Fine mapping of S37, a locus responsible for pollen and embryo sac sterility in hybrids between Oryza sativa L. and O. glaberrima Steud.

Science.gov (United States)

Shen, Yumin; Zhao, Zhigang; Ma, Hongyang; Bian, Xiaofeng; Yu, Yang; Yu, Xiaowen; Chen, Haiyuan; Liu, Linglong; Zhang, Wenwei; Jiang, Ling; Zhou, Jiawu; Tao, Dayun; Wan, Jianmin

2015-11-01

Hybrid sterility locus S37 between Oryza glaberrima and Oryza sativa results in both pollen and embryo sac sterility. Interspecific crossing between African cultivated rice Oryza glaberrima and Oryza sativa cultivars is hindered by hybrid sterility. To dissect the mechanism of interspecific hybrid sterility, we developed a near-isogenic line (NIL)-S37 using Dianjingyou1 (DJY1) as the recipient parent and an African cultivated rice variety as the donor parent. Empty pollen and embryo sac sterility were observed in F1 hybrids between DJY1 and NIL-S37. Cytological analyses showed that pollen abortion in the F1 hybrids occurred at the late binucleate stage due to a failure of starch accumulation in pollen grains. In addition, partial abortion of the embryo sac in the F1 hybrid was observed during function megaspore developing into mature embryo sac. Molecular analysis revealed that the semi-sterility was largely caused by the abortion of male and female gametophytes carrying the S37 allele from DJY1. A population of 25,600 plants derived from the hybrid DJY1/NIL-S37 was developed to fine map S37. Based on the physical location of molecular markers, S37 locus was finally delimited to a region of 205 kb on the short arm of chromosome 1 in terms of reference sequences of cv. Nipponbare. Interestingly, an about 97-kb DNA segment was deleted in the NIL-S37 based on BAC clone information of O. glaberrima. Fifty-four open reading frames (ORF) were predicted in this 205-kb region of DJY1, whereas only 31 ORFs were in that of NIL-S37. These results are valuable for cloning of S37 gene and further breaking reproductive isolation between Oryza glaberrima and Oryza sativa cultivars, as well as marker-assisted transferring of the corresponding neutral allele in rice breeding programs.

Alien DNA introgression and wheat DNA rearrangements in a stable wheat line derived from the early generation of distant hybridization.

Science.gov (United States)

Zhang, Lianquan; Liu, Dengcai; Yan, Zehong; Zheng, Youliang

2005-10-01

Polyploidy has been found to be common in plants. Bread or common wheat (Triticum aestivum L., 2n=42) is a good example of allopolyploid made up of three diploid genomes A, B and D. In recent years, by the study of mimicking the origination of common wheat, it was found that changes of DNA sequence and gene expression occurred at the early stages of artificial allohexaploid between tetraploid wheat and Aegilops tauschii, which was probably favorable to genetic diploidization of new synthetic hexaploid wheat. Common wheat 99L2 is a new line stable in genetic, which was derived from the early self-pollinated generation of wide hybrids between common wheat and rye. In this study, it was found that at least two rye DNA segments had been introgressed into 99L2. This result suggested that a mechanism of alien DNA introgression may exist, which was different from the traditional mechanism of chromosome pairing and DNA recombination between wheat and alien species. Meanwhile, during the introgression process of alien rye DNA segments, the changes in DNA sequences of wheat itself occurred.

Introgression of leginsulin, a cysteine-rich protein, and high-protein trait from an Asian soybean plant introduction genotype into a North American experimental soybean line.

Science.gov (United States)

Krishnan, Hari B; Kim, Won-Seok; Oehrle, Nathan W; Alaswad, Alaa A; Baxter, Ivan; Wiebold, William J; Nelson, Randall L

2015-03-25

Soybean is an important protein source for both humans and animals. However, soybean proteins are relatively poor in the sulfur-containing amino acids, cysteine and methionine. Improving the content of endogenous proteins rich in sulfur-containing amino acids could enhance the nutritive value of soybean meal. Leginsulin, a cysteine-rich peptide, predominantly accumulates in Asian soybean accessions but not in most North American cultivars. By screening diverse soybean accessions from the USDA Soybean Germplasm Collection, we were able to identify one plant introduction, PI 427138, as a high-protein line with relatively high amounts of both elemental sulfur and leginsulin. We introgressed these desirable traits from PI 427138 into an experimental line with the aim of improving the overall protein content and quality of seed proteins. Biochemical characterization of inbred progenies from the cross of LD00-3309 with PI 427138 grown at six locations revealed stable ingression of high protein, high elemental sulfur, and high leginsulin accumulation. Comparison of soybean seed proteins resolved by high-resolution 2-D gel electrophoresis in combination with Delta2D image analysis software revealed preferential accumulation of a few glycinin subunits contributed to the increased protein content in the introgressed lines. Amino acid analysis revealed that even though the leginsulin introgressed lines had higher protein, leginsulin, and elemental sulfur, the overall concentration of sulfur-containing amino acids was not significantly altered when compared with the parental lines. The experimental soybean lines developed during this study (Leg-3, Leg-7, and Leg-8) lack A5, A4, and B3 glycinin subunits and could be utilized in breeding programs to develop high-quality tofu cultivars.

Genetic analysis of a novel broad-spectrum powdery mildew resistance gene from the wheat-Agropyron cristatum introgression line Pubing 74.

Science.gov (United States)

Lu, Yuqing; Yao, Miaomiao; Zhang, Jinpeng; Song, Liqiang; Liu, Weihua; Yang, Xinming; Li, Xiuquan; Li, Lihui

2016-09-01

A novel broad-spectrum powdery mildew resistance gene PmPB74 was identified in wheat- Agropyron cristatum introgression line Pubing 74. Development of wheat cultivars with broad-spectrum, durable resistance to powdery mildew has been restricted by lack of superior genetic resources. In this study, a wheat-A. cristatum introgression line Pubing 74, originally selected from a wide cross between the common wheat cultivar Fukuhokomugi (Fukuho) and Agropyron cristatum (L.) Gaertn (2n = 4x = 28; genome PPPP), displayed resistance to powdery mildew at both the seedling and adult stages. The putative alien chromosomal fragment in Pubing 74 was below the detection limit of genomic in situ hybridization (GISH), but evidence for other non-GISH-detectable introgressions was provided by the presence of three STS markers specific to A. cristatum. Genetic analysis indicated that Pubing 74 carried a single dominant gene for powdery mildew resistance, temporarily designated PmPB74. Molecular mapping showed that PmPB74 was located on wheat chromosome arm 5DS, and flanked by markers Xcfd81 and HRM02 at genetic distances of 2.5 and 1.7 cM, respectively. Compared with other lines with powdery mildew resistance gene(s) on wheat chromosome arm 5DS, Pubing 74 was resistant to all 28 Blumeria graminis f. sp tritici (Bgt) isolates from different wheat-producing regions of northern China. Allelism tests indicated that PmPB74 was not allelic to PmPB3558 or Pm2. Our work showed that PmPB74 is a novel gene with broad resistance to powdery mildew, and hence will be helpful in broadening the genetic basis of powdery mildew resistance in wheat.

Home Bodies and Wanderers: Sympatric Lineages of the Deep-Sea Black Coral Leiopathes glaberrima.

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Dannise V Ruiz-Ramos

Full Text Available Colonial corals occur in a wide range of marine benthic habitats from the shallows to the deep ocean, often defining the structure of their local community. The black coral Leiopathes glaberrima is a long-lived foundation species occurring on carbonate outcrops in the Northern Gulf of Mexico (GoM. Multiple color morphs of L. glaberrima grow sympatrically in the region. Morphological, mitochondrial and nuclear ribosomal markers supported the hypothesis that color morphs constituted a single biological species and that colonies, regardless of color, were somewhat genetically differentiated east and west of the Mississippi Canyon. Ten microsatellite loci were used to determine finer-scale population genetic structure and reproductive characteristics. Gene flow was disrupted between and within two nearby (distance = 36.4 km hardground sites and two sympatric microsatellite lineages, which might constitute cryptic species, were recovered. Lineage one was outbred and found in all sampled locations (N = 5 across 765.6 km in the Northern Gulf of Mexico. Lineage two was inbred, reproducing predominantly by fragmentation, and restricted to sites around Viosca Knoll. In these sites the lineages and the color phenotypes occurred in different microhabitats, and models of maximum entropy suggested that depth and slope influence the distribution of the color phenotypes within the Vioska Knolls. We conclude that L. glaberrima is phenotypically plastic with a mixed reproductive strategy in the Northern GoM. Such strategy might enable this long-lived species to balance local recruitment with occasional long-distance dispersal to colonize new sites in an environment where habitat is limited.

Improvement of local varieties of rice (Oryza glaberrima) for resistance to shattering and grain quality by induced mutations

Energy Technology Data Exchange (ETDEWEB)

Cisse, F; Dione, M; Kelly, S [Institute d` Economie Rurale, Station de Recherche Agronomique, Mopti (Mali)

1997-12-01

In Mali, a large area of rice is planted with the local rice, O. glaberrima which under conditions of low rainfall and flood water is more hardy to stress than the introduced O. sativa cultivars. A program to improve the local varieties of O. glaberrima by induced mutations was started in 1988. Ten local varieties were irradiated with 20 and 30 krad. In M{sub 4} of cv. `Gorbal`, irradiated with 20 krads, 13 variants were selected. Five of these were evaluated in M{sub 5} for their agronomic performance. The induced mutants in the remaining 9 varieties were highly sterile with 90% or more sterility in the M{sub 2} and M{sub 3}. Irradiation with 20-30 krad gave high survival (70-95%), and several mutants with white kernel were obtained from the red seeded types. Nearly two-third of the identified mutants had white caryopsis. There is better consumer acceptance of the white seeded type of rice than the red seeded varieties in Mali and the white seeded mutants may have an added premium in the market. The field performance of the M{sub 5} mutants was investigated. Preliminary results showed that some of mutants derived from cv. `Gorbal` were early in maturity and had more panicles per plant, but had a lower 1000-kernel weight, and did not differ from the parent in grain yield. Additional trials are planned to establish potential of the mutants for yield and quality. Three more cultivars of O. glaberrima - `Haira`, `Tombo` and `Yele` - were irradiated with 20 and 60 krads, and gave 75, 81 and 72% seed viability, respectively. M{sub 1} showed reduced plant height. Selection for non-shattering of grains shall be carried out in M{sub 2}. Any plants which are non-shattering but sterile shall be crossed with the parent to recover the mutant types. The taxonomic status of cv. `Gorbal` is not very clear. Isozyme patterns suggest that this cultivar may belong to O. sativa and not to O. glaberrima. To establish its taxonomic status, crosses shall be made with O. sativa and O

Improvement of local varieties of rice (Oryza glaberrima) for resistance to shattering and grain quality by induced mutations

International Nuclear Information System (INIS)

Cisse, F.; Dione, M.; Kelly, S.

1997-01-01

In Mali, a large area of rice is planted with the local rice, O. glaberrima which under conditions of low rainfall and flood water is more hardy to stress than the introduced O. sativa cultivars. A program to improve the local varieties of O. glaberrima by induced mutations was started in 1988. Ten local varieties were irradiated with 20 and 30 krad. In M 4 of cv. 'Gorbal', irradiated with 20 krads, 13 variants were selected. Five of these were evaluated in M 5 for their agronomic performance. The induced mutants in the remaining 9 varieties were highly sterile with 90% or more sterility in the M 2 and M 3 . Irradiation with 20-30 krad gave high survival (70-95%), and several mutants with white kernel were obtained from the red seeded types. Nearly two-third of the identified mutants had white caryopsis. There is better consumer acceptance of the white seeded type of rice than the red seeded varieties in Mali and the white seeded mutants may have an added premium in the market. The field performance of the M 5 mutants was investigated. Preliminary results showed that some of mutants derived from cv. 'Gorbal' were early in maturity and had more panicles per plant, but had a lower 1000-kernel weight, and did not differ from the parent in grain yield. Additional trials are planned to establish potential of the mutants for yield and quality. Three more cultivars of O. glaberrima - 'Haira', 'Tombo' and 'Yele' - were irradiated with 20 and 60 krads, and gave 75, 81 and 72% seed viability, respectively. M 1 showed reduced plant height. Selection for non-shattering of grains shall be carried out in M 2 . Any plants which are non-shattering but sterile shall be crossed with the parent to recover the mutant types. The taxonomic status of cv. 'Gorbal' is not very clear. Isozyme patterns suggest that this cultivar may belong to O. sativa and not to O. glaberrima. To establish its taxonomic status, crosses shall be made with O. sativa and O. glaberrima. (author). 2 tabs

SNP Discovery for mapping alien introgressions in wheat

Science.gov (United States)

2014-01-01

Background Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L). Results The short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL · 5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines with Lr57 and Yr40 genes. Conclusion This approach should be widely applicable for the identification of species/genome-specific SNPs. The development of a large number of SNP markers will facilitate the precise introgression and

SNP Discovery for mapping alien introgressions in wheat.

Science.gov (United States)

Tiwari, Vijay K; Wang, Shichen; Sehgal, Sunish; Vrána, Jan; Friebe, Bernd; Kubaláková, Marie; Chhuneja, Praveen; Doležel, Jaroslav; Akhunov, Eduard; Kalia, Bhanu; Sabir, Jamal; Gill, Bikram S

2014-04-10

Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L). The short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL · 5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines with Lr57 and Yr40 genes. This approach should be widely applicable for the identification of species/genome-specific SNPs. The development of a large number of SNP markers will facilitate the precise introgression and monitoring of alien segments in crop

African Journal of Biotechnology - Vol 9, No 26 (2010)

African Journals Online (AJOL)

Evaluation of Oryza sativa x O. glaberrima derived progenies for resistance to rootknot nematode and identification of introgressed alien chromosome segments ... Genetic characterization of mango anthracnose pathogen Colletotrichum gloeosporioides Penz. by random amplified polymorphic DNA analysis · EMAIL FREE ...

Quantifying introgression risk with realistic population genetics.

Science.gov (United States)

Ghosh, Atiyo; Meirmans, Patrick G; Haccou, Patsy

2012-12-07

Introgression is the permanent incorporation of genes from the genome of one population into another. This can have severe consequences, such as extinction of endemic species, or the spread of transgenes. Quantification of the risk of introgression is an important component of genetically modified crop regulation. Most theoretical introgression studies aimed at such quantification disregard one or more of the most important factors concerning introgression: realistic genetical mechanisms, repeated invasions and stochasticity. In addition, the use of linkage as a risk mitigation strategy has not been studied properly yet with genetic introgression models. Current genetic introgression studies fail to take repeated invasions and demographic stochasticity into account properly, and use incorrect measures of introgression risk that can be manipulated by arbitrary choices. In this study, we present proper methods for risk quantification that overcome these difficulties. We generalize a probabilistic risk measure, the so-called hazard rate of introgression, for application to introgression models with complex genetics and small natural population sizes. We illustrate the method by studying the effects of linkage and recombination on transgene introgression risk at different population sizes.

Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations.

Science.gov (United States)

Zhang, Xueli; Ge, Xianhong; Shao, Yujiao; Sun, Genlou; Li, Zaiyun

2013-01-01

Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP), sequence-specific amplification polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8%) and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

Genotype × environment interactions of yield traits in backcross introgression lines derived from Oryza sativa cv. Swarna /Oryza nivara

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Divya Balakrishnan

2016-10-01

Full Text Available Advanced backcross introgression lines (BILs developed from crosses of Oryza sativa var. Swarna/O. nivara accessions were grown and evaluated for yield and related traits. Trials were conducted for consecutive three seasons in field conditions in a randomized complete block design with three replications. Data on yield traits under irrigated conditions were analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI, Genotype and Genotype × Environment Interaction (GGE and modified rank-sum statistic (YSi for yield stability. BILs viz., G3 (14S and G6 (166S showed yield stability across the seasons along with high mean yield performance. G3 is early in flowering with high yield and has good grain quality and medium height, hence could be recommended for most of the irrigated locations. G6 is a late duration genotype, with strong culm strength, high grain number and panicle weight. G6 has higher yield and stability than Swarna but has Swarna grain type. Among the varieties tested DRRDhan 40 and recurrent parent Swarna showed stability for yield traits across the seasons. The component traits thousand grain weight, panicle weight, panicle length, grain number and plant height explained highest genotypic percentage over environment and interaction factors and can be prioritized to dissect stable QTLs/ genes. These lines were genotyped using microsatellite markers covering the entire rice genome and also using a set of markers linked to previously reported yield QTLs. It was observed that wild derived lines with more than 70% of recurrent parent genome were stable and showed enhanced yield levels compared to genotypes with higher donor genome introgressions.

Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima

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Caijin Chen

2017-11-01

Conclusions: Genetic diversity studies revealed that 50 rice types were clustered into different subpopulations whereas three genotypes were admixtures. Molecular fingerprinting and 10 specific markers were obtained to identify the 53 rice genotypes. These results can facilitate the potential utilization of sibling species in rice breeding and molecular classification of O. sativa and O. glaberrima germplasms.

Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations.

Directory of Open Access Journals (Sweden)

Xueli Zhang

Full Text Available Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP, sequence-specific amplification polymorphism (SSAP and methylation-sensitive amplified polymorphism (MSAP were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8% and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background

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Pietro Gramazio

2017-08-01

Full Text Available Advanced backcrosses (ABs and introgression lines (ILs of eggplant (Solanum melongena can speed up genetics and genomics studies and breeding in this crop. We have developed the first full set of ABs and ILs in eggplant using Solanum incanum, a wild eggplant that has a relatively high tolerance to drought, as a donor parent. The development of these ABs and IL eggplant populations had a low efficiency in the early stages, because of the lack of molecular markers and genomic tools. However, this dramatically improved after performing genotyping-by-sequencing in the first round of selfing, followed by high-resolution-melting single nucleotide polymorphism genotyping in subsequent selection steps. A set of 73 selected ABs covered 99% of the S. incanum genome, while 25 fixed immortal ILs, each carrying a single introgressed fragment in homozygosis, altogether spanned 61.7% of the S. incanum genome. The introgressed size fragment in the ILs contained between 0.1 and 10.9% of the S. incanum genome, with a mean value of 4.3%. Sixty-eight candidate genes involved in drought tolerance were identified in the set of ILs. This first set of ABs and ILs of eggplant will be extremely useful for the genetic dissection of traits of interest for eggplant, and represents an elite material for introduction into the breeding pipelines for developing new eggplant cultivars adapted to the challenges posed by the climate-change scenario.

Quantifying introgression risk with realistic population genetics

OpenAIRE

Ghosh, Atiyo; Meirmans, Patrick G.; Haccou, Patsy

2012-01-01

Introgression is the permanent incorporation of genes from the genome of one population into another. This can have severe consequences, such as extinction of endemic species, or the spread of transgenes. Quantification of the risk of introgression is an important component of genetically modified crop regulation. Most theoretical introgression studies aimed at such quantification disregard one or more of the most important factors concerning introgression: realistic genetical mechanisms, rep...

Molecular cytogenetic characterization of alien introgressions with gene Fhb3 for resistance to Fusarium head blight disease of wheat

Science.gov (United States)

Fusarium head blight (FHB) resistance was identified in the alien species Leymus racemosus, and wheat-Leymus introgression lines with FHB resistance were reported previously. Detailed molecular cytogenetic analysis of alien introgressions T01, T09, and T14 and the mapping of Fhb3, a new gene for FHB...

Physiological basis of genetic variation in leaf photosynthesis among rice (Oryza sativa L.) introgression lines under drought and well-watered conditions

Science.gov (United States)

Yin, Xinyou

2012-01-01

To understand the physiological basis of genetic variation and resulting quantitative trait loci (QTLs) for photosynthesis in a rice (Oryza sativa L.) introgression line population, 13 lines were studied under drought and well-watered conditions, at flowering and grain filling. Simultaneous gas exchange and chlorophyll fluorescence measurements were conducted at various levels of incident irradiance and ambient CO2 to estimate parameters of a model that dissects photosynthesis into stomatal conductance (g s), mesophyll conductance (g m), electron transport capacity (J max), and Rubisco carboxylation capacity (V cmax). Significant genetic variation in these parameters was found, although drought and leaf age accounted for larger proportions of the total variation. Genetic variation in light-saturated photosynthesis and transpiration efficiency (TE) were mainly associated with variation in g s and g m. One previously mapped major QTL of photosynthesis was associated with variation in g s and g m, but also in J max and V cmax at flowering. Thus, g s and g m, which were demonstrated in the literature to be responsible for environmental variation in photosynthesis, were found also to be associated with genetic variation in photosynthesis. Furthermore, relationships between these parameters and leaf nitrogen or dry matter per unit area, which were previously found across environmental treatments, were shown to be valid for variation across genotypes. Finally, the extent to which photosynthesis rate and TE can be improved was evaluated. Virtual ideotypes were estimated to have 17.0% higher photosynthesis and 25.1% higher TE compared with the best genotype investigated. This analysis using introgression lines highlights possibilities of improving both photosynthesis and TE within the same genetic background. PMID:22888131

Genetic and Epigenetic Alterations of Brassica nigra Introgression Lines from Somatic Hybridization: A Resource for Cauliflower Improvement.

Science.gov (United States)

Wang, Gui-Xiang; Lv, Jing; Zhang, Jie; Han, Shuo; Zong, Mei; Guo, Ning; Zeng, Xing-Ying; Zhang, Yue-Yun; Wang, You-Ping; Liu, Fan

2016-01-01

Broad phenotypic variations were obtained previously in derivatives from the asymmetric somatic hybridization of cauliflower "Korso" (Brassica oleracea var. botrytis, 2n = 18, CC genome) and black mustard "G1/1" (Brassica nigra, 2n = 16, BB genome). However, the mechanisms underlying these variations were unknown. In this study, 28 putative introgression lines (ILs) were pre-selected according to a series of morphological (leaf shape and color, plant height and branching, curd features, and flower traits) and physiological (black rot/club root resistance) characters. Multi-color fluorescence in situ hybridization revealed that these plants contained 18 chromosomes derived from "Korso." Molecular marker (65 simple sequence repeats and 77 amplified fragment length polymorphisms) analysis identified the presence of "G1/1" DNA segments (average 7.5%). Additionally, DNA profiling revealed many genetic and epigenetic differences among the ILs, including sequence alterations, deletions, and variation in patterns of cytosine methylation. The frequency of fragments lost (5.1%) was higher than presence of novel bands (1.4%), and the presence of fragments specific to Brassica carinata (BBCC 2n = 34) were common (average 15.5%). Methylation-sensitive amplified polymorphism analysis indicated that methylation changes were common and that hypermethylation (12.4%) was more frequent than hypomethylation (4.8%). Our results suggested that asymmetric somatic hybridization and alien DNA introgression induced genetic and epigenetic alterations. Thus, these ILs represent an important, novel germplasm resource for cauliflower improvement that can be mined for diverse traits of interest to breeders and researchers.

Breeding for resistance to grain shattering in Oryza glaberrima Steud. Through induced mutations

Energy Technology Data Exchange (ETDEWEB)

Cisse, F [Institut d` Economie Rurale, Station de Recherche Agronomique de Sikasso, Sikasso (Mali)

1997-07-01

Several local varieties of African rice, O. glaberrima, which is an important crop in the inland Niger River Delta in Mali, were irradiated with gamma rays in two different experiments. Several mutants with changed kernel colour from red to white and improved characters such as early maturity, non-shattering of grain, and reduced plant height were selected among the advanced segregating generations. Some of the selected mutants are being tested in multi-location trials. (author). 2 refs, 5 tabs.

Breeding for resistance to grain shattering in Oryza glaberrima Steud. Through induced mutations

International Nuclear Information System (INIS)

Cisse, F.

1997-01-01

Several local varieties of African rice, O. glaberrima, which is an important crop in the inland Niger River Delta in Mali, were irradiated with gamma rays in two different experiments. Several mutants with changed kernel colour from red to white and improved characters such as early maturity, non-shattering of grain, and reduced plant height were selected among the advanced segregating generations. Some of the selected mutants are being tested in multi-location trials. (author). 2 refs, 5 tabs

Detection of alien genetic introgressions in bread wheat using dot-blot genomic hybridisation.

Science.gov (United States)

Rey, María-Dolores; Prieto, Pilar

2017-01-01

Simple, reliable methods for the identification of alien genetic introgressions are required in plant breeding programmes. The use of genomic dot-blot hybridisation allows the detection of small Hordeum chilense genomic introgressions in the descendants of genetic crosses between wheat and H. chilense addition or substitution lines in wheat when molecular markers are difficult to use. Based on genomic in situ hybridisation, DNA samples from wheat lines carrying putatively H. chilense introgressions were immobilised on a membrane, blocked with wheat genomic DNA and hybridised with biotin-labelled H. chilense genomic DNA as a probe. This dot-blot screening reduced the number of plants necessary to be analysed by molecular markers or in situ hybridisation, saving time and money. The technique was sensitive enough to detect a minimum of 5 ng of total genomic DNA immobilised on the membrane or about 1/420 dilution of H. chilense genomic DNA in the wheat background. The robustness of the technique was verified by in situ hybridisation. In addition, the detection of other wheat relative species such as Hordeum vulgare , Secale cereale and Agropyron cristatum in the wheat background was also reported .

Genetic and epigenetic alterations of Brassica nigra introgression lines from somatic hybridization: a resource for cauliflower improvement

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Guixiang Wang

2016-08-01

Full Text Available Broad phenotypic variations were obtained previously in derivatives from the asymmetric somatic hybridization of cauliflower ‘Korso’ (Brassica oleracea var. botrytis, 2n = 18, CC genome and black mustard ‘G1/1’ (Brassica nigra, 2n = 16, BB genome. However, the mechanisms underlying these variations were unknown. In this study, 28 putative introgression lines (ILs were pre-selected according to a series of morphological (leaf shape and color, plant height and branching, curd features, and flower traits and physiological (black rot/club root resistance characters. Multi-color fluorescence in situ hybridization revealed that these plants contained 18 chromosomes derived from ‘Korso’. Molecular marker (65 simple sequence repeats and 77 amplified fragment length polymorphisms analysis identified the presence of ‘G1/1’ DNA segments (average 7.5%. Additionally, DNA profiling revealed many genetic and epigenetic differences among the ILs, including sequence alterations, deletions, and variation in patterns of cytosine methylation. The frequency of fragments lost (5.1% was significantly higher than presence of novel bands (1.4%, and the presence of fragments specific to B. carinata (BBCC 2n = 34 were common (average 15.5%. Methylation-sensitive amplified polymorphism analysis indicated that methylation changes were common and that hypermethylation (12.4% was more frequent than hypomethylation (4.8%. Our results suggested that asymmetric somatic hybridization and alien DNA introgression induced genetic and epigenetic alterations. Thus, these ILs represent an important, novel germplasm resource for cauliflower improvement that can be mined for diverse traits of interest to breeders and researchers.

Introgression of a Block of Genome Under Infinitesimal Selection.

Science.gov (United States)

Sachdeva, Himani; Barton, Nicholas H

2018-06-12

Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of loci, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection are qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how their length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish the long-term introgression of a block of genome with a single strongly selected locus from the introgression of a block with multiple, tightly linked and weakly selected loci. Copyright © 2018, Genetics.

Assessing hybrid sterility in Oryza glaberrima x O. sativa hybrid progenies by PCR marker analysis and crossing with wide compatibility varieties.

Science.gov (United States)

Heuer, Sigrid; Miézan, Kouamé M

2003-09-01

Interspecific crossing of the African indigenous rice Oryza glaberrima with Oryza sativa cultivars is hindered by crossing barriers causing 100% spikelet sterility in F(1) hybrids. Since hybrids are partially female fertile, fertility can be restored by back crossing (BC) to a recurrent male parent. Distinct genetic models on spikelet sterility have been developed predicting, e.g., the existence of a gamete eliminator and/or a pollen killer. Linkage of sterility to the waxy starch synthase gene and the chromogen gene C, both located on chromosome 6, have been demonstrated. We selected a segregating BC(2)F(3) population of semi-sterile O. glaberrima x O. sativa indica hybrid progenies for analyses with PCR markers located at the respective chromosome-6 region. These analyses revealed that semi-sterile plants were heterozygous for a marker (OSR25) located in the waxy promoter, whereas fertile progenies were homozygous for the O. glaberrima allele. Adjacent markers showed no linkage to spikelet sterility. Semi-sterility of hybrid progenies was maintained at least until the F(4) progeny generation, suggesting the existence of a pollen killer in this plant material. Monitoring of reproductive plant development showed that spikelet sterility was at least partially due to an arrest of pollen development at the microspore stage. In order to address the question whether genes responsible for F(1) sterility in intraspecific hybrids ( O. sativa indica x japonica) also cause spikelet sterility in interspecific hybrids, crossings with wide compatibility varieties (WCV) were performed. WCV accessions possess "neutral" S-loci ( S(n)) improving fertility in intraspecific hybrids. This experiment showed that the tested S(n)-loci had no fertility restoring effect in F(1) interspecific hybrids. Pollen development was completely arrested at the microspore stage and grains were never obtained after selfing. This suggests that distinct or additional S-loci are responsible for sterility

Genomewide variation in an introgression line of rice-Zizania revealed by whole-genome re-sequencing.

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Zhen-Hui Wang

Full Text Available BACKGROUND: Hybridization between genetically diverged organisms is known as an important avenue that drives plant genome evolution. The possible outcomes of hybridization would be the occurrences of genetic instabilities in the resultant hybrids. It remained under-investigated however whether pollination by alien pollens of a closely related but sexually "incompatible" species could evoke genomic changes and to what extent it may result in phenotypic novelties in the derived progenies. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we have re-sequenced the genomes of Oryza sativa ssp. japonica cv. Matsumae and one of its derived introgressant RZ35 that was obtained from an introgressive hybridization between Matsumae and Zizanialatifolia Griseb. in general, 131 millions 90 base pair (bp paired-end reads were generated which covered 13.2 and 21.9 folds of the Matsumae and RZ35 genomes, respectively. Relative to Matsumae, a total of 41,724 homozygous single nucleotide polymorphisms (SNPs and 17,839 homozygous insertions/deletions (indels were identified in RZ35, of which 3,797 SNPs were nonsynonymous mutations. Furthermore, rampant mobilization of transposable elements (TEs was found in the RZ35 genome. The results of pathogen inoculation revealed that RZ35 exhibited enhanced resistance to blast relative to Matsumae. Notably, one nonsynonymous mutation was found in the known blast resistance gene Pid3/Pi25 and real-time quantitative (q RT-PCR analysis revealed constitutive up-regulation of its expression, suggesting both altered function and expression of Pid3/Pi25 may be responsible for the enhanced resistance to rice blast by RZ35. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that introgressive hybridization by Zizania has provoked genomewide, extensive genomic changes in the rice genome, and some of which have resulted in important phenotypic novelties. These findings suggest that introgressive hybridization by alien pollens of even a

Effects of asymmetric nuclear introgression, introgressive mitochondrial sweep, and purifying selection on phylogenetic reconstruction and divergence estimates in the Pacific clade of Locustella warblers.

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Drovetski, Sergei V; Semenov, Georgy; Red'kin, Yaroslav A; Sotnikov, Vladimir N; Fadeev, Igor V; Koblik, Evgeniy A

2015-01-01

When isolated but reproductively compatible populations expand geographically and meet, simulations predict asymmetric introgression of neutral loci from a local to invading taxon. Genetic introgression may affect phylogenetic reconstruction by obscuring topology and divergence estimates. We combined phylogenetic analysis of sequences from one mtDNA and 12 nuDNA loci with analysis of gene flow among 5 species of Pacific Locustella warblers to test for presence of genetic introgression and its effects on tree topology and divergence estimates. Our data showed that nuDNA introgression was substantial and asymmetrical among all members of superspecies groups whereas mtDNA showed no introgression except a single species pair where the invader's mtDNA was swept by mtDNA of the local species. This introgressive sweep of mtDNA had the opposite direction of the nuDNA introgression and resulted in the paraphyly of the local species' mtDNA haplotypes with respect to those of the invader. Тhe multilocus nuDNA species tree resolved all inter- and intraspecific relationships despite substantial introgression. However, the node ages on the species tree may be underestimated as suggested by the differences in node age estimates based on non-introgressing mtDNA and introgressing nuDNA. In turn, the introgressive sweep and strong purifying selection appear to elongate internal branches in the mtDNA gene tree.

Introgression of a leaf rust resistance gene from Aegilops caudata to ...

Indian Academy of Sciences (India)

tance genes (Lr) and 48 stripe rust resistance genes (Yr) have .... Leaf rust reaction of the parents, wheat – Ae. caudata introgression lines and representative F2 plants developed from the cross: .... segregation ratio, which is otherwise a serious problem with ... Financial assistance was provided by the USDA-ARS under the.

Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers.

Science.gov (United States)

Edet, Offiong Ukpong; Kim, June-Sik; Okamoto, Masanori; Hanada, Kousuke; Takeda, Tomoyuki; Kishii, Masahiro; Gorafi, Yasir Serag Alnor; Tsujimoto, Hisashi

2018-03-27

The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses. We generated de novo DNA and mRNA sequence information of L. racemosus and developed 110 polymorphic PCR-based markers from the data, and to complement the PCR markers, DArT-seq genotyping was applied to develop additional 9990 SNP markers. Approximately 52% of all the markers enabled us to clearly genotype 22 wheat-L. racemosus chromosome introgression lines, and L. racemosus chromosome-specific markers were highly efficient in detailed characterization of the translocation and recombination lines analyzed. A further analysis revealed remarkable transferability of the PCR markers to three other important Triticeae perennial species: L. mollis, Psathyrostachys huashanica and Elymus ciliaris, indicating their suitability for characterizing wheat-alien chromosome introgressions carrying chromosomes of these genomes. The efficiency of the markers in characterizing wheat-L. racemosus chromosome introgression lines proves their reliability, and their high transferability further broadens their scope of application. This is the first report on sequencing and development of markers from L. racemosus genome and the application of DArT-seq to develop markers from a perennial wild relative of wheat, marking a paradigm shift from the seeming concentration of the technology on cultivated species. Integration of these markers with appropriate cytogenetic methods would accelerate development and characterization of wheat-alien chromosome introgression lines.

Common cellular events occur during wound healing and organ regeneration in the sea cucumber Holothuria glaberrima

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García-Arrarás José E

2007-10-01

Full Text Available Abstract Background All animals possess some type of tissue repair mechanism. In some species, the capacity to repair tissues is limited to the healing of wounds. Other species, such as echinoderms, posses a striking repair capability that can include the replacement of entire organs. It has been reported that some mechanisms, namely extracellular matrix remodeling, appear to occur in most repair processes. However, it remains unclear to what extent the process of organ regeneration, particularly in animals where loss and regeneration of complex structures is a programmed natural event, is similar to wound healing. We have now used the sea cucumber Holothuria glaberrima to address this question. Results Animals were lesioned by making a 3–5 mm transverse incision between one of the longitudinal muscle pairs along the bodywall. Lesioned tissues included muscle, nerve, water canal and dermis. Animals were allowed to heal for up to four weeks (2, 6, 12, 20, and 28 days post-injury before sacrificed. Tissues were sectioned in a cryostat and changes in cellular and tissue elements during repair were evaluated using classical dyes, immmuohistochemistry and phalloidin labeling. In addition, the temporal and spatial distribution of cell proliferation in the animals was assayed using BrdU incorporation. We found that cellular events associated with wound healing in H. glaberrima correspond to those previously shown to occur during intestinal regeneration. These include: (1 an increase in the number of spherule-containing cells, (2 remodeling of the extracellular matrix, (3 formation of spindle-like structures that signal dedifferentiation of muscle cells in the area flanking the lesion site and (4 intense cellular division occurring mainly in the coelomic epithelium after the first week of regeneration. Conclusion Our data indicate that H. glaberrima employs analogous cellular mechanisms during wound healing and organ regeneration. Thus, it is possible

Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

Science.gov (United States)

Bapteste, Eric; Lopez, Philippe; Bouchard, Frédéric; Baquero, Fernando; McInerney, James O; Burian, Richard M

2012-11-06

All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.

Identification of tomato introgression lines with enhanced susceptibility or resistance to infection by parasitic giant dodder (Cuscuta reflexa).

Science.gov (United States)

Krause, Kirsten; Johnsen, Hanne R; Pielach, Anna; Lund, Leidulf; Fischer, Karsten; Rose, Jocelyn K C

2018-02-01

The parasitic flowering plant genus Cuscuta (dodder) is a parasitic weed that infects many important crops. Once it winds around the shoots of potential host plants and initiates the development of penetration organs, called haustoria, only a few plant species have been shown to deploy effective defense mechanisms to ward off Cuscuta parasitization. However, a notable exception is Solanum lycopersicum (tomato), which exhibits a local hypersensitive reaction when attacked by giant dodder (Cuscuta reflexa). Interestingly, the closely related wild desert tomato, Solanum pennellii, is unable to stop the penetration of its tissue by the C. reflexa haustoria. In this study, we observed that grafting a S. pennellii scion onto the rootstock of the resistant S. lycopersicum did not change the susceptibility phenotype of S. pennellii. This suggests that hormones, or other mobile substances, produced by S. lycopersicum do not induce a defense reaction in the susceptible tissue. Screening of a population of introgression lines harboring chromosome fragments from S. pennellii in the genome of the recurrent parent S. lycopersicum, revealed that most lines exhibit the same defense reaction as shown by the S. lycopersicum parental line. However, several lines showed different responses and exhibited either susceptibility, or cell death that extended considerably beyond the infection site. These lines will be valuable for the future identification of key loci involved in the perception of, and resistance to, C. reflexa and for developing strategies to enhance resistance to infection in crop species. © 2017 Scandinavian Plant Physiology Society.

Transcriptome alteration in a rice introgression line with enhanced alkali tolerance.

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Zhang, Yunhong; Lin, Xiuyun; Ou, Xiufang; Hu, Lanjuan; Wang, Jinming; Yang, Chunwu; Wang, Shucai; Liu, Bao

2013-07-01

Alkali stress inhibits plant growth and development and thus limits crop productivity. To investigate the possible genetic basis of alkali tolerance in rice, we generated an introgressed rice line (K83) with significantly enhanced tolerance to alkali stress compared to its recipient parental cultivar (Jijing88). By using microarray analysis, we examined the global gene expression profiles of K83 and Jijing88, and found that more than 1200 genes were constitutively and differentially expressed in K83 in comparison to Jijing88 with 572 genes up- and 654 down-regulated. Upon alkali treatment, a total of 347 genes were found up- and 156 down-regulated in K83 compared to 591 and 187, respectively, in Jijing88. Among the up-regulated genes in both K83 and Jijing88, only 34 were constitutively up-regulated in K83, suggesting that both the constitutive differentially expressed genes in K83 and those induced by alkali treatment are most likely responsible for enhanced alkali tolerance. A gene ontology analysis based on all annotated, differentially expressed genes revealed that genes with expression alterations were enriched in pathways involved in metabolic processes, catalytic activity, and transport and transcription factor activities, suggesting that these pathways are associated with alkali stress tolerance in rice. Our results illuminated the novel genetic aspects of alkali tolerance in rice and established a repertory of potential target genes for biotechnological manipulations that can be used to generate alkali-tolerant rice cultivars. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Characterization of new allele influencing flowering time in bread wheat introgressed from Triticum militinae.

Science.gov (United States)

Ivaničová, Zuzana; Jakobson, Irena; Reis, Diana; Šafář, Jan; Milec, Zbyněk; Abrouk, Michael; Doležel, Jaroslav; Järve, Kadri; Valárik, Miroslav

2016-09-25

Flowering time variation was identified within a mapping population of doubled haploid lines developed from a cross between the introgressive line 8.1 and spring bread wheat cv. Tähti. The line 8.1 carried introgressions from tetraploid Triticum militinae in the cv. Tähti genetic background on chromosomes 1A, 2A, 4A, 5A, 7A, 1B and 5B. The most significant QTL for the flowering time variation was identified within the introgressed region on chromosome 5A and its largest effect was associated with the VRN-A1 locus, accounting for up to 70% of phenotypic variance. The allele of T. militinae origin was designated as VRN-A1f-like. The effect of the VRN-A1f-like allele was verified in two other mapping populations. QTL analysis identified that in cv. Tähti and cv. Mooni genetic background, VRN-A1f-like allele incurred a delay of 1.9-18.6 days in flowering time, depending on growing conditions. Sequence comparison of the VRN-A1f-like and VRN-A1a alleles from the parental lines of the mapping populations revealed major mutations in the promoter region as well as in the first intron, including insertion of a MITE element and a large deletion. The sequence variation allowed construction of specific diagnostic PCR markers for VRN-A1f-like allele determination. Identification and quantification of the effect of the VRN-A1f-like allele offers a useful tool for wheat breeding and for studying fine-scale regulation of flowering pathways in wheat. Copyright © 2016 Elsevier B.V. All rights reserved.

African rice (Oryza glaberrima) cultivation in the Togo Hills: ecological and socio-cultural cues in farmer seed selection and development

NARCIS (Netherlands)

Teeken, B.W.E.

2015-01-01

Abstract

Teeken B (2015). African rice (Oryza glaberrima) cultivation in the Togo Hills: ecological and socio-cultural cues in farmer seed selection and development. PhD thesis, Wageningen University, The Netherlands, 306 pp. The low adoption rates of

The biosynthesis, structure and gelatinization properties of starches from wild and cultivated African rice species (Oryza barthii and Oryza glaberrima).

Science.gov (United States)

Wang, Kai; Wambugu, Peterson W; Zhang, Bin; Wu, Alex Chi; Henry, Robert J; Gilbert, Robert G

2015-09-20

The molecular structure and gelatinization properties of starches from domesticated African rice (Oryza glaberrima) and its wild progenitor (Oryza barthii) are determined and comparison made with Asian domesticated rice (Oryza sativa), the commonest commercial rice. This suggests possible enzymatic processes contributing to the unique traits of the African varieties. These have similar starch structures, including smaller amylose molecules, but larger amounts of amylose chains across the whole amylose chain-length distribution, and higher amylose contents, than O. sativa. They also show a higher proportion of two- and three-lamellae spanning amylopectin branch chains (degree of polymerization 34-100) than O. sativa, which contributes to their higher gelatinization temperatures. Fitting amylopectin chain-length distribution with a biosynthesis-based mathematical model suggests that the reason for this difference might be because O. glaberrima and O. barthii have more active SSIIIa and/or less active SBEIIb enzymes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparative transmission genetics of introgressed chromatin in Gossypium (cotton) polyploids.

Science.gov (United States)

Waghmare, Vijay N; Rong, Junkang; Rogers, Carl J; Bowers, John E; Chee, Peng W; Gannaway, John R; Katageri, Ishwarappa; Paterson, Andrew H

2016-04-01

Introgression is widely acknowledged as a potential source of valuable genetic variation, and growing effort is being invested in analysis of interspecific crosses conferring transgressive variation. Experimental backcross populations provide an opportunity to study transmission genetics following interspecific hybridization, identifying opportunities and constraints to introgressive crop improvement. The evolutionary consequences of introgression have been addressed at the theoretical level, however, issues related to levels and patterns of introgression among (plant) species remain inadequately explored, including such factors as polyploidization, subgenome interaction inhabiting a common nucleus, and the genomic distribution and linkage relationships of introgressant alleles. We analyze introgression into the polyploid Gossypium hirsutum (upland cotton) from its sister G. tomentosum and compare the level and pattern with that of G. barbadense representing a different clade tracing to the same polyploidization. Across the genome, recurrent backcrossing to Gossypium hirsutum yielded only one-third of the expected average frequency of the G. tomentosum allele, although one unusual region showed preferential introgression. Although a similar rate of introgression is found in the two subgenomes of polyploid (AtDt) G. hirsutum, a preponderance of multilocus interactions were largely within the Dt subgenome. Skewed G. tomentosum chromatin transmission is polymorphic among two elite G. hirsutum genotypes, which suggests that genetic background may profoundly affect introgression of particular chromosomal regions. Only limited correspondence is found between G. hirsutum chromosomal regions that are intolerant to introgression from the two species, G. barbadense and G. tomentosum, concentrated near possible inversion polymorphisms. Complex transmission of introgressed chromatin highlights the challenges to utilization of exotic germplasm in crop improvement. © 2016

Robustness and strategies of adaptation among farmer varieties of African Rice (Oryza glaberrima) and Asian Rice (Oryza sativa) across West Africa.

Science.gov (United States)

Mokuwa, Alfred; Nuijten, Edwin; Okry, Florent; Teeken, Béla; Maat, Harro; Richards, Paul; Struik, Paul C

2013-01-01

This study offers evidence of the robustness of farmer rice varieties (Oryza glaberrima and O. sativa) in West Africa. Our experiments in five West African countries showed that farmer varieties were tolerant of sub-optimal conditions, but employed a range of strategies to cope with stress. Varieties belonging to the species Oryza glaberrima - solely the product of farmer agency - were the most successful in adapting to a range of adverse conditions. Some of the farmer selections from within the indica and japonica subspecies of O. sativa also performed well in a range of conditions, but other farmer selections from within these two subspecies were mainly limited to more specific niches. The results contradict the rather common belief that farmer varieties are only of local value. Farmer varieties should be considered by breeding programmes and used (alongside improved varieties) in dissemination projects for rural food security.

Robustness and Strategies of Adaptation among Farmer Varieties of African Rice (Oryza glaberrima) and Asian Rice (Oryza sativa) across West Africa

Science.gov (United States)

Maat, Harro; Richards, Paul; Struik, Paul C.

2013-01-01

This study offers evidence of the robustness of farmer rice varieties (Oryza glaberrima and O. sativa) in West Africa. Our experiments in five West African countries showed that farmer varieties were tolerant of sub-optimal conditions, but employed a range of strategies to cope with stress. Varieties belonging to the species Oryza glaberrima – solely the product of farmer agency – were the most successful in adapting to a range of adverse conditions. Some of the farmer selections from within the indica and japonica subspecies of O. sativa also performed well in a range of conditions, but other farmer selections from within these two subspecies were mainly limited to more specific niches. The results contradict the rather common belief that farmer varieties are only of local value. Farmer varieties should be considered by breeding programmes and used (alongside improved varieties) in dissemination projects for rural food security. PMID:23536754

Robustness and Strategies of Adaptation among Farmer Varieties of African Rice (Oryza glaberrima) and Asian Rice (Oryza sativa) across West Africa

NARCIS (Netherlands)

Mokuwa, A.; Nuijten, H.A.C.P.; Okry, F.; Teeken, B.W.E.; Maat, H.; Richards, P.; Struik, P.C.

2013-01-01

This study offers evidence of the robustness of farmer rice varieties (Oryza glaberrima and O. sativa) in West Africa. Our experiments in five West African countries showed that farmer varieties were tolerant of sub-optimal conditions, but employed a range of strategies to cope with stress.

Quantifying introgression risk with realistic population genetics

NARCIS (Netherlands)

Ghosh, A.; Meirmans, P.G.; Haccou, P.

2012-01-01

Introgression is the permanent incorporation of genes from the genome of one population into another. This can have severe consequences, such as extinction of endemic species, or the spread of transgenes. Quantification of the risk of introgression is an important component of genetically modified

Systematic design for trait introgression projects

OpenAIRE

Cameron, John N.; Han, Ye; Wang, Lizhi; Beavis, William D.

2017-01-01

Key message Using an Operations Research approach, we demonstrate design of optimal trait introgression projects with respect to competing objectives. Abstract We demonstrate an innovative approach for designing Trait Introgression (TI) projects based on optimization principles from Operations Research. If the designs of TI projects are based on clear and measurable objectives, they can be translated into mathematical models with decision variables and constraints that can be translated into ...

Introgression and pyramiding into common bean market class fabada of genes conferring resistance to anthracnose and potyvirus.

Science.gov (United States)

Ferreira, Juan José; Campa, Ana; Pérez-Vega, Elena; Rodríguez-Suárez, Cristina; Giraldez, Ramón

2012-03-01

Anthracnose and bean common mosaic (BCM) are considered major diseases in common bean crop causing severe yield losses worldwide. This work describes the introgression and pyramiding of genes conferring genetic resistance to BCM and anthracnose local races into line A25, a bean genotype classified as market class fabada. Resistant plants were selected using resistance tests or combining resistance tests and marker-assisted selection. Lines A252, A321, A493, Sanilac BC6-Are, and BRB130 were used as resistance sources. Resistance genes to anthracnose (Co-2 ( C ), Co-2 ( A252 ) and Co-3/9) and/or BCM (I and bc-3) were introgressed in line A25 through six parallel backcrossing programs, and six breeding lines showing a fabada seed phenotype were obtained after six backcross generations: line A1258 from A252; A1231 from A321; A1220 from A493; A1183 and A1878 from Sanilac BC6-Are; and line A2418 from BRB130. Pyramiding of different genes were developed using the pedigree method from a single cross between lines obtained in the introgression step: line A1699 (derived from cross A1258 × A1220), A2438 (A1220 × A1183), A2806 (A1878 × A2418), and A3308 (A1699 × A2806). A characterization based on eight morpho-agronomic traits revealed a limited differentiation among the obtained breeding lines and the recurrent line A25. However, using a set of seven molecular markers linked to the loci used in the breeding programs it was possible to differentiate the 11 fabada lines. Considering the genetic control of the resistance in resistant donor lines, the observed segregations in the last backcrossing generation, the reaction against the pathogens, and the expression of the molecular markers it was also possible to infer the genotype conferring resistance in the ten fabada breeding lines obtained. As a result of these breeding programs, genetic resistance to three anthracnose races controlled by genes included in clusters Co-2 and Co-3/9, and genetic resistance to BCM controlled

Studies in tissue culture of some indigenous rice (Oryza glaberrima Steud.) accessions in Ghana

International Nuclear Information System (INIS)

Diawuoh, R.G.

2011-01-01

A study was conducted with the aim of developing separate protocols for callus induction and plant regeneration from different parts of three O. glaberrima accessions indigenous to Ghana. The three O. glaberrima accessions, Guame, N/4 and SARI 1 were assessed for their callus induction and plant regeneration ability from leaf segments, mature dehusked seeds and anthers on different concentrations of plant growth regulators, incorporated into Murashige and Skoog, (1962) (MS) basal medium. For leaf segments, callus was induced on MS supplemented with (0-10) mg/l 2,4-D. Callus induction frequency was significantly (p≤0.05) different among accessions, as well as among the 2,4-dichlorophenoxyacetic acid (2,4-D) levels tested. Highest callus induction frequency was exhibited at a concentration of 6 mg/l 2,4-D for all accessions tested. Callus obtained was sub-cultured on regeneration medium consisting of MS supplemented with (1:0-5) mg.l NAA:BAP. Plant regeneration was nil. Instead, prolific root formation was observed. For mature dehusked seeds, callus induction medium consisted of MS supplemented with (0-6) mg/l 2,4-D. All tested accessions exhibited highest callus frequency at 4 mg/l 2,4-D. Similarly callus induction frequency was significantly (p≤0.05) different among accessions, as well as among concentrations of 2,4-D tested. Calli obtained were sub-cultured on MS medium supplemented with (0-2.5) mg/l 6-benzylaminopurine (BAP) and exhibited the highest regeneration frequency on medium containing 2.0 mg/l BAP. However, callus induced on a concentration of 3 mg/l 2,4-D and sub-cultured on a concentration of 2 mg/l BAP gave the best response n terms of shoot proliferation, growth and root development and therefore were considered to be the optimum concentrations for callus induction and plant regeneration respectively. Plantlet regeneration was achieved only in accession N/4 while Guame and SARI 1 exhibited poor regeneration response. Among the three rice

The in silico identification and characterization of a bread wheat/Triticum militinae introgression line

Czech Academy of Sciences Publication Activity Database

Abrouk, Michael; Balcárková, Barbora; Šimková, Hana; Komínková, Eva; Martis, M.M.; Jakobson, I.; Timofejeva, L.; Rey, Elodie; Vrána, Jan; Kilian, A.; Jarve, K.; Doležel, Jaroslav; Valárik, Miroslav

2017-01-01

Roč. 15, č. 2 (2017), s. 249-256 ISSN 1467-7644 R&D Projects: GA MŠk(CZ) LO1204; GA ČR(CZ) GA14-07164S Institutional support: RVO:61389030 Keywords : crop improvement * powdery mildew * common wheat * chromosomes * genome * resistance * plant * recombination * evolution * barley * GenomeZipper * alien introgression * comparative analysis * chromosome rearrangement * chromosome translocation * linkage drag Subject RIV: EB - Gene tics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 7.443, year: 2016

An HMM-based comparative genomic framework for detecting introgression in eukaryotes.

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Kevin J Liu

2014-06-01

Full Text Available One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on PhyloNet-HMM-a new comparative genomic framework for detecting introgression in genomes. PhyloNet-HMM combines phylogenetic networks with hidden Markov models (HMMs to simultaneously capture the (potentially reticulate evolutionary history of the genomes and dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus genome detected a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgressed genomic regions. Based on our analysis, it is estimated that about 9% of all sites within chromosome 7 are of introgressive origin (these cover about 13 Mbp of chromosome 7, and over 300 genes. Further, our model detected no introgression in a negative control data set. We also found that our model accurately detected introgression and other evolutionary processes from synthetic data sets simulated under the coalescent model with recombination, isolation, and migration. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism.

Broadening the genetic base of Abyssinian mustard (Brassica carinata A. Braun through introgression of genes from related allotetraploid species

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Farooq A. Sheikh

2014-07-01

Full Text Available Brassica carinata (BBCC, 2n=34 has still to emerge as a major oilseed crop owing to poor agronomic attributes like long stature, long maturity duration and low seed yield. The restricted amount of genetic variability available in natural B. carinata necessitates utilization of new sources of variability for broadening its genetic base. Interspecific hybridization followed by selection in selfed and back cross progenies was employed to generate useful variability into B. carinata cv ˈPC5ˈ from elite lines of Brassica napus (AACC, 2n=38 and Brassica juncea (AABB, 2n=36. The morphological evaluation of 24 stable introgressed progenies revealed wide range of variability for key economic traits. The progenies with mean maturity duration of 161 ± 2.1 days, short stature of 139.5 ± 6.5 cm and seed yield per plant of 18.6 ± 2.0 g in comparison to the corresponding figures of 168 ± 4.6 days, 230.6 ± 12.7 cm and 12.0 ± 2.4 g in ˈPC5ˈ (recurrent parent were recovered. Diversity analysis at morphological level revealed that 22 out of 24 stable introgressed progenies were grouped with B. carinata ˈPC5ˈ at average taxonomic distance of 1.19. The diversity at molecular level using 25 polymorphic and reproducible RAPD primers revealed that 19 out of 21 introgressed progenies grouped with B. carinata ˈPC5ˈ at a similarity coefficient of 0.68. The clusters in general represent a wide range of genetic diversity in the back cross lines of B. carinata as a result of introgression of genes from elite lines of B. napus and B. juncea parents.

Fine scale mapping of genomic introgressions within the Drosophila yakuba clade.

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Turissini, David A; Matute, Daniel R

2017-09-01

The process of speciation involves populations diverging over time until they are genetically and reproductively isolated. Hybridization between nascent species was long thought to directly oppose speciation. However, the amount of interspecific genetic exchange (introgression) mediated by hybridization remains largely unknown, although recent progress in genome sequencing has made measuring introgression more tractable. A natural place to look for individuals with admixed ancestry (indicative of introgression) is in regions where species co-occur. In west Africa, D. santomea and D. yakuba hybridize on the island of São Tomé, while D. yakuba and D. teissieri hybridize on the nearby island of Bioko. In this report, we quantify the genomic extent of introgression between the three species of the Drosophila yakuba clade (D. yakuba, D. santomea), D. teissieri). We sequenced the genomes of 86 individuals from all three species. We also developed and applied a new statistical framework, using a hidden Markov approach, to identify introgression. We found that introgression has occurred between both species pairs but most introgressed segments are small (on the order of a few kilobases). After ruling out the retention of ancestral polymorphism as an explanation for these similar regions, we find that the sizes of introgressed haplotypes indicate that genetic exchange is not recent (>1,000 generations ago). We additionally show that in both cases, introgression was rarer on X chromosomes than on autosomes which is consistent with sex chromosomes playing a large role in reproductive isolation. Even though the two species pairs have stable contemporary hybrid zones, providing the opportunity for ongoing gene flow, our results indicate that genetic exchange between these species is currently rare.

Flooding tolerance in interspecific introgression lines containing chromosome segments from teosinte (Zea nicaraguensis) in maize (Zea mays subsp. mays)

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Mano, Y.; Omori, F.

2013-01-01

Background and Aims Nicaraguan teosinte (Zea nicaraguensis), a species found in frequently flooded areas, provides useful germplasm for breeding flooding-tolerant maize (Z. mays subsp. mays). The objective of this study was to select flooding-tolerant lines using a library of introgression lines (ILs), each containing a chromosome segment from Z. nicaraguensis in the maize inbred line Mi29. Methods To produce the ILs, a single F1 plant derived from a cross between maize Mi29 and Z. nicaraguensis was backcrossed to Mi29 three times, self-pollinated four times and genotyped using simple sequence repeat markers. Flooding tolerance was evaluated at the seedling stage under reducing soil conditions. Key Results By backcrossing and selfing, a series of 45 ILs were developed covering nearly the entire maize genome. Five flooding-tolerant lines were identified from among the ILs by evaluating leaf injury. Among these, line IL#18, containing a Z. nicaraguensis chromosome segment on the long arm of chromosome 4, showed the greatest tolerance to flooding, suggesting the presence of a major quantitative trait locus (QTL) in that region. The presence of the QTL was verified by examining flooding tolerance in a population segregating for the candidate region of chromosome 4. There was no significant relationship between the capacity to form constitutive aerenchyma and flooding tolerance in the ILs, indicating the presence of other factors related to flooding tolerance under reducing soil conditions. Conclusions A flooding-tolerant genotype, IL#18, was identified; this genotype should be useful for maize breeding. In addition, because the chromosome segments of Z. nicaraguensis in the ILs cover nearly the entire genome and Z. nicaraguensis possesses several unique traits related to flooding tolerance, the ILs should be valuable material for additional QTL detection and the development of flooding-tolerant maize lines. PMID:23877074

Flooding tolerance in interspecific introgression lines containing chromosome segments from teosinte (Zea nicaraguensis) in maize (Zea mays subsp. mays).

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Mano, Y; Omori, F

2013-10-01

Nicaraguan teosinte (Zea nicaraguensis), a species found in frequently flooded areas, provides useful germplasm for breeding flooding-tolerant maize (Z. mays subsp. mays). The objective of this study was to select flooding-tolerant lines using a library of introgression lines (ILs), each containing a chromosome segment from Z. nicaraguensis in the maize inbred line Mi29. To produce the ILs, a single F1 plant derived from a cross between maize Mi29 and Z. nicaraguensis was backcrossed to Mi29 three times, self-pollinated four times and genotyped using simple sequence repeat markers. Flooding tolerance was evaluated at the seedling stage under reducing soil conditions. By backcrossing and selfing, a series of 45 ILs were developed covering nearly the entire maize genome. Five flooding-tolerant lines were identified from among the ILs by evaluating leaf injury. Among these, line IL#18, containing a Z. nicaraguensis chromosome segment on the long arm of chromosome 4, showed the greatest tolerance to flooding, suggesting the presence of a major quantitative trait locus (QTL) in that region. The presence of the QTL was verified by examining flooding tolerance in a population segregating for the candidate region of chromosome 4. There was no significant relationship between the capacity to form constitutive aerenchyma and flooding tolerance in the ILs, indicating the presence of other factors related to flooding tolerance under reducing soil conditions. A flooding-tolerant genotype, IL#18, was identified; this genotype should be useful for maize breeding. In addition, because the chromosome segments of Z. nicaraguensis in the ILs cover nearly the entire genome and Z. nicaraguensis possesses several unique traits related to flooding tolerance, the ILs should be valuable material for additional QTL detection and the development of flooding-tolerant maize lines.

Introgression of a Rare Haplotype from Southeastern Africa to Breed California Blackeyes with Larger Seeds

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Mitchell R Lucas

2015-03-01

Full Text Available Seed size distinguishes most crops from their wild relatives and is an important quality trait for the grain legume cowpea. In order to breed cowpea varieties with larger seeds we introgressed a rare haplotype associated with large seeds at the Css-1 locus from an African buff seed type cultivar, IT82E-18 (18.5g/100 seeds, into a blackeye seed type cultivar, CB27 (22g/100 seed. Four RILs derived from these two parents were chosen for marker-assisted breeding based on SNP genotyping with a goal of stacking large seed haplotypes into a CB27 background. Foreground and background selection were performed during two cycles of backcrossing based on genome-wide SNP markers. The average seed size of introgression lines homozygous for haplotypes associated with large seeds was 28.7g/100 seed and 24.8g/100 seed for cycles 1 and 2, respectively. One cycle 1 introgression line with desirable seed quality was selfed for two generations to make families with very large seeds (28-35g/100 seeds. Field-based performance trials helped identify breeding lines that not only have large seeds but are also desirable in terms of yield, maturity, and plant architecture when compared to industry standards. A principal component analysis was used to explore the relationships between the parents relative to a core set of landraces and improved varieties based on high-density SNP data. The geographic distribution of haplotypes at the Css-1 locus suggest the haplotype associated with large seeds is unique to accessions collected from Southeastern Africa. Therefore this QTL has a strong potential to develop larger seeded varieties for other growing regions which is demonstrated in this work using a California pedigree.

QTL Mapping of Grain Quality Traits Using Introgression Lines Carrying Oryza rufipogon Chromosome Segments in Japonica Rice.

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Yun, Yeo-Tae; Chung, Chong-Tae; Lee, Young-Ju; Na, Han-Jung; Lee, Jae-Chul; Lee, Sun-Gye; Lee, Kwang-Won; Yoon, Young-Hwan; Kang, Ju-Won; Lee, Hyun-Sook; Lee, Jong-Yeol; Ahn, Sang-Nag

2016-12-01

Improved eating quality is a major breeding target in japonica rice due to market demand. Consequently, quantitative trait loci (QTL) for glossiness of cooked rice and amylose content associated with eating quality have received much research focus because of their importance in rice quality. In this study, QTL associated with 12 grain quality traits were identified using 96 introgression lines (IL) of rice developed from an interspecific cross between the Korean elite O. sativa japonica cultivar 'Hwaseong' and O. rufipogon over 7 years. QTL analyses indicated that QTL qDTH6 for heading date, detected on chromosome 6 is associated with variance in grain traits. Most QTLs detected in this study clustered near the qDTH6 locus on chromosome 6, suggesting the effect of qDTH6. O. rufipogon alleles negatively affected grain quality traits except for a few QTLs, including qGCR9 for glossiness of cooked rice on chromosome 9. To characterize the effect of the O. rufipogon locus harboring qGCR9, four lines with a single but different O. rufipogon segment near qGCR9 were compared to Hwaseong. Three lines (O. rufipopgon ILs) having O. rufipogon segment between RM242 and RM245 in common showed higher glossiness of cooked rice than Hwaseong and the other line (Hwaseong IL), indicating that qGCR9 is located in the 3.4-Mb region between RM242 and RM245. Higher glossiness of cooked rice conferred by the O. rufipogon allele might be associated with protein content considering that three lines had lower protein content than Hwaseong (P < 0.1). These three O. rufipogon ILs showed higher yield than Hwaseong and Hwaseong IL due to increase in spikelets per panicle and grain weight indicating the linkage of qGCR9 and yield component QTLs. The qGCR9 locus is of particular interest because of its independence from other undesirable grain quality traits in O. rufipogon. SSR markers linked to qGCR9 can be used to develop high-quality japonica lines and offer a starting point for map

Repeated adaptive introgression at a gene under multiallelic balancing selection.

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Vincent Castric

2008-08-01

Full Text Available Recently diverged species typically have incomplete reproductive barriers, allowing introgression of genetic material from one species into the genomic background of the other. The role of natural selection in preventing or promoting introgression remains contentious. Because of genomic co-adaptation, some chromosomal fragments are expected to be selected against in the new background and resist introgression. In contrast, natural selection should favor introgression for alleles at genes evolving under multi-allelic balancing selection, such as the MHC in vertebrates, disease resistance, or self-incompatibility genes in plants. Here, we test the prediction that negative, frequency-dependent selection on alleles at the multi-allelic gene controlling pistil self-incompatibility specificity in two closely related species, Arabidopsis halleri and A. lyrata, caused introgression at this locus at a higher rate than the genomic background. Polymorphism at this gene is largely shared, and we have identified 18 pairs of S-alleles that are only slightly divergent between the two species. For these pairs of S-alleles, divergence at four-fold degenerate sites (K = 0.0193 is about four times lower than the genomic background (K = 0.0743. We demonstrate that this difference cannot be explained by differences in effective population size between the two types of loci. Rather, our data are most consistent with a five-fold increase of introgression rates for S-alleles as compared to the genomic background, making this study the first documented example of adaptive introgression facilitated by balancing selection. We suggest that this process plays an important role in the maintenance of high allelic diversity and divergence at the S-locus in flowering plant families. Because genes under balancing selection are expected to be among the last to stop introgressing, their comparison in closely related species provides a lower-bound estimate of the time since the

Sequence-based SSR marker development and their application in defining the Introgressions of LA0716 (Solanum pennellii in the background of cv. M82 (Solanum lycopersicum.

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Wenbo Long

Full Text Available The introgression lines (ILs from cv. M82 (Solanum lycopersicum × LA0716 (S. pennellii have been proven to be exceptionally useful for genetic analysis and gene cloning. The introgressions were originally defined by RFLP markers at their development. The objectives of this study are to develop polymorphic SSR markers, and to re-define the DNA introgression from LA0716 in the ILs. Tomato sequence data was scanned by software to generate SSR markers. In total, 829 SSRs, which could be robustly amplified by PCR, were developed. Among them, 658 SSRs were dinucleotide repeats, 162 were trinucleotide repeats, and nine were tetranucleotide repeats. The 829 SSRs together with 96 published RFLPs were integrated into the physical linkage map of S. lycopersicum. Introgressions of DNA fragments from LA0716 were re-defined among the 75 ILs using the newly developed SSRs. A specific introgression of DNA fragment from LA0716 was identified in 72 ILs as described previously by RFLP, whereas the specific DNA introgression described previously were not detected in the ILs LA4035, LA4059 and LA4091. The physical location of each investigated DNA introgression was finely determined by SSR mapping. Among the 72 ILs, eight ILs showed a shorter and three ILs (IL3-2, IL12-3 and IL12-3-1 revealed a longer DNA introgression than that framed by RFLPs. Furthermore, 54 previously undefined segments were found in 21 ILs, ranging from 1 to 11 DNA introgressions per IL. Generally, the newly developed SSRs provide additional markers for genetic studies of tomatoes, and the fine definition of DNA introgressions from LA0716 would facilitate the use of the ILs for genetic analysis and gene cloning.

IDENTIFICATION AND MAPPING OF A GENE FOR RICE SLENDER KERNEL USING Oryza glumaepatula INTROGRESSION LINES

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Sobrizal Sobrizal

2016-10-01

Full Text Available World demand for superior rice grain quality tends to increase. One of the  criteria of appearance quality of rice grain is grain shape. Rice consumers  exhibit wide preferences for grain shape, but most Indonesian rice consumers prefer long and slender grain. The objectives of this study were to identify and map a gene for rice slender kernel trait using Oryza  glumaepatula introgression lines with O. sativa cv. Taichung 65 genetic background. A segregation analysis of BC4F2 population derived from backcrosses of a donor parent O. glumaepatula into a recurrent parent Taichung 65 showed that the slender kernel was controlled by a single recessive gene. This new identified gene was designated as sk1 (slender kernel 1. Moreover, based on the RFLP analyses using 14 RFLP markers located on chromosomes 2, 8, 9, and 10 in which the O. glumaepatula chromosomal segments were retained in BC4F2 population, the sk1 was located between RFLP markers C679 and C560 on the long arm of chromosome 2, with map distances of 2.8 and 1.5 cM, respectively. The wild rice O. glumaepatula carried a recessive allele for slender kernel. This allele may be useful in breeding of rice with slender kernel types. In addition, the development of plant materials and RFLP map associated with slender kernel in this study is the preliminary works in the effort to isolate this important grain shape gene.

Introgression of genetic material from Zea mays ssp. Mexicana into cultivated maize was facilitated by tissue culture

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Wang, L.; Gu, X.; Qu, M.; Luan, J.; Zhang, J.

2012-01-01

Zea mays ssp. mexicana, a wild relative of cultivated maize (Z. mays ssp. mays), is a useful gene resource for maize breeding. In this study, two populations were generated by conventional breeding scheme (population I) or tissue culture regime (population II), respectively, to introgress genetic material of Z. mays ssp. mexicana into maize. Karyotype analysis showed that the arm ratios of 10 pairs of chromosomes in parent maize Ye515 and derivative lines from 2 different populations with 26% and 38% chromosome variation frequencies, respectively. Alien chromatin was detected in the root tip cells of progeny plants through genomic in situ hybridization (GISH). There were 3.3 chromosomes carrying alien chromatin on average in population I and 6.5 in population II. The hybridization signals were located mainly at the terminal or sub terminal regions of the chromosomes and the sizes were notably variant among lines. Based on those results, it is concluded that the introgression of genetic material from Z. mays ssp. mexicana into cultivated maize was facilitated by tissue culture, and subsequently some excellent materials for maize breeding were created. (author)

Introgression of mitochondrial DNA among Myodes voles: consequences for energetics?

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Boratyński Zbyszek

2011-12-01

Full Text Available Abstract Background Introgression of mitochondrial DNA (mtDNA is among the most frequently described cases of reticulate evolution. The tendency of mtDNA to cross interspecific barriers is somewhat counter-intuitive considering the key function of enzymes that it encodes in the oxidative-phosphorylation process, which could give rise to hybrid dysfunction. How mtDNA reticulation affects the evolution of metabolic functions is, however, uncertain. Here we investigated how morpho-physiological traits vary in natural populations of a common rodent (the bank vole, Myodes glareolus and whether this variation could be associated with mtDNA introgression. First, we confirmed that M. glareolus harbour mtDNA introgressed from M. rutilus by analyzing mtDNA (cytochrome b, 954 bp and nuclear DNA (four markers; 2333 bp in total sequence variation and reconstructing loci phylogenies among six natural populations in Finland. We then studied geographic variation in body size and basal metabolic rate (BMR among the populations of M. glareolus and tested its relationship with mtDNA type. Results Myodes glareolus and its arctic neighbour, M. rutilus, are reciprocally monophyletic at the analyzed nuclear DNA loci. In contrast, the two northernmost populations of M. glareolus have a fixed mitotype that is shared with M. rutilus, likely due to introgressive hybridization. The analyses of phenotypic traits revealed that the body mass and whole-body, but not mass corrected, BMR are significantly reduced in M. glareolus females from northern Finland that also have the introgressed mitotype. Restricting the analysis to the single population where the mitotypes coexist, the association of mtDNA type with whole-body BMR remained but those with mass corrected BMR and body mass did not. Mitochondrial sequence variation in the introgressed haplotypes is compatible with demographic growth of the populations, but may also be a result of positive selection. Conclusion Our

Widespread introgression of mountain hare genes into Fennoscandian brown hare populations.

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Riikka Levänen

Full Text Available In Fennoscandia, mountain hare (Lepus timidus and brown hare (Lepus europaeus hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the low levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.

Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae).

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Leduc-Robert, Geneviève; Maddison, Wayne P

2018-02-22

Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict. To infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave almost completely congruent results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial data are incongruent with the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus groups, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the relative contributions of ILS and introgression, we analyzed gene tree discordance for nuclear loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517 loci) and found signals of introgression in both. Finally, we tested specifically for introgression in the concatenated nuclear matrix with Patterson's D statistics and D FOIL . We found nuclear introgression resulting in substantial admixture between americanus group species, between H. roberti

Mating, hybridisation and introgression in Lasius ants (Hymenoptera: Formicidae)

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Van der Have, Tom; Pedersen, Jes Søe; Boomsma, Jacobus Jan

2011-01-01

Recent reviews have shown that hybridisation among ant species is likely to be more common than previously appreci-ated, but that documented cases of introgression remain rare. After molecular phylogenetic work had shown that Euro-pean Lasius niger (LINNAEUS, 1758) and L. psammophilus SEIFERT, 1992...... (formerly L. alienus (FOERSTER, 1850)) are unlikely to be very closely related, we decided to analyse an old data set confirming the conclusion by PEARSON (1983) that these two ants can indeed form viable hybrids. We show that signatures of introgression can be detected in a Danish site...... sympatrically. This would imply that multiple accessible field sites are available to study the molecular details of hybridisation and in-trogression between two ant species that have variable degrees of sympatry throughout their distributional ranges...

Progressive introgression between ¤Brassica napus¤ (oilseed rape) and ¤B-rapa¤

DEFF Research Database (Denmark)

Hansen, L.B.; Siegismund, H.R.; Bagger Jørgensen, Rikke

2003-01-01

We have earlier shown extensive introgression between oilseed rape (Brassica napus) and B. rapa in a weedy population using AFLP markers specific for the nuclear genomes. In order to describe the progress of this introgression, we examined 117 offspring from 12 maternal plants from the introgress...

The introgression of RNAi silencing of γ-gliadins into commercial lines of bread wheat changes the mixing and technological properties of the dough.

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Javier Gil-Humanes

Full Text Available In the present work the effects on dough quality by the down-regulation of γ-gliadins in different genetic backgrounds of bread wheat were investigated. RNAi-mediated silencing of γ-gliadins was introgressed by conventional crossing into three commercial bread wheat lines (namely 'Gazul', 'Podenco' and 'Arpain', and along with the transgenic line A1152 (cv. Bobwhite compared with their respective wild types. The protein fractions were quantified by RP-HPLC, whereas the technological and mixing properties were assessed by SDSS test and by the Mixograph instrument. Principal component analysis (PCA was carried out for both the wild types and the transgenic lines, showing differences in the factors affecting the technological and mixing properties of the dough as a consequence of the reduction of the γ-gliadins. In transgenic lines, the α- and ω-gliadins, and total gliadins negatively affected the dough strength and tolerance to over-mixing, whereas the L/H ratio showed the opposite effect, positively influencing the dough quality. The increase of the SDSS volume in the transgenic lines of 'Gazul', 'Podenco' and 'Arpain' indicates increased gluten strength and quality respect to the wild types. SDSS volume was found to be positively influenced by the amount of glutenins, which were also increased in the transgenic lines. In addition, a positive effect was observed in the MT, PR1 and RBD in some of the transgenic lines of 'Podenco' and 'Arpain'. In conclusion, the down-regulation of γ-gliadins resulted in stronger doughs and a better tolerance to over-mixing in some transgenic lines. Although the reduction of γ-gliadins seems not to have a direct effect on the mixing and bread-making properties, the compensatory effect on the synthesis of the other prolamins may result in stronger doughs with improved over-mixing resistance.

The introgression of RNAi silencing of γ-gliadins into commercial lines of bread wheat changes the mixing and technological properties of the dough.

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Gil-Humanes, Javier; Pistón, Fernando; Giménez, María J; Martín, Antonio; Barro, Francisco

2012-01-01

In the present work the effects on dough quality by the down-regulation of γ-gliadins in different genetic backgrounds of bread wheat were investigated. RNAi-mediated silencing of γ-gliadins was introgressed by conventional crossing into three commercial bread wheat lines (namely 'Gazul', 'Podenco' and 'Arpain'), and along with the transgenic line A1152 (cv. Bobwhite) compared with their respective wild types. The protein fractions were quantified by RP-HPLC, whereas the technological and mixing properties were assessed by SDSS test and by the Mixograph instrument. Principal component analysis (PCA) was carried out for both the wild types and the transgenic lines, showing differences in the factors affecting the technological and mixing properties of the dough as a consequence of the reduction of the γ-gliadins. In transgenic lines, the α- and ω-gliadins, and total gliadins negatively affected the dough strength and tolerance to over-mixing, whereas the L/H ratio showed the opposite effect, positively influencing the dough quality. The increase of the SDSS volume in the transgenic lines of 'Gazul', 'Podenco' and 'Arpain' indicates increased gluten strength and quality respect to the wild types. SDSS volume was found to be positively influenced by the amount of glutenins, which were also increased in the transgenic lines. In addition, a positive effect was observed in the MT, PR1 and RBD in some of the transgenic lines of 'Podenco' and 'Arpain'. In conclusion, the down-regulation of γ-gliadins resulted in stronger doughs and a better tolerance to over-mixing in some transgenic lines. Although the reduction of γ-gliadins seems not to have a direct effect on the mixing and bread-making properties, the compensatory effect on the synthesis of the other prolamins may result in stronger doughs with improved over-mixing resistance.

Introgression in Lake Malaŵi

DEFF Research Database (Denmark)

Stauffer, Jay R.; Madsen, Henry; Rollinson, David

2014-01-01

with the indigenous strain of S. haematobium, which ultimately produced via introgression a strain that can use both B. globosus and B. nyassanus as intermediate hosts. This actively evolving situation involving intermediate snail-host switching and decline of Trematocranus placodon, a natural cichlid snail predator...

A maize introgression library reveals ample genetic variability for root architecture, water use efficiency and grain yield under different water regimes

OpenAIRE

Salvi, S.; Giuliani, S.; Cané, M.; Sciara, G.; Bovina, R.; Welcker, Claude; Cabrera Bosquet, Llorenç; Grau, Antonin; Tardieu, Francois; Meriggi, P.

2015-01-01

The genetic dissection of root system architecture (RSA) provides valuable opportunities towards a better understanding of its role in determining yield under different water regimes. To this end, a maize introgression library comprised of 75 BC5 lines derived from the cross between Gaspé Flint (an early line; donor parent) and B73 (an elite line; recurrent parent) were evaluated in two experiments conducted under well-watered and water-deficit conditions (WW and WD, respectively) in order to...

Detecting slow introgression of invasive alleles in an extensively restocked game bird

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Ines eSanchez-Donoso

2014-04-01

Full Text Available Interbreeding of two species in the wild implies introgression of alleles from one species into the other only when admixed individuals survive and successfully backcross with the parental species. Consequently, estimating the proportion of first generation hybrids in a population may not inform about the evolutionary impact of hybridization. Samples obtained over a long time span may offer a more accurate view of the spreading of introgressed alleles in a species’ gene pool. Common quail (Coturnix coturnix populations in Europe have been restocked extensively with farm quails of hybrid origin (crosses with Japanese quails, C. japonica. We genetically monitored a common quail population over 15 years to investigate whether genetic introgression is occurring and used simulations to investigate our power to detect it. Our results revealed that some introgression has occurred, but we did not observe a significant increase over time in the proportion of admixed individuals. However, simulations showed that the degree of admixture may be larger than anticipated due to the limited power of analyses over a short time span, and that observed data was compatible with a low rate of introgression, probably resulting from reduced fitness of admixed individuals. Simulations predicted this could result in extensive admixture in the near future.

Introgressive hybridization: brown bears as vectors for polar bear alleles.

Science.gov (United States)

Hailer, Frank

2015-03-01

The dynamics and consequences of introgression can inform about numerous evolutionary processes. Biologists have therefore long been interested in hybridization. One challenge, however, lies in the identification of nonadmixed genotypes that can serve as a baseline for accurate quantification of admixture. In this issue of Molecular Ecology, Cahill et al. (2015) analyse a genomic data set of 28 polar bears, eight brown bears and one American black bear. Polar bear alleles are found to be introgressed into brown bears not only near a previously identified admixture zone on the Alaskan Admiralty, Baranof and Chichagof (ABC) Islands, but also far into the North American mainland. Elegantly contrasting admixture levels at autosomal and X chromosomal markers, Cahill and colleagues infer that male-biased dispersal has spread these introgressed alleles away from the Late Pleistocene contact zone. Compared to a previous study on the ABC Island population in which an Alaskan brown bear served as a putatively admixture-free reference, Cahill et al. (2015) utilize a newly sequenced Swedish brown bear as admixture baseline. This approach reveals that brown bears have been impacted by introgression from polar bears to a larger extent (up to 8.8% of their genome), than previously known, including the bear that had previously served as admixture baseline. No evidence for introgression of brown bear into polar bear is found, which the authors argue could be a consequence of selection. Besides adding new exciting pieces to the puzzle of polar/brown bear evolutionary history, the study by Cahill and colleagues highlights that wildlife genomics is moving from analysing single genomes towards a landscape genomics approach. © 2015 John Wiley & Sons Ltd.

Systematic design for trait introgression projects.

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Cameron, John N; Han, Ye; Wang, Lizhi; Beavis, William D

2017-10-01

Using an Operations Research approach, we demonstrate design of optimal trait introgression projects with respect to competing objectives. We demonstrate an innovative approach for designing Trait Introgression (TI) projects based on optimization principles from Operations Research. If the designs of TI projects are based on clear and measurable objectives, they can be translated into mathematical models with decision variables and constraints that can be translated into Pareto optimality plots associated with any arbitrary selection strategy. The Pareto plots can be used to make rational decisions concerning the trade-offs between maximizing the probability of success while minimizing costs and time. The systematic rigor associated with a cost, time and probability of success (CTP) framework is well suited to designing TI projects that require dynamic decision making. The CTP framework also revealed that previously identified 'best' strategies can be improved to be at least twice as effective without increasing time or expenses.

Molecular mapping of the novel powdery mildew resistance gene Pm36 introgressed from Triticum turgidum var. dicoccoides in durum wheat.

Science.gov (United States)

Blanco, Antonio; Gadaleta, A; Cenci, A; Carluccio, A V; Abdelbacki, A M M; Simeone, R

2008-06-01

Powdery mildew, caused by Blumeria graminis f.sp. tritici, is one of the most important wheat diseases in many regions of the world. Triticum turgidum var. dicoccoides (2n=4x=AABB), the progenitor of cultivated wheats, shows particular promises as a donor of useful genetic variation for several traits, including disease resistances. The wild emmer accession MG29896, resistant to powdery mildew, was backcrossed to the susceptible durum wheat cultivar Latino, and a set of backcross inbred lines (BC(5)F(5)) was produced. Genetic analysis of F(3) populations from two resistant introgression lines (5BIL-29 x Latino and 5BIL-42 x Latino) indicated that the powdery mildew resistance is controlled by a single dominant gene. Molecular markers and the bulked segregant analysis were used to characterize and map the powdery mildew resistance. Five AFLP markers (XP43M32((250)), XP46M31((410)), XP41M37((100)), XP41M39((250)), XP39M32((120))), three genomic SSR markers (Xcfd07, Xwmc75, Xgwm408) and one EST-derived SSR marker (BJ261635) were found to be linked to the resistance gene in 5BIL-29 and only the BJ261635 marker in 5BIL-42. By means of Chinese Spring nullisomic-tetrasomic, ditelosomic and deletion lines, the polymorphic markers and the resistance gene were assigned to chromosome bin 5BL6-0.29-0.76. These results indicated that the two lines had the same resistance gene and that the introgressed dicoccoides chromosome segment was longer (35.5 cM) in 5BIL-29 than that introgressed in 5BIL-42 (less than 1.5 cM). As no powdery mildew resistance gene has been reported on chromosome arm 5BL, the novel resistance gene derived from var. dicoccoides was designated Pm36. The 244 bp allele of BJ261635 in 5BIL-42 can be used for marker-assisted selection during the wheat resistance breeding process for facilitating gene pyramiding.

Interspecies introgressive hybridization in spiny frogs Quasipaa (Family Dicroglossidae) revealed by analyses on multiple mitochondrial and nuclear genes.

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Zhang, Qi-Peng; Hu, Wen-Fang; Zhou, Ting-Ting; Kong, Shen-Shen; Liu, Zhi-Fang; Zheng, Rong-Quan

2018-01-01

Introgression may lead to discordant patterns of variation among loci and traits. For example, previous phylogeographic studies on the genus Quasipaa detected signs of genetic introgression from genetically and morphologically divergent Quasipaa shini or Quasipaa spinosa . In this study, we used mitochondrial and nuclear DNA sequence data to verify the widespread introgressive hybridization in the closely related species of the genus Quasipaa , evaluate the level of genetic diversity, and reveal the formation mechanism of introgressive hybridization. In Longsheng, Guangxi Province, signs of asymmetrical nuclear introgression were detected between Quasipaa boulengeri and Q. shini . Unidirectional mitochondrial introgression was revealed from Q. spinosa to Q. shini . By contrast, bidirectional mitochondrial gene introgression was detected between Q. spinosa and Q. shini in Lushan, Jiangxi Province. Our study also detected ancient hybridizations between a female Q. spinosa and a male Q. jiulongensis in Zhejiang Province. Analyses on mitochondrial and nuclear genes verified three candidate cryptic species in Q. spinosa , and a cryptic species may also exist in Q. boulengeri . However, no evidence of introgressive hybridization was found between Q. spinosa and Q. boulengeri . Quasipaa exilispinosa from all the sampling localities appeared to be deeply divergent from other communities. Our results suggest widespread introgressive hybridization in closely related species of Quasipaa and provide a fundamental basis for illumination of the forming mechanism of introgressive hybridization, classification of species, and biodiversity assessment in Quasipaa .

When and how did Bos indicus introgress into Mongolian cattle?

Science.gov (United States)

Yue, Xiangpeng; Li, Ran; Liu, Li; Zhang, Yunsheng; Huang, Jieping; Chang, Zhenhua; Dang, Ruihua; Lan, Xianyong; Chen, Hong; Lei, Chuzhao

2014-03-10

The Mongolian cattle are one of the most widespread breeds with strictly Bos taurus morphological features in northern China. In our current study, we presented a diversity of mitochondrial DNA (mtDNA) D-loop region and Y chromosome SNP markers in 25 male and 8 female samples of Mongolian cattle from the Xinjiang Uygur autonomous region in Western China, and detected 21 B. taurus and four Bos indicus (zebu) mtDNA haplotypes. Among four B. indicus mtDNA haplotypes, two haplotypes belonged to I1 haplogroup and the remaining two haplotypes belonged to I2 haplogroup. In contrast, all 25 male Mongolian cattle samples revealed B. taurus Y chromosome haplotype and no B. indicus haplotypes were found. Historical and archeological records indicate that B. taurus was introduced to Xinjiang during the second millennium BC and B. indicus appeared in this region by the second century AD. The two types of cattle coexisted for many centuries in Xinjiang, as depicted in clay and wooden figurines unearthed in the Astana cemetery in Turfan (3rd-8th century AD). Multiple lines of evidence suggest that the earliest B. indicus introgression in the Mongolian cattle may have occurred during the 2nd-7th centuries AD through the Silk Road around the Xinjiang region. This conclusion differs from the previous hypothesis that zebu introgression to Mongolian cattle happened during the Mongol Empire era in the 13th century. Copyright © 2014 Elsevier B.V. All rights reserved.

Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash

Science.gov (United States)

Holdsworth, William L.; LaPlant, Kyle E.; Bell, Duane C.; Jahn, Molly M.; Mazourek, Michael

2016-01-01

Powdery mildew is a major fungal disease on squash and pumpkin (Cucurbita spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within Cucurbita pepo and only infrequently in Cucurbita moschata, but has been achieved in both species through the introgression of a major resistance gene from the wild species Cucurbita okeechobeensis subsp. martinezii. At present, this gene, Pm-0, is used extensively in breeding, and is found in nearly all powdery mildew-resistant C. pepo and C. moschata commercial cultivars. In this study, we mapped C. okeechobeensis subsp. martinezii-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant C. pepo and C. moschata cultivars bred at Cornell University that, by common possession of Pm-0, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 de novo SNP markers in each of the three Cucurbita species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the Pm-0 introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a C. pepo cultivar panel that included the Cornell lines, heirlooms, and 68 additional C. pepo cultivars and with an independent F2 population derived from C. okeechobeensis subsp. martinezii x C. moschata. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection. PMID:27936008

Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash.

Science.gov (United States)

Holdsworth, William L; LaPlant, Kyle E; Bell, Duane C; Jahn, Molly M; Mazourek, Michael

2016-01-01

Powdery mildew is a major fungal disease on squash and pumpkin (Cucurbita spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within Cucurbita pepo and only infrequently in Cucurbita moschata, but has been achieved in both species through the introgression of a major resistance gene from the wild species Cucurbita okeechobeensis subsp. martinezii. At present, this gene, Pm-0, is used extensively in breeding, and is found in nearly all powdery mildew-resistant C. pepo and C. moschata commercial cultivars. In this study, we mapped C. okeechobeensis subsp. martinezii-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant C. pepo and C. moschata cultivars bred at Cornell University that, by common possession of Pm-0, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 de novo SNP markers in each of the three Cucurbita species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the Pm-0 introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a C. pepo cultivar panel that included the Cornell lines, heirlooms, and 68 additional C. pepo cultivars and with an independent F2 population derived from C. okeechobeensis subsp. martinezii x C. moschata. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection.

Rapid and targeted introgression of genes into popular wheat cultivars using marker-assisted background selection.

Directory of Open Access Journals (Sweden)

Harpinder S Randhawa

Full Text Available A marker-assisted background selection (MABS-based gene introgression approach in wheat (Triticum aestivum L. was optimized, where 97% or more of a recurrent parent genome (RPG can be recovered in just two backcross (BC generations. A four-step MABS method was developed based on 'Plabsim' computer simulations and wheat genome structure information. During empirical optimization of this method, double recombinants around the target gene were selected in a step-wise fashion during the two BC cycles followed by selection for recurrent parent genotype on non-carrier chromosomes. The average spacing between carrier chromosome markers was <4 cM. For non-carrier chromosome markers that flanked each of the 48 wheat gene-rich regions, this distance was approximately 12 cM. Employed to introgress seedling stripe rust (Puccinia striiformis f. sp. tritici resistance gene Yr15 into the spring wheat cultivar 'Zak', marker analysis of 2,187 backcross-derived progeny resulted in the recovery of a BC(2F(2ratio3 plant with 97% of the recurrent parent genome. In contrast, only 82% of the recurrent parent genome was recovered in phenotypically selected BC(4F(7 plants developed without MABS. Field evaluation results from 17 locations indicated that the MABS-derived line was either equal or superior to the recurrent parent for the tested agronomic characteristics. Based on these results, MABS is recommended as a strategy for rapidly introgressing a targeted gene into a wheat genotype in just two backcross generations while recovering 97% or more of the recurrent parent genotype.

Transcriptomic analysis of fiber strength in upland cotton chromosome introgression lines carrying different Gossypium barbadense chromosomal segments.

Directory of Open Access Journals (Sweden)

Lei Fang

Full Text Available Fiber strength is the key trait that determines fiber quality in cotton, and it is closely related to secondary cell wall synthesis. To understand the mechanism underlying fiber strength, we compared fiber transcriptomes from different G. barbadense chromosome introgression lines (CSILs that had higher fiber strengths than their recipient, G. hirsutum acc. TM-1. A total of 18,288 differentially expressed genes (DEGs were detected between CSIL-35431 and CSIL-31010, two CSILs with stronger fiber and TM-1 during secondary cell wall synthesis. Functional classification and enrichment analysis revealed that these DEGs were enriched for secondary cell wall biogenesis, glucuronoxylan biosynthesis, cellulose biosynthesis, sugar-mediated signaling pathways, and fatty acid biosynthesis. Pathway analysis showed that these DEGs participated in starch and sucrose metabolism (328 genes, glycolysis/gluconeogenesis (122 genes, phenylpropanoid biosynthesis (101 genes, and oxidative phosphorylation (87 genes, etc. Moreover, the expression of MYB- and NAC-type transcription factor genes were also dramatically different between the CSILs and TM-1. Being different to those of CSIL-31134, CSIL-35431 and CSIL-31010, there were many genes for fatty acid degradation and biosynthesis, and also for carbohydrate metabolism that were down-regulated in CSIL-35368. Metabolic pathway analysis in the CSILs showed that different pathways were changed, and some changes at the same developmental stage in some pathways. Our results extended our understanding that carbonhydrate metabolic pathway and secondary cell wall biosynthesis can affect the fiber strength and suggested more genes and/or pathways be related to complex fiber strength formation process.

Mating, hybridisation and introgression in Lasius ants

NARCIS (Netherlands)

Have, van der T.M.; Pedersen, J.S.; Boomsma, J.J.

2011-01-01

Recent reviews have shown that hybridisation among ant species is likely to be more common than previously appreciated. but that documented cases of introgression remain rare. After molecular phylogenetic work had shown that European Lasius niger (LINNAEUS, 1758) and L. psammophilus SEIFERT, 1992

Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia.

Science.gov (United States)

Schrider, Daniel R; Ayroles, Julien; Matute, Daniel R; Kern, Andrew D

2018-04-01

Hybridization and gene flow between species appears to be common. Even though it is clear that hybridization is widespread across all surveyed taxonomic groups, the magnitude and consequences of introgression are still largely unknown. Thus it is crucial to develop the statistical machinery required to uncover which genomic regions have recently acquired haplotypes via introgression from a sister population. We developed a novel machine learning framework, called FILET (Finding Introgressed Loci via Extra-Trees) capable of revealing genomic introgression with far greater power than competing methods. FILET works by combining information from a number of population genetic summary statistics, including several new statistics that we introduce, that capture patterns of variation across two populations. We show that FILET is able to identify loci that have experienced gene flow between related species with high accuracy, and in most situations can correctly infer which population was the donor and which was the recipient. Here we describe a data set of outbred diploid Drosophila sechellia genomes, and combine them with data from D. simulans to examine recent introgression between these species using FILET. Although we find that these populations may have split more recently than previously appreciated, FILET confirms that there has indeed been appreciable recent introgression (some of which might have been adaptive) between these species, and reveals that this gene flow is primarily in the direction of D. simulans to D. sechellia.

Widespread hybridization and bidirectional introgression in sympatric species of coral reef fish

KAUST Repository

Harrison, Hugo B.

2017-10-28

Coral reefs are highly diverse ecosystems, where numerous closely related species often coexist. How new species arise and are maintained in these high geneflow environments have been long-standing conundrums. Hybridization and patterns of introgression between sympatric species provide a unique insight into the mechanisms of speciation and the maintenance of species boundaries. In this study, we investigate the extent of hybridization between two closely related species of coral reef fish: the common coral trout (Plectropomus leopardus) and the bar-cheek coral trout (Plectropomus maculatus). Using a complementary set of 25 microsatellite loci, we distinguish pure genotype classes from first- and later-generation hybrids, identifying 124 interspecific hybrids from a collection of 2,991 coral trout sampled in inshore and mid-shelf reefs of the southern Great Barrier Reef. Hybrids were ubiquitous among reefs, fertile and spanned multiple generations suggesting both ecological and evolutionary processes are acting to maintain species barriers. We elaborate on these finding to investigate the extent of genomic introgression and admixture from 2,271 SNP loci recovered from a ddRAD library of pure and hybrid individuals. An analysis of genomic clines on recovered loci indicates that 261 SNP loci deviate from a model of neutral introgression, of which 132 indicate a pattern of introgression consistent with selection favouring both hybrid and parental genotypes. Our findings indicate genome-wide, bidirectional introgression between two sympatric species of coral reef fishes and provide further support to a growing body of evidence for the role of hybridization in the evolution of coral reef fishes.

Chemical communication, sexual selection, and introgression in wall lizards.

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MacGregor, Hannah E A; Lewandowsky, Rachel A M; d'Ettorre, Patrizia; Leroy, Chloé; Davies, Noel W; While, Geoffrey M; Uller, Tobias

2017-10-01

Divergence in communication systems should influence the likelihood that individuals from different lineages interbreed, and consequently shape the direction and rate of hybridization. Here, we studied the role of chemical communication in hybridization, and its contribution to asymmetric and sexually selected introgression between two lineages of the common wall lizard (Podarcis muralis). Males of the two lineages differed in the chemical composition of their femoral secretions. Chemical profiles provided information regarding male secondary sexual characters, but the associations were variable and inconsistent between lineages. In experimental contact zones, chemical composition was weakly associated with male reproductive success, and did not predict the likelihood of hybridization. Consistent with these results, introgression of chemical profiles in a natural hybrid zone resembled that of neutral nuclear genetic markers overall, but one compound in particular (tocopherol methyl ether) matched closely the introgression of visual sexual characters. These results imply that associations among male chemical profiles, sexual characters, and reproductive success largely reflect transient and environmentally driven effects, and that genetic divergence in chemical composition is largely neutral. We therefore suggest that femoral secretions in wall lizards primarily provide information about residency and individual identity rather than function as sexual signals. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha.

Science.gov (United States)

Ray, Soham; Bose, Lotan K; Ray, Joshitha; Ngangkham, Umakanta; Katara, Jawahar L; Samantaray, Sanghamitra; Behera, Lambodar; Anumalla, Mahender; Singh, Onkar N; Chen, Meingsheng; Wing, Rod A; Mohapatra, Trilochan

2016-08-01

African wild rice Oryza brachyantha (FF), a distant relative of cultivated rice Oryza sativa (AA), carries genes for pests and disease resistance. Molecular marker assisted alien gene introgression from this wild species to its domesticated counterpart is largely impeded due to the scarce availability of cross-transferable and polymorphic molecular markers that can clearly distinguish these two species. Availability of the whole genome sequence (WGS) of both the species provides a unique opportunity to develop markers, which are cross-transferable. We observed poor cross-transferability (~0.75 %) of O. sativa specific sequence tagged microsatellite (STMS) markers to O. brachyantha. By utilizing the genome sequence information, we developed a set of 45 low cost PCR based co-dominant polymorphic markers (STS and CAPS). These markers were found cross-transferrable (84.78 %) between the two species and could distinguish them from each other and thus allowed tracing alien genome introgression. Finally, we validated a Monosomic Alien Addition Line (MAAL) carrying chromosome 1 of O. brachyantha in O. sativa background using these markers, as a proof of concept. Hence, in this study, we have identified a set molecular marker (comprising of STMS, STS and CAPS) that are capable of detecting alien genome introgression from O. brachyantha to O. sativa.

Detection of nitrogen deficiency QTL in juvenile wild barley introgression lines growing in a hydroponic system

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Hoffmann Astrid

2012-10-01

Full Text Available Abstract Background In this report we studied the genetic regulation of juvenile development of wild barley introgression lines (S42ILs under two contrasting hydroponic nitrogen (N supplies. Ten shoot and root related traits were examined among 42 S42ILs and the recurrent parent ‘Scarlett’. The traits included tiller number, leaf number, plant height, leaf and root length, leaf to root length ratio, shoots and root dry weight, shoot to root weight ratio, and chlorophyll content. Our aims were (1 to test the suitability of a hydroponic system for early detection of favourable S42ILs, (2 to locate quantitative trait loci (QTL that control the examined traits, (3 to identify favourable wild barley alleles that improve trait performances in regard to N treatment and, finally, (4 to validate the identified QTL through comparison with previously reported QTL originating from the same parental cross. Results The phenotypic data were analysed in a mixed model association study to detect QTL. The post-hoc Dunnett test identified 28 S42ILs that revealed significant (P Hsp effects for tiller number, leaf number, leaf length, plant height and leaf to root ratio on the long arm of chromosome 7H. These QTL correspond to QTL for ears per plant and plant height that were previously detected in field trials conducted with the same S42ILs or with the S42 population. Conclusion Our results suggest that the QTL we identified under hydroponic N cultivation partly correspond to QTL detected in field experiments. Due to this finding, screening of plants in early developmental stages grown in a hydroponic system may be a fast and cost effective method for early QTL detection and marker-assisted allelic selection, potentially speeding up elite barley breeding programs.

Archaic adaptive introgression in TBX15/WARS2

DEFF Research Database (Denmark)

Racimo, Fernando; Gokhman, David; Fumagalli, Matteo

2017-01-01

A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using SNP chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related...... to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been...... under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15....

Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models

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Wielstra Ben

2012-08-01

Full Text Available Abstract Background If the geographical displacement of one species by another is accompanied by hybridization, mitochondrial DNA can introgress asymmetrically, from the outcompeted species into the invading species, over a large area. We explore this phenomenon using the two parapatric crested newt species, Triturus macedonicus and T. karelinii, distributed on the Balkan Peninsula in south-eastern Europe, as a model. Results We first delimit a ca. 54,000 km2 area in which T. macedonicus contains T. karelinii mitochondrial DNA. This introgression zone bisects the range of T. karelinii, cutting off a T. karelinii enclave. The high similarity of introgressed mitochondrial DNA haplotypes with those found in T. karelinii suggests a recent transfer across the species boundary. We then use ecological niche modeling to explore habitat suitability of the location of the present day introgression zone under current, mid-Holocene and Last Glacial Maximum conditions. This area was inhospitable during the Last Glacial Maximum for both species, but would have been habitable at the mid-Holocene. Since the mid-Holocene, habitat suitability generally increased for T. macedonicus, whereas it decreased for T. karelinii. Conclusion The presence of a T. karelinii enclave suggests that T. karelinii was the first to colonize the area where the present day introgression zone is positioned after the Last Glacial Maximum. Subsequently, we propose T. karelinii was outcompeted by T. macedonicus, which captured T. karelinii mitochondrial DNA via introgressive hybridization in the process. Ecological niche modeling suggests that this replacement was likely facilitated by a shift in climate since the mid-Holocene. We suggest that the northwestern part of the current introgression zone was probably never inhabited by T. karelinii itself, and that T. karelinii mitochondrial DNA spread there through T. macedonicus exclusively. Considering the spatial distribution of the

Introgression from domestic goat generated variation at the major histocompatibility complex of Alpine ibex.

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Christine Grossen

2014-06-01

Full Text Available The major histocompatibility complex (MHC is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex. At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2, Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus. We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8% to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection.

Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

Science.gov (United States)

Grossen, Christine; Keller, Lukas; Biebach, Iris; Croll, Daniel

2014-01-01

The major histocompatibility complex (MHC) is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex). At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2), Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus). We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8%) to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection. PMID:24945814

Introgression Browser: High throughput whole-genome SNP visualization

NARCIS (Netherlands)

Aflitos, S.A.; Sanchez Perez, G.F.; Ridder, de D.; Fransz, P.; Schranz, M.E.; Jong, de J.H.S.G.M.; Peters, S.A.

2015-01-01

Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not

Introgression browser: high-throughput whole-genome SNP visualization

NARCIS (Netherlands)

Alves Aflitos, S.; Sanchez-Perez, G.; de Ridder, D.; Fransz, P.; Schranz, M.E.; de Jong, H.; Peters, S.A.

2015-01-01

Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not

A molecular cytogenetic analysis of introgression in Alstroemeria

NARCIS (Netherlands)

Kamstra, S.A.

1999-01-01

This thesis describes the results of a molecular cytogenetic investigation of the process of introgression in Alstroemeria . The aim of this study was to transfer chromosomes or genes from one Alstroemeria species into another. For this, two

Pm55, a developmental-stage and tissue-specific powdery mildew resistance gene introgressed from Dasypyrum villosum into common wheat.

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Zhang, Ruiqi; Sun, Bingxiao; Chen, Juan; Cao, Aizhong; Xing, Liping; Feng, Yigao; Lan, Caixia; Chen, Peidu

2016-10-01

Powdery mildew resistance gene Pm55 was physically mapped to chromosome arm 5VS FL 0.60-0.80 of Dasypyrum villosum . Pm55 is present in T5VS·5AL and T5VS·5DL translocations, which should be valuable resources for wheat improvement. Powdery mildew caused by Blumeria graminis f. sp. tritici is a major wheat disease worldwide. Exploiting novel genes effective against powdery mildew from wild relatives of wheat is a promising strategy for controlling this disease. To identify novel resistance genes for powdery mildew from Dasypyrum villosum, a wild wheat relative, we evaluated a set of Chinese Spring-D. villosum disomic addition and whole-arm translocation lines for reactions to powdery mildew. Based on the evaluation data, we concluded that the D. villosum chromosome 5V controls post-seedling resistance to powdery mildew. Subsequently, three introgression lines were developed and confirmed by molecular and cytogenetic analysis following ionizing radiation of the pollen of a Chinese Spring-D. villosum 5V disomic addition line. A homozygous T5VS·5AL translocation line (NAU421) with good plant vigor and full fertility was further characterized using sequential genomic in situ hybridization, C-banding, and EST-STS marker analysis. A dominant gene permanently named Pm55 was located in chromosome bin 5VS 0.60-0.80 based on the responses to powdery mildew of all wheat-D. villosum 5V introgression lines evaluated at both seeding and adult stages. This study demonstrated that Pm55 conferred growth-stage and tissue-specific dependent resistance; therefore, it provides a novel resistance type for powdery mildew. The T5VS·5AL translocation line with additional softness loci Dina/Dinb of D. villosum provides a possibility of extending the range of grain textures to a super-soft category. Accordingly, this stock is a new source of resistance to powdery mildew and may be useful in both resistance mechanism studies and soft wheat improvement.

Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus.

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Fabian Staubach

Full Text Available General parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression, are still insufficiently understood. The house mouse (Mus musculus is a particularly well-suited model system to approach such questions, since it has a defined history of splits into subspecies and populations and since extensive genome information is available. We have used high-density single-nucleotide polymorphism (SNP typing arrays to assess genomic patterns of positive selection and introgression of alleles in two natural populations of each of the subspecies M. m. domesticus and M. m. musculus. Applying different statistical procedures, we find a large number of regions subject to apparent selective sweeps, indicating frequent positive selection on rare alleles or novel mutations. Genes in the regions include well-studied imprinted loci (e.g. Plagl1/Zac1, homologues of human genes involved in adaptations (e.g. alpha-amylase genes or in genetic diseases (e.g. Huntingtin and Parkin. Haplotype matching between the two subspecies reveals a large number of haplotypes that show patterns of introgression from specific populations of the respective other subspecies, with at least 10% of the genome being affected by partial or full introgression. Using neutral simulations for comparison, we find that the size and the fraction of introgressed haplotypes are not compatible with a pure migration or incomplete lineage sorting model. Hence, it appears that introgressed haplotypes can rise in frequency due to positive selection and thus can contribute to the adaptive genomic landscape of natural populations. Our data support the notion that natural genomes are subject to complex adaptive processes, including the introgression of haplotypes from other differentiated populations or species at a larger scale than previously assumed for animals. This implies that some of the admixture found in inbred strains of mice

Characterization of QTL for unique agronomic traits of new-plant-type rice varieties using introgression lines of IR64

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Analiza G. Tagle

2016-02-01

Full Text Available To enhance the yield potential of an elite indica rice cultivar, an introgression (BC3-derived line of IR64, YTH288, was developed using a new-plant-type cultivar, IR66215-44-2-3, as a donor parent. YTH288 has agronomically valuable characteristics such as large panicles, few unproductive tillers, and large leaves inherited from NPT. To identify the genetic basis of these traits, we used 167 F2 plants derived from a cross between IR64 and YTH288 to conduct QTL analysis for five agronomic traits: days to heading (DTH, culm length (CL, flag leaf length (FLL, flag leaf width (FLW, and filled spikelet number per panicle (FSN. Six putative QTL were detected: four on chromosome 4 (for CL, FLL, FLW, and FSN and two on chromosome 2 (for DTH and FLL. All QTL with the IR66215-44-2-3 allele, except that for FLL on chromosome 2, had positive effects on each trait. To confirm the effects of these putative QTL, we developed NILs with the IR64 genetic background by marker-assisted selection. We observed significant differences in several agronomic traits between IR64 and NILs that carried these QTL on chromosomes 2 and 4. Additionally, four IR64-NILs carrying chromosomal segments derived from different NPT varieties on the long arm of chromosome 4 exhibited similar pleiotropic effects for unique agronomic traits. These NILs can be used as research materials for studying each trait and as breeding materials for yield improvement of indica rice cultivars.

Detection of nitrogen deficiency QTL in juvenile wild barley introgression lines growing in a hydroponic system.

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Hoffmann, Astrid; Maurer, Andreas; Pillen, Klaus

2012-10-20

In this report we studied the genetic regulation of juvenile development of wild barley introgression lines (S42ILs) under two contrasting hydroponic nitrogen (N) supplies. Ten shoot and root related traits were examined among 42 S42ILs and the recurrent parent 'Scarlett'. The traits included tiller number, leaf number, plant height, leaf and root length, leaf to root length ratio, shoots and root dry weight, shoot to root weight ratio, and chlorophyll content. Our aims were (1) to test the suitability of a hydroponic system for early detection of favourable S42ILs, (2) to locate quantitative trait loci (QTL) that control the examined traits, (3) to identify favourable wild barley alleles that improve trait performances in regard to N treatment and, finally, (4) to validate the identified QTL through comparison with previously reported QTL originating from the same parental cross. The phenotypic data were analysed in a mixed model association study to detect QTL. The post-hoc Dunnett test identified 28 S42ILs that revealed significant (P hydroponic N study corresponded to QTL that were also detected in field trials with adult plants of a similar S42IL set or of the original S42 population. For instance, S42IL-135, -136 and -137, revealed increasing Hsp effects for tiller number, leaf number, leaf length, plant height and leaf to root ratio on the long arm of chromosome 7H. These QTL correspond to QTL for ears per plant and plant height that were previously detected in field trials conducted with the same S42ILs or with the S42 population. Our results suggest that the QTL we identified under hydroponic N cultivation partly correspond to QTL detected in field experiments. Due to this finding, screening of plants in early developmental stages grown in a hydroponic system may be a fast and cost effective method for early QTL detection and marker-assisted allelic selection, potentially speeding up elite barley breeding programs.

Introgression from cultivated rice alters genetic structures of wild relative populations: implications for in situ conservation

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Jin, Xin; Chen, Yu; Liu, Ping; Li, Chen; Cai, Xingxing; Rong, Jun

2018-01-01

Abstract Maintaining genetic integrity is essential for in situ and ex situ conservation of crop wild relative (CWR) species. However, introgression of crop alleles into CWR species/populations may change their genetic structure and diversity, resulting in more invasive weeds or, in contrast, the extinction of endangered populations. To determine crop-wild introgression and its consequences, we examined the genetic structure and diversity of six wild rice (Oryza rufipogon) populations under in situ conservation in China. Thirty-four simple sequence repeat (SSR) and 34 insertion/deletion markers were used to genotype the wild rice populations and two sets of rice cultivars (O. sativa), corresponding to the two types of molecular markers. Shared alleles and STRUCTURE analyses suggested a variable level of crop-wild introgression and admixture. Principal coordinates and cluster analyses indicated differentiation of wild rice populations, which was associated with the spatial distances to cultivated rice fields. The level of overall genetic diversity was comparable between wild rice populations and rice cultivars, but a great number of wild-specific alleles was detected in the wild populations. We conclude based on the results that crop-wild introgression can considerably alter the pattern of genetic structure and relationships of CWR populations. Appropriate measures should be taken for effective in situ conservation of CWR species under the scenario of crop-wild introgression. PMID:29308123

Characterisation of some Accessions of Indigenous Rice (Oryza glaberrima Steud) in Ghana

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Doku, H. A

2011-07-15

African rice (Oryza glaberrima Steud), a relative of the commonly consumed Asian (white) rice (Oryza sativa L.) is resistant to a number of biotic and abiotic stress factors and contains higher amounts of some essential mineral elements required for human health and growth, compared to the latter. Seventeen local accessions collected from four geographical regions in Ghana were characterised alongside NERICA 1, a high yielding, protein-rich hybrid line purposely bred for Africa, using 32 IBPGR-IRRI agro-botanical traits. Molecular characterisation was done using 24 standard simple sequence repeat markers. The accessions were also evaluated for seven essential mineral elements: calcium (Ca), copper (Cu), iron (Fe), magnesium (Mg), Manganese (Mn), potassium (K) and zinc (Zn) in the caryopsis, using Atomic Absorption Spectrophotometry (AAS) supported by Neutron Activation Analysis (NAA). The aim was to assess genetic diversity of the accessions and identify superior ones for incorporation in future breeding programmes. Cluster analysis (UPGMA), principal component analysis (Axes), correlation and population genetic analysis were used to group the accessions. The single link cluster technique classified the qualitative and quantitative traits of 18 accessions into six and four clusters respectively while the use of molecular traits grouped them into four clusters. Principal component analysis (PCA) re-ordered the accessions into four broad groups which had within-cluster and inter-cluster variations. Two pairs of duplicate accessions were revealed from the dendogram generated using morphological characters. SSRs were highly polymorphic, more discriminatory and informative at 77.3% and 80.0% similarity distance respectively, they were able to discriminate between these pairs of accessions earlier identified as duplicates using botanical descriptors. The overall genetic diversity of the accessions was relatively high (He = 0.625; Nei's He = 0.608 and I = 1.178) with

Characterisation of some Accessions of Indigenous Rice (Oryza glaberrima Steud) in Ghana

International Nuclear Information System (INIS)

Doku, H. A

2011-07-01

African rice (Oryza glaberrima Steud), a relative of the commonly consumed Asian (white) rice (Oryza sativa L.) is resistant to a number of biotic and abiotic stress factors and contains higher amounts of some essential mineral elements required for human health and growth, compared to the latter. Seventeen local accessions collected from four geographical regions in Ghana were characterised alongside NERICA 1, a high yielding, protein-rich hybrid line purposely bred for Africa, using 32 IBPGR-IRRI agro-botanical traits. Molecular characterisation was done using 24 standard simple sequence repeat markers. The accessions were also evaluated for seven essential mineral elements: calcium (Ca), copper (Cu), iron (Fe), magnesium (Mg), Manganese (Mn), potassium (K) and zinc (Zn) in the caryopsis, using Atomic Absorption Spectrophotometry (AAS) supported by Neutron Activation Analysis (NAA). The aim was to assess genetic diversity of the accessions and identify superior ones for incorporation in future breeding programmes. Cluster analysis (UPGMA), principal component analysis (Axes), correlation and population genetic analysis were used to group the accessions. The single link cluster technique classified the qualitative and quantitative traits of 18 accessions into six and four clusters respectively while the use of molecular traits grouped them into four clusters. Principal component analysis (PCA) re-ordered the accessions into four broad groups which had within-cluster and inter-cluster variations. Two pairs of duplicate accessions were revealed from the dendogram generated using morphological characters. SSRs were highly polymorphic, more discriminatory and informative at 77.3% and 80.0% similarity distance respectively, they were able to discriminate between these pairs of accessions earlier identified as duplicates using botanical descriptors. The overall genetic diversity of the accessions was relatively high (He = 0.625; Nei's He = 0.608 and I = 1.178) with

Male mating strategy and the introgression of a growth hormone transgene.

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Valosaari, Kata-Riina; Aikio, Sami; Kaitala, Veijo

2008-11-01

Escaped transgenic organisms (GMO's) may threaten the populations of their wild relatives if able to hybridize with each other. The introgression of a growth enhancement transgene into a wild Atlantic salmon population may be affected by the transgene's effects not only on fitness parameters, but also on mating behaviour. Large anadromous GMO males are most preferred in mating, but a transgene can also give the large sneakers a reproductive advantage over the smaller wild individuals. With a simulation model, we studied whether the increase in the proportion and mating success of sneakers in transgenic and hybrid genotypes could facilitate the introgression of a transgene into wild population after the release of GMOs. The model combines population dynamics and Mendelian inheritance of a transgenic trait. We found that the introgression of the transgene is strongly affected by the greater mating preference of large GMO males. Furthermore, the difference in reproductive success between the anadromous versus sneaker strategy defines how much GMO's have to be preferred to be able to invade. These results emphasize the importance of detailed knowledge of reproductive systems and the effect of a transgene on the phenotype and behaviour of GMOs when assessing the consequences of their release or escape to the wild.

Introgression of wild alleles into the tetraploid peanut crop to improve water use efficiency, earliness and yield.

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Wellison F Dutra

Full Text Available The introduction of genes from wild species is a practice little adopted by breeders for the improvement of commercial crops, although it represents an excellent opportunity to enrich the genetic basis and create new cultivars. In peanut, this practice is being increasingly adopted. In this study we present results of introgression of wild alleles from the wild species Arachis duranensis and A. batizocoi improving photosynthetic traits and yield in a set of lines derived from the cross of an induced allotetraploid and cultivated peanut with selection under water stress. The assays were carried out in greenhouse and field focusing on physiological and agronomic traits. A multivariate model (UPGMA was adopted in order to classify drought tolerant lines. Several lines showed improved levels of tolerance, with values similar to or greater than the tolerant control. Two BC1F6 lines (53 P4 and 96 P9 were highlighted for good drought-related traits, earliness and pod yield, having better phenotypic profile to the drought tolerant elite commercial cultivar BR1. These lines are good candidates for the creation of peanut cultivars suitable for production in semiarid environments.

Extensive hybridization and introgression between Melastoma candidum and M. sanguineum.

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Ting Liu

Full Text Available Natural hybridization can lead to various evolutionary outcomes in plants, including hybrid speciation and interspecific gene transfer. It can also cause taxonomic problems, especially in plant genera containing multiple species. In this study, the hybrid status of Melastoma affine, the most widespread taxon in this genus, and introgression between its putative parental species, M. candidum and M. sanguineum, were assessed on two sites, Hainan and Guangdong, using 13 SSR markers and sequences of a chloroplast intergenic spacer. Bayesian-based STRUCTURE analysis detected two most likely distinct clusters for the three taxa, and 76.0% and 73.9% of the morphologically identified individuals of M. candidum and M. sanguineum were correctly assigned, respectively. 74.5% of the M. affine individuals had a membership coefficient to either parental species between 0.1 and 0.9, suggesting admixture between M. candidum and M. sanguineum. Furthermore, NewHybrids analysis suggested that most individuals of M. affine were F2 hybrids or backcross hybrids to M. candidum, and that there was extensive introgression between M. candidum and M. sanguineum. These SSR data thus provides convincing evidence for hybrid origin of M. affine and extensive introgression between M. candidum and M. sanguineum. Chloroplast DNA results were consistent with this conclusion. Much higher hybrid frequency on the more disturbed Guangdong site suggests that human disturbance might offer suitable habitats for the survival of hybrids, a hypothesis that is in need of further testing.

Termometria infravermelha na fenotipagem para resistência à seca de linhagens inter e intraespecíficas de arroz Infrared thermometry for drought phenotyping of inter and intra specific upland rice lines

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Cleber M. Guimarães

2010-02-01

Full Text Available Propôs-se avaliar, no presente estudo, a técnica da termometria ao infravermelho na caracterização de linhagens interespecíficas (Oryza glaberrima x Oryza sativa cv Caiapó e intraespecíficas de arroz para tolerância a seca. O experimento, conduzido em Porangatu, GO, foi submetido a condições adequadas de umidade no solo até 30 dias após a emergência, quando então foi implantado um tratamento com deficiência hídrica moderada (aproximadamente 50% da irrigação aplicada em uma parcela testemunha, com condições adequadas de umidade no solo. Verificou-se que as linhagens mais produtivas em condições de deficiência hídrica apresentaram plantas mais altas, com panículas mais densas e com grãos mais bem formados, com menor esterilidade de espiguetas. Observou-se, também, que a temperatura das folhas se correlacionou positivamente com a esterilidade de espiguetas e negativamente com a massa de 100 grãos, altura das plantas, fertilidade de perfilhos e produtividade. Exceto a fertilidade de perfilhos, os demais componentes se correlacionaram com a produtividade de grãos, sendo que com a esterilidade de espiguetas a correlação foi negativa. Concluiu-se que a O. glaberrima confere, às suas progênies, maior rusticidade à deficiência hídrica e que a termometria ao infravermelho é uma técnica auxiliar importante na fenotipagem para tolerância a seca.The purpose of the present study was to evaluate the use of infrared thermometry in the characterization of inter specific (Oryza glaberrima x Oryza sativa cv Caiapó and intra specific upland rice lines for drought tolerance. The experiment, carried out at Porangatu in the State of Goiás, was submitted to adequate soil moisture for up to 30 days following emergence when a moderate water stress treatment was imposed (about 50% of the applied irrigation in a control plot in which adequate conditions of soil moisture were maintained. It has been observed that lines with higher

The responses of crop - wild Brassica hybrids to simulated herbivory and interspecific competition: implications for transgene introgression.

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Sutherland, Jamie P; Justinova, Lenka; Poppy, Guy M

2006-01-01

Brassica rapa grows as a wild and weedy species throughout the world and is the most likely recipient of transgenes from GM oilseed rape. For transgene introgression to occur, the critical step which must be realized, is the formation of an F1 hybrid. Concerns exist that hybrid populations could be more vigorous and competitive compared to the parental species. This study examines the effect of simulated herbivory and interspecific competition on the vegetative and reproductive performance of non-transgenic F1 hybrids and their parental lines. Several vegetative and reproductive performance measures were used to determine the effect of simulated herbivory and competition on the Brassica lines, including leaf length and biomass for herbivory and seedling height and biomass for competition. For defoliation experiments, B. rapa showed little response in terms of leaf length but B. napus and the F1 hybrid responded negatively. Brassica rapa showed elevated biomass responses, but B. napus and the hybrid demonstrated negative responses to defoliation. Defoliation at the cotyledon stage had a slight effect upon final biomass with the F1 hybrid performing significantly worse than B. napus, although seed counts were not significantly different. For the series of competition experiments, hybrids seemed to be more similar to B. rapa in terms of early seedling growth and reproductive measures. The underperformance of hybrid plants when challenged by herbivory and competition, could potentially decrease survivorship and explain the rarity of hybrids in field surveys. However, should transgene introgression occur, the dynamics of hybrids could change radically thus increasing the risk of gene flow from a transgenic oilseed rape crop to the wild recipient.

Marker-assisted introgression of drought tolerance from wild ancestors into popular Indian rice varieties using a 7K Infinium SNP array

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Ravindra Donde

2017-10-01

Full Text Available Recent advances in the area of genomics have led to the development of high throughput genotyping platforms that have immensely contributed to molecular breeding programs. Custom-designed single nucleotide polymorphism (SNP arrays provide an efficient, cost effective, high throughput genotyping tool for QTL/gene mapping, variety identification, marker-assisted selection, etc. In the current study, two interspecific libraries of Chromosome Segment Substitution Lines (CSSLs were evaluated under both drought and control conditions to identify lines with superior yield under drought. The CSSL libraries consisted of 48 BC4F3 lines derived from O. sativa cv. Curinga (tropical japonica x O. rufipogon, and 32 BC4F3 lines derived from O. sativa cv. Curinga (tropical japonica x O. meridionalis. The phenotypic screening of these 80 CSSLs led to the identification of three lines, MER-20, RUF-16, and RUF-44, that yielded well under drought stress. This line was backcrossed with popular rice variety of India, Swarna-Sub1 to introgress wild chromosome segments responsible for reproductive stage drought tolerance. During backcrossing, tracking of wild introgressions and monitoring of recurrent parent genome recovery was facilitated by the use of the Cornell 6K and 7K Infinium rice SNP arrays. The 6K and 7K SNP arrays assayed 5275 SNPs and 7099 SNPs, respectively, distributed across the 12 chromosomes. In our populations of (MER-20X Swarna sub1 BC2F1 lines, 1775 SNPs were polymorphic using the 6K array. The percentage of recurrent parent genome in these backcrossed lines ranged from 33-92% and the percentage of wild donor genome ranged from 8-67%. Using genotypic selection, 5% of plants were identified for further marker assisted backcrossing, based on the presence of the target donor (wild segment and maximum recovery of recurrent parent background. In the next generation, BC3F1 lines were genotyped using the 7K SNP array, which identified 2521 polymorphic SNPs

An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes.

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Hohmann, Nora; Koch, Marcus A

2017-10-23

Gene flow between species, across ploidal levels, and even between evolutionary lineages is a common phenomenon in the genus Arabidopsis. However, apart from two genetically fully stabilized allotetraploid species that have been investigated in detail, the extent and temporal dynamics of hybridization are not well understood. An introgression zone, with tetraploid A. arenosa introgressing into A. lyrata subsp. petraea in the Eastern Austrian Forealps and subsequent expansion towards pannonical lowlands, was described previously based on morphological observations as well as molecular data using microsatellite and plastid DNA markers. Here we investigate the spatio-temporal context of this suture zone, making use of the potential of next-generation sequencing and whole-genome data. By utilizing a combination of nuclear and plastid genomic data, the extent, direction and temporal dynamics of gene flow are elucidated in detail and Late Pleistocene evolutionary processes are resolved. Analysis of nuclear genomic data significantly recognizes the clinal structure of the introgression zone, but also reveals that hybridization and introgression is more common and substantial than previously thought. Also tetraploid A. lyrata and A. arenosa subsp. borbasii from outside the previously defined suture zone show genomic signals of past introgression. A. lyrata is shown to serve usually as the maternal parent in these hybridizations, but one exception is identified from plastome-based phylogenetic reconstruction. Using plastid phylogenomics with secondary time calibration, the origin of A. lyrata and A. arenosa lineages is pre-dating the last three glaciation complexes (approx. 550,000 years ago). Hybridization and introgression followed during the last two glacial-interglacial periods (since approx. 300,000 years ago) with later secondary contact at the northern and southern border of the introgression zone during the Holocene. Footprints of adaptive introgression in the

Introgression of A- and B-genome of tetraploid triticale chromatin into tetraploid rye.

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Wiśniewska, H; Kwiatek, M; Kulak-Książczyk, S; Apolinarska, B

2013-11-01

An improvement of rye is one of the mainstream goals of current breeding. Our study is concerned with the introduction of the tetraploid triticale (ABRR) into the 4x rye (RRRR) using classical methods of distant crossing. One hundred fifty BC1F9 hybrid plants [(4x rye × 4x triticales) × 4x rye] obtained from a backcrossing program were studied. The major aim of this work was to verify the presence of an introgressed A- and B- genome chromatin of triticale in a collection of the 4x rye-tiritcale hybrids and to determine their chromosome compositions. In the present study, karyotypes of the previously reported BC1F2s and BC1F3s were compared with that of the BC1F9 generation as obtained after several subsequent open pollinations. The genomic in situ hybridisation (GISH) allowed us to identify 133 introgression forms in which chromosome numbers ranged between 26 and 32. Using four DNA probes (5S rDNA, 25S rDNA, pSc119.2 and pAs1), the fluorescence in situ hybridisation (FISH) was carried out to facilitate an exact chromosome identification in the hybrid plants. The combination of the multi-colour GISH with the repetitive DNA FISH singled out five types of translocated chromosomes: 2A.2R, 4A.4R, 5A.5R, 5B.5R and 7A.7R among the examined BC1F9s. The reported translocation lines could serve as valuable sources of wheat chromatin suitable for further improvements of rye.

Introgression of a Tombusvirus Resistance Locus from Nicotiana edwardsonii var. Columbia to N. clevelandii.

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Schoelz, James E; Wiggins, B Elizabeth; Wintermantel, William M; Ross, Kathleen

2006-05-01

ABSTRACT A new variety of Nicotiana, N. edwardsonii var. Columbia, was evaluated for its capacity to serve as a new source for virus resistance genes. Columbia was developed from a hybridization between N. glutinosa and N. clevelandii, the same parents used for the formation of the original N. edwardsonii. However, in contrast to the original N. edwardsonii, crosses between Columbia and either of its parents are fertile. Thus, the inheritance of virus resistance genes present in N. glutinosa could be characterized by using Columbia as a bridge plant in crosses with the susceptible parent, N. clevelandii. To determine how virus resistance genes would segregate in interspecific crosses between Columbia and N. clevelandii, we followed the fate of the N gene, a single dominant gene that specifies resistance to Tobacco mosaic virus (TMV). Our genetic evidence indicated that the entire chromosome containing the N gene was introgressed into N. clevelandii to create an addition line, designated N. clevelandii line 19. Although line 19 was homozygous for resistance to TMV, it remained susceptible to Tomato bushy stunt virus (TBSV) and Cauliflower mosaic virus (CaMV) strain W260, indicating that resistance to these viruses must reside on other N. glutinosa chromosomes. We also developed a second addition line, N. clevelandii line 36, which was homozygous for resistance to TBSV. Line 36 was susceptible to TMV and CaMV strain W260, but was resistant to other tombusviruses, including Cucumber necrosis virus, Cymbidium ringspot virus, Lettuce necrotic stunt virus, and Carnation Italian ringspot virus.

Asymmetric hybridization and introgression between pink salmon and chinook salmon in the Laurentian Great Lakes

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Rosenfield, Jonathan A.; Todd, Thomas; Greil, Roger

2000-01-01

Among Pacific salmon collected in the St. Marys River, five natural hybrids of pink salmon Oncorhynchus gorbuscha and chinook salmon Oncorhynchus tshawytscha and one suspected backcross have been detected using morphologic, meristic, and color evidence. One allozyme (LDH, l-lactate dehydrogenase from muscle) and one nuclear DNA locus (growth hormone) for which species-specific fixed differences exist were analyzed to detect additional hybrids and to determine if introgression had occurred. Restriction fragment length polymorphism of mitochondrial DNA (mtDNA) was used to identify the maternal parent of each hybrid. Evidence of introgression was found among the five previously identified hybrids. All hybrid specimens had chinook salmon mtDNA, indicating that hybridization between chinook salmon and pink salmon in the St. Marys River is asymmetric and perhaps unidirectional. Ecological, physiological, and sexual selection forces may contribute to this asymmetric hybridization. Introgression between these highly differentiated species has implications for management, systematics, and conservation of Pacific salmon.

Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression

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Clark, Lindsay V.; Stewart, J. Ryan; Nishiwaki, Aya; Toma, Yo; Kjeldsen, Jens Bonderup; Jørgensen, Uffe; Zhao, Hua; Peng, Junhua; Yoo, Ji Hye; Heo, Kweon; Yu, Chang Yeon; Yamada, Toshihiko

2015-01-01

Unilateral introgression from diploids to tetraploids has been hypothesized to be an important evolutionary mechanism in plants. However, few examples have been definitively identified, perhaps because data of sufficient depth and breadth were difficult to obtain before the advent of affordable high-density genotyping. Throughout Japan, tetraploid Miscanthus sacchariflorus and diploid Miscanthus sinensis are common, and occasionally hybridize. In this study, 667 M. sinensis and 78 M. sacchariflorus genotypes from Japan were characterized using 20 704 SNPs and ten plastid microsatellites. Similarity of SNP genotypes between diploid and tetraploid M. sacchariflorus indicated that the tetraploids originated through autopolyploidy. Structure analysis indicated a gradient of introgression from diploid M. sinensis into tetraploid M. sacchariflorus throughout Japan; most tetraploids had some M. sinensis DNA. Among phenotypically M. sacchariflorus tetraploids, M. sinensis ancestry averaged 7% and ranged from 1–39%, with introgression greatest in southern Japan. Unexpectedly, rare (~1%) diploid M. sinensis individuals from northern Japan were found with 6–27% M. sacchariflorus ancestry. Population structure of M. sinensis in Japan included three groups, and was driven primarily by distance, and secondarily by geographic barriers such as mountains and straits. Miscanthus speciation is a complex and dynamic process. In contrast to limited introgression between diploid M. sacchariflorus and M. sinensis in northern China, selection for adaptation to a moderate maritime climate probably favoured cross-ploidy introgressants in southern Japan. These results will help guide the selection of Miscanthus accessions for the breeding of biomass cultivars. PMID:25618143

Discordant introgression in a rapidly expanding hybrid swarm

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Ward, Jessica L.; Blum, Mike J.; Walters, David M.; Porter, Brady A.; Burkhead, Noel; Freeman, Byron

2012-01-01

The erosion of species boundaries can involve rapid evolutionary change. Consequently, many aspects of the process remain poorly understood, including the formation, expansion, and evolution of hybrid swarms. Biological invasions involving hybridization present exceptional opportunities to study the erosion of species boundaries because timelines of interactions and outcomes are frequently well known. Here, we examined clinal variation across codominant and maternally inherited genetic markers as well as phenotypic traits to characterize the expansion and evolution of a hybrid swarm between native Cyprinella venusta and invasive Cyprinella lutrensis minnows. Discordant introgression of phenotype, microsatellite multilocus genotype, and mtDNA haplotype indicates that the observable expansion of the C. venusta x C. lutrensis hybrid swarm is a false invasion front. Both parental and hybrid individuals closely resembling C. lutrensis are numerically dominant in the expansion wake, indicating that the non-native parental phenotype may be selectively favored. These findings show that cryptic introgression can extend beyond the phenotypic boundaries of hybrid swarms and that hybrid swarms likely expand more rapidly than can be documented from phenotypic variation alone. Similarly, dominance of a single parental phenotype following an introduction event may lead to instances of species erosion being mistaken for species displacement without hybridization.

Quantifying rooting at depth in a wheat doubled haploid population with introgression from wild emmer.

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Clarke, Christina K; Gregory, Peter J; Lukac, Martin; Burridge, Amanda J; Allen, Alexandra M; Edwards, Keith J; Gooding, Mike J

2017-09-01

The genetic basis of increased rooting below the plough layer, post-anthesis in the field, of an elite wheat line (Triticum aestivum 'Shamrock') with recent introgression from wild emmer (T. dicoccoides), is investigated. Shamrock has a non-glaucous canopy phenotype mapped to the short arm of chromosome 2B (2BS), derived from the wild emmer. A secondary aim was to determine whether genetic effects found in the field could have been predicted by other assessment methods. Roots of doubled haploid (DH) lines from a winter wheat ('Shamrock' × 'Shango') population were assessed using a seedling screen in moist paper rolls, in rhizotrons to the end of tillering, and in the field post-anthesis. A linkage map was produced using single nucleotide polymorphism markers to identify quantitative trait loci (QTLs) for rooting traits. Shamrock had greater root length density (RLD) at depth than Shango, in the field and within the rhizotrons. The DH population exhibited diversity for rooting traits within the three environments studied. QTLs were identified on chromosomes 5D, 6B and 7B, explaining variation in RLD post-anthesis in the field. Effects associated with the non-glaucous trait on RLD interacted significantly with depth in the field, and some of this interaction mapped to 2BS. The effect of genotype was strongly influenced by the method of root assessment, e.g. glaucousness expressed in the field was negatively associated with root length in the rhizotrons, but positively associated with length in the seedling screen. To our knowledge, this is the first study to identify QTLs for rooting at depth in field-grown wheat at mature growth stages. Within the population studied here, our results are consistent with the hypothesis that some of the variation in rooting is associated with recent introgression from wild emmer. The expression of genetic effects differed between the methods of root assessment. © The Author 2017. Published by Oxford University Press on behalf of the

A matter of genes? Possible consequences of genetic introgression from domestic forms in two problematic species

DEFF Research Database (Denmark)

Scandura, Massimo; Canu, Antonio; Bassi, Elena

wildlife managers and public administrations. Here, we present an updated review on the extent and the possible effects of hybridization in the two species. Specifically, we will focus on i) the methods to track introgression and their main limitations, ii) the life-history traits possibly affected...... by the introgression, iii) the conditions for introgressive hybridization to occur and iv) the management implications. After its historical minimum in the early XX century, the wild boar came back to be a common presence in the Italian countryside, becoming a pest. Crossbreeding between wild boar and domestic pigs...... has been historically important and is likely to have shaped the present-day genetic make-up of both forms. Although intensive farming has reduced the chance of hybridization in nature, gene flow between wild and domestic S. scrofa still takes place either spontaneously in areas where open-air pig...

Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression.

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Li, Runsheng; Ren, Xiaoliang; Bi, Yu; Ho, Vincy Wing Sze; Hsieh, Chia-Ling; Young, Amanda; Zhang, Zhihong; Lin, Tingting; Zhao, Yanmei; Miao, Long; Sarkies, Peter; Zhao, Zhongying

2016-09-01

Hybrid incompatibility (HI) prevents gene flow between species, thus lying at the heart of speciation genetics. One of the most common HIs is male sterility. Two superficially contradictory observations exist for hybrid male sterility. First, an introgression on the X Chromosome is more likely to produce male sterility than on autosome (so-called large-X theory); second, spermatogenesis genes are enriched on the autosomes but depleted on the X Chromosome (demasculinization of X Chromosome). Analysis of gene expression in Drosophila hybrids suggests a genetic interaction between the X Chromosome and autosomes that is essential for male fertility. However, the prevalence of such an interaction and its underlying mechanism remain largely unknown. Here we examine the interaction in nematode species by contrasting the expression of both coding genes and transposable elements (TEs) between hybrid sterile males and its parental nematode males. We use two lines of hybrid sterile males, each carrying an independent introgression fragment from Caenorhabditis briggsae X Chromosome in an otherwise Caenorhabditis nigoni background, which demonstrate similar defects in spermatogenesis. We observe a similar pattern of down-regulated genes that are specific for spermatogenesis between the two hybrids. Importantly, the down-regulated genes caused by the X Chromosome introgressions show a significant enrichment on the autosomes, supporting an epistatic interaction between the X Chromosome and autosomes. We investigate the underlying mechanism of the interaction by measuring small RNAs and find that a subset of 22G RNAs specifically targeting the down-regulated spermatogenesis genes is significantly up-regulated in hybrids, suggesting that perturbation of small RNA-mediated regulation may contribute to the X-autosome interaction. © 2016 Li et al.; Published by Cold Spring Harbor Laboratory Press.

Maize x Teosinte Hybrid Cobs Do Not Prevent Crop Gene Introgression.

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Chavez, Nancy B; Flores, Jose J; Martin, Joseph; Ellstrand, Norman C; Guadagnuolo, Roberto; Heredia, Sylvia; Welles, Shana R

2012-06-01

Maize x Teosinte Hybrid Cobs Do Not Prevent Crop Gene Introgression. Whether introgression from crops to wild relatives can occur is an important component of transgene risk assessment. In the case of maize, which co-occurs with its wild relative teosinte in Mexico, the possibility of introgression has been controversial. Maize is cross-compatible with teosinte, and spontaneous hybridization is known to occur. Some scientists have hypothesized that the maize x teosinte cob infructescence will prevent progeny dispersal, thus preventing introgression. Motivated by a prior study where we found maize x teosinte hybrid fruits naturally dispersed under field conditions, we tested whether hybrid cobs hold their fruits as tightly as maize cobs. We found the force required to detach hybrid fruits was substantially and significantly less than that for maize. Consequently, we expect that introgression of transgenes from maize into teosinte in Mexico should occur largely unimpeded by the hybrid cob.La mazorca o elote híbrido de maíz x teocintle no impide la introgresión de genes transgénicos provenientes del cultivo. La introgresión entre el maíz cultivado y el maíz silvestre, o teocintle, es un componente importante en la evaluación ambiental relacionada con los riesgos de la introducción de genes transgénicos. La posibilidad de introgresión entre el maíz domesticado y el teocintle ha sido un tema controversial, en particular en México, donde maíz y teocintle coexisten. El maíz es compatible con el teocintle y la hibridización espontánea ocurre entre ellos. Algunos científicos han planteado como hipótesis que al cruzar el maíz con teocintle, la estructura interna de la infrutescencia que sujeta los frutos conocida como la mazorca de maíz o el elote, impide la dispersión de la progenie evitando que la introgresión ocurra. Los resultados de un estudio previo evidencian la dispersión de los frutos híbridos del maíz x teocintle en condiciones naturales

Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles.

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Labate, Joanne A; Robertson, Larry D

2012-08-07

Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. Each marker was mapped with high confidence (etomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help

Detecting genetic introgression: high levels of intersubspecific recombination found in Xylella fastidiosa in Brazil.

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Nunney, Leonard; Yuan, Xiaoli; Bromley, Robin E; Stouthamer, Richard

2012-07-01

Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (leuA, petC, malF, cysG, and holC). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another X. fastidiosa subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that X. fastidiosa subsp. pauca became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly X. fastidiosa subsp. multiplex). This hypothesis predicts that nonrecombinant native X. fastidiosa subsp. pauca (not yet isolated) does not cause disease in citrus or coffee.

Genetic introgression of ethylene-suppressed transgenic tomatoes with higher-polyamines trait overcomes many unintended effects due to reduced ethylene on the primary metabolome

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Anatoly P Sobolev

2014-12-01

Full Text Available Ethylene regulates a myriad physiological and biochemical processes in ripening fruits and is accepted as the ripening hormone for the climacteric fruits. However, its effects on metabolome and resulting fruit quality are not yet fully understood, particularly when some of the ripening-associated biochemical changes are independent of ethylene action. We have generated a homozygous transgenic tomato genotype (2AS-AS that exhibits reduced ethylene production as a result of impaired expression of 1-aminocyclopropane-1-carboxylate synthase 2 gene by its antisense RNA and had a longer shelf life. Double transgenic hybrid (2AS-AS x 579HO developed through a genetic cross between 2AS-AS and 579HO (Mehta et al., 2002 lines resulted in significantly higher ethylene production than either the WT or 2AS-AS fruit. To determine the effects of reduced ethylene and introgression of higher polyamines’ trait, the metabolic profiles of ripening fruits from WT (556AZ, 2AS-AS, and 2AS-AS x 579HO lines were determined using 1H-NMR spectroscopy. The levels of Glu, Asp, AMP, Adenosine, Nucl1 and Nucl2 increased during ripening of the WT fruit. The increases in Glu, Asp, and AMP levels were attenuated in 2AS-AS fruit but recovered in the double hybrid with higher ethylene and polyamine levels. The ripening-associated decreases in Ala, Tyr, Val, Ile, Phe, malate and myo-inositol levels in the 2AS-AS line were not reversed in the double hybrid line suggesting a developmental/ripening regulated accumulation of these metabolites independent of ethylene. Significant increases in the levels of fumarate, formate, choline, Nucl1 and Nucl2 at most stages of ripening fruit were found in the double transgenic line due to introgression with higher-polyamines trait. Taken together these results show that the ripening-associated metabolic changes are both ethylene dependent and independent, and that the fruit metabolome is under the control of multiple regulators, including

The myth of natural barriers. Is transgene introgression by genetically modified crops an environmental risk?

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Guarnieri, Vincenzo; Benessia, Alice; Camino, Elena; Barbiero, Giuseppe

2008-01-01

Genetically modified (GM) crops under open field conditions are a complex and controversial issue. Ecologists are discussing about the possibility that a transgene belonging to GM plants could spread to native populations through a process known as introgression the stable incorporation of a gene in the host genome able to generate a differentiated population. The ecological consequences of a transgene introgression in plants or bacteria are not yet well understood, but could be significant. In this critical review we consider vertical and horizontal introgression. We analyse the biochemical and genetic constraints, and environmental factors that limit the possibility of transgene spread; meanwhile we show cases in which the natural barriers are overcome. Then we discuss the overall management of GM crops, noting the shortcomings and approximations of risk assessment based on linear thinking typical of the biomolecular approach. Finally we suggest to explicitly weight facts together with values and we encourage the undertaking of an ecological perspective, encompassing the complexity of (non-linear) relations between organisms and the environment.

Chromosome engineering for alien gene introgression in wheat: Progress and prospective

Science.gov (United States)

Chromosome engineering is a useful strategy for introgression of desirable genes from wild relatives into cultivated wheat. However, it has been a challenge to transfer a small amount of alien chromatin containing the gene of interest from one genome to another non-homologous genome through classic...

Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype.

Science.gov (United States)

Mascher, Martin; Gerlach, Nina; Gahrtz, Manfred; Bucher, Marcel; Scholz, Uwe; Dresselhaus, Thomas

2014-01-01

Maize (Zea mays) is the most widely grown crop species in the world and a classical model organism for plant research. The completion of a high-quality reference genome sequence and the advent of high-throughput sequencing have greatly empowered re-sequencing studies in maize. In this study, plants of maize inbred line B73 descended from two different sets of seed material grown for several generations either in the field or in the greenhouse were found to show a different growth phenotype and ionome under phosphate starvation conditions and moreover a different responsiveness towards mycorrhizal fungi of the species Glomus intraradices (syn: Rhizophagus irregularis). Whole genome re-sequencing of individuals from both sets and comparison to the B73 reference sequence revealed three cryptic introgressions on chromosomes 1, 5 and 10 in the line grown in the greenhouse summing up to a total of 5,257 single-nucleotide polymorphisms (SNPs). Transcriptome sequencing of three individuals from each set lent further support to the location of the introgression intervals and confirmed them to be fixed in all sequenced individuals. Moreover, we identified >120 genes differentially expressed between the two B73 lines. We thus have found a nearly-isogenic line (NIL) of maize inbred line B73 that is characterized by an altered growth phenotype under phosphate starvation conditions and an improved responsiveness towards symbiosis with mycorrhizal fungi. Through next-generation sequencing of the genomes and transcriptomes we were able to delineate exact introgression intervals. Putative de novo mutations appeared approximately uniformly distributed along the ten maize chromosomes mainly representing G:C -> A:T transitions. The plant material described in this study will be a valuable tool both for functional studies of genes differentially expressed in both B73 lines and for research on growth behavior especially in response to symbiosis between maize and mycorrhizal fungi.

Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype.

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Martin Mascher

Full Text Available Maize (Zea mays is the most widely grown crop species in the world and a classical model organism for plant research. The completion of a high-quality reference genome sequence and the advent of high-throughput sequencing have greatly empowered re-sequencing studies in maize. In this study, plants of maize inbred line B73 descended from two different sets of seed material grown for several generations either in the field or in the greenhouse were found to show a different growth phenotype and ionome under phosphate starvation conditions and moreover a different responsiveness towards mycorrhizal fungi of the species Glomus intraradices (syn: Rhizophagus irregularis. Whole genome re-sequencing of individuals from both sets and comparison to the B73 reference sequence revealed three cryptic introgressions on chromosomes 1, 5 and 10 in the line grown in the greenhouse summing up to a total of 5,257 single-nucleotide polymorphisms (SNPs. Transcriptome sequencing of three individuals from each set lent further support to the location of the introgression intervals and confirmed them to be fixed in all sequenced individuals. Moreover, we identified >120 genes differentially expressed between the two B73 lines. We thus have found a nearly-isogenic line (NIL of maize inbred line B73 that is characterized by an altered growth phenotype under phosphate starvation conditions and an improved responsiveness towards symbiosis with mycorrhizal fungi. Through next-generation sequencing of the genomes and transcriptomes we were able to delineate exact introgression intervals. Putative de novo mutations appeared approximately uniformly distributed along the ten maize chromosomes mainly representing G:C -> A:T transitions. The plant material described in this study will be a valuable tool both for functional studies of genes differentially expressed in both B73 lines and for research on growth behavior especially in response to symbiosis between maize and

Genomic markers reveal introgressive hybridization in the Indo-West Pacific mangroves: a case study.

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Mei Sun

2011-05-01

Full Text Available Biodiversity of mangrove ecosystems is difficult to assess, at least partly due to lack of genetic verification of morphology-based documentation of species. Natural hybridization, on the one hand, plays an important role in evolution as a source of novel gene combinations and a mechanism of speciation. However, on the other hand, recurrent introgression allows gene flow between species and could reverse the process of genetic differentiation among populations required for speciation. To understand the dynamic evolutionary consequences of hybridization, this study examines genomic structure of hybrids and parental species at the population level. In the Indo-West Pacific, Bruguiera is one of the dominant mangrove genera and species ranges overlap extensively with one another. Morphological intermediates between sympatric Bruguiera gymnorrhiza and Bruguiera sexangula have been reported as a variety of B. sexangula or a new hybrid species, B. × rhynchopetala. However, the direction of hybridization and extent of introgression are unclear. A large number of species-specific inter-simple sequence repeat (ISSR markers were found in B. gymnorrhiza and B. sexangula, and the additive ISSR profiling of B. × rhynchopetala ascertained its hybrid status and identified its parental origin. The varying degree of scatterness among hybrid individuals in Principal Coordinate Analysis and results from NewHybrids analysis indicate that B. × rhynchopetala comprises different generations of introgressants in addition to F(1s. High genetic relatedness between B. × rhynchopetala and B. gymnorrhiza based on nuclear and chloroplast sequences suggests preferential hybrid backcrosses to B. gymnorrhiza. We conclude that B. × rhynchopetala has not evolved into an incipient hybrid species, and its persistence can be explained by recurrent hybridization and introgression. Genomic data provide insights into the hybridization dynamics of mangrove plants. Such information

LPS-induced genes in intestinal tissue of the sea cucumber Holothuria glaberrima.

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Francisco Ramírez-Gómez

2009-07-01

Full Text Available Metazoan immunity is mainly associated with specialized cells that are directly involved with the immune response. Nevertheless, both in vertebrates and invertebrates other organs might respond to immune activation and participate either directly or indirectly in the ongoing immune process. However, most of what is known about invertebrate immunity has been restricted to immune effector cells and little information is available on the immune responses of other tissues or organs. We now focus on the immune reactions of the intestinal tissue of an echinoderm. Our study employs a non-conventional model, the echinoderm Holothuria glaberrima, to identify intestinal molecules expressed after an immune challenge presented by an intra-coelomic injection of lipopolysaccharides (LPS. The expression profiles of intestinal genes expressed differentially between LPS-injected animals and control sea water-injected animals were determined using a custom-made Agilent microarray with 7209 sea cucumber intestinal ESTs. Fifty (50 unique sequences were found to be differentially expressed in the intestine of LPS-treated sea cucumbers. Seven (7 of these sequences represented homologues of known proteins, while the remaining (43 had no significant similarity with any protein, EST or RNA database. The known sequences corresponded to cytoskeletal proteins (Actin and alpha-actinin, metabolic enzymes (GAPDH, Ahcy and Gnmt, metal ion transport/metabolism (major yolk protein and defense/recognition (fibrinogen-like protein. The expression pattern of 11 genes was validated using semi-quantitative RT-PCR. Nine of these corroborated the microarray results and the remaining two showed a similar trend but without statistical significance. Our results show some of the molecular events by which the holothurian intestine responds to an immune challenge and provide important information to the study of the evolution of the immune response.

Genomic Analysis Reveals Hypoxia Adaptation in the Tibetan Mastiff by Introgression of the Gray Wolf from the Tibetan Plateau.

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Miao, Benpeng; Wang, Zhen; Li, Yixue

2017-03-01

The Tibetan Mastiff (TM), a native of the Tibetan Plateau, has quickly adapted to the extreme highland environment. Recently, the impact of positive selection on the TM genome was studied and potential hypoxia-adaptive genes were identified. However, the origin of the adaptive variants remains unknown. In this study, we investigated the signature of genetic introgression in the adaptation of TMs with dog and wolf genomic data from different altitudes in close geographic proximity. On a genome-wide scale, the TM was much more closely related to other dogs than wolves. However, using the 'ABBA/BABA' test, we identified genomic regions from the TM that possibly introgressed from Tibetan gray wolf. Several of the regions, including the EPAS1 and HBB loci, also showed the dominant signature of selective sweeps in the TM genome. We validated the introgression of the two loci by excluding the possibility of convergent evolution and ancestral polymorphisms and examined the haplotypes of all available canid genomes. The estimated time of introgression based on a non-coding region of the EPAS1 locus mostly overlapped with the Paleolithic era. Our results demonstrated that the introgression of hypoxia adaptive genes in wolves from the highland played an important role for dogs living in hypoxic environments, which indicated that domestic animals could acquire local adaptation quickly by secondary contact with their wild relatives. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus revealed by analyses of multiple mitochondrial and nuclear DNA loci

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Wu Shi-Fang

2011-07-01

Full Text Available Abstract Background Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion. Results Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species. Conclusion This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.

Sequence-Based Introgression Mapping Identifies Candidate White Mold Tolerance Genes in Common Bean

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Sujan Mamidi

2016-07-01

Full Text Available White mold, caused by the necrotrophic fungus (Lib. de Bary, is a major disease of common bean ( L.. WM7.1 and WM8.3 are two quantitative trait loci (QTL with major effects on tolerance to the pathogen. Advanced backcross populations segregating individually for either of the two QTL, and a recombinant inbred (RI population segregating for both QTL were used to fine map and confirm the genetic location of the QTL. The QTL intervals were physically mapped using the reference common bean genome sequence, and the physical intervals for each QTL were further confirmed by sequence-based introgression mapping. Using whole-genome sequence data from susceptible and tolerant DNA pools, introgressed regions were identified as those with significantly higher numbers of single-nucleotide polymorphisms (SNPs relative to the whole genome. By combining the QTL and SNP data, WM7.1 was located to a 660-kb region that contained 41 gene models on the proximal end of chromosome Pv07, while the WM8.3 introgression was narrowed to a 1.36-Mb region containing 70 gene models. The most polymorphic candidate gene in the WM7.1 region encodes a BEACH-domain protein associated with apoptosis. Within the WM8.3 interval, a receptor-like protein with the potential to recognize pathogen effectors was the most polymorphic gene. The use of gene and sequence-based mapping identified two candidate genes whose putative functions are consistent with the current model of pathogenicity.

Heritability studies for seed quality traits in introgressed segregating populations of brassica

International Nuclear Information System (INIS)

Farhatullah, S.; Nasim, A.; Fayyaz, L.

2014-01-01

Estimation of genetic parameters in the context of trait characterization is an essential component of future targeted crop improvement programs. Collection of knowledge about genetic behavior such as genetic variability and heritability etc., of the germplasm is the basic step for initiation of any breeding program. Genetic variability and Broad sense heritability for various seed quality traits in 10 brassica genotypes and their 12 F2 progenies comprising of introgressed hybrids were studied. The genotypes had highly significant variation for oil content, protein, glucosinolates contents, oleic, linolenic and erucic acid contents. Glucosinolates content and erucic acid showed high heritability in all F2 populations, while rest of the traits showed variable trends. The cross combination 547 x 118 (B. napus x B. campestris) proved to be a good interspecific hybrid that had high proportion of introgression and has high heritability for beneficial traits. The individual plants having combination of desirable traits were also identified from the F2 populations. (author)

Fitness of crop-wild hybrid sunflower under competitive conditions: implications for crop-to-wild introgression.

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Mercer, Kristin L; Emry, D Jason; Snow, Allison A; Kost, Matthew A; Pace, Brian A; Alexander, Helen M

2014-01-01

Understanding the likelihood and extent of introgression of novel alleles in hybrid zones requires comparison of lifetime fitness of parents and hybrid progeny. However, fitness differences among cross types can vary depending on biotic conditions, thereby influencing introgression patterns. Based on past work, we predicted that increased competition would enhance introgression between cultivated and wild sunflower (Helianthus annuus) by reducing fitness advantages of wild plants. To test this prediction, we established a factorial field experiment in Kansas, USA where we monitored the fitness of four cross types (Wild, F1, F2, and BCw hybrids) under different levels of interspecific and intraspecific competition. Intraspecific manipulations consisted both of density of competitors and of frequency of crop-wild hybrids. We recorded emergence of overwintered seeds, survival to reproduction, and numbers of seeds produced per reproductive plant. We also calculated two compound fitness measures: seeds produced per emerged seedling and seeds produced per planted seed. Cross type and intraspecific competition affected emergence and survival to reproduction, respectively. Further, cross type interacted with competitive treatments to influence all other fitness traits. More intense competition treatments, especially related to density of intraspecific competitors, repeatedly reduced the fitness advantage of wild plants when considering seeds produced per reproductive plant and per emerged seedling, and F2 plants often became indistinguishable from the wilds. Wild fitness remained superior when seedling emergence was also considered as part of fitness, but the fitness of F2 hybrids relative to wild plants more than quadrupled with the addition of interspecific competitors and high densities of intraspecific competitors. Meanwhile, contrary to prediction, lower hybrid frequency reduced wild fitness advantage. These results emphasize the importance of taking a full life cycle

Fitness of crop-wild hybrid sunflower under competitive conditions: implications for crop-to-wild introgression.

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Kristin L Mercer

Full Text Available Understanding the likelihood and extent of introgression of novel alleles in hybrid zones requires comparison of lifetime fitness of parents and hybrid progeny. However, fitness differences among cross types can vary depending on biotic conditions, thereby influencing introgression patterns. Based on past work, we predicted that increased competition would enhance introgression between cultivated and wild sunflower (Helianthus annuus by reducing fitness advantages of wild plants. To test this prediction, we established a factorial field experiment in Kansas, USA where we monitored the fitness of four cross types (Wild, F1, F2, and BCw hybrids under different levels of interspecific and intraspecific competition. Intraspecific manipulations consisted both of density of competitors and of frequency of crop-wild hybrids. We recorded emergence of overwintered seeds, survival to reproduction, and numbers of seeds produced per reproductive plant. We also calculated two compound fitness measures: seeds produced per emerged seedling and seeds produced per planted seed. Cross type and intraspecific competition affected emergence and survival to reproduction, respectively. Further, cross type interacted with competitive treatments to influence all other fitness traits. More intense competition treatments, especially related to density of intraspecific competitors, repeatedly reduced the fitness advantage of wild plants when considering seeds produced per reproductive plant and per emerged seedling, and F2 plants often became indistinguishable from the wilds. Wild fitness remained superior when seedling emergence was also considered as part of fitness, but the fitness of F2 hybrids relative to wild plants more than quadrupled with the addition of interspecific competitors and high densities of intraspecific competitors. Meanwhile, contrary to prediction, lower hybrid frequency reduced wild fitness advantage. These results emphasize the importance of taking

Fitness of Crop-Wild Hybrid Sunflower under Competitive Conditions: Implications for Crop-to-Wild Introgression

Science.gov (United States)

Mercer, Kristin L.; Emry, D. Jason; Snow, Allison A.; Kost, Matthew A.; Pace, Brian A.; Alexander, Helen M.

2014-01-01

Understanding the likelihood and extent of introgression of novel alleles in hybrid zones requires comparison of lifetime fitness of parents and hybrid progeny. However, fitness differences among cross types can vary depending on biotic conditions, thereby influencing introgression patterns. Based on past work, we predicted that increased competition would enhance introgression between cultivated and wild sunflower (Helianthus annuus) by reducing fitness advantages of wild plants. To test this prediction, we established a factorial field experiment in Kansas, USA where we monitored the fitness of four cross types (Wild, F1, F2, and BCw hybrids) under different levels of interspecific and intraspecific competition. Intraspecific manipulations consisted both of density of competitors and of frequency of crop-wild hybrids. We recorded emergence of overwintered seeds, survival to reproduction, and numbers of seeds produced per reproductive plant. We also calculated two compound fitness measures: seeds produced per emerged seedling and seeds produced per planted seed. Cross type and intraspecific competition affected emergence and survival to reproduction, respectively. Further, cross type interacted with competitive treatments to influence all other fitness traits. More intense competition treatments, especially related to density of intraspecific competitors, repeatedly reduced the fitness advantage of wild plants when considering seeds produced per reproductive plant and per emerged seedling, and F2 plants often became indistinguishable from the wilds. Wild fitness remained superior when seedling emergence was also considered as part of fitness, but the fitness of F2 hybrids relative to wild plants more than quadrupled with the addition of interspecific competitors and high densities of intraspecific competitors. Meanwhile, contrary to prediction, lower hybrid frequency reduced wild fitness advantage. These results emphasize the importance of taking a full life cycle

Introgression of novel traits from a wild wheat relative improves drought adaptation in wheat.

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Placido, Dante F; Campbell, Malachy T; Folsom, Jing J; Cui, Xinping; Kruger, Greg R; Baenziger, P Stephen; Walia, Harkamal

2013-04-01

Root architecture traits are an important component for improving water stress adaptation. However, selection for aboveground traits under favorable environments in modern cultivars may have led to an inadvertent loss of genes and novel alleles beneficial for adapting to environments with limited water. In this study, we elucidate the physiological and molecular consequences of introgressing an alien chromosome segment (7DL) from a wild wheat relative species (Agropyron elongatum) into cultivated wheat (Triticum aestivum). The wheat translocation line had improved water stress adaptation and higher root and shoot biomass compared with the control genotypes, which showed significant drops in root and shoot biomass during stress. Enhanced access to water due to higher root biomass enabled the translocation line to maintain more favorable gas-exchange and carbon assimilation levels relative to the wild-type wheat genotypes during water stress. Transcriptome analysis identified candidate genes associated with root development. Two of these candidate genes mapped to the site of translocation on chromosome 7DL based on single-feature polymorphism analysis. A brassinosteroid signaling pathway was predicted to be involved in the novel root responses observed in the A. elongatum translocation line, based on the coexpression-based gene network generated by seeding the network with the candidate genes. We present an effective and highly integrated approach that combines root phenotyping, whole-plant physiology, and functional genomics to discover novel root traits and the underlying genes from a wild related species to improve drought adaptation in cultivated wheat.

Marker-assisted introgression of broad-spectrum blast resistance genes into the cultivated MR219 rice variety.

Science.gov (United States)

Miah, Gous; Rafii, Mohd Y; Ismail, Mohd R; Puteh, Adam B; Rahim, Harun A; Latif, Mohammad A

2017-07-01

The rice cultivar MR219 is famous for its better yield and long and fine grain quality; however, it is susceptible to blast disease. The main objective of this study was to introgress blast resistance genes into MR219 through marker-assisted selection (MAS). The rice cultivar MR219 was used as the recurrent parent, and Pongsu Seribu 1 was used as the donor. Marker-assisted foreground selection was performed using RM6836 and RM8225 to identify plants possessing blast resistance genes. Seventy microsatellite markers were used to estimate recurrent parent genome (RPG) recovery. Our analysis led to the development of 13 improved blast resistant lines with Piz, Pi2 and Pi9 broad-spectrum blast resistance genes and an MR219 genetic background. The RPG recovery of the selected improved lines was up to 97.70% with an average value of 95.98%. Selected improved lines showed a resistance response against the most virulent blast pathogen pathotype, P7.2. The selected improved lines did not express any negative effect on agronomic traits in comparison with MR219. The research findings of this study will be a conducive approach for the application of different molecular techniques that may result in accelerating the development of new disease-resistant rice varieties, which in turn will match rising demand and food security worldwide. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Genetic introgression and the survival of Florida panther kittens

Science.gov (United States)

Hostetler, Jeffrey A.; Onorato, David P.; Nichols, James D.; Johnson, Warren E.; Roelke, Melody E.; O'Brien, Stephen J.; Jansen, Deborah; Oli, Madan K.

2010-01-01

Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982–2008 and a live-recapture dead-recovery modeling framework to estimate and model survival of Florida panther (Puma concolor coryi) kittens (age 0–1 year). Overall, annual survival of Florida panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were released into occupied panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F1 admixed and backcrossed to Texas kittens survived better than canonical Florida panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older panther survival, whereas index of panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data.

Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective

Directory of Open Access Journals (Sweden)

Rosa Alicia Jiménez

2016-01-01

Full Text Available The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds, Amazilia beryllina, Amazilia cyanura and Amazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA sequence data and microsatellite loci scores for populations throughout the range of the three Amazilia species, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of this Amazilia species complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA supported three genetic groups with signs of genetic admixture, corresponding to: (1 A. beryllina populations located west of the Isthmus of Tehuantepec; (2 A. cyanura populations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America; and (3 A. saucerottei populations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses

Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective

Science.gov (United States)

Jiménez, Rosa Alicia

2016-01-01

The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds, Amazilia beryllina, Amazilia cyanura and Amazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the three Amazilia species, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of this Amazilia species complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1) A. beryllina populations located west of the Isthmus of Tehuantepec; (2) A. cyanura populations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3) A. saucerottei populations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence

Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.

Directory of Open Access Journals (Sweden)

Keyan Zhao

2010-05-01

Full Text Available The domestication of Asian rice (Oryza sativa was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers.In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations.Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.

Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species.

Science.gov (United States)

Peris, David; Arias, Armando; Orlić, Sandi; Belloch, Carmela; Pérez-Través, Laura; Querol, Amparo; Barrio, Eladio

2017-03-01

Horizontal gene transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested between S. cerevisiae and S. paradoxus. However, few strains have been explored given the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur, and their role in cytonuclear incompatibilities and fitness. Indeed, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. We herein explored the mitochondrial inheritance of several worldwide distributed wild Saccharomyces species and their hybrids isolated from different sources and geographic origins. We demonstrated the existence of several recombination points in mitochondrial region COX2-ORF1, likely mediated by either the activity of the protein encoded by the ORF1 (F-SceIII) gene, a free-standing homing endonuclease, or mostly facilitated by A+T tandem repeats and regions of integration of GC clusters. These introgressions were shown to occur among strains of the same species and among strains of different species, which suggests a complex model of Saccharomyces evolution that involves several ancestral hybridization events in wild environments. Copyright © 2017 Elsevier Inc. All rights reserved.

Introgressing subgenome components from Brassica rapa and B. carinata to B. juncea for broadening its genetic base and exploring intersubgenomic heterosis

Directory of Open Access Journals (Sweden)

Zili Wei

2016-11-01

Full Text Available Brassica juncea (AjAjBjBj, is an allotetraploid that arose from two diploid species, B. rapa (ArAr and B. nigra (BnBn. It is an old oilseed crop with unique favorable traits, but the genetic improvement on this species is limited. We developed an approach to broaden its genetic base within several generations by intensive selection. The Ar subgenome from the Asian oil crop B. rapa (ArAr and the Bc subgenome from the African oil crop B. carinata (BcBcCcCc were combined in a synthesized allohexaploid (ArArBcBcCcCc, which was crossed with traditional B. juncea to generate pentaploid F1 hybrids (ArAjBcBjCc, with subsequent self-pollination to obtain newly synthesized B. juncea (Ar/jAr/jBc/jBc/j. After intensive cytological screening and phenotypic selection of fertility and agronomic traits, a population of new-type B. juncea was obtained and was found to be genetically stable at the F6 generation. The new-type B. juncea possesses good fertility and rich genetic diversity and is distinctly divergent but not isolated from traditional B. juncea, as revealed by population genetic analysis with molecular markers. More than half of its genome was modified, showing exotic introgression and novel variation. In addition to the improvement in some traits of the new-type B. juncea lines, a considerable potential for heterosis was observed in inter-subgenomic hybrids between new-type B. juncea lines and traditional B. juncea accessions. The new-type B. juncea exhibited a stable chromosome number and a novel genome composition through multiple generations, providing insight into how to significantly broaden the genetic base of crops with subgenome introgression from their related species and the potential of exploring inter-subgenomic heterosis for hybrid breeding.

Genetic dissection of black grain rice by the development of a near isogenic line.

Science.gov (United States)

Maeda, Hiroaki; Yamaguchi, Takuya; Omoteno, Motoyasu; Takarada, Takeshi; Fujita, Kenji; Murata, Kazumasa; Iyama, Yukihide; Kojima, Yoichiro; Morikawa, Makiko; Ozaki, Hidenobu; Mukaino, Naoyuki; Kidani, Yoshinori; Ebitani, Takeshi

2014-06-01

Rice (Oryza sativa L.) can produce black grains as well as white. In black rice, the pericarp of the grain accumulates anthocyanin, which has antioxidant activity and is beneficial to human health. We developed a black rice introgression line in the genetic background of Oryza sativa L. 'Koshihikari', which is a leading variety in Japan. We used Oryza sativa L. 'Hong Xie Nuo' as the donor parent and backcrossed with 'Koshihikari' four times, resulting in a near isogenic line (NIL) for black grains. A whole genome survey of the introgression line using DNA markers suggested that three regions, on chromosomes 1, 3 and 4 are associated with black pigmentation. The locus on chromosome 3 has not been identified previously. A mapping analysis with 546 F2 plants derived from a cross between the black rice NIL and 'Koshihikari' was evaluated. The results indicated that all three loci are essential for black pigmentation. We named these loci Kala1, Kala3 and Kala4. The black rice NIL was evaluated for eating quality and general agronomic traits. The eating quality was greatly superior to that of 'Okunomurasaki', an existing black rice variety. The isogenicity of the black rice NIL to 'Koshihikari' was very high.

Population diversity and evidence of introgression among the black oaks of California

Science.gov (United States)

Richard S. Dodd; Nasser Kashani; Zara Afzal-Rafii

2002-01-01

The black oaks of California include 4 tree species (California black oak, coast live oak, Shreve oak, interior live oak) that are known to hybridize. Complex patterns of population variation within each species are likely to result from these hybrid combinations and from subsequent introgressions. We have been studying population variation using biochemical and...

Evidence for introgressive hybridization of captive markhor (Capra falconeri) with domestic goat: cautions for reintroduction.

Science.gov (United States)

Hammer, Sabine E; Schwammer, Harald M; Suchentrunk, Franz

2008-04-01

Markhors (Capra falconeri) are among the most endangered mammal species, and several conservation measures, including ex situ breeding, are implemented to prevent their extinction. We studied sequence diversity and differentiation of the first hypervariable segment of the mitochondrial DNA control region among C. f. heptneri and C. f. megaceros kept in four zoos in relationship to lineages of other wild and domestic goats, to assess for the first time the level of molecular distinctness and variability among those subspecies, and to check for possible introgression by related Capra taxa, such as domestic goats. Levels of differentiation between some Capra falconeri lineages and modern domestic goats were similar to levels between other wild goat species (i.e., Capra aegagrus, Capra ibex) and domestic goats. Among pure markhor lineages, paraphyly was observed for C. f. heptneri, suggesting occurrence of shared ancestral polymorphism among markhor subspecies and/or ancient or recent gene exchange between subspecies. Interestingly, 35.7% of all studied markhors from three zoos are introgressed by the domestic goat. Furthermore, despite relatively small breeding group sizes, markhors have maintained a relatively high proportion of mtDNA variation within zoo groups. In any case, the existence of markhors introgressed with domestic goat DNA in zoos should be considered when selecting markhors for ex situ breeding programs with the aim of building up a stock for later reintroduction into the wild.

Natural hybridization and introgression between Ligularia cymbulifera and L. tongolensis (Asteraceae, Senecioneae) in four different locations.

Science.gov (United States)

Yu, Jiaojun; Kuroda, Chiaki; Gong, Xun

2014-01-01

Natural hybridization has been considered to represent an important factor influencing the high diversity of the genus Ligularia Cass. in the Hengduan Mountains, China. Natural hybridization has been confirmed to occur frequently in Ligularia. To date, however, it has been demonstrated only within a single population. In this paper, we present evidence of natural hybridization in Ligularia from four different locations. The internal transcribed spacer (ITS) region of the nuclear ribosomal DNA and three chloroplast intergenic spacers (trnK-rps16, trnL-rpl32 and trnQ-5'rps16) of 149 accessions of putative hybrids and their putative parents (L. cymbulifera and L. tongolensis) were analyzed for evidence of hybridization. The ITS data clearly distinguished two putative parental species and sympatric L. vellerea and supported the hypothesis that those morphological intermediates were products of natural hybridization between L. cymbulifera and L. tongolensis. Moreover, several identified morphological parents were actual introgressed products. Because of hybridization and introgression, chloroplast DNA sequences generated a poorly resolved network. The present results indicate that varying degrees of hybridization and introgression occur differently depending on the habitat context. We conclude that gene flow caused by natural hybridization in Ligularia indeed plays an important role in the species diversity.

Introgressive hybridization as a promoter of genome reshuffling in natural homoploid fish hybrids (Cyprinidae, Leuciscinae)

Czech Academy of Sciences Publication Activity Database

Pereira, C. S.; Aboim, M. A.; Ráb, Petr; Collares-Pereira, M. J.

2014-01-01

Roč. 112, č. 3 (2014), s. 343-350 ISSN 0018-067X Institutional support: RVO:67985904 Keywords : comparative genome hybridization * hybrid zones * introgression Subject RIV: EG - Zoology Impact factor: 3.805, year: 2014

Recent introgressive hybridization revealed by exclusive mtDNA transfer from Oreochromis leucostictus (Trewavas, 1933) to Oreochromis niloticus (Linnaeus, 1758) in Lake Baringo, Kenya

OpenAIRE

Nyingi, Dorothy W.; Agnèse, Jean-François

2007-01-01

Nuclear DNA and mtDNA polymorphisms were surveyed in various species of East African Oreochromis. In Lake Baringo, where only Oreochromis niloticus baringoensis is present, alien mtDNA haplotypes were observed, apparently the result of introgressive hybridization with Oreochromis leucostictus. This introgression is not accompanied by any substantial or recorded transfer of nuclear genes into O. n. baringoensis.

Yield-enhancing heterotic QTL transferred from wild species to cultivated rice Oryza sativa L.

Science.gov (United States)

Gaikwad, Kiran B; Singh, Naveen; Bhatia, Dharminder; Kaur, Rupinder; Bains, Navtej S; Bharaj, Tajinder S; Singh, Kuldeep

2014-01-01

Utilization of "hidden genes" from wild species has emerged as a novel option for enrichment of genetic diversity for productivity traits. In rice we have generated more than 2000 lines having introgression from 'A' genome-donor wild species of rice in the genetic background of popular varieties PR114 and Pusa44 were developed. Out of these, based on agronomic acceptability, 318 lines were used for developing rice hybrids to assess the effect of introgressions in heterozygous state. These introgression lines and their recurrent parents, possessing fertility restoration ability for wild abortive (WA) cytoplasm, were crossed with cytoplasmic male sterile (CMS) line PMS17A to develop hybrids. Hybrids developed from recurrent parents were used as checks to compare the performance of 318 hybrids developed by hybridizing alien introgression lines with PMS17A. Seventeen hybrids expressed a significant increase in yield and its component traits over check hybrids. These 17 hybrids were re-evaluated in large-size replicated plots. Of these, four hybrids, viz., ILH299, ILH326, ILH867 and ILH901, having introgressions from O. rufipogon and two hybrids (ILH921 and ILH951) having introgressions from O. nivara showed significant heterosis over parental introgression line, recurrent parents and check hybrids for grain yield-related traits. Alien introgressions were detected in the lines taken as male parents for developing six superior hybrids, using a set of 100 polymorphic simple sequence repeat (SSR) markers. Percent introgression showed a range of 2.24 from in O. nivara to 7.66 from O. rufipogon. The introgressed regions and their putative association with yield components in hybrids is reported and discussed.

Repeated unidirectional introgression towards Populus balsamifera in contact zones of exotic and native poplars

NARCIS (Netherlands)

Thompson, S.L.; Lamothe, M.; Meirmans, P.G.; Périnet, P.; Isabel, N.

2010-01-01

As the evolutionary significance of hybridization is largely dictated by its extent beyond the first generation, we broadly surveyed patterns of introgression across a sympatric zone of two native poplars (Populus balsamifera, Populus deltoides) in Quebec, Canada within which European exotic Populus

Genetic dissection of black grain rice by the development of a near isogenic line

OpenAIRE

Maeda, Hiroaki; Yamaguchi, Takuya; Omoteno, Motoyasu; Takarada, Takeshi; Fujita, Kenji; Murata, Kazumasa; Iyama, Yukihide; Kojima, Yoichiro; Morikawa, Makiko; Ozaki, Hidenobu; Mukaino, Naoyuki; Kidani, Yoshinori; Ebitani, Takeshi

2014-01-01

Rice (Oryza sativa L.) can produce black grains as well as white. In black rice, the pericarp of the grain accumulates anthocyanin, which has antioxidant activity and is beneficial to human health. We developed a black rice introgression line in the genetic background of Oryza sativa L. ‘Koshihikari’, which is a leading variety in Japan. We used Oryza sativa L. ‘Hong Xie Nuo’ as the donor parent and backcrossed with ‘Koshihikari’ four times, resulting in a near isogenic line (NIL) for black g...

Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts.

Science.gov (United States)

Hulse-Kemp, Amanda M; Ashrafi, Hamid; Zheng, Xiuting; Wang, Fei; Hoegenauer, Kevin A; Maeda, Andrea B V; Yang, S Samuel; Stoffel, Kevin; Matvienko, Marta; Clemons, Kimberly; Udall, Joshua A; Van Deynze, Allen; Jones, Don C; Stelly, David M

2014-10-30

Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection. Using transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3-79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays. This large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in

Multilocus analysis of introgression between two sympatric sister species of Drosophila: Drosophila yakuba and D. santomea.

Science.gov (United States)

Llopart, Ana; Lachaise, Daniel; Coyne, Jerry A

2005-09-01

Drosophila yakuba is widely distributed in sub-Saharan Africa, while D. santomea is endemic to the volcanic island of São Tomé in the Atlantic Ocean, 280 km west of Gabon. On São Tomé, D. yakuba is found mainly in open lowland forests, and D. santomea is restricted to the wet misty forests at higher elevations. At intermediate elevations, the species form a hybrid zone where hybrids occur at a frequency of approximately 1%. To determine the extent of gene flow between these species we studied polymorphism and divergence patterns in 29 regions distributed throughout the genome, including mtDNA and three genes on the Y chromosome. This multilocus approach, together with the comparison to the two allopatric species D. mauritiana and D. sechellia, allowed us to distinguish between forces that should affect all genes and forces that should act on some genes (e.g., introgression). Our results show that D. yakuba mtDNA has replaced that of D. santomea and that there is also significant introgression for two nuclear genes, yellow and salr. The majority of genes, however, has remained distinct. These two species therefore do not form a "hybrid swarm" in which much of the genome shows substantial introgression while disruptive selection maintains distinctness for only a few traits (e.g., pigmentation and male genitalia).

The complex biogeography of the plant pathogen Xylella fastidiosa: genetic evidence of introductions and Subspecific introgression in Central America.

Science.gov (United States)

Nunney, Leonard; Ortiz, Beatriz; Russell, Stephanie A; Ruiz Sánchez, Rebeca; Stouthamer, Richard

2014-01-01

The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST) of isolates from Costa Rica. Six (five from oleander, one from coffee) defined a new sequence type (ST53) that carried alleles at six of the eight loci sequenced (five of the seven MLST loci) diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee) showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa.

The complex biogeography of the plant pathogen Xylella fastidiosa: genetic evidence of introductions and Subspecific introgression in Central America.

Directory of Open Access Journals (Sweden)

Leonard Nunney

Full Text Available The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST of isolates from Costa Rica. Six (five from oleander, one from coffee defined a new sequence type (ST53 that carried alleles at six of the eight loci sequenced (five of the seven MLST loci diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa.

Multilocus analysis of divergence and introgression in sympatric and allopatric sibling species of the Lutzomyia longipalpis complex in Brazil.

Science.gov (United States)

Araki, Alejandra S; Ferreira, Gabriel E M; Mazzoni, Camila J; Souza, Nataly A; Machado, Ricardo C; Bruno, Rafaela V; Peixoto, Alexandre A

2013-01-01

Lutzomyia longipalpis, the main vector of visceral leishmaniasis in Latin America, is a complex of sibling species. In Brazil, a number of very closely related sibling species have been revealed by the analyses of copulation songs, sex pheromones and molecular markers. However, the level of divergence and gene flow between the sibling species remains unclear. Brazilian populations of this vector can be divided in two main groups: one producing Burst-type songs and the Cembrene-1 pheromone and a second more diverse group producing various Pulse song subtypes and different pheromones. We analyzed 21 nuclear loci in two pairs of Brazilian populations: two sympatric populations from the Sobral locality (1S and 2S) in northeastern Brazil and two allopatric populations from the Lapinha and Pancas localities in southeastern Brazil. Pancas and Sobral 2S are populations of the Burst/Cembrene-1 species while Lapinha and Sobral 1S are two putative incipient species producing the same pheromone and similar Pulse song subtypes. The multilocus analysis strongly suggests the occurrence of gene flow during the divergence between the sibling species, with different levels of introgression between loci. Moreover, this differential introgression is asymmetrical, with estimated gene flow being higher in the direction of the Burst/Cembrene-1 species. The results indicate that introgressive hybridization has been a crucial phenomenon in shaping the genome of the L. longipalpis complex. This has possible epidemiological implications and is particularly interesting considering the potential for increased introgression caused by man-made environmental changes and the current trend of leishmaniasis urbanization in Brazil.

Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression.

Science.gov (United States)

Murray, Gemma G R; Woolhouse, Mark E J; Tapio, Miika; Mbole-Kariuki, Mary N; Sonstegard, Tad S; Thumbi, Samuel M; Jennings, Amy E; van Wyk, Ilana Conradie; Chase-Topping, Margo; Kiara, Henry; Toye, Phil; Coetzer, Koos; deC Bronsvoort, Barend M; Hanotte, Olivier

2013-11-09

Positive multi-locus heterozygosity-fitness correlations have been observed in a number of natural populations. They have been explained by the correlation between heterozygosity and inbreeding, and the negative effect of inbreeding on fitness (inbreeding depression). Exotic introgression in a locally adapted population has also been found to reduce fitness (outbreeding depression) through the breaking-up of co-adapted genes, or the introduction of non-locally adapted gene variants. In this study we examined the inter-relationships between genome-wide heterozygosity, introgression, and death or illness as a result of infectious disease in a sample of calves from an indigenous population of East African Shorthorn Zebu (crossbred Bos taurus x Bos indicus) in western Kenya. These calves were observed from birth to one year of age as part of the Infectious Disease in East African Livestock (IDEAL) project. Some of the calves were found to be genetic hybrids, resulting from the recent introgression of European cattle breed(s) into the indigenous population. European cattle are known to be less well adapted to the infectious diseases present in East Africa. If death and illness as a result of infectious disease have a genetic basis within the population, we would expect both a negative association of these outcomes with introgression and a positive association with heterozygosity. In this indigenous livestock population we observed negative associations between heterozygosity and both death and illness as a result of infectious disease and a positive association between European taurine introgression and episodes of clinical illness. We observe the effects of both inbreeding and outbreeding depression in the East African Shorthorn Zebu, and therefore find evidence of a genetic component to vulnerability to infectious disease. These results indicate that the significant burden of infectious disease in this population could, in principle, be reduced by altered breeding

Multilocus Analysis of Divergence and Introgression in Sympatric and Allopatric Sibling Species of the Lutzomyia longipalpis Complex in Brazil

Science.gov (United States)

Mazzoni, Camila J.; Souza, Nataly A.; Machado, Ricardo C.; Bruno, Rafaela V.

2013-01-01

Background Lutzomyia longipalpis, the main vector of visceral leishmaniasis in Latin America, is a complex of sibling species. In Brazil, a number of very closely related sibling species have been revealed by the analyses of copulation songs, sex pheromones and molecular markers. However, the level of divergence and gene flow between the sibling species remains unclear. Brazilian populations of this vector can be divided in two main groups: one producing Burst-type songs and the Cembrene-1 pheromone and a second more diverse group producing various Pulse song subtypes and different pheromones. Methodology/Principal Findings We analyzed 21 nuclear loci in two pairs of Brazilian populations: two sympatric populations from the Sobral locality (1S and 2S) in northeastern Brazil and two allopatric populations from the Lapinha and Pancas localities in southeastern Brazil. Pancas and Sobral 2S are populations of the Burst/Cembrene-1 species while Lapinha and Sobral 1S are two putative incipient species producing the same pheromone and similar Pulse song subtypes. The multilocus analysis strongly suggests the occurrence of gene flow during the divergence between the sibling species, with different levels of introgression between loci. Moreover, this differential introgression is asymmetrical, with estimated gene flow being higher in the direction of the Burst/Cembrene-1 species. Conclusions/Significance The results indicate that introgressive hybridization has been a crucial phenomenon in shaping the genome of the L. longipalpis complex. This has possible epidemiological implications and is particularly interesting considering the potential for increased introgression caused by man-made environmental changes and the current trend of leishmaniasis urbanization in Brazil. PMID:24147172

Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon)

KAUST Repository

Bernal, Moisés A.

2016-11-22

Closely related marine species with large overlapping ranges provide opportunities to study mechanisms of speciation, particularly when there is evidence of gene flow between such lineages. Here, we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via restriction site-associated DNA sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister-species. On the other hand, complete lineage sorting was observed at the nuclear loci and most of the SNPs. Under neutral expectations, the smaller effective population size of mtDNA should lead to fixation of mutations faster than nDNA. Thus, these results suggest that hybridization in the recent past (0.174-0.263Ma) led to introgression of the mtDNA, with little effect on the nuclear genome. Analyses of the SNP data revealed 28 loci potentially under divergent selection between the two species. The combination of mtDNA introgression and limited nuclear DNA introgression provides a mechanism for the evolution of independent lineages despite recurrent hybridization events. This study adds to the growing body of research that exemplifies how genetic divergence can be maintained in the presence of gene flow between closely related species.

Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon)

KAUST Repository

Bernal, Moisé s A.; Gaither, Michelle R.; Simison, W. Brian; Rocha, Luiz A.

2016-01-01

Closely related marine species with large overlapping ranges provide opportunities to study mechanisms of speciation, particularly when there is evidence of gene flow between such lineages. Here, we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via restriction site-associated DNA sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister-species. On the other hand, complete lineage sorting was observed at the nuclear loci and most of the SNPs. Under neutral expectations, the smaller effective population size of mtDNA should lead to fixation of mutations faster than nDNA. Thus, these results suggest that hybridization in the recent past (0.174-0.263Ma) led to introgression of the mtDNA, with little effect on the nuclear genome. Analyses of the SNP data revealed 28 loci potentially under divergent selection between the two species. The combination of mtDNA introgression and limited nuclear DNA introgression provides a mechanism for the evolution of independent lineages despite recurrent hybridization events. This study adds to the growing body of research that exemplifies how genetic divergence can be maintained in the presence of gene flow between closely related species.

Introgression lines of Triticum aestivum x Aegilops tauschii: Agronomic and nutritional value

Science.gov (United States)

Eighty-five single homozygous substitution lines (SLs) of the Aegilops tauschii D genome in Chinese Spring (CS) hexaploid wheat (Triticum aestivum L.) genetic background were evaluated for agronomic, phenotypic and ionome profiles during three years of field experiments. An augmented design with a r...

The eastern migratory caribou: the role of genetic introgression in ecotype evolution.

Science.gov (United States)

Klütsch, Cornelya F C; Manseau, Micheline; Trim, Vicki; Polfus, Jean; Wilson, Paul J

2016-02-01

Understanding the evolutionary history of contemporary animal groups is essential for conservation and management of endangered species like caribou (Rangifer tarandus). In central Canada, the ranges of two caribou subspecies (barren-ground/woodland caribou) and two woodland caribou ecotypes (boreal/eastern migratory) overlap. Our objectives were to reconstruct the evolutionary history of the eastern migratory ecotype and to assess the potential role of introgression in ecotype evolution. STRUCTURE analyses identified five higher order groups (i.e. three boreal caribou populations, eastern migratory ecotype and barren-ground). The evolutionary history of the eastern migratory ecotype was best explained by an early genetic introgression from barren-ground into a woodland caribou lineage during the Late Pleistocene and subsequent divergence of the eastern migratory ecotype during the Holocene. These results are consistent with the retreat of the Laurentide ice sheet and the colonization of the Hudson Bay coastal areas subsequent to the establishment of forest tundra vegetation approximately 7000 years ago. This historical reconstruction of the eastern migratory ecotype further supports its current classification as a conservation unit, specifically a Designatable Unit, under Canada's Species at Risk Act. These findings have implications for other sub-specific contact zones for caribou and other North American species in conservation unit delineation.

Natural hybridization and asymmetric introgression at the distribution margin of two Buddleja species with a large overlap.

Science.gov (United States)

Liao, Rong-Li; Ma, Yong-Peng; Gong, Wei-Chang; Chen, Gao; Sun, Wei-Bang; Zhou, Ren-Chao; Marczewski, Tobias

2015-06-18

Natural hybridization in plants is universal and plays an important role in evolution. Based on morphology it has been presumed that hybridization occurred in the genus Buddleja, though genetic studies confirming this assumption have not been conducted to date. The two species B. crispa and B. officinalis overlap in their distributions over a wide range in South-West China, and we aimed to provide genetic evidence for ongoing hybridization in this study. We investigated the occurrence of hybrids between the two species at the southern-most edge of the distribution of B. crispa using five nuclear loci and pollination experiments. The genetic data suggest substantial differentiation between the two species as species-specific alleles are separated by at least 7-28 mutations. The natural hybrids found were nearly all F1s (21 of 23), but backcrosses were detected, and some individuals, morphologically indistinguishable from the parental species, showed introgression. Pollen viability test shows that the percentage of viable pollen grains was 50 ± 4% for B. crispa, and 81 ± 2% for B. officinalis. This difference is highly significant (t = 7.382, p < 0.0001). Hand cross-pollination experiments showed that B. crispa is not successful as pollen-parent, but B. officinalis is able to pollinate B. crispa to produce viable hybrid seed. Inter-specific seed-set is low (8 seeds per fruit, as opposed to about 65 for intra-specific pollinations), suggesting post-zygotic reproductive barriers. In addition, one of the reference populations also suggests a history of introgression at other localities. The occurrence of morphologically intermediate individuals between B. crispa and B. officinalis at Xishan Mountain is unequivocally linked to hybridization and almost all examined individuals of the putative hybrids were likely F1s. Despite pollination experiments indicating higher chances for introgression into B. officinalis (hybrids only produced viable seed when

Introgression of physiological traits for a comprehensive improvement of drought adaptation in crop plants

Science.gov (United States)

Sreeman, Sheshshayee M.; Vijayaraghavareddy, Preethi; Sreevathsa, Rohini; Rajendrareddy, Sowmya; Arakesh, Smitharani; Bharti, Pooja; Dharmappa, Prathibha; Soolanayakanahally, Raju

2018-04-01

Burgeoning population growth, industrial demand and the predicted global climate change resulting in erratic monsoon rains are expected to severely limit fresh water availability for agriculture both in irrigated and rainfed ecosystems. In order to remain food and nutrient secure, agriculture research needs to focus on devising strategies to save water in irrigated conditions and to develop superior cultivars with improved water productivity to sustain yield under rainfed conditions. Recent opinions accruing in the scientific literature strongly favour the adoption of a “trait based” approach for increasing water productivity especially the traits associated with maintenance of positive tissue turgor and maintenance of increased carbon assimilation as the most relevant traits to improve crop growth rates under water limiting conditions and to enhance water productivity. The advent of several water saving agronomic practices notwithstanding, a genetic enhancement strategy of introgressing distinct physiological, morphological and cellular mechanisms on to a single elite genetic background is essential for achieving a comprehensive improvement in drought adaptation in crop plants. The significant progress made in genomics, though would provide the necessary impetus, a clear understanding of the “traits” to be introgressed is the most essential need of the hour. Water uptake by a better root architecture, water conservation by preventing unproductive transpiration is crucial for maintaining positive tissue water relations. Improved carbon assimilation associated with carboxylation capacity and mesophyll conductance is equally important in sustaining crop growth rates under water limited conditions. Besides these major traits, we summarized the available information in literature on classifying various drought adaptive traits. We provide evidences that water-use efficiency when introgressed with moderately higher transpiration, would significantly enhance

Introgression of Physiological Traits for a Comprehensive Improvement of Drought Adaptation in Crop Plants

Directory of Open Access Journals (Sweden)

Sheshshayee M. Sreeman

2018-04-01

Full Text Available Burgeoning population growth, industrial demand, and the predicted global climate change resulting in erratic monsoon rains are expected to severely limit fresh water availability for agriculture both in irrigated and rainfed ecosystems. In order to remain food and nutrient secure, agriculture research needs to focus on devising strategies to save water in irrigated conditions and to develop superior cultivars with improved water productivity to sustain yield under rainfed conditions. Recent opinions accruing in the scientific literature strongly favor the adoption of a “trait based” crop improvement approach for increasing water productivity. Traits associated with maintenance of positive tissue turgor and maintenance of increased carbon assimilation are regarded as most relevant to improve crop growth rates under water limiting conditions and to enhance water productivity. The advent of several water saving agronomic practices notwithstanding, a genetic enhancement strategy of introgressing distinct physiological, morphological, and cellular mechanisms on to a single elite genetic background is essential for achieving a comprehensive improvement in drought adaptation in crop plants. The significant progress made in genomics, though would provide the necessary impetus, a clear understanding of the “traits” to be introgressed is the most essential need of the hour. Water uptake by a better root architecture, water conservation by preventing unproductive transpiration are crucial for maintaining positive tissue water relations. Improved carbon assimilation associated with carboxylation capacity and mesophyll conductance is important in sustaining crop growth rates under water limited conditions. Besides these major traits, we summarize the available information in literature on classifying various drought adaptive traits. We provide evidences that Water-Use Efficiency when introgressed with moderately higher transpiration, would

Introgression of Blast Resistance Genes (Putative Pi-b and Pi-kh) into Elite Rice Cultivar MR219 through Marker-Assisted Selection

Science.gov (United States)

Tanweer, Fatah A.; Rafii, Mohd Y.; Sijam, Kamaruzaman; Rahim, Harun A.; Ahmed, Fahim; Ashkani, Sadegh; Latif, Mohammad A.

2015-01-01

Blast is the most common biotic stress leading to the reduction of rice yield in many rice-growing areas of the world, including Malaysia. Improvement of blast resistance of rice varieties cultivated in blast endemic areas is one of the most important objectives of rice breeding programs. In this study, the marker-assisted backcrossing strategy was applied to improve the blast resistance of the most popular Malaysian rice variety MR219 by introgressing blast resistance genes from the Pongsu Seribu 2 variety. Two blast resistance genes, Pi-b and Pi-kh, were pyramided into MR219. Foreground selection coupled with stringent phenotypic selection identified 15 plants homozygous for the Pi-b and Pi-kh genes, and background selection revealed more than 95% genome recovery of MR219 in advanced blast resistant lines. Phenotypic screening against blast disease indicated that advanced homozygous blast resistant lines were strongly resistant against pathotype P7.2 in the blast disease endemic areas. The morphological, yield, grain quality, and yield-contributing characteristics were significantly similar to those of MR219. The newly developed blast resistant improved lines will retain the high adoptability of MR219 by farmers. The present results will also play an important role in sustaining the rice production of Malaysia. PMID:26734013

The elusive nature of adaptive mitochondrial DNA evolution of an Arctic lineage prone to frequent introgression

DEFF Research Database (Denmark)

Melo-Ferreira, Jose; Vilela, Joana; Fonseca, Miguel M.

2014-01-01

understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread...

Introgression of mountain hare (Lepus timidus mitochondrial DNA into wild brown hares (Lepus europaeus in Denmark

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Villesen Palle

2006-11-01

Full Text Available Abstract Background In Europe the mountain hare (Lepus timidus exists in Great Britain, Norway, Sweden, Finland, parts of the Alps and in Eastern Europe, but not in Denmark. Interspecific hybridization has been demonstrated between native Swedish mountain hares and introduced brown hares (Lepus europaeus. During the data collection in a study concerning Danish brown hares we identified 16 hares with a single very divergent haplotype. Results Phylogenetic analysis shows that the divergent Danish haplotype is most closely related to the Swedish mountain hare. The frequency of Lepus timidus mtDNA haplotype in the Eastern Danish hare populations is estimated to 6%. Conclusion In contrast to what is known, the Danish hare populations are not pure L. europaeus populations but include introgressed brown hares with Swedish L. timidus mtDNA. The most probable explanation of this is natural migration or translocation of introgressed brown hares from Sweden. The impurity of hare populations has implications for conservation and population genetics.

Evidence to support natural hybridization between Anopheles sinensis and Anopheles kleini (Diptera: Culicidae): possibly a significant mechanism for gene introgression in sympatric populations

Science.gov (United States)

2014-01-01

Background Malaria caused by Plasmodium vivax is still a public health problem in the Republic of Korea (ROK), particularly regarding the recent re-emergence of this malarial species near the demilitarized zone in northwestern Paju City, Gyeonggi-do Province. Currently, at least 4 species (An. kleini, An. pullus, An. belenrae and An. lesteri) of the Hyrcanus Group are reported as possible natural vectors of vivax malaria in the ROK, and An. sinensis, which is the most dominant species, has long been incriminated as an important natural vector of this P. vivax. However, An. sinensis was ranked recently as a low potential vector. According to the discovery of natural hybrids between An. sinensis (a low potential vector for P. vivax) and An. kleini (a high potential vector for P. vivax) in Paju City, intensive investigation of this phenomenon is warranted under laboratory conditions. Methods Mosquitoes were collected during 2010-2012 from Paju City, ROK. Hybridization experiments used iso-female line colonies of these anophelines together with DNA analysis of ribosomal DNA [second internal transcribed spacer (ITS2)] and mitochondrial DNA [cytochrome c oxidase subunit I (COI)] of the parental colonies, F1-hybrids and repeated backcross progenies were performed intensively by using a PCR-based assay and pyrosequencing technology. Results The results from hybridization experiments and molecular investigations revealed that the mitochondrial COI gene was introgressed from An. sinensis into An. kleini. The An. sinensis progenies obtained from consecutive repeated backcrosses in both directions, i.e., F2-11 progeny [(An. sinensis x An. kleini) x An. sinensis] and F3-5 progeny [(An. kleini x An. sinensis) x An. kleini] provided good supportive evidence. Conclusions This study revealed introgression of the mitochondrial COI gene between An. sinensis and An. kleini through consecutive repeated backcrosses under laboratory conditions. This new body of knowledge will be

Effects of introgression on the genetic population structure of two ecologically and economically important conifer species: lodgepole pine (Pinus contorta var. latifolia) and jack pine (Pinus banksiana).

Science.gov (United States)

Cullingham, Catherine I; Cooke, Janice E K; Coltman, David W

2013-10-01

Forest trees exhibit a remarkable range of adaptations to their environment, but as a result of frequent and long-distance gene flow, populations are often only weakly differentiated. Lodgepole and jack pine hybridize in western Canada, which adds the opportunity for introgression through hybridization to contribute to population structure and (or) adaptive variation. Access to large sample size, high density SNP datasets for these species would improve our ability to resolve population structure, parameterize introgression, and separate the influence of demography from adaptation. To accomplish this, 454 transcriptome reads for lodgepole and jack pine were assembled using Newbler and MIRA, the assemblies mined for SNPs, and 1536 SNPs were selected for typing on lodgepole pine, jack pine, and their hybrids (N = 536). We identified population structure using both Bayesian clustering and discriminate analysis of principle components. Introgressed SNP loci were identified and their influence on observed population structure was assessed. We found that introgressed loci resulted in increased differentiation both within lodgepole and jack pine populations. These findings are timely given the recent mountain pine beetle population expansion in the hybrid zone, and will facilitate future studies of adaptive traits in these ecologically important species.

Climate, demography, and zoogeography predict introgression thresholds in salmonid hybrid zones in Rocky Mountain streams

Science.gov (United States)

Michael K. Young; Daniel J. Isaak; Kevin S. McKelvey; Taylor M. Wilcox; Daniel M. Bingham; Kristine L. Pilgrim; Kellie J. Carim; Matthew R. Campbell; Matthew P. Corsi; Dona L. Horan; David E. Nagel; Michael K. Schwartz

2016-01-01

Among the many threats posed by invasions of nonnative species is introgressive hybridization, which can lead to the genomic extinction of native taxa. This phenomenon is regarded as common and perhaps inevitable among native cutthroat trout and introduced rainbow trout in western North America, despite that these taxa naturally co-occur in some locations. We conducted...

Assessing multilocus introgression patterns: a case study on the mouse X chromosome in Central Europe

Czech Academy of Sciences Publication Activity Database

Macholán, Miloš; Baird, S. J. E.; Dufková, Petra; Munclinger, P.; Vošlajerová Bímová, Barbora; Piálek, Jaroslav

2011-01-01

Roč. 65, č. 5 (2011), s. 1428-1446 ISSN 0014-3820 R&D Projects: GA ČR GA206/08/0640 Institutional research plan: CEZ:AV0Z50450515; CEZ:AV0Z60930519 Keywords : genetic conflict * hybrid zone movement * sex biased introgression * mice * X chromosome Subject RIV: EG - Zoology Impact factor: 5.146, year: 2011

Semi-permeable species boundaries in the coral genus Madracis: introgression in a brooding coral system.

Science.gov (United States)

Frade, P R; Reyes-Nivia, M C; Faria, J; Kaandorp, J A; Luttikhuizen, P C; Bak, R P M

2010-12-01

Introgressive hybridization is described in several phylogenetic studies of mass-spawning corals. However, the prevalence of this process among brooding coral species is unclear. We used a mitochondrial (mtDNA: nad5) and two nuclear (nDNA: ATPSα and SRP54) intron markers to explore species barriers in the coral genus Madracis and address the role of hybridization in brooding systems. Specimens of six Caribbean Madracis morphospecies were collected from 5 to 60 m depth at Buoy One, Curaçao, supplemented by samples from Aruba, Trinidad & Tobago and Bermuda. Polymerase chain reaction and denaturing gradient gel electrophoresis were coupled to detect distinct alleles within single colonies. The recurrent nDNA phylogenetic non-monophyly among taxa is only challenged by Madracis senaria, the single monophyletic species within the genus. nDNA AMOVAs indicated overall statistical divergence (0.1% significance level) among species but pairwise comparisons of genetic differentiation revealed some gene exchange between Madracis taxa. mtDNA sequences clustered in two main groups representing typical shallow and deep water Madracis species. Madracis pharensis shallow and deep colonies (with threshold at about 23-24 m) clustered in different mtDNA branches, together with their depth-sympatric congenerics. This divergence was repeated for the nDNA (ATPSα) suggestive of distinct M. pharensis depth populations. These matched the vertical distribution of the dinoflagellate symbionts hosted by M. pharensis, with Symbiodinium ITS2 type B7 in the shallows but type B15 in the deep habitats, suggesting symbiont-related disruptive selection. Recurrent non-monophyly of Madracis taxa and high levels of shared polymorphism reflected in ambiguous phylogenetic networks indicate that hybridization is likely to have played a role in the evolution of the genus. Using coalescent forward-in-time simulations, lineage sorting alone was rejected as an explanation to the SRP54 genetic variation

Introgression between ecologically distinct species following increased salinity in the Colorado Delta- Worldwide implications for impacted estuary diversity.

Science.gov (United States)

Lau, Clive L F; Jacobs, David K

2017-01-01

We investigate hybridization and introgression between ecologically distinct sister species of silverside fish in the Gulf of California through combined analysis of morphological, sequence, and genotypic data. Water diversions in the past century turned the Colorado River Delta from a normal estuary to a hypersaline inverse estuary, raising concerns for the local fauna, much of which is endangered. Salinity differences are known to generate ecological species pairs and we anticipated that loss of the fresher-water historic salinity regime could alter the adaptive factors maintaining distinction between the broadly distributed Gulf-endemic Colpichthys regis and the narrowly restricted Delta-endemic Colpichthys hubbsi , the species that experienced dramatic environmental change. In this altered environmental context, these long-isolated species (as revealed by Cytochrome b sequences) show genotypic (RAG1, microsatellites) evidence of active hybridization where the species ranges abut, as well as directional introgression from C. regis into the range center of C. hubbsi . Bayesian group assignment (STRUCTURE) on six microsatellite loci and multivariate analyses (DAPC) on both microsatellites and phenotypic data further support substantial recent admixture between the sister species. Although we find no evidence for recent population decline in C. hubbsi based on mitochondrial sequence, introgression may be placing an ancient ecological species at risk of extinction. Such introgressive extinction risk should also pertain to other ecological species historically sustained by the now changing Delta environment. More broadly, salinity gradient associated ecological speciation is evident in silverside species pairs in many estuarine systems around the world. Ecological species pairs among other taxa in such systems are likely poorly understood or cryptic. As water extraction accelerates in river systems worldwide, salinity gradients will necessarily be altered, impacting

Introgression between ecologically distinct species following increased salinity in the Colorado Delta- Worldwide implications for impacted estuary diversity

Directory of Open Access Journals (Sweden)

Clive L.F. Lau

2017-12-01

Full Text Available We investigate hybridization and introgression between ecologically distinct sister species of silverside fish in the Gulf of California through combined analysis of morphological, sequence, and genotypic data. Water diversions in the past century turned the Colorado River Delta from a normal estuary to a hypersaline inverse estuary, raising concerns for the local fauna, much of which is endangered. Salinity differences are known to generate ecological species pairs and we anticipated that loss of the fresher-water historic salinity regime could alter the adaptive factors maintaining distinction between the broadly distributed Gulf-endemic Colpichthys regis and the narrowly restricted Delta-endemic Colpichthys hubbsi, the species that experienced dramatic environmental change. In this altered environmental context, these long-isolated species (as revealed by Cytochrome b sequences show genotypic (RAG1, microsatellites evidence of active hybridization where the species ranges abut, as well as directional introgression from C. regis into the range center of C. hubbsi. Bayesian group assignment (STRUCTURE on six microsatellite loci and multivariate analyses (DAPC on both microsatellites and phenotypic data further support substantial recent admixture between the sister species. Although we find no evidence for recent population decline in C. hubbsi based on mitochondrial sequence, introgression may be placing an ancient ecological species at risk of extinction. Such introgressive extinction risk should also pertain to other ecological species historically sustained by the now changing Delta environment. More broadly, salinity gradient associated ecological speciation is evident in silverside species pairs in many estuarine systems around the world. Ecological species pairs among other taxa in such systems are likely poorly understood or cryptic. As water extraction accelerates in river systems worldwide, salinity gradients will necessarily be

Reduced SNP panels for genetic identification and introgression analysis in the dark honey bee (Apis mellifera mellifera.

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Irene Muñoz

Full Text Available Beekeeping activities, especially queen trading, have shaped the distribution of honey bee (Apis mellifera subspecies in Europe, and have resulted in extensive introductions of two eastern European C-lineage subspecies (A. m. ligustica and A. m. carnica into the native range of the M-lineage A. m. mellifera subspecies in Western Europe. As a consequence, replacement and gene flow between native and commercial populations have occurred at varying levels across western European populations. Genetic identification and introgression analysis using molecular markers is an important tool for management and conservation of honey bee subspecies. Previous studies have monitored introgression by using microsatellite, PCR-RFLP markers and most recently, high density assays using single nucleotide polymorphism (SNP markers. While the latter are almost prohibitively expensive, the information gained to date can be exploited to create a reduced panel containing the most ancestry-informative markers (AIMs for those purposes with very little loss of information. The objective of this study was to design reduced panels of AIMs to verify the origin of A. m. mellifera individuals and to provide accurate estimates of the level of C-lineage introgression into their genome. The discriminant power of the SNPs using a variety of metrics and approaches including the Weir & Cockerham's FST, an FST-based outlier test, Delta, informativeness (In, and PCA was evaluated. This study shows that reduced AIMs panels assign individuals to the correct origin and calculates the admixture level with a high degree of accuracy. These panels provide an essential tool in Europe for genetic stock identification and estimation of admixture levels which can assist management strategies and monitor honey bee conservation programs.

Identification of Mutant Genes and Introgressed Tiger Salamander DNA in the Laboratory Axolotl, Ambystoma mexicanum.

Science.gov (United States)

Woodcock, M Ryan; Vaughn-Wolfe, Jennifer; Elias, Alexandra; Kump, D Kevin; Kendall, Katharina Denise; Timoshevskaya, Nataliya; Timoshevskiy, Vladimir; Perry, Dustin W; Smith, Jeramiah J; Spiewak, Jessica E; Parichy, David M; Voss, S Randal

2017-01-31

The molecular genetic toolkit of the Mexican axolotl, a classic model organism, has matured to the point where it is now possible to identify genes for mutant phenotypes. We used a positional cloning-candidate gene approach to identify molecular bases for two historic axolotl pigment phenotypes: white and albino. White (d/d) mutants have defects in pigment cell morphogenesis and differentiation, whereas albino (a/a) mutants lack melanin. We identified in white mutants a transcriptional defect in endothelin 3 (edn3), encoding a peptide factor that promotes pigment cell migration and differentiation in other vertebrates. Transgenic restoration of Edn3 expression rescued the homozygous white mutant phenotype. We mapped the albino locus to tyrosinase (tyr) and identified polymorphisms shared between the albino allele (tyr a ) and tyr alleles in a Minnesota population of tiger salamanders from which the albino trait was introgressed. tyr a has a 142 bp deletion and similar engineered alleles recapitulated the albino phenotype. Finally, we show that historical introgression of tyr a significantly altered genomic composition of the laboratory axolotl, yielding a distinct, hybrid strain of ambystomatid salamander. Our results demonstrate the feasibility of identifying genes for traits in the laboratory Mexican axolotl.

Molecular identification of vectors of Leishmania in Colombia: mitochondrial introgression in the Lutzomyia townsendi series.

Science.gov (United States)

Testa, J M; Montoya-Lerma, J; Cadena, H; Oviedo, M; Ready, P D

2002-12-01

The identity of the sandfly vectors of Leishmania braziliensis in Valle del Cauca Department, Colombia, was originally given as Lutzomyia townsendi, but then changed to L. youngi, another member of the L. townsendi series (Verrucarum group) with isomorphic females. To identify members of this series in Valle del Cauca, we analyzed the nuclear gene elongation factor-alpha (EF-alpha) and the mitochondrial gene cytochrome b (Cyt b). DNA sequences from the L. verrucarum series (L. columbiana, L. evansi and L. ovallesi) were used as outgroups. Flies from two locations on the western cordillera of the Andes were identified as L. townsendi s.s., according to male morphology and distinctive gene lineages. In the third location, on the central cordillera of the Andes, most specimens were identified as belonging to a geographical population of L. youngi, according to male morphology, an EF-alpha lineage shared with L. youngi from the Venezuelan-type locality, and a distinctive Cyt b sub-lineage. All other specimens were identified as L. youngi with the introgressed Cyt b sequences of L. townsendi. Such interspecific introgression implies that vectorial traits and ecological associations may no longer be viewed as fixed properties of different morphospecies.

Non-introgressive genome chimerisation by malsegregation in autodiploidised allotetraploids during meiosis of Saccharomyces kudriavzevii x Saccharomyces uvarum hybrids.

Science.gov (United States)

Karanyicz, Edina; Antunovics, Zsuzsa; Kallai, Z; Sipiczki, M

2017-06-01

Saccharomyces strains with chimerical genomes consisting of mosaics of the genomes of different species ("natural hybrids") occur quite frequently among industrial and wine strains. The most widely endorsed hypothesis is that the mosaics are introgressions acquired via hybridisation and repeated backcrosses of the hybrids with one of the parental species. However, the interspecies hybrids are sterile, unable to mate with their parents. Here, we show by analysing synthetic Saccharomyces kudriavzevii x Saccharomyces uvarum hybrids that mosaic (chimeric) genomes can arise without introgressive backcrosses. These species are biologically separated by a double sterility barrier (sterility of allodiploids and F1 sterility of allotetraploids). F1 sterility is due to the diploidisation of the tetraploid meiosis resulting in MAT a /MAT α heterozygosity which suppresses mating in the spores. This barrier can occasionally be broken down by malsegregation of autosyndetically paired chromosomes carrying the MAT loci (loss of MAT heterozygosity). Subsequent malsegregation of additional autosyndetically paired chromosomes and occasional allosyndetic interactions chimerise the hybrid genome. Chromosomes are preferentially lost from the S. kudriavzevii subgenome. The uniparental transmission of the mitochondrial DNA to the hybrids indicates that nucleo-mitochondrial interactions might affect the direction of the genomic changes. We propose the name GARMe (Genome AutoReduction in Meiosis) for this process of genome reduction and chimerisation which involves no introgressive backcrossings. It opens a way to transfer genetic information between species and thus to get one step ahead after hybridisation in the production of yeast strains with beneficial combinations of properties of different species.

Features of Ppd-B1 expression regulation and their impact on the flowering time of wheat near-isogenic lines.

Science.gov (United States)

Kiseleva, Antonina A; Potokina, Elena K; Salina, Elena A

2017-11-14

Photoperiod insensitive Ppd-1a alleles determine early flowering of wheat. Increased expression of homoeologous Ppd-D1a and Ppd-A1a result from deletions in the promoter region, and elevated expression of Ppd-B1a is determined by an increased copy number. In this study, using bread wheat cultivars Sonora and PSL2, which contrast in flowering time, and near-isogenic lines resulting from their cross, "Ppd-m" and "Ppd-w" with Ppd-B1a introgressed from Sonora, we investigated the putative factors that influence Ppd-B1a expression. By analyzing the Ppd-B1a three distinct copies, we identified an indel and the two SNPs, which distinguished the investigated allele from other alleles with a copy number variation. We studied the expression of the Ppd-A1, Ppd-B1a, and Ppd-D1 genes along with genes that are involved in light perception (PhyA, PhyB, PhyC) and the flowering initiation (Vrn-1, TaFT1) and discussed their interactions. Expression of Ppd-B1a in the "Ppd-m" line, which flowered four days earlier than "Ppd-w", was significantly higher. We found PhyC to be up-regulated in lines with Ppd-B1a alleles. Expression of PhyC was higher in "Ppd-m". Microsatellite genotyping demonstrated that in the line "Ppd-m", there is an introgression in the pericentromeric region of chromosome 5B from the early flowering parental Sonora, while the "Ppd-w" does not have this introgression. FHY3/FAR1 is known to be located in this region. Expression of the transcription factor FHY3/FAR1 was higher in the "Ppd-m" line than in "Ppd-w", suggesting that FHY3/FAR1 is important for the wheat flowering time and may cause earlier flowering of "Ppd-m" as compared to "Ppd-w". We propose that there is a positive bidirectional regulation of Ppd-B1a and PhyC with an FHY3/FAR1 contribution. The bidirectional regulation can be proposed for Ppd-A1a and Ppd-D1a. Using in silico analysis, we demonstrated that the specificity of the Ppd-B1 regulation compared to that of homoeologous genes involves not only a

A Phylogenetic Synthesis for Oceanic Dolphins: Total Evidence, Cytonuclear Discordance, and Possible Introgressive Hybridization

OpenAIRE

Haisten, David

2016-01-01

Introgressive hybridization is increasingly being detected in vertebrate taxa but was thought to be rare in mammals. Recent evidence suggests that this view might not correct and cetaceans may be pre-disposed for the capacity to hybridize. Numerous instances of cetacean (dolphins, whales, and porpoises) hybridization have been reported both in captivity and in the wild, many of which occurred in oceanic dolphins: family Delphinidae. The rapid radiation of Delphinidae commenced during the Mio...

Study on the introgression of beef breeds in Canchim cattle using single nucleotide polymorphism markers.

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Marcos Eli Buzanskas

Full Text Available The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais-37.5% Zebu and MA genetic group (MA: 65.6% Charolais-34.4% Zebu cattle using genomic information on Charolais (CH, Nelore (NE, and Indubrasil (IB breeds. The number of animals used was 395 (CA and MA, 763 (NE, 338 (CH, and 37 (IB. The Bovine50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle.

Water deficit affects primary metabolism differently in two Lolium multiflorum/Festuca arundinacea introgression forms with a distinct capacity for photosynthesis and membrane regeneration.

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Dawid Perlikowski

2016-07-01

Full Text Available Understanding how plants respond to drought at different levels of cell metabolism is an important aspect of research on the mechanisms involved in stress tolerance. Furthermore, a dissection of drought tolerance into its crucial components by the use of plant introgression forms facilitates to analyze this trait more deeply. The important components of plant drought tolerance are the capacity for photosynthesis under drought conditions, and the ability of cellular membrane regeneration after stress cessation. Two closely related introgression forms of Lolium multiflorum/Festuca arundinacea, differing in the level of photosynthetic capacity during stress, and in the ability to regenerate their cellular membranes after stress cessation, were used as forage grass models in a primary metabolome profiling and in an evaluation of chloroplast 1,6-bisphosphate aldolase accumulation level and activity, during 11 days of water deficit, followed by 10 days of rehydration. It was revealed here that the introgression form, characterized by the ability to regenerate membranes after rehydration, contained higher amounts of proline, melibiose, galactaric acid, myo-inositol and myo-inositol-1-phosphate involved in osmoprotection and stress signaling under drought. Moreover, during the rehydration period, this form also maintained elevated accumulation levels of most the primary metabolites, analyzed here. The other introgression form, characterized by the higher capacity for photosynthesis, revealed a higher accumulation level and activity of chloroplast aldolase under drought conditions, and higher accumulation levels of most photosynthetic products during control and drought periods. The potential impact of the observed metabolic alterations on cellular membrane recovery after stress cessation, and on a photosynthetic capacity under drought conditions in grasses, are discussed.

Genome-wide signatures of complex introgression and adaptive evolution in the big cats

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Figueiró, Henrique V.; Li, Gang; Trindade, Fernanda J.; Assis, Juliana; Pais, Fabiano; Fernandes, Gabriel; Santos, Sarah H. D.; Hughes, Graham M.; Komissarov, Aleksey; Antunes, Agostinho; Trinca, Cristine S.; Rodrigues, Maíra R.; Linderoth, Tyler; Bi, Ke; Silveira, Leandro; Azevedo, Fernando C. C.; Kantek, Daniel; Ramalho, Emiliano; Brassaloti, Ricardo A.; Villela, Priscilla M. S.; Nunes, Adauto L. V.; Teixeira, Rodrigo H. F.; Morato, Ronaldo G.; Loska, Damian; Saragüeta, Patricia; Gabaldón, Toni; Teeling, Emma C.; O’Brien, Stephen J.; Nielsen, Rasmus; Coutinho, Luiz L.; Oliveira, Guilherme; Murphy, William J.; Eizirik, Eduardo

2017-01-01

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages. PMID:28776029

Marked hybridization and introgression in Ophrys sect. Pseudophrys in the western Iberian Peninsula.

Science.gov (United States)

Cotrim, Helena; Monteiro, Filipa; Sousa, Eva; Pinto, Manuel J; Fay, Michael F

2016-04-01

Orchids in the genus Ophrys represent extraordinary cases of tight coevolution between plants and their pollinators, and as a result, they present opportunities for studying hybridization, or a lack thereof, during speciation. However, few studies assess the real effect of hybridization in diversification. The three most representative species of section Pseudophrys in the western Iberian Peninsula-O. dyris, O. fusca, and O. lutea-were chosen to study evolutionary relationships and examine speciation. Using eight specific nuclear microsatellite loci, 357 individuals from 28 locations were studied; 142 of these samples were also studied with four plastid microsatellite loci. Data were analyzed using Bayesian cluster analysis, a median-joint network, and multivariate analysis. Many O. dyris and O. fusca specimens had three or four alleles and were therefore treated as tetraploid. Ophrys dyris is poorly genetically separated from O. fusca, and pure populations are rare. Ophrys fusca and O. lutea are distinct, but hybrids/introgressed individuals were detected in most of the populations and supported by plastid haplotypes. Ophrys fusca is subdivided into three well-delimited genetic lineages with a strict geographic correspondence confirmed by plastid haplotypes. Because postzygotic barriers are weak, leakage in this highly specialized orchid-pollinator system contributes to hybridization and introgression. These leakages may have occurred during periods of past climate change, promoting homogenization and the potential for generations of new biodiversity via production of novel genotypes/phenotypes interacting with pollinators. © 2016 Botanical Society of America.

Heritability and genetic advance studies for biochemical traits in F2-3 introgressed families of Brassica

International Nuclear Information System (INIS)

Farhatullah, N.K.; Khalil, I.H.; Nahed, H.

2015-01-01

Higher heritability estimates along with high genetic advance values are effective in envisaging gain under selection in developing genotypes. The objective of the present study was to evaluate variability, heritability and genetic advance in 10 interspecific F2-3 families of Brassica species (B. napus * B. juncea, B. napus * B. rapa). These families were studied for heterospecific introgression of biochemical traits. Low to high heritability estimates were recorded for seed quality traits. Considerable variations within F2-3 families were observed for biochemical traits. Most of the F2-3 families for oil content and erucic showed moderate to high heritability indicating the slightest influence of environment thus modification of trait by selection would be more effective. Among F2-3 introgressed families Bn-510 x Bj-109 produced high oil i.e., 49.5% while Bn-532 x Br-118 (24.4%), Bn-533 x Bj-109 (24.1%) and high protein percentage in terms of mean performance. In the present research, individual segregating progenies of interspecific cross populations i.e., which possessed combination of desirable traits, were identified which could be incorporated in the future Breeding programs and it may facilitate varietal development. (author)

Introgression of the callipyge mutation into the Assaf fat tail breed

International Nuclear Information System (INIS)

Gootwine, E.; Rosov, A.; Bor, A.; Yossafi, S.; Zenue, A.

2003-01-01

Introgression of the callipyge (CLPG) mutation into the fat-tail Assaf breed was initiated by inseminating Assaf ewes with Dorset-Hampshire semen from a ram that was heterozygous for the callipyge mutation. Presence of the mutation in the F1 generation and the first backcross generation (BC1) was validated using molecular markers linked to the CLPG locus. Carcasses of callipyge BC1-CN lambs had significantly (P less than 0.01) better conformation than carcasses of normal BC1-NN lambs and straightbred Assaf lambs. Computerized tomography analysis of live BC1 and Assaf lambs showed that carrying the callipyge mutation increased Longissimus dorsi and Quadriceps femoris muscles by about 30

A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.).

Science.gov (United States)

Pfennig, Karin S; Allenby, Ashley; Martin, Ryan A; Monroy, Anaïs; Jones, Corbin D

2012-09-01

Two congeneric species of spadefoot toad, Spea multiplicata and Spea bombifrons, have been the focus of hybridization studies since the 1970s. Because complex hybrids are not readily distinguished phenotypically, genetic markers are needed to identify introgressed individuals. We therefore developed a set of molecular markers (amplified fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and single nucleotide polymorphism) for identifying pure-species, F1 hybrids and more complex introgressed types. To do so, we tested a series of markers across both species and known hybrids using populations in both allopatry and sympatry. We retained those markers that differentiated the two pure-species and also consistently identified known species hybrids. These markers are well suited for identifying hybrids between these species. Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow. © 2012 Blackwell Publishing Ltd.

Accelerated Generation of Selfed Pure Line Plants for Gene Identification and Crop Breeding

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Guijun Yan

2017-10-01

Full Text Available Production of pure lines is an important step in biological studies and breeding of many crop plants. The major types of pure lines for biological studies and breeding include doubled haploid (DH lines, recombinant inbred lines (RILs, and near isogenic lines (NILs. DH lines can be produced through microspore and megaspore culture followed by chromosome doubling while RILs and NILs can be produced through introgressions or repeated selfing of hybrids. DH approach was developed as a quicker method than conventional method to produce pure lines. However, its drawbacks of genotype-dependency and only a single chance of recombination limited its wider application. A recently developed fast generation cycling system (FGCS achieved similar times to those of DH for the production of selfed pure lines but is more versatile as it is much less genotype-dependent than DH technology and does not restrict recombination to a single event. The advantages and disadvantages of the technologies and their produced pure line populations for different purposes of biological research and breeding are discussed. The development of a concept of complete in vitro meiosis and mitosis system is also proposed. This could integrate with the recently developed technologies of single cell genomic sequencing and genome wide selection, leading to a complete laboratory based pre-breeding scheme.

Source-sink estimates of genetic introgression show influence of hatchery strays on wild chum salmon populations in Prince William Sound, Alaska.

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James R Jasper

Full Text Available The extent to which stray, hatchery-reared salmon affect wild populations is much debated. Although experiments show that artificial breeding and culture influence the genetics of hatchery salmon, little is known about the interaction between hatchery and wild salmon in a natural setting. Here, we estimated historical and contemporary genetic population structures of chum salmon (Oncorhynchus keta in Prince William Sound (PWS, Alaska, with 135 single nucleotide polymorphism (SNP markers. Historical population structure was inferred from the analysis of DNA from fish scales, which had been archived since the late 1960's for several populations in PWS. Parallel analyses with microsatellites and a test based on Hardy-Weinberg proportions showed that about 50% of the fish-scale DNA was cross-contaminated with DNA from other fish. These samples were removed from the analysis. We used a novel application of the classical source-sink model to compare SNP allele frequencies in these archived fish-scales (1964-1982 with frequencies in contemporary samples (2008-2010 and found a temporal shift toward hatchery allele frequencies in some wild populations. Other populations showed markedly less introgression, despite moderate amounts of hatchery straying. The extent of introgression may reflect similarities in spawning time and life-history traits between hatchery and wild fish, or the degree that hybrids return to a natal spawning area. The source-sink model is a powerful means of detecting low levels of introgression over several generations.

Genetic and epigenetic variations induced by wheat-rye 2R and 5R monosomic addition lines.

Science.gov (United States)

Fu, Shulan; Sun, Chuanfei; Yang, Manyu; Fei, Yunyan; Tan, Feiqun; Yan, Benju; Ren, Zhenglong; Tang, Zongxiang

2013-01-01

Monosomic alien addition lines (MAALs) can easily induce structural variation of chromosomes and have been used in crop breeding; however, it is unclear whether MAALs will induce drastic genetic and epigenetic alterations. In the present study, wheat-rye 2R and 5R MAALs together with their selfed progeny and parental common wheat were investigated through amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analyses. The MAALs in different generations displayed different genetic variations. Some progeny that only contained 42 wheat chromosomes showed great genetic/epigenetic alterations. Cryptic rye chromatin has introgressed into the wheat genome. However, one of the progeny that contained cryptic rye chromatin did not display outstanding genetic/epigenetic variation. 78 and 49 sequences were cloned from changed AFLP and MSAP bands, respectively. Blastn search indicated that almost half of them showed no significant similarity to known sequences. Retrotransposons were mainly involved in genetic and epigenetic variations. Genetic variations basically affected Gypsy-like retrotransposons, whereas epigenetic alterations affected Copia-like and Gypsy-like retrotransposons equally. Genetic and epigenetic variations seldom affected low-copy coding DNA sequences. The results in the present study provided direct evidence to illustrate that monosomic wheat-rye addition lines could induce different and drastic genetic/epigenetic variations and these variations might not be caused by introgression of rye chromatins into wheat. Therefore, MAALs may be directly used as an effective means to broaden the genetic diversity of common wheat.

Stress response of the black coral Leiopathes glaberrima when exposed to sub-lethal amounts of crude oil and dispersant

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Dannise V. Ruiz-Ramos

2017-12-01

Full Text Available The 2010 Deep Water Horizon oil well failure released billions of gallons of crude oil into the deep Gulf of Mexico, and, combined with chemical dispersants, this oil caused significant coral mortality. However, the mechanisms by which oil and dispersed oil impact deep marine fauna are not well understood. Here, we investigate the effects of oil and dispersed oil on a black coral common in the deep Gulf of Mexico, 'Leiopathes glaberrima. 'This coral occurs in several color morphs that show ecological and genetic differences. We hypothesized that dispersed oil would be more detrimental to coral health than oil alone and that this difference would be detectable in the gene expression response of the colonies even at sub-lethal concentrations. In two experiments, four and six colonies of red and white color morphs were exposed to oil, dispersant, and dispersed oil for a minimum of 96 hours. Visual assessment indicated that indeed dispersant and dispersed oil treatments were more damaging than oil alone, for target concentrations of 25 mg L–1. Decline in health was observed for all treatments, independently of color morphotype, but the decline was faster in the white colonies exposed to dispersant. The responses to the treatments were also investigated by monitoring gene expression after 24 hours of sub-lethal chemical exposure. Coral gene expression differed by chemical stressor. Interestingly, the polycyclic aromatic hydrocarbon biomarker gene, cytochrome P450, was only up-regulated in dispersed oil but not oil alone, suggesting that the dispersant increased the availability of such hydrocarbons in the tissue. The gene expression response was apparent at 24 hours when visual impacts were not (yet detectable. The use of chemical dispersants in oil-spill remediation may cause health declines in deep-water corals and deserves further study.

Interspecific Hybridization in Pilot Whales and Asymmetric Genetic Introgression in Northern Globicephala melas under the Scenario of Global Warming.

Science.gov (United States)

Miralles, Laura; Oremus, Marc; Silva, Mónica A; Planes, Serge; Garcia-Vazquez, Eva

2016-01-01

Pilot whales are two cetacean species (Globicephala melas and G. macrorhynchus) whose distributions are correlated with water temperature and partially overlap in some areas like the North Atlantic Ocean. In the context of global warming, distribution range shifts are expected to occur in species affected by temperature. Consequently, a northward displacement of the tropical pilot whale G. macrorynchus is expected, eventually leading to increased secondary contact areas and opportunities for interspecific hybridization. Here, we describe genetic evidences of recurrent hybridization between pilot whales in northeast Atlantic Ocean. Based on mitochondrial DNA sequences and microsatellite loci, asymmetric introgression of G. macrorhynchus genes into G. melas was observed. For the latter species, a significant correlation was found between historical population growth rate estimates and paleotemperature oscillations. Introgressive hybridization, current temperature increases and lower genetic variation in G. melas suggest that this species could be at risk in its northern range. Under increasing environmental and human-mediated stressors in the North Atlantic Ocean, it seems recommendable to develop a conservation program for G. melas.

Introgression Between Cultivars and Wild Populations of Momordica charantia L. (Cucurbitaceae) in Taiwan

Science.gov (United States)

Liao, Pei-Chun; Tsai, Chi-Chu; Chou, Chang-Hung; Chiang, Yu-Chung

2012-01-01

The landrace strains of Momordica charantia are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native to Taiwan. Because of the introduction of cultivars for agricultural purposes, these two accessions currently exhibit a sympatric or parapatric distribution in Taiwan. In this study, the cultivars and wild samples from Taiwan, India, and Korea were collected for testing of their hybridization and evolutionary patterns. The cpDNA marker showed a clear distinction between accessions of cultivars and wild populations of Taiwan and a long divergence time. In contrast, an analysis of eight selectively neutral nuclear microsatellite loci did not reveal a difference between the genetic structures of these two accessions. A relatively short divergence time and frequent but asymmetric gene flows were estimated based on the isolation-with-migration model. Historical and current introgression from cultivars to wild populations of Taiwan was also inferred using MIGRATE-n and BayesAss analyses. Our results showed that these two accessions shared abundant common ancestral polymorphisms, and the timing of the divergence and colonization of the Taiwanese wild populations is consistent with the geohistory of the Taiwan Strait land bridge of the Last Glacial Maximum (LGM). Long-term and recurrent introgression between accessions indicated the asymmetric capacity to receive foreign genes from other accessions. The modern introduction of cultivars of M. charantia during the colonization of Taiwan by the Han Chinese ethnic group enhanced the rate of gene replacement in the native populations and resulted in the loss of native genes. PMID:22754378

Introgression between cultivars and wild populations of Momordica charantia L. (Cucurbitaceae) in Taiwan.

Science.gov (United States)

Liao, Pei-Chun; Tsai, Chi-Chu; Chou, Chang-Hung; Chiang, Yu-Chung

2012-01-01

The landrace strains of Momordica charantia are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native to Taiwan. Because of the introduction of cultivars for agricultural purposes, these two accessions currently exhibit a sympatric or parapatric distribution in Taiwan. In this study, the cultivars and wild samples from Taiwan, India, and Korea were collected for testing of their hybridization and evolutionary patterns. The cpDNA marker showed a clear distinction between accessions of cultivars and wild populations of Taiwan and a long divergence time. In contrast, an analysis of eight selectively neutral nuclear microsatellite loci did not reveal a difference between the genetic structures of these two accessions. A relatively short divergence time and frequent but asymmetric gene flows were estimated based on the isolation-with-migration model. Historical and current introgression from cultivars to wild populations of Taiwan was also inferred using MIGRATE-n and BayesAss analyses. Our results showed that these two accessions shared abundant common ancestral polymorphisms, and the timing of the divergence and colonization of the Taiwanese wild populations is consistent with the geohistory of the Taiwan Strait land bridge of the Last Glacial Maximum (LGM). Long-term and recurrent introgression between accessions indicated the asymmetric capacity to receive foreign genes from other accessions. The modern introduction of cultivars of M. charantia during the colonization of Taiwan by the Han Chinese ethnic group enhanced the rate of gene replacement in the native populations and resulted in the loss of native genes.

Feasible introgression of an anti-pathogen transgene into an urban mosquito population without using gene-drive.

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Kenichi W Okamoto

2014-07-01

Full Text Available Introgressing anti-pathogen constructs into wild vector populations could reduce disease transmission. It is generally assumed that such introgression would require linking an anti-pathogen gene with a selfish genetic element or similar technologies. Yet none of the proposed transgenic anti-pathogen gene-drive mechanisms are likely to be implemented as public health measures in the near future. Thus, much attention now focuses instead on transgenic strategies aimed at mosquito population suppression, an approach generally perceived to be practical. By contrast, aiming to replace vector competent mosquito populations with vector incompetent populations by releasing mosquitoes carrying a single anti-pathogen gene without a gene-drive mechanism is widely considered impractical.Here we use Skeeter Buster, a previously published stochastic, spatially explicit model of Aedes aegypti to investigate whether a number of approaches for releasing mosquitoes with only an anti-pathogen construct would be efficient and effective in the tropical city of Iquitos, Peru. To assess the performance of such releases using realistic release numbers, we compare the transient and long-term effects of this strategy with two other genetic control strategies that have been developed in Ae. aegypti: release of a strain with female-specific lethality, and a strain with both female-specific lethality and an anti-pathogen gene. We find that releasing mosquitoes carrying only an anti-pathogen construct can substantially decrease vector competence of a natural population, even at release ratios well below that required for the two currently feasible alternatives that rely on population reduction. Finally, although current genetic control strategies based on population reduction are compromised by immigration of wild-type mosquitoes, releasing mosquitoes carrying only an anti-pathogen gene is considerably more robust to such immigration.Contrary to the widely held view that

Genetic structure of Miscanthus sinensis and M. sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression

DEFF Research Database (Denmark)

Clark, Lindsay V; Stewart, J Ryan; Nishiwaki, Aya

2015-01-01

Unilateral introgression from diploids to tetraploids has been hypothesized to be an important evolutionary mechanism in plants. However, few examples have been definitively identified, perhaps because data of sufficient depth and breadth were difficult to obtain before the advent of affordable...

Interspecific introgression and changes in population structure in a flatfish species complex after the Prestige accident

International Nuclear Information System (INIS)

Crego-Prieto, V.; Danancher, D.; Campo, D.; Perez, J.; Garcia-Vazquez, E.; Roca, A.

2013-01-01

Highlights: • Impact of Prestige oil spill was studied on two sympatric megrim fish populations. • Samples before and nine years after the accident were genetically analyzed. • A large proportion of post-F1 interspecific hybrids was found in the polluted area. • Both species’ population structure was altered by introgression of foreign alleles. • The spillage likely promoted a hybrid zone for Lepidorhombus in the areas affected. -- Abstract: Oil spills cause aggressive impacts on marine ecosystems affecting immense areas and the species inhabiting them. If wastes are not cleaned up properly, the remnants may affect local populations for a long time. This work focuses on the long-term impacts of the Prestige spillage that occurred off Galician coast (Spain) in November 2002. Model species were two sympatric flatfish, the megrims Lepidorhombus whiffiagonis and Lepidorhombus boscii. Samples obtained before and nine years after the Prestige accident from affected and unaffected areas were genotyped for six hypervariable nuclear markers and for the mitochondrial D-loop sequence. The results revealed a high proportion of post-F1 interspecific hybrids in the area affected, and also increased intraspecific population differentiation likely due to such localized introgression of foreign genes. These changes suggest the appearance of a hybrid zone following the accident and emphasize the need of paying special attention to potential evolutionary impacts of oil spills

Analysis of root-knot nematode and fusarium wilt disease resistance in cotton (Gossypium spp.) using chromosome substitution lines from two alien species.

Science.gov (United States)

Ulloa, M; Wang, C; Saha, S; Hutmacher, R B; Stelly, D M; Jenkins, J N; Burke, J; Roberts, P A

2016-04-01

Chromosome substitution (CS) lines in plants are a powerful genetic resource for analyzing the contribution of chromosome segments to phenotypic variance. In this study, a series of interspecific cotton (Gossypium spp.) CS lines were used to identify a new germplasm resource, and to validate chromosomal regions and favorable alleles associated with nematode or fungal disease resistance traits. The CS lines were developed in the G. hirsutum L. TM-1 background with chromosome or chromosome segment substitutions from G. barbadense L. Pima 3-79 or G. tomentosum. Root-knot nematode (Meloidogyne incognita) and fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) (races 1 and 4) resistance alleles and quantitative trait loci (QTL) previously placed on cotton chromosomes using SSR markers in two interspecific recombinant inbred line populations were chosen for testing. Phenotypic responses of increased resistance or susceptibility in controlled inoculation and infested field assays confirmed the resistance QTLs, based on substitution with the positive or negative allele for resistance. Lines CS-B22Lo, CS-B04, and CS-B18 showed high resistance to nematode root-galling, confirming QTLs on chromosomes 4 and 22 (long arm) with resistance alleles from Pima 3-79. Line CS-B16 had less fusarium race 1-induced vascular root staining and higher percent survival than the TM-1 parent, confirming a major resistance QTL on chromosome 16. Lines CS-B(17-11) and CS-B17 had high fusarium race 4 vascular symptoms and low survival due to susceptible alleles introgressed from Pima 3-79, confirming the localization on chromosome 17 of an identified QTL with resistance alleles from TM1 and other resistant lines. Analyses validated regions on chromosomes 11, 16, and 17 harboring nematode and fusarium wilt resistance genes and demonstrated the value of CS lines as both a germplasm resource for breeding programs and as a powerful genetic analysis tool for determining QTL effects for disease

The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

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Mark Ravinet

2018-05-01

Full Text Available Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus and the Japan Sea stickleback (G. nipponicus, which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

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Ravinet, Mark; Yoshida, Kohta; Shigenobu, Shuji; Toyoda, Atsushi; Fujiyama, Asao; Kitano, Jun

2018-05-01

Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

Genetic and epigenetic variations induced by wheat-rye 2R and 5R monosomic addition lines.

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Shulan Fu

Full Text Available BACKGROUND: Monosomic alien addition lines (MAALs can easily induce structural variation of chromosomes and have been used in crop breeding; however, it is unclear whether MAALs will induce drastic genetic and epigenetic alterations. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, wheat-rye 2R and 5R MAALs together with their selfed progeny and parental common wheat were investigated through amplified fragment length polymorphism (AFLP and methylation-sensitive amplification polymorphism (MSAP analyses. The MAALs in different generations displayed different genetic variations. Some progeny that only contained 42 wheat chromosomes showed great genetic/epigenetic alterations. Cryptic rye chromatin has introgressed into the wheat genome. However, one of the progeny that contained cryptic rye chromatin did not display outstanding genetic/epigenetic variation. 78 and 49 sequences were cloned from changed AFLP and MSAP bands, respectively. Blastn search indicated that almost half of them showed no significant similarity to known sequences. Retrotransposons were mainly involved in genetic and epigenetic variations. Genetic variations basically affected Gypsy-like retrotransposons, whereas epigenetic alterations affected Copia-like and Gypsy-like retrotransposons equally. Genetic and epigenetic variations seldom affected low-copy coding DNA sequences. CONCLUSIONS/SIGNIFICANCE: The results in the present study provided direct evidence to illustrate that monosomic wheat-rye addition lines could induce different and drastic genetic/epigenetic variations and these variations might not be caused by introgression of rye chromatins into wheat. Therefore, MAALs may be directly used as an effective means to broaden the genetic diversity of common wheat.

Introgression evidence and phylogenetic relationships among three (ParaMisgurnus species as revealed by mitochondrial and nuclear DNA markers

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Jakovlić I.

2013-01-01

Full Text Available The taxonomy of (ParaMisgurnus genera is still debated. We therefore used mitochondrial and nuclear DNA markers to analyze the phylogenetic relationships among Misgurnus anguillicaudatus, Paramisgurnus dabryanus and Misgurnus fossilis. Differing phylogenetic signals from mitochondrial and nuclear marker data suggest an introgression event in the history of M. anguillicaudatus and M. mohoity. No substantial genetic evidence was found that Paramisgurnus dabryanus should be classified as a separate genus.

Marker-assisted pyramiding of brown planthopper (Nilaparvata lugens Stål) resistance genes Bph1 and Bph2 on rice chromosome 12.

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Sharma, Prem N; Torii, Akihide; Takumi, Shigeo; Mori, Naoki; Nakamura, Chiharu

2004-01-01

Brown planthopper (BPH) (Nilaparvata lugens Stål) is a significant insect pest of rice (Oryza sativa L.). We constructed a gene-pyramided japonica line, in which two BPH resistance genes Bph1 and Bph2 on the long arm of chromosome 12 independently derived from two indica resistance lines were combined through the recombinant selection. The gene-pyramiding was achieved based on the previously constructed high-resolution linkage maps of the two genes. Two co-dominant and four dominant PCR-based markers flanking the loci were used to select for a homozygous recombinant line in a segregating population that was derived from a cross between the parental homozygous single-gene introgression lines. BPH bioassay showed that the resistance level of the pyramided line was equivalent to that of the Bph1-single introgression line, which showed a higher level of resistance than the Bph2-single introgression line. The pyramid line should provide a useful experimental means for studying the fine structure of the chromosomal region covering these two major BPH resistance genes.

Incompatibility and competitive exclusion of genomic segments between sibling Drosophila species.

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Fang, Shu; Yukilevich, Roman; Chen, Ying; Turissini, David A; Zeng, Kai; Boussy, Ian A; Wu, Chung-I

2012-06-01

The extent and nature of genetic incompatibilities between incipient races and sibling species is of fundamental importance to our view of speciation. However, with the exception of hybrid inviability and sterility factors, little is known about the extent of other, more subtle genetic incompatibilities between incipient species. Here we experimentally demonstrate the prevalence of such genetic incompatibilities between two young allopatric sibling species, Drosophila simulans and D. sechellia. Our experiments took advantage of 12 introgression lines that carried random introgressed D. sechellia segments in different parts of the D. simulans genome. First, we found that these introgression lines did not show any measurable sterility or inviability effects. To study if these sechellia introgressions in a simulans background contained other fitness consequences, we competed and genetically tracked the marked alleles within each introgression against the wild-type alleles for 20 generations. Strikingly, all marked D. sechellia introgression alleles rapidly decreased in frequency in only 6 to 7 generations. We then developed computer simulations to model our competition results. These simulations indicated that selection against D. sechellia introgression alleles was high (average s = 0.43) and that the marker alleles and the incompatible alleles did not separate in 78% of the introgressions. The latter result likely implies that most introgressions contain multiple genetic incompatibilities. Thus, this study reveals that, even at early stages of speciation, many parts of the genome diverge to a point where introducing foreign elements has detrimental fitness consequences, but which cannot be seen using standard sterility and inviability assays.

Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance.

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Ali, N; Heslop-Harrison, Js Pat; Ahmad, H; Graybosch, R A; Hein, G L; Schwarzacher, T

2016-08-01

Pyramiding of alien-derived Wheat streak mosaic virus (WSMV) resistance and resistance enhancing genes in wheat is a cost-effective and environmentally safe strategy for disease control. PCR-based markers and cytogenetic analysis with genomic in situ hybridisation were applied to identify alien chromatin in four genetically diverse populations of wheat (Triticum aestivum) lines incorporating chromosome segments from Thinopyrum intermedium and Secale cereale (rye). Out of 20 experimental lines, 10 carried Th. intermedium chromatin as T4DL*4Ai#2S translocations, while, unexpectedly, 7 lines were positive for alien chromatin (Th. intermedium or rye) on chromosome 1B. The newly described rye 1RS chromatin, transmitted from early in the pedigree, was associated with enhanced WSMV resistance. Under field conditions, the 1RS chromatin alone showed some resistance, while together with the Th. intermedium 4Ai#2S offered superior resistance to that demonstrated by the known resistant cultivar Mace. Most alien wheat lines carry whole chromosome arms, and it is notable that these lines showed intra-arm recombination within the 1BS arm. The translocation breakpoints between 1BS and alien chromatin fell in three categories: (i) at or near to the centromere, (ii) intercalary between markers UL-Thin5 and Xgwm1130 and (iii) towards the telomere between Xgwm0911 and Xbarc194. Labelled genomic Th. intermedium DNA hybridised to the rye 1RS chromatin under high stringency conditions, indicating the presence of shared tandem repeats among the cereals. The novel small alien fragments may explain the difficulty in developing well-adapted lines carrying Wsm1 despite improved tolerance to the virus. The results will facilitate directed chromosome engineering producing agronomically desirable WSMV-resistant germplasm.

Mapping of powdery mildew resistance gene Pm53 introgressed from Aegilops speltoides into soft red winter wheat.

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Petersen, Stine; Lyerly, Jeanette H; Worthington, Margaret L; Parks, Wesley R; Cowger, Christina; Marshall, David S; Brown-Guedira, Gina; Murphy, J Paul

2015-02-01

A powdery mildew resistance gene was introgressed from Aegilops speltoides into winter wheat and mapped to chromosome 5BL. Closely linked markers will permit marker-assisted selection for the resistance gene. Powdery mildew of wheat (Triticum aestivum L.) is a major fungal disease in many areas of the world, caused by Blumeria graminis f. sp. tritici (Bgt). Host plant resistance is the preferred form of disease prevention because it is both economical and environmentally sound. Identification of new resistance sources and closely linked markers enable breeders to utilize these new sources in marker-assisted selection as well as in gene pyramiding. Aegilops speltoides (2n = 2x = 14, genome SS), has been a valuable disease resistance donor. The powdery mildew resistant wheat germplasm line NC09BGTS16 (NC-S16) was developed by backcrossing an Ae. speltoides accession, TAU829, to the susceptible soft red winter wheat cultivar 'Saluda'. NC-S16 was crossed to the susceptible cultivar 'Coker 68-15' to develop F2:3 families for gene mapping. Greenhouse and field evaluations of these F2:3 families indicated that a single gene, designated Pm53, conferred resistance to powdery mildew. Bulked segregant analysis showed that multiple simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers specific to chromosome 5BL segregated with the resistance gene. The gene was flanked by markers Xgwm499, Xwmc759, IWA6024 (0.7 cM proximal) and IWA2454 (1.8 cM distal). Pm36, derived from a different wild wheat relative (T. turgidum var. dicoccoides), had previously been mapped to chromosome 5BL in a durum wheat line. Detached leaf tests revealed that NC-S16 and a genotype carrying Pm36 differed in their responses to each of three Bgt isolates. Pm53 therefore appears to be a new source of powdery mildew resistance.

Features of Ppd-B1 expression regulation and their impact on the flowering time of wheat near-isogenic lines

OpenAIRE

Kiseleva, Antonina A.; Potokina, Elena K.; Salina, Elena A.

2017-01-01

Background Photoperiod insensitive Ppd-1a alleles determine early flowering of wheat. Increased expression of homoeologous Ppd-D1a and Ppd-A1a result from deletions in the promoter region, and elevated expression of Ppd-B1a is determined by an increased copy number. Results In this study, using bread wheat cultivars Sonora and PSL2, which contrast in flowering time, and near-isogenic lines resulting from their cross, “Ppd-m” and “Ppd-w” with Ppd-B1a introgressed from Sonora, we investigated t...

Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks.

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Corrigan, Shannon; Maisano Delser, Pierpaolo; Eddy, Corey; Duffy, Clinton; Yang, Lei; Li, Chenhong; Bazinet, Adam L; Mona, Stefano; Naylor, Gavin J P

2017-05-01

We use a genomic sampling of both nuclear and mitochondrial DNA markers to examine a pattern of genetic admixture between Carcharhinus galapagensis (Galapagos sharks) and Carcharhinus obscurus (dusky sharks), two well-known and closely related sharks that have been recognized as valid species for more than 100years. We describe widespread mitochondrial-nuclear discordance in which these species are readily distinguishable based on 2152 nuclear single nucleotide polymorphisms from 910 independent autosomal regions, but show pervasive mitochondrial admixture. The species are superficially morphologically cryptic as adults but show marked differences in internal anatomy, as well as niche separation. There was no indication of ongoing hybridization between the species. We conclude that the observed mitochondrial-nuclear discordance is likely due to historical mitochondrial introgression following a range expansion. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification, introgression, and molecular marker genetic analysis and selection of a highly effective novel oat crown rust resistance from diploid oat, Avena strigosa

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A new highly effective resistance to oat crown rust (Puccinia coronata f. sp. avenae) was identified in the diploid oat Avena strigosa PI 258731 and introgressed into hexaploid cultivated oat. Young plants with this resistance show moderate susceptibility, whereas older plant tissues and adult plant...

Metabolic and molecular changes of the phenylpropanoid pathway in tomato (Solanum lycopersicum lines carrying different Solanum pennellii wild chromosomal regions

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Maria Manuela Rigano

2016-10-01

Full Text Available Solanum lycopersicum represents an important dietary source of bioactive compounds including the antioxidants flavonoids and phenolic acids. We previously identified two genotypes (IL7-3 and IL12-4 carrying loci from the wild species Solanum pennellii, which increased antioxidants in the fruit. Successively, these lines were crossed and two genotypes carrying both introgressions at the homozygous condition (DHO88 and DHO88-SL were selected. The amount of total antioxidant compounds was increased in DHOs compared to both ILs and the control genotype M82. In order to understand the genetic mechanisms underlying the positive interaction between the two wild regions pyramided in DHO genotypes, detailed analyses of the metabolites accumulated in the fruit were carried out by colorimetric methods and LC/MS/MS. These analyses evidenced a lower content of flavonoids in DHOs and in ILs, compared to M82. By contrast, in the DHOs the relative content of phenolic acids increased, particularly the fraction of hexoses, thus evidencing a redirection of the phenylpropanoid flux towards the biosynthesis of phenolic acid glycosides in these genotypes. In addition, the line DHO88 exhibited a lower content of free phenolic acids compared to M82. Interestingly, the two DHOs analyzed differ in the size of the wild region on chromosome 12. Genes mapping in the introgression regions were further investigated. Several genes of the phenylpropanoid biosynthetic pathway were identified, such as one 4-coumarate:CoA ligase and two UDP-glycosyltransferases in the region 12-4 and one chalcone isomerase and one UDP-glycosyltransferase in the region 7-3. Transcriptomic analyses demonstrated a different expression of the detected genes in the ILs and in the DHOs compared to M82.These analyses, combined with biochemical analyses, suggested a central role of the 4-coumarate:CoA ligase in redirecting the phenylpropanoid pathways towards the biosynthesis of phenolic acids in the

Distinguishing between incomplete lineage sorting and genomic introgressions: complete fixation of allospecific mitochondrial DNA in a sexually reproducing fish (Cobitis; Teleostei, despite clonal reproduction of hybrids.

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Lukas Choleva

Full Text Available Distinguishing between hybrid introgression and incomplete lineage sorting causing incongruence among gene trees in that they exhibit topological differences requires application of statistical approaches that are based on biologically relevant models. Such study is especially challenging in hybrid systems, where usual vectors mediating interspecific gene transfers--hybrids with Mendelian heredity--are absent or unknown. Here we study a complex of hybridizing species, which are known to produce clonal hybrids, to discover how one of the species, Cobitis tanaitica, has achieved a pattern of mito-nuclear mosaic genome over the whole geographic range. We appplied three distinct methods, including the method using solely the information on gene tree topologies, and found that the contrasting mito-nuclear signal might not have resulted from the retention of ancestral polymorphism. Instead, we found two signs of hybridization events related to C. tanaitica; one concerning nuclear gene flow and the other suggested mitochondrial capture. Interestingly, clonal inheritance (gynogenesis of contemporary hybrids prevents genomic introgressions and non-clonal hybrids are either absent or too rare to be detected among European Cobitis. Our analyses therefore suggest that introgressive hybridizations are rather old episodes, mediated by previously existing hybrids whose inheritance was not entirely clonal. Cobitis complex thus supports the view that the type of resulting hybrids depends on a level of genomic divergence between sexual species.

SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera).

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Muñoz, Irene; Henriques, Dora; Jara, Laura; Johnston, J Spencer; Chávez-Galarza, Julio; De La Rúa, Pilar; Pinto, M Alice

2017-07-01

The honeybee (Apis mellifera) has been threatened by multiple factors including pests and pathogens, pesticides and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A. m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify pure-bred A. m. mellifera colonies. Microsatellites have been preferred for identification of A. m. mellifera stocks across conservation centres. However, owing to high throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite set to detect structure and introgression with that of different sets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellite loci. Contrary to every SNP data set, microsatellites did not discriminate between the two lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level, microsatellites' performance was relatively poor at the upper range of Q-values, a result reflected by their lower precision. Our results suggest that SNPs are more accurate and powerful than microsatellites for identification of A. m. mellifera colonies, especially when they are selected by information content. © 2016 John Wiley & Sons Ltd.

Targeted introgression of a wheat stem rust resistance gene by DNA marker-assisted chromosome engineering.

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Niu, Zhixia; Klindworth, Daryl L; Friesen, Timothy L; Chao, Shiaoman; Jin, Yue; Cai, Xiwen; Xu, Steven S

2011-04-01

Chromosome engineering is a useful strategy for transfer of alien genes from wild relatives into modern crops. However, this strategy has not been extensively used for alien gene introgression in most crops due to low efficiency of conventional cytogenetic techniques. Here, we report an improved scheme of chromosome engineering for efficient elimination of a large amount of goatgrass (Aegilops speltoides) chromatin surrounding Sr39, a gene that provides resistance to multiple stem rust races, including Ug99 (TTKSK) in wheat. The wheat ph1b mutation, which promotes meiotic pairing between homoeologous chromosomes, was employed to induce recombination between wheat chromosome 2B and goatgrass 2S chromatin using a backcross scheme favorable for inducing and detecting the homoeologous recombinants with small goatgrass chromosome segments. Forty recombinants with Sr39 with reduced surrounding goatgrass chromatin were quickly identified from 1048 backcross progenies through disease screening and molecular marker analysis. Four of the recombinants carrying Sr39 with a minimal amount of goatgrass chromatin (2.87-9.15% of the translocated chromosomes) were verified using genomic in situ hybridization. Approximately 97% of the goatgrass chromatin was eliminated in one of the recombinants, in which a tiny goatgrass chromosome segment containing Sr39 was retained in the wheat genome. Localization of the goatgrass chromatin in the recombinants led to rapid development of three molecular markers tightly linked to Sr39. The new wheat lines and markers provide useful resources for the ongoing global effort to combat Ug99. This study has demonstrated great potential of chromosome engineering in genome manipulation for plant improvement.

Processes underpinning development and maintenance of diversity in rice in West Africa: evidence from combining morphological and molecular markers.

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Alfred Mokuwa

Full Text Available We assessed the interplay of artificial and natural selection in rice adaptation in low-input farming systems in West Africa. Using 20 morphological traits and 176 molecular markers, 182 farmer varieties of rice (Oryza spp. from 6 West African countries were characterized. Principal component analysis showed that the four botanical groups (Oryza sativa ssp. indica, O. sativa ssp. japonica, O. glaberrima, and interspecific farmer hybrids exhibited different patterns of morphological diversity. Regarding O. glaberrima, morphological and molecular data were in greater conformity than for the other botanical groups. A clear difference in morphological features was observed between O. glaberrima rices from the Togo hills and those from the Upper Guinea Coast, and among O. glaberrima rices from the Upper Guinea Coast. For the other three groups such clear patterns were not observed. We argue that this is because genetic diversity is shaped by different environmental and socio-cultural selection pressures. For O. glaberrima, recent socio-cultural selection pressures seemed to restrict genetic diversity while this was not observed for the other botanical groups. We also show that O. glaberrima still plays an important role in the selection practices of farmers and resulting variety development pathways. This is particularly apparent in the case of interspecific farmer hybrids where a relationship was found between pericarp colour, panicle attitude and genetic diversity. Farmer varieties are the product of long and complex trajectories of selection governed by local human agency. In effect, rice varieties have emerged that are adapted to West African farming conditions through genotype × environment × society interactions. The diversity farmers maintain in their rice varieties is understood to be part of a risk-spreading strategy that also facilitates successful and often serendipitous variety innovations. We advocate, therefore, that farmers and

Processes underpinning development and maintenance of diversity in rice in West Africa: evidence from combining morphological and molecular markers.

Science.gov (United States)

Mokuwa, Alfred; Nuijten, Edwin; Okry, Florent; Teeken, Béla; Maat, Harro; Richards, Paul; Struik, Paul C

2014-01-01

We assessed the interplay of artificial and natural selection in rice adaptation in low-input farming systems in West Africa. Using 20 morphological traits and 176 molecular markers, 182 farmer varieties of rice (Oryza spp.) from 6 West African countries were characterized. Principal component analysis showed that the four botanical groups (Oryza sativa ssp. indica, O. sativa ssp. japonica, O. glaberrima, and interspecific farmer hybrids) exhibited different patterns of morphological diversity. Regarding O. glaberrima, morphological and molecular data were in greater conformity than for the other botanical groups. A clear difference in morphological features was observed between O. glaberrima rices from the Togo hills and those from the Upper Guinea Coast, and among O. glaberrima rices from the Upper Guinea Coast. For the other three groups such clear patterns were not observed. We argue that this is because genetic diversity is shaped by different environmental and socio-cultural selection pressures. For O. glaberrima, recent socio-cultural selection pressures seemed to restrict genetic diversity while this was not observed for the other botanical groups. We also show that O. glaberrima still plays an important role in the selection practices of farmers and resulting variety development pathways. This is particularly apparent in the case of interspecific farmer hybrids where a relationship was found between pericarp colour, panicle attitude and genetic diversity. Farmer varieties are the product of long and complex trajectories of selection governed by local human agency. In effect, rice varieties have emerged that are adapted to West African farming conditions through genotype × environment × society interactions. The diversity farmers maintain in their rice varieties is understood to be part of a risk-spreading strategy that also facilitates successful and often serendipitous variety innovations. We advocate, therefore, that farmers and farmer varieties should

1729-IJBCS-Article-Montcho David

African Journals Online (AJOL)

Pr GATSING

(Linares, 2002). Because of the history of O. glaberrima in Africa, the species is expected to be a rich genetic source for adaptability to. African environments as compared to O. sativa. In fact O. glaberrima can provide resistance to various indigenous biotic constraints: rice yellow mottle virus. (Thiémélé et al., 2010), bacterial ...

A resource of large-scale molecular markers for monitoring Agropyron cristatum chromatin introgression in wheat background based on transcriptome sequences.

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Zhang, Jinpeng; Liu, Weihua; Lu, Yuqing; Liu, Qunxing; Yang, Xinming; Li, Xiuquan; Li, Lihui

2017-09-20

Agropyron cristatum is a wild grass of the tribe Triticeae and serves as a gene donor for wheat improvement. However, very few markers can be used to monitor A. cristatum chromatin introgressions in wheat. Here, we reported a resource of large-scale molecular markers for tracking alien introgressions in wheat based on transcriptome sequences. By aligning A. cristatum unigenes with the Chinese Spring reference genome sequences, we designed 9602 A. cristatum expressed sequence tag-sequence-tagged site (EST-STS) markers for PCR amplification and experimental screening. As a result, 6063 polymorphic EST-STS markers were specific for the A. cristatum P genome in the single-receipt wheat background. A total of 4956 randomly selected polymorphic EST-STS markers were further tested in eight wheat variety backgrounds, and 3070 markers displaying stable and polymorphic amplification were validated. These markers covered more than 98% of the A. cristatum genome, and the marker distribution density was approximately 1.28 cM. An application case of all EST-STS markers was validated on the A. cristatum 6 P chromosome. These markers were successfully applied in the tracking of alien A. cristatum chromatin. Altogether, this study provided a universal method of large-scale molecular marker development to monitor wild relative chromatin in wheat.

Introgression Between Cultivars and Wild Populations of Momordica charantia L. (Cucurbitaceae in Taiwan

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Yu-Chung Chiang

2012-05-01

Full Text Available The landrace strains of Momordica charantia are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native to Taiwan. Because of the introduction of cultivars for agricultural purposes, these two accessions currently exhibit a sympatric or parapatric distribution in Taiwan. In this study, the cultivars and wild samples from Taiwan, India, and Korea were collected for testing of their hybridization and evolutionary patterns. The cpDNA marker showed a clear distinction between accessions of cultivars and wild populations of Taiwan and a long divergence time. In contrast, an analysis of eight selectively neutral nuclear microsatellite loci did not reveal a difference between the genetic structures of these two accessions. A relatively short divergence time and frequent but asymmetric gene flows were estimated based on the isolation-with-migration model. Historical and current introgression from cultivars to wild populations of Taiwan was also inferred using MIGRATE-n and BayesAss analyses. Our results showed that these two accessions shared abundant common ancestral polymorphisms, and the timing of the divergence and colonization of the Taiwanese wild populations is consistent with the geohistory of the Taiwan Strait land bridge of the Last Glacial Maximum (LGM. Long-term and recurrent introgression between accessions indicated the asymmetric capacity to receive foreign genes from other accessions. The modern introduction of cultivars of M. charantia during the colonization of Taiwan by the Han Chinese ethnic group enhanced the rate of gene replacement in the native populations and resulted in the loss of native genes.

Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line.

Science.gov (United States)

Hou, Liyuan; Zhang, Xiaojun; Li, Xin; Jia, Juqing; Yang, Huizhen; Zhan, Haixian; Qiao, Linyi; Guo, Huijuan; Chang, Zhijian

2015-07-28

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68-0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs.

Oryza glaberrima

African Journals Online (AJOL)

GNACADJA

Technologies Alimentaires, Faculté des Sciences Agronomiques, Université .... dans la mesure où la littérature a montré que ... culturelle, sociale et symbolique. ..... Revue. Ivoirienne d'Histoire, 19 : 41 - 60. Yacouba AS, Moussa OZ, Kadri A, ...

Oryza glaberrima

African Journals Online (AJOL)

GNACADJA

4Centre du riz pour l'Afrique (AfricaRice), Madagascar. ... Ouest et Est qui assurent près de 95% de la production rizicole (Sié et .... limitée au Nord par les préfectures de Wawa et d'Amou ... vue partielle illustrant le relief de Danyi qui une zone ...

Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression.

Science.gov (United States)

McCoy, Rajiv C; Wakefield, Jon; Akey, Joshua M

2017-02-23

Regulatory variation influencing gene expression is a key contributor to phenotypic diversity, both within and between species. Unfortunately, RNA degrades too rapidly to be recovered from fossil remains, limiting functional genomic insights about our extinct hominin relatives. Many Neanderthal sequences survive in modern humans due to ancient hybridization, providing an opportunity to assess their contributions to transcriptional variation and to test hypotheses about regulatory evolution. We developed a flexible Bayesian statistical approach to quantify allele-specific expression (ASE) in complex RNA-seq datasets. We identified widespread expression differences between Neanderthal and modern human alleles, indicating pervasive cis-regulatory impacts of introgression. Brain regions and testes exhibited significant downregulation of Neanderthal alleles relative to other tissues, consistent with natural selection influencing the tissue-specific regulatory landscape. Our study demonstrates that Neanderthal-inherited sequences are not silent remnants of ancient interbreeding but have measurable impacts on gene expression that contribute to variation in modern human phenotypes. Copyright © 2017 Elsevier Inc. All rights reserved.

Targeted introgression of cotton fibre quality quantitative trait loci using molecular markers

International Nuclear Information System (INIS)

Lacape, J.M.; Trung-Bieu Nguyen; Hau, B.; Giband, M.

2007-01-01

Within the framework of a cotton breeding programme, molecular markers are used to improve the efficiency of the introgression of fibre quality traits of Gossypium barbadense into G. hirsutum. A saturated genetic map was developed based on genotyping data obtained from the BC 1 (75 plants) and BC 2 (200 plants) generations. Phenotypic measurements conducted over three generations (BC 1 , BC 2 and BC 2 S 1 ) allowed 80 quantitative trait loci (QTL) to be detected for fibre length, uniformity, strength, elongation, fineness and colour. Positive QTL, i.e. those for which favourable alleles came from the G. barbadense parent, were harboured by 19 QTL-rich regions on 15 'carrier' chromosomes. In subsequent generations (BC 3 and BC 4 ), markers framing the QTL-rich regions were used to select about 10 percent of over 400 plants analysed in each generation. Although BC plants selected through the marker-assisted selection (MAS) process show promising fibre quality, only their full field evaluation will allow validation of the procedure. (author)

Effectiveness of the Ty-3 Introgression for Conferring Resistance in Recombinant Inbred Lines of Tomato to Bipartite Begomoviruses in Guatemala

Science.gov (United States)

Management of begomovirus-incited diseases on tomatoes in Guatemala continues to be a challenge and there continues to be a need to better understand the genetics of resistance to begomoviruses. In this study, the resistant line, Gh13, was crossed with the susceptible line, HUJ-VF, that lacked the ...

Introgression of lineage c honey bees into black honey bee populations: a genome-wide estimation using single nucleotide polymorphisms (SNPS)

OpenAIRE

Henriques, Dora; Chavez-Galarza, Julio; Kryger, Per; Johnston, J. Spencer; De la Rúa, Pilar; Rufino, José; Dall'Olio, Raffaele; Garnery, Lionel; Pinto, M. Alice

2012-01-01

The black honey bee, Apis mellifera mellifera L., is probably the honey bee subspecies more threatened by introgression from foreign subspecies, specially lineage C A. m. carnica and A. m. ligustica. In fact, in some areas of its distributional range, intensive beekeeping with foreign subspecies has driven A. m. mellifera populations to nearly replacement. While massive and repeated introductions may lead to loss of native genetic patrimony, a low level of gene flow can also be detrimental be...

Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line

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Liyuan Hou

2015-07-01

Full Text Available Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt, is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68–0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs.

Genetic Analysis of Kernel Traits in Maize-Teosinte Introgression Populations

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Zhengbin Liu

2016-08-01

Full Text Available Seed traits have been targeted by human selection during the domestication of crop species as a way to increase the caloric and nutritional content of food during the transition from hunter-gather to early farming societies. The primary seed trait under selection was likely seed size/weight as it is most directly related to overall grain yield. Additional seed traits involved in seed shape may have also contributed to larger grain. Maize (Zea mays ssp. mays kernel weight has increased more than 10-fold in the 9000 years since domestication from its wild ancestor, teosinte (Z. mays ssp. parviglumis. In order to study how size and shape affect kernel weight, we analyzed kernel morphometric traits in a set of 10 maize-teosinte introgression populations using digital imaging software. We identified quantitative trait loci (QTL for kernel area and length with moderate allelic effects that colocalize with kernel weight QTL. Several genomic regions with strong effects during maize domestication were detected, and a genetic framework for kernel traits was characterized by complex pleiotropic interactions. Our results both confirm prior reports of kernel domestication loci and identify previously uncharacterized QTL with a range of allelic effects, enabling future research into the genetic basis of these traits.

Identification of heat-sensitive QTL derived from common wild rice (Oryza rufipogon Griff.).

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Lei, Dongyang; Tan, Lubin; Liu, Fengxia; Chen, Liyun; Sun, Chuanqing

2013-03-01

Understanding the responses of rice plants to heat-stress is a challenging, yet crucial, endeavor. A set of introgression lines was previously developed using an advanced backcrossing strategy that involved the elite indica cultivar Teqing as the recipient and an accession of common wild rice (Oryza rufipongon Griff.) as the donor. In this study, we evaluated the responses of 90 of these previously developed introgression lines to heat stress. Five quantitative trait loci (QTLs) related to heat response were detected. The phenotypic variances explained by these QTLs ranged from 6.83% to 14.63%, and O. rufipogon-derived alleles at one locus reduced sensitivity to heat. A heat-sensitive introgression line, YIL106, was identified and characterized. Genotypic analysis demonstrated that YIL106 contained four introgressed segments derived from O. rufipongon and two QTLs (qHTS1-1 and qHTS3) related to heat response. Physiological tests, including measurements of chlorophyll content, electrolyte leakage, malondialdehyde content, and soluble sugar content, were consistent with the heat sensitivity observed in YIL106. Ultrastructural analysis of YIL106 mesophyll cells showed that they were severely damaged following heat stress. This suggests that modification of the cell membrane system is a primary response to heat stress in plants. Identification and characterization of the heat-sensitive line YIL106 may facilitate the isolation of genes associated with the response of rice plants to heat stress. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Historical introgression of the downy mildew resistance gene Rpv12 from the Asian species Vitis amurensis into grapevine varieties.

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Silvia Venuti

Full Text Available The Amur grape (Vitis amurensis Rupr. thrives naturally in cool climates of Northeast Asia. Resistance against the introduced pathogen Plasmopara viticola is common among wild ecotypes that were propagated from Manchuria into Chinese vineyards or collected by Soviet botanists in Siberia, and used for the introgression of resistance into wine grapes (Vitis vinifera L.. A QTL analysis revealed a dominant gene Rpv12 that explained 79% of the phenotypic variance for downy mildew resistance and was inherited independently of other resistance genes. A Mendelian component of resistance-a hypersensitive response in leaves challenged with P. viticola-was mapped in an interval of 0.2 cM containing an array of coiled-coil NB-LRR genes on chromosome 14. We sequenced 10-kb genic regions in the Rpv12(+ haplotype and identified polymorphisms in 12 varieties of V. vinifera using next-generation sequencing. The combination of two SNPs in single-copy genes flanking the NB-LRR cluster distinguished the resistant haplotype from all others found in 200 accessions of V. vinifera, V. amurensis, and V. amurensis x V. vinifera crosses. The Rpv12(+ haplotype is shared by 15 varieties, the most ancestral of which are the century-old 'Zarja severa' and 'Michurinets'. Before this knowledge, the chromosome segment around Rpv12(+ became introgressed, shortened, and pyramided with another downy mildew resistance gene from North American grapevines (Rpv3 only by phenotypic selection. Rpv12(+ has an additive effect with Rpv3(+ to protect vines against natural infections, and confers foliar resistance to strains that are virulent on Rpv3(+ plants.

Gene diversity, agroecological structure and introgression patterns among village chicken populations across North, West and Central Africa

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Leroy Grégoire

2012-05-01

Full Text Available Abstract Background Chickens represent an important animal genetic resource for improving farmers’ income in Africa. The present study provides a comparative analysis of the genetic diversity of village chickens across a subset of African countries. Four hundred seventy-two chickens were sampled in 23 administrative provinces across Cameroon, Benin, Ghana, Côte d’Ivoire, and Morocco. Geographical coordinates were recorded to analyze the relationships between geographic distribution and genetic diversity. Molecular characterization was performed with a set of 22 microsatellite markers. Five commercial lines, broilers and layers, were also genotyped to investigate potential gene flow. A genetic diversity analysis was conducted both within and between populations. Results High heterozygosity levels, ranging from 0.51 to 0.67, were reported for all local populations, corresponding to the values usually found in scavenging populations worldwide. Allelic richness varied from 2.04 for a commercial line to 4.84 for one population from Côte d’Ivoire. Evidence of gene flow between commercial and local populations was observed in Morocco and in Cameroon, which could be related to long-term improvement programs with the distribution of crossbred chicks. The impact of such introgressions seemed rather limited, probably because of poor adaptation of exotic birds to village conditions, and because of the consumers’ preference for local chickens. No such gene flow was observed in Benin, Ghana, and Côte d’Ivoire, where improvement programs are also less developed. The clustering approach revealed an interesting similarity between local populations found in regions sharing high levels of precipitation, from Cameroon to Côte d’Ivoire. Restricting the study to Benin, Ghana, and Côte d’Ivoire, did not result in a typical breed structure but a south-west to north-east gradient was observed. Three genetically differentiated areas (P  Conclusions

Obtaining of interspecific hybrids for pea introgressive breeding

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Sergey Vasilevich Bobkov

2015-09-01

Full Text Available Background. Overcoming of reproductive isolation, identification and transfer of agronomic value genes from wild relatives into cultivated pea genomes is an important task for pea introgressive breeding. Materials and methods. Reciprocal hybridization of cultivated pea with wide set of P. fulvum accessions was conducted. Identification of hybrids was carried out with use of biochemical and morphological markers. Identification of unique protein was conducted with use of electrophoretic spectra of mature seeds. Results. Pea interspecific hybrids were obtained in two reciprocal directions of crosses. Cross efficiency in Р. sativum × P. fulvum and P. fulvum × Р. sativum combinations was 36 % and 7 %, respectively. All tested seeds in crosses Р. sativum × P. fulvum were hybrids. Crosses in direction P. fulvum × Р. sativum led to formation of puny seeds restricted in embryo growth. Protein markers of one seed derived in cross P. fulvum × Р. sativum proved its hybrid nature. Morphological markers demonstrated that plant derived from another cross was also a hybrid. Culture of immature embryos was developed for recovering plants in interspecific crosses. Morphogenic calli and regenerated plants were obtained in culture of immature embryos P. fulvum (И592589 × Р. sativum (Aest. Identification of unique protein 7 of P. fulvum was conducted. Inheritance of that protein was proved as monogenic dominant. Conclusion. Efficiency of hybridization in combination P. fulvum × Р. sativum was significantly less in compare to reciprocal one. All products of that cross combination were tested as hybrids. Unique protein 7 of P. fulvum was revealed as a result of mature seed electrophoretic spectra analysis. Inheritance of that protein was determined as monogenic dominant.

Anatomy and Cytogenetic Identification of a Wheat-Psathyrostachys huashanica Keng Line with Early Maturation.

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Liangming Wang

Full Text Available In previous studies, our research team successfully transferred the Ns genome from Psathyrostachys huashanica Keng into Triticum aestivum (common wheat cv. 7182 using embryo culture. In the present study, one of these lines, i.e., hybrid progeny 25-10-3, which matured about 10-14 days earlier than its wheat parent, was assessed using sequenced characterized amplified region (SCAR analysis, EST-SSR and EST-STS molecular markers, and genomic in situ hybridization (GISH. We found that this was a stable wheat-P. huashanica disomic addition line (2n = 44 = 22 II and the results demonstrated that it was a 6Ns disomic chromosome addition line, but it exhibited many different features compared with previously characterized lines, i.e., a longer awn, early maturation, and no twin spikelets. It was considered to be an early-maturing variety based on the early stage of inflorescence initiation in field experiments and binocular microscope observations over three consecutive years. This characteristic was distinct, especially from the single ridge stage and double ridge stage until the glume stage. In addition, it had a higher photosynthesis rate and economic values than common wheat cv. 7182, i.e., more spikelets per spike, more florets per spikelet, more kernels per spike, and a higher thousand-grain weight. These results suggest that this material may comprise a genetic pool of beneficial genes or chromosome segments, which are suitable for introgression to improve the quality of common wheat.

The high-quality genome of Brassica napus cultivar 'ZS11' reveals the introgression history in semi-winter morphotype.

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Sun, Fengming; Fan, Guangyi; Hu, Qiong; Zhou, Yongming; Guan, Mei; Tong, Chaobo; Li, Jiana; Du, Dezhi; Qi, Cunkou; Jiang, Liangcai; Liu, Weiqing; Huang, Shunmou; Chen, Wenbin; Yu, Jingyin; Mei, Desheng; Meng, Jinling; Zeng, Peng; Shi, Jiaqin; Liu, Kede; Wang, Xi; Wang, Xinfa; Long, Yan; Liang, Xinming; Hu, Zhiyong; Huang, Guodong; Dong, Caihua; Zhang, He; Li, Jun; Zhang, Yaolei; Li, Liangwei; Shi, Chengcheng; Wang, Jiahao; Lee, Simon Ming-Yuen; Guan, Chunyun; Xu, Xun; Liu, Shengyi; Liu, Xin; Chalhoub, Boulos; Hua, Wei; Wang, Hanzhong

2017-11-01

Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (A r ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with A r , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

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Daniel Fulop

2016-10-01

Full Text Available Quantitative Trait Loci (QTL mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum and its more distant interfertile relatives typically follow a near isogenic line (NIL design, such as the S. pennellii Introgression Line (IL population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii. This so-called Backcrossed Inbred Line (BIL population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping.

Common raven occurrence in relation to energy transmission line corridors transiting human-altered sagebrush steppe

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Coates, Peter S.; Howe, Kristy B.; Casazza, Michael L.; Delehanty, David J.

2014-01-01

Energy-related infrastructure and other human enterprises within sagebrush steppe of the American West often results in changes that promote common raven (Corvus corax; hereafter, raven) populations. Ravens, a generalist predator capable of behavioral innovation, present a threat to many species of conservation concern. We evaluate the effects of detailed features of an altered landscape on the probability of raven occurrence using extensive raven survey (n= 1045) and mapping data from southern Idaho, USA. We found nonlinear relationships between raven occurrence and distances to transmission lines, roads, and facilities. Most importantly, raven occurrence was greater with presence of transmission lines up to 2.2 km from the corridor.We further explain variation in raven occurrence along anthropogenic features based on the amount of non-native vegetation and cover type edge, such that ravens select fragmented sagebrush stands with patchy, exotic vegetative introgression. Raven occurrence also increased with greater length of edge formed by the contact of big sagebrush (Artemisia tridentate spp.) with non-native vegetation cover types. In consideration of increasing alteration of sagebrush steppe, these findings will be useful for planning energy transmission corridor placement and other management activities where conservation of sagebrush obligate species is a priority.

wMel limits zika and chikungunya virus infection in a Singapore Wolbachia-introgressed Ae. aegypti strain, wMel-Sg.

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Cheong Huat Tan

2017-05-01

Full Text Available Zika (ZIKV and Chikungunya (CHIKV viruses are emerging Aedes-borne viruses that are spreading outside their known geographic range and causing wide-scale epidemics. It has been reported that these viruses can be transmitted efficiently by Ae. aegypti. Recent studies have shown that Ae. aegypti when transinfected with certain Wolbachia strains shows a reduced replication and dissemination of dengue (DENV, Chikungunya (CHIKV, and Yellow Fever (YFV viruses. The aim of this study was to determine whether the wMel strain of Wolbachia introgressed onto a Singapore Ae. aegypti genetic background was able to limit ZIKV and CHIKV infection in the mosquito.Five to seven-day old mosquitoes either infected or uninfected with wMel Wolbachia were orally infected with a Ugandan strain of ZIKV and several outbreak strains of CHIKV. The midgut and salivary glands of each mosquito were sampled at days 6, 9 and 13 days post infectious blood meal to determine midgut infection and salivary glands dissemination rates, respectively. In general, all wild type Ae. aegypti were found to have high ZIKV and CHIKV infections in their midguts and salivary glands, across all sampling days, compared to Wolbachia infected counterparts. Median viral titre for all viruses in Wolbachia infected mosquitoes were significantly lower across all time points when compared to wild type mosquitoes. Most significantly, all but two and one of the wMel infected mosquitoes had no detectable ZIKV and CHIKV, respectively, in their salivary glands at 14 days post-infectious blood meal.Our results showed that wMel limits both ZIKV and CHIKV infection when introgressed into a Singapore Ae. aegypti genetic background. These results also strongly suggest that female Aedes aegypti carrying Wolbachia will have a reduced capacity to transmit ZIKV and CHIKV.

Introgression of heat shock protein (Hsp70 and sHsp) genes into the Malaysian elite chilli variety Kulai (Capsicum annuum L.) through the application of marker-assisted backcrossing (MAB).

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Usman, Magaji G; Rafii, Mohd Y; Martini, Mohammad Y; Yusuff, Oladosu A; Ismail, Mohd R; Miah, Gous

2018-03-01

Backcrossing together with simple sequence repeat marker strategy was adopted to improve popular Malaysian chilli Kulai (Capsicum annuum L.) for heat tolerance. The use of molecular markers in backcross breeding and selection contributes significantly to overcoming the main drawbacks such as increase linkage drag and time consumption, in the ancient manual breeding approach (conventional), and speeds up the genome recovery of the recurrent parent. The strategy was adopted to introgress heat shock protein gene(s) from AVPP0702 (C. annuum L.), which are heat-tolerant, into the genetic profile of Kulai, a popular high-yielding chilli but which is heat sensitive. The parents were grown on seed trays, and parental screening was carried out with 252 simple sequence repeat markers. The selected parents were crossed and backcrossed to generate F 1 hybrids and backcross generations. Sixty-eight markers appeared to be polymorphic and were used to assess the backcross generation; BC 1 F 1 , BC 2 F 1 and BC 3 F 1 . The average recipient allele of the selected four BC 1 F 1 plants was 80.75% which were used to produce the BC 2 F 1 generation. BC 1 -P 7 was the best BC 1 F 1 plant because it had the highest recovery at 83.40% and was positive to Hsp-linked markers (Hsp70-u2 and AGi42). After three successive generations of backcrossing, the average genome recovery of the recurrent parent in the selected plants in BC 3 F 1 was 95.37%. Hsp gene expression analysis was carried out on BC 1 F 1 , BC 2 F 1 and BC 3 F 1 selected lines. The Hsp genes were found to be up-regulated when exposed to heat treatment. The pattern of Hsp expression in the backcross generations was similar to that of the donor parent. This confirms the successful introgression of a stress-responsive gene (Hsp) into a Kulai chilli pepper variety. Furthermore, the yield performance viz. plant height, number of fruits, fruit length and weight and total yield of the improved plant were similar with the recurrent

Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite

DEFF Research Database (Denmark)

McMullan, Mark; Gardiner, Anastasia; Bailey, Kate

2015-01-01

How generalist parasites with wide host ranges can evolve is a central question in parasite evolution. Albugo candida is an obligate biotrophic parasite that consists of many physiological races that each specialize on distinct Brassicaceae host species. By analyzing genome sequence assemblies...... by normally non-infecting races. This facilitates introgression and the exchange of effector repertoires, and may enable the evolution of novel races that can undergo clonal population expansion on new hosts. We discuss recent studies on hybridization in other eukaryotes such as yeast, Heliconius butterflies...

Development and characterization of a Psathyrostachys huashanica Keng 7Ns chromosome addition line with leaf rust resistance.

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Wanli Du

Full Text Available The aim of this study was to characterize a Triticum aestivum-Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs disomic addition line 2-1-6-3. Individual line 2-1-6-3 plants were analyzed using cytological, genomic in situ hybridization (GISH, EST-SSR, and EST-STS techniques. The alien addition line 2-1-6-3 was shown to have two P. huashanica chromosomes, with a meiotic configuration of 2n = 44 = 22 II. We tested 55 EST-SSR and 336 EST-STS primer pairs that mapped onto seven different wheat chromosomes using DNA from parents and the P. huashanica addition line. One EST-SSR and nine EST-STS primer pairs indicated that the additional chromosome of P. huashanica belonged to homoeologous group 7, the diagnostic fragments of five EST-STS markers (BE404955, BE591127, BE637663, BF482781 and CD452422 were cloned, sequenced and compared. The results showed that the amplified polymorphic bands of P. huashanica and disomic addition line 2-1-6-3 shared 100% sequence identity, which was designated as the 7Ns disomic addition line. Disomic addition line 2-1-6-3 was evaluated to test the leaf rust resistance of adult stages in the field. We found that one pair of the 7Ns genome chromosomes carried new leaf rust resistance gene(s. Moreover, wheat line 2-1-6-3 had a superior numbers of florets and grains per spike, which were associated with the introgression of the paired P. huashanica chromosomes. These high levels of disease resistance and stable, excellent agronomic traits suggest that this line could be utilized as a novel donor in wheat breeding programs.

Development of a genetic sexing strain in Bactrocera carambolae (Diptera: Tephritidae) by introgression of sex sorting components from B. dorsalis, Salaya1 strain.

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Isasawin, Siriwan; Aketarawong, Nidchaya; Lertsiri, Sittiwat; Thanaphum, Sujinda

2014-01-01

The carambola fruit fly, Bactrocera carambolae Drew & Hancock is a high profile key pest that is widely distributed in the southwestern ASEAN region. In addition, it has trans-continentally invaded Suriname, where it has been expanding east and southward since 1975. This fruit fly belongs to Bactrocera dorsalis species complex. The development and application of a genetic sexing strain (Salaya1) of B. dorsalis sensu stricto (s.s.) (Hendel) for the sterile insect technique (SIT) has improved the fruit fly control. However, matings between B. dorsalis s.s. and B. carambolae are incompatible, which hinder the application of the Salaya1 strain to control the carambola fruit fly. To solve this problem, we introduced genetic sexing components from the Salaya1 strain into the B. carambolae genome by interspecific hybridization. Morphological characteristics, mating competitiveness, male pheromone profiles, and genetic relationships revealed consistencies that helped to distinguish Salaya1 and B. carambolae strains. A Y-autosome translocation linking the dominant wild-type allele of white pupae gene and a free autosome carrying a recessive white pupae homologue from the Salaya1 strain were introgressed into the gene pool of B. carambolae. A panel of Y-pseudo-linked microsatellite loci of the Salaya1 strain served as markers for the introgression experiments. This resulted in a newly derived genetic sexing strain called Salaya5, with morphological characteristics corresponding to B. carambolae. The rectal gland pheromone profile of Salaya5 males also contained a distinctive component of B. carambolae. Microsatellite DNA analyses confirmed the close genetic relationships between the Salaya5 strain and wild B. carambolae populations. Further experiments showed that the sterile males of Salaya5 can compete with wild males for mating with wild females in field cage conditions. Introgression of sex sorting components from the Salaya1 strain to a closely related B. carambolae

Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations.

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Uwimana, Brigitte; Smulders, Marinus J M; Hooftman, Danny A P; Hartman, Yorike; van Tienderen, Peter H; Jansen, Johannes; McHale, Leah K; Michelmore, Richard W; Visser, Richard G F; van de Wiel, Clemens C M

2012-03-26

After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F(1) hybrid was backcrossed to L. serriola to generate BC(1) and BC(2) populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC(1)S(1) and BC(2)S(1)). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC(1)S(1) and BC(2)S(1) hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC(1) and BC(2) hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. As it was shown that the crop contributed QTLs with either a positive

Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations

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Uwimana Brigitte

2012-03-01

Full Text Available Abstract Background After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (transgenes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F1 hybrid was backcrossed to L. serriola to generate BC1 and BC2 populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC1S1 and BC2S1. Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency. Results Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC1S1 and BC2S1 hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC1 and BC2 hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. Conclusion As it was shown that the crop

Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations

Science.gov (United States)

2012-01-01

Background After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F1 hybrid was backcrossed to L. serriola to generate BC1 and BC2 populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC1S1 and BC2S1). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Results Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC1S1 and BC2S1 hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC1 and BC2 hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. Conclusion As it was shown that the crop contributed QTLs with either a

Weak population structure in European roe deer (Capreolus capreolus and evidence of introgressive hybridization with Siberian roe deer (C. pygargus in northeastern Poland.

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Juanita Olano-Marin

Full Text Available We investigated contemporary and historical influences on the pattern of genetic diversity of European roe deer (Capreolus capreolus. The study was conducted in northeastern Poland, a zone where vast areas of primeval forests are conserved and where the European roe deer was never driven to extinction. A total of 319 unique samples collected in three sampling areas were genotyped at 16 microsatellites and one fragment (610 bp of mitochondrial DNA (mtDNA control region. Genetic diversity was high, and a low degree of genetic differentiation among sampling areas was observed with both microsatellites and mtDNA. No evidence of genetic differentiation between roe deer inhabiting open fields and forested areas was found, indicating that the ability of the species to exploit these contrasting environments might be the result of its phenotypic plasticity. Half of the studied individuals carried an mtDNA haplotype that did not belong to C. capreolus, but to a related species that does not occur naturally in the area, the Siberian roe deer (C. pygargus. No differentiation between individuals with Siberian and European mtDNA haplotypes was detected at microsatellite loci. Introgression of mtDNA of Siberian roe deer into the genome of European roe deer has recently been detected in eastern Europe. Such introgression might be caused by human-mediated translocations of Siberian roe deer within the range of European roe deer or by natural hybridization between these species in the past.

Detection of an inversion in the Ty-2 region between S. lycopersicum and S. habrochaites by a combination of de novo genome assembly and BAC cloning.

Science.gov (United States)

Wolters, Anne-Marie A; Caro, Myluska; Dong, Shufang; Finkers, Richard; Gao, Jianchang; Visser, Richard G F; Wang, Xiaoxuan; Du, Yongchen; Bai, Yuling

2015-10-01

A chromosomal inversion associated with the tomato Ty - 2 gene for TYLCV resistance is the cause of severe suppression of recombination in a tomato Ty - 2 introgression line. Among tomato and its wild relatives inversions are often observed, which result in suppression of recombination. Such inversions hamper the transfer of important traits from a related species to the crop by introgression breeding. Suppression of recombination was reported for the TYLCV resistance gene, Ty-2, which has been introgressed in cultivated tomato (Solanum lycopersicum) from the wild relative S. habrochaites accession B6013. Ty-2 was mapped to a 300-kb region on the long arm of chromosome 11. The suppression of recombination in the Ty-2 region could be caused by chromosomal rearrangements in S. habrochaites compared with S. lycopersicum. With the aim of visualizing the genome structure of the Ty-2 region, we compared the draft de novo assembly of S. habrochaites accession LYC4 with the sequence of cultivated tomato ('Heinz'). Furthermore, using populations derived from intraspecific crosses of S. habrochaites accessions, the order of markers in the Ty-2 region was studied. Results showed the presence of an inversion of approximately 200 kb in the Ty-2 region when comparing S. lycopersicum and S. habrochaites. By sequencing a BAC clone from the Ty-2 introgression line, one inversion breakpoint was identified. Finally, the obtained results are discussed with respect to introgression breeding and the importance of a priori de novo sequencing of the species involved.

A novel PCR-based marker for identifying Ns chromosomes in wheat-Psathyrostachys huashanica Keng derivative lines

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J. Wang

2013-10-01

Full Text Available Psathyrostachys huashanica Keng is an endangered species that is endemic to China, which provides an important gene pool for wheat improvement. We developed a quick and reliable PCR-based diagnostic assay to accurately and efficiently detect P. huashanica DNA sequences from introgression lines, which was based on a species-specific marker derived from genomic DNA. The 900-bp PCR-amplified band used as a P. huashanica-specific RAPD marker was tested with 21 different plant species and was converted into a sequence-characterized amplified region (SCAR marker by cloning and sequencing the selected fragments (pHs11. This SCAR marker, which was designated as RHS23, could clearly distinguish the presence of P. huashanica DNA repetitive sequences in wheat-P. huashanica derivative lines. The specificity of the marker was validated using 21 different plant species and a complete set of wheat-P. huashanica disomic addition lines (1Ns–7Ns, 2n=44=22II. This specific sequence targeted the Ns genome of P. huashanica and it was present in all the seven P. huashanica chromosomes. Therefore, this SCAR marker is specific for P. huashanica chromosomes and may be used in the identification of alien repetitive sequences in large gene pools. This diagnostic PCR assay for screening the target genetic material may play a key role in marker-assisted selective breeding programs.

Introgression of tomato chromosomes into the potato genome : an analysis through molecular marker and in situ hybridisation techniques = [Introgressie van tomatenchromosomen in het aardappelgenoom : een analyse met behulp van moleculaire merker en in situ hybridisatie technieken

NARCIS (Netherlands)

Garriga Caldere, F.

1998-01-01

Transfer of alien chromosomes and genes across intergeneric boundaries can be useful not only for the introgression of desirable characters but also for fundamental genetic studies. The successful demonstration of hybridisation of potato ( Solanum tuberosum ) and tomato

Do competitive conditions affect introgression of transgenes from oilseed rape (Brassica napus) to weedy Brassica rapa? AS case study with special reference to transplastomic oilseed rape

DEFF Research Database (Denmark)

Johannessen, Marina

In species where chloroplast inheritance is exclusively or predominantly maternal, pollen-mediated flow of transgenes is reduced if transgenes are inserted in chloroplast DNA instead of nuclear DNA. However, transmission of chloroplast-encoded transgeneswill still occur if transgenic individuals ...... affected the thousand-kernel weight significantly. It was concluded that further introgression of transgenes from transplastomic oilseed rape to B. rapa is mostlikely at current field densities of B. napus and when B. rapa is an abundant weed....

Biochemical and molecular analysis of pink tomatoes: deregulated expression of the gene encoding transcription factor SlMYB12 leads to pink tomato fruit colour

NARCIS (Netherlands)

Ballester, A.R.; Molthoff, J.W.; Vos, de C.H.; Lintel Hekkert, B.; Orzaez, D.; Fernandez-Moreno, J.P.; Tripodi, S.; Grandillo, S.; Martin, C.; Heldens, J.; Ykema, M.; Granell, A.; Bovy, A.G.

2010-01-01

The color of tomato fruit is mainly determined by carotenoids and flavonoids. Phenotypic analysis of an introgression line (IL) population derived from a cross between Solanum lycopersicum 'Moneyberg' and the wild species Solanum chmielewskii revealed three ILs with a pink fruit color. These lines

Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika – the result of repeated introgressive hybridization

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Blanc Michel

2007-01-01

Full Text Available Abstract Background The tribe Lamprologini is the major substrate breeding lineage of Lake Tanganyika's cichlid species flock. Among several different life history strategies found in lamprologines, the adaptation to live and breed in empty gastropod shells is probably the most peculiar. Although shell-breeding arose several times in the evolutionary history of the lamprologines, all obligatory and most facultative shell-breeders belong to the so called "ossified group", a monophyletic lineage within the lamprologine cichlids. Since their distinctive life style enables these species to live and breed in closest vicinity, we hypothesized that these cichlids might be particularly prone to accidental hybridization, and that introgression might have affected the evolutionary history of this cichlid lineage. Results Our analyses revealed discrepancies between phylogenetic hypotheses based on mitochondrial and nuclear (AFLP data. While the nuclear phylogeny was congruent with morphological, behavioral and ecological characteristics, several species – usually highly specialized shell-breeders – were placed at contradicting positions in the mitochondrial phylogeny. The discordant phylogenies strongly suggest repeated incidents of introgressive hybridization between several distantly related shell-breeding species, which reticulated the phylogeny of this group of cichlids. Long interior branches and high bootstrap support for many interior nodes in the mitochondrial phylogeny argue against a major effect of ancient incomplete lineage sorting on the phylogenetic reconstruction. Moreover, we provide morphological and genetic (mtDNA and microsatellites evidence for ongoing hybridization among distantly related shell-breeders. In these cases, the territorial males of the inferred paternal species are too large to enter the shells of their mate, such that they have to release their sperm over the entrance of the shell to fertilize the eggs. With sperm

Production and molecular characterization of bread wheat lines with reduced amount of α-type gliadins.

Science.gov (United States)

Camerlengo, Francesco; Sestili, Francesco; Silvestri, Marco; Colaprico, Giuseppe; Margiotta, Benedetta; Ruggeri, Roberto; Lupi, Roberta; Masci, Stefania; Lafiandra, Domenico

2017-12-19

Among wheat gluten proteins, the α-type gliadins are the major responsible for celiac disease, an autoimmune disorder that affects about 1% of the world population. In fact, these proteins contain several toxic and immunogenic epitopes that trigger the onset of the disease. The α-type gliadins are a multigene family, encoded by genes located at the complex Gli-2 loci. Here, three bread wheat deletion lines (Gli-A2, Gli-D2 and Gli-A2/Gli-D2) at the Gli-2 loci were generated by the introgression in the bread wheat cultivar Pegaso of natural mutations, detected in different bread wheat cultivars. The molecular characterization of these lines allowed the isolation of 49 unique expressed genes coding α-type gliadins, that were assigned to each of the three Gli-2 loci. The number and the amount of α-type gliadin transcripts were drastically reduced in the deletion lines. In particular, the line Gli-A2/Gli-D2 contained only 12 active α-type gliadin genes (-75.6% respect to the cv. Pegaso) and a minor level of transcripts (-80% compared to cv. Pegaso). Compensatory pleiotropic effects were observed in the two other classes of gliadins (ω- and γ-gliadins) either at gene expression or protein levels. Although the comparative analysis of the deduced amino acid sequences highlighted the typical structural features of α-type gliadin proteins, substantial differences were displayed among the 49 proteins for the presence of toxic and immunogenic epitopes. The deletion line Gli-A2/Gli-D2 did not contain the 33-mer peptide, one of the major epitopes triggering the celiac disease, representing an interesting material to develop less "toxic" wheat varieties.

Genomic divergence and lack of introgressive hybridization between two 13-year periodical cicadas support life cycle switching in the face of climate change.

Science.gov (United States)

Koyama, Takuya; Ito, Hiromu; Fujisawa, Tomochika; Ikeda, Hiroshi; Kakishima, Satoshi; Cooley, John R; Simon, Chris; Yoshimura, Jin; Sota, Teiji

2016-11-01

Life history evolution spurred by post-Pleistocene climatic change is hypothesized to be responsible for the present diversity in periodical cicadas (Magicicada), but the mechanism of life cycle change has been controversial. To understand the divergence process of 13-year and 17-year cicada life cycles, we studied genetic relationships between two synchronously emerging, parapatric 13-year periodical cicada species in the Decim group, Magicicada tredecim and M. neotredecim. The latter was hypothesized to be of hybrid origin or to have switched from a 17-year cycle via developmental plasticity. Phylogenetic analysis using restriction-site-associated DNA sequences for all Decim species and broods revealed that the 13-year M. tredecim lineage is genomically distinct from 17-year Magicicada septendecim but that 13-year M. neotredecim is not. We detected no significant introgression between M. tredecim and M. neotredecim/M. septendecim thus refuting the hypothesis that M. neotredecim are products of hybridization between M. tredecim and M. septendecim. Further, we found that introgressive hybridization is very rare or absent in the contact zone between the two 13-year species evidenced by segregation patterns in single nucleotide polymorphisms, mitochondrial lineage identity and head width and abdominal sternite colour phenotypes. Our study demonstrates that the two 13-year Decim species are of independent origin and nearly completely reproductively isolated. Combining our data with increasing observations of occasional life cycle change in part of a cohort (e.g. 4-year acceleration of emergence in 17-year species), we suggest a pivotal role for developmental plasticity in Magicicada life cycle evolution. © 2016 John Wiley & Sons Ltd.

Evidence for the introduction of the Asian red alga Neosiphonia japonica and its introgression with Neosiphonia harveyi (Ceramiales, Rhodophyta) in the Northwest Atlantic.

Science.gov (United States)

Savoie, Amanda M; Saunders, Gary W

2015-12-01

There is currently conflict in the literature on the taxonomic status of the reportedly cosmopolitan species Neosiphonia harveyi, a common red alga along the coast of Atlantic Canada and New England, USA. Neosiphonia harveyi sensu lato was assessed using three molecular markers: COI-5P, ITS and rbcL. All three markers clearly delimited three genetic species groups within N. harveyi sensu lato in this region, which we identified as N. harveyi, N. japonica and Polysiphonia akkeshiensis (here resurrected from synonymy with N. japonica). Although Neosiphonia harveyi is considered by some authors to be introduced to the Atlantic from the western Pacific, it was only confirmed from the North Atlantic suggesting it is native to this area. In contrast, Neosiphonia japonica was collected from only two sites in Rhode Island, USA, as well as from its reported native range in Asia (South Korea), which when combined with data in GenBank indicates that this species was introduced to the Northwest Atlantic. The GenBank data further indicate that N. japonica was also introduced to North Carolina, Spain, Australia and New Zealand. Despite the fact that all three markers clearly delimited N. harveyi and N. japonica as distinct genetic species groups, the ITS sequences for some N. harveyi individuals displayed mixed patterns and additivity indicating introgression of nuclear DNA from N. japonica into N. harveyi in the Northwest Atlantic. Introgression of DNA from an introduced species to a native species (i.e. 'genetic pollution') is one of the possible consequences of species introductions, and we believe this is the first documented evidence for this phenomenon in red algae. © 2015 John Wiley & Sons Ltd.

Fine mapping of a quantitative resistance gene for gray leaf spot of maize (Zea mays L.) derived from teosinte (Z. mays ssp. parviglumis)

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In previous work, using near isogenic line (NIL) populations in which segments of the tesosinte (Zea mays ssp. parviglumis) genome had been introgressed into the background of the maize line B73, we had identified a QTL on chromosome 8, here called Qgls8, for gray leaf spot resistance. We identified...

Interspecific introgression in cetaceans: DNA markers reveal post-F1 status of a pilot whale.

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Laura Miralles

Full Text Available Visual species identification of cetacean strandings is difficult, especially when dead specimens are degraded and/or species are morphologically similar. The two recognised pilot whale species (Globicephala melas and Globicephala macrorhynchus are sympatric in the North Atlantic Ocean. These species are very similar in external appearance and their morphometric characteristics partially overlap; thus visual identification is not always reliable. Genetic species identification ensures correct identification of specimens. Here we have employed one mitochondrial (D-Loop region and eight nuclear loci (microsatellites as genetic markers to identify six stranded pilot whales found in Galicia (Northwest Spain, one of them of ambiguous phenotype. DNA analyses yielded positive amplification of all loci and enabled species identification. Nuclear microsatellite DNA genotypes revealed mixed ancestry for one individual, identified as a post-F1 interspecific hybrid employing two different Bayesian methods. From the mitochondrial sequence the maternal species was Globicephala melas. This is the first hybrid documented between Globicephala melas and G. macrorhynchus, and the first post-F1 hybrid genetically identified between cetaceans, revealing interspecific genetic introgression in marine mammals. We propose to add nuclear loci to genetic databases for cetacean species identification in order to detect hybrid individuals.

Studying the Genetics of Resistance to CyHV-3 Disease Using Introgression from Feral to Cultured Common Carp Strains

Science.gov (United States)

Tadmor-Levi, Roni; Asoulin, Efrat; Hulata, Gideon; David, Lior

2017-01-01

Sustainability and further development of aquaculture production are constantly challenged by outbreaks of fish diseases, which are difficult to prevent or control. Developing fish strains that are genetically resistant to a disease is a cost-effective and a sustainable solution to address this challenge. To do so, heritable genetic variation in disease resistance should be identified and combined together with other desirable production traits. Aquaculture of common carp has suffered substantial losses from the infectious disease caused by the cyprinid herpes virus type 3 (CyHV-3) virus and the global spread of outbreaks indicates that many cultured strains are susceptible. In this research, CyHV-3 resistance from the feral strain “Amur Sassan” was successfully introgressed into two susceptible cultured strains up to the first backcross (BC1) generation. Variation in resistance of families from F1 and BC1 generations was significantly greater compared to that among families of any of the susceptible parental lines, a good starting point for a family selection program. Considerable additive genetic variation was found for CyHV-3 resistance. This phenotype was transferable between generations with contributions to resistance from both the resistant feral and the susceptible cultured strains. Reduced scale coverage (mirror phenotype) is desirable and common in cultured strains, but so far, cultured mirror carp strains were found to be susceptible. Here, using BC1 families ranging from susceptible to resistant, no differences in resistance levels between fully scaled and mirror full-sib groups were found, indicating that CyHV-3 resistance was successfully combined with the desirable mirror phenotype. In addition, the CyHV-3 viral load in tissues throughout the infection of susceptible and resistant fish was followed. Although resistant fish get infected, viral loads in tissues of these fish are significantly lesser than in those of susceptible fish, allowing them

Sources of stem rust resistance in wheat-alien introgression lines

Science.gov (United States)

Stem rust, caused by Puccinia graminis f. sp. tritici, is one of the most devastating diseases of wheat and the novel highly virulent race of TTKSK and its lineage are threatening wheat production worldwide. The objective of the study was to identify new sources of resistance in wheat-alien introgre...

The Birth of a Black Rice Gene and Its Local Spread by Introgression.

Science.gov (United States)

Oikawa, Tetsuo; Maeda, Hiroaki; Oguchi, Taichi; Yamaguchi, Takuya; Tanabe, Noriko; Ebana, Kaworu; Yano, Masahiro; Ebitani, Takeshi; Izawa, Takeshi

2015-09-01

The origin and spread of novel agronomic traits during crop domestication are complex events in plant evolution. Wild rice (Oryza rufipogon) has red grains due to the accumulation of proanthocyanidins, whereas most cultivated rice (Oryza sativa) varieties have white grains induced by a defective allele in the Rc basic helix-loop-helix (bHLH) gene. Although the events surrounding the origin and spread of black rice traits remain unknown, varieties with black grains due to anthocyanin accumulation are distributed in various locations throughout Asia. Here, we show that the black grain trait originated from ectopic expression of the Kala4 bHLH gene due to rearrangement in the promoter region. Both the Rc and Kala4 genes activate upstream flavonol biosynthesis genes, such as chalcone synthase and dihydroflavonol-4-reductase, and downstream genes, such as leucoanthocyanidin reductase and leucoanthocyanidin dioxygenase, to produce the respective specific pigments. Genome analysis of 21 black rice varieties as well as red- and white-grained landraces demonstrated that black rice arose in tropical japonica and its subsequent spread to the indica subspecies can be attributed to the causal alleles of Kala4. The relatively small size of genomic fragments of tropical japonica origin in some indica varieties indicates that refined introgression must have occurred by natural crossbreeding in the course of evolution of the black trait in rice. © 2015 American Society of Plant Biologists. All rights reserved.

Multi-locus phylogeny reveals instances of mitochondrial introgression and unrecognized diversity in Kenyan barbs (Cyprininae: Smiliogastrini).

Science.gov (United States)

Schmidt, Ray C; Bart, Henry L; Nyingi, Wanja Dorothy

2017-06-01

The phylogenetics and taxonomic status of small African barbs (Cyprininae: Smiliogastrini) remains unresolved despite the recent decision to elevate the genus name Enteromius for the group. The main barrier to understanding the origin of African small barbs and evolutionary relationships within the group is the poor resolution of phylogenies published to date. These phylogenies usually rely on mitochondrial markers and have limited taxon sampling. Here we investigate the phylogenetic relationships of small barbs of Kenya utilizing cytochrome b, Growth Hormone (GH) intron 2, and RAG1 markers from multiple populations of many species in the region. This multi-locus study produced well-supported phylogenies and revealed additional issues that complicate understanding the relationships among East African barbs. We observed widespread mtDNA introgression within the Kenyan barbs, highlighting the need to include nuclear markers in phylogenetic studies of the group. The GH intron 2 resolved heterospecific individuals and aided in inferring the species level phylogeny. The study reveals unrecognized diversity within the group, including within species reported to occur throughout East Africa, and it provides the groundwork for future taxonomic work in the region and across Africa. Copyright © 2017 Elsevier Inc. All rights reserved.

Multiple disease resistance to fungal and oomycete pathogens using a recombinant inbred line population in pepper

Science.gov (United States)

Incorporating disease resistance into cultivars is a primary focus of modern breeding programs. Resistance to pathogens is often introgressed from landrace or wild individuals with poor fruit quality into commercial-quality cultivars. Sites of multiple disease resistance (MDR) are regions or “hotspo...

Stomatal conductance, mesophyll conductance, and transpiration efficiency in relation to leaf anatomy in rice and wheat genotypes under drought.

Science.gov (United States)

Ouyang, Wenjing; Struik, Paul C; Yin, Xinyou; Yang, Jianchang

2017-11-02

Increasing leaf transpiration efficiency (TE) may provide leads for growing rice like dryland cereals such as wheat (Triticum aestivum). To explore avenues for improving TE in rice, variations in stomatal conductance (gs) and mesophyll conductance (gm) and their anatomical determinants were evaluated in two cultivars from each of lowland, aerobic, and upland groups of Oryza sativa, one cultivar of O. glaberrima, and two cultivars of T. aestivum, under three water regimes. The TE of upland rice, O. glaberrima, and wheat was more responsive to the gm/gs ratio than that of lowland and aerobic rice. Overall, the explanatory power of the particular anatomical trait varied among species. Low stomatal density mostly explained the low gs in drought-tolerant rice, whereas rice genotypes with smaller stomata generally responded more strongly to drought. Compared with rice, wheat had a higher gm, which was associated with thicker mesophyll tissue, mesophyll and chloroplasts more exposed to intercellular spaces, and thinner cell walls. Upland rice, O. glaberrima, and wheat cultivars minimized the decrease in gm under drought by maintaining high ratios of chloroplasts to exposed mesophyll cell walls. Rice TE could be improved by increasing the gm/gs ratio via modifying anatomical traits. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Barrier to gene flow between two ecologically divergent Populus species, P. alba (white poplar) and P. tremula (European aspen): the role of ecology and life history in gene introgression.

Science.gov (United States)

Lexer, C; Fay, M F; Joseph, J A; Nica, M-S; Heinze, B

2005-04-01

The renewed interest in the use of hybrid zones for studying speciation calls for the identification and study of hybrid zones across a wide range of organisms, especially in long-lived taxa for which it is often difficult to generate interpopulation variation through controlled crosses. Here, we report on the extent and direction of introgression between two members of the "model tree" genus Populus: Populus alba (white poplar) and Populus tremula (European aspen), across a large zone of sympatry located in the Danube valley. We genotyped 93 hybrid morphotypes and samples from four parental reference populations from within and outside the zone of sympatry for a genome-wide set of 20 nuclear microsatellites and eight plastid DNA restriction site polymorphisms. Our results indicate that introgression occurs preferentially from P. tremula to P. alba via P. tremula pollen. This unidirectional pattern is facilitated by high levels of pollen vs. seed dispersal in P. tremula (pollen/seed flow = 23.9) and by great ecological opportunity in the lowland floodplain forest in proximity to P. alba seed parents, which maintains gene flow in the direction of P. alba despite smaller effective population sizes (N(e)) in this species (P. alba N(e)c. 500-550; P. tremula N(e)c. 550-700). Our results indicate that hybrid zones will be valuable tools for studying the genetic architecture of the barrier to gene flow between these two ecologically divergent Populus species.

Functional Marker Assisted Improvement of Stable Cytoplasmic Male Sterile Lines of Rice for Bacterial Blight Resistance

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Jegadeesan Ramalingam

2017-06-01

Full Text Available Bacterial blight (BB, caused by Xanthomonas oryzae pv.oryzae is one among the major diseases in rice, which in severe condition cause losses up to 60% in total yield. Marker assisted pyramiding of three broad spectrum BB resistance genes (xa5, xa13, and Xa21 in prominent rice varieties is the most economical and effective strategy for the management of the BB disease. We report here the pyramiding of three genes (xa5, xa13, and Xa21 in maintainer lines (CO 2B, CO 23B, and CO 24B of three promising wild abortive cytoplasmic male sterile lines (CO 2A, CO 23A, and CO 24A through functional markers assisted back cross breeding. IRBB60 with xa5, xa13, and Xa21 genes is used as a donor parent. BC2F1 and BC2F2 generations from a cross of CO 2B, CO 23B, and CO 24B with IRBB60 were evaluated for bacterial blight and non-fertility restoration. In BC2F1, plants with all three resistance genes (xa5, xa13, and Xa21 and high parent genome recovery was identified. In BC2F2, plants with all resistance genes and without fertility restorer (Rf3 and Rf4 were selected. Based on agronomic traits, BB resistance and maintenance of sterility, two plants each in CO 2B × IRBB60, CO 24B × IRBB60 and one plant in CO 23B × IRBB60 combinations were identified. The identified lines were crossed with respective male sterile lines for conversion of improved B line into CMS line through back-crossing, in addition to selfing. The plants with high recurrent genome and phenotypically similar to parental lines and sterile are being used for the hybrid rice development program. Currently, using these lines (improved CMS line, test crosses were made to develop new rice hybrids. Hybrids combinations viz., CO 23A × AD08009R and CO 24A × IET20898R were found to be stable at different locations with high yield. The R line used in this study has been introgressed with xa5, xa13, and Xa21 genes in a separate breeding program. These new hybrids with resistance against bacterial blight

Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat.

Science.gov (United States)

Rey, Elodie; Abrouk, Michael; Keeble-Gagnère, Gabriel; Karafiátová, Miroslava; Vrána, Jan; Balzergue, Sandrine; Soubigou-Taconnat, Ludivine; Brunaud, Véronique; Martin-Magniette, Marie-Laure; Endo, Takashi R; Bartoš, Jan; Appels, Rudi; Doležel, Jaroslav

2018-03-06

Despite a long history, the production of useful alien introgression lines in wheat remains difficult mainly due to linkage drag and incomplete genetic compensation. In addition, little is known about the molecular mechanisms underlying the impact of foreign chromatin on plant phenotype. Here, a comparison of the transcriptomes of barley, wheat and a wheat-barley 7HL addition line allowed the transcriptional impact both on 7HL genes of a non-native genetic background and on the wheat gene complement as a result of the presence of 7HL to be assessed. Some 42% (389/923) of the 7HL genes assayed were differentially transcribed, which was the case for only 3% (960/35 301) of the wheat gene complement. The absence of any transcript in the addition line of a suite of chromosome 7A genes implied the presence of a 36 Mbp deletion at the distal end of the 7AL arm; this deletion was found to be in common across the full set of Chinese Spring/Betzes barley addition lines. The remaining differentially transcribed wheat genes were distributed across the whole genome. The up-regulated barley genes were mostly located in the proximal part of the 7HL arm, while the down-regulated ones were concentrated in the distal part; as a result, genes encoding basal cellular functions tended to be transcribed, while those encoding specific functions were suppressed. An insight has been gained into gene transcription in an alien introgression line, thereby providing a basis for understanding the interactions between wheat and exotic genes in introgression materials. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Exploration of wild relatives of tomato for enhanced stress tolerance

NARCIS (Netherlands)

Junming Li,

2010-01-01

Among the different abiotic and biotic stresses, Botrytis cinerea, Phytophthora infestans and high salt concentrations are world-wide the most destructive. Several wild relatives of tomato were identified as source for tolerance to these stresses. Three introgression line (IL) populations derived

Cytological and morphological analysis of hybrids between Brassicoraphanus, and Brassica napus for introgression of clubroot resistant trait into Brassica napus L.

Science.gov (United States)

Zhan, Zongxiang; Nwafor, Chinedu Charles; Hou, Zhaoke; Gong, Jianfang; Zhu, Bin; Jiang, Yingfen; Zhou, Yongming; Wu, Jiangsheng; Piao, Zhongyun; Tong, Yue; Liu, Chao; Zhang, Chunyu

2017-01-01

Interspecific hybridization is a powerful tool for improvement of crop species, it has the potential to broaden the genetic base and create new plant forms for breeding programs. Synthetic allopolyploid is a widely-used model for the study of genetic recombination and fixed heterosis in Brassica. In Brassica napus breeding, identification and introgression of new sources of clubroot resistance trait from wild or related species into it by hybridization is a long-term crop management strategy for clubroot disease. Radish (Raphanus sativus L.) is a close relative of the Brassica and most radish accessions are immune to the clubroot disease. A synthesized allotetraploid Brassicoraphanus (RRCC, 2n = 36) between R. sativus cv. HQ-04 (2n = 18, RR) and Brassica oleracea var. alboglabra (L.H Bailey) (2n = 18, CC) proved resistant of multiple clubroot disease pathogen P. brassicae. To predict the possibility to transfer the clubroot resistance trait from the RR subgenome of allotetraploid Brassicoraphanus (RRCC, 2n = 36) into Brassica napus (AACC, 2n = 38), we analyzed the frequency of chromosome pairings in the F1 hybrids produced from a cross between B. napus cv. HS5 and the allotetraploid, characterize the genomic composition of some backcrossed progeny (BC1) using GISH, BAC-FISH and AFLP techniques. The level of intergenomic pairing between A and R genomes in the F1 hybrid was high, allosyndetic bivalents formed in 73.53% PMCs indicative of significant level of homeologous recombination between two genomes and high probability of incorporating chromosomal segments/genes from R-genome into A/C-genomes. The BC1 plants inherited variant extra R chromosomes or fragments from allotetraploid as revealed by GISH and AFLP analysis. 13.51% BC2 individuals were resistant to clubroot disease, and several resistance lines had high pollen fertility, Overall, the genetic material presented in this work represents a potential new genetic resource for practical use in breeding B. napus

A new 2DS·2RL Robertsonian translocation transfers stem rust resistance gene Sr59 into wheat.

Science.gov (United States)

Rahmatov, Mahbubjon; Rouse, Matthew N; Nirmala, Jayaveeramuthu; Danilova, Tatiana; Friebe, Bernd; Steffenson, Brian J; Johansson, Eva

2016-07-01

A new stem rust resistance gene Sr59 from Secale cereale was introgressed into wheat as a 2DS·2RL Robertsonian translocation. Emerging new races of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici), from Africa threaten global wheat (Triticum aestivum L.) production. To broaden the resistance spectrum of wheat to these widely virulent African races, additional resistance genes must be identified from all possible gene pools. From the screening of a collection of wheat-rye (Secale cereale L.) chromosome substitution lines developed at the Swedish University of Agricultural Sciences, we described the line 'SLU238' 2R (2D) as possessing resistance to many races of P. graminis f. sp. tritici, including the widely virulent race TTKSK (isolate synonym Ug99) from Africa. The breakage-fusion mechanism of univalent chromosomes was used to produce a new Robertsonian translocation: T2DS·2RL. Molecular marker analysis and stem rust seedling assays at multiple generations confirmed that the stem rust resistance from 'SLU238' is present on the rye chromosome arm 2RL. Line TA5094 (#101) was derived from 'SLU238' and was found to be homozygous for the T2DS·2RL translocation. The stem rust resistance gene on chromosome 2RL arm was designated as Sr59. Although introgressions of rye chromosome arms into wheat have most often been facilitated by irradiation, this study highlights the utility of the breakage-fusion mechanism for rye chromatin introgression. Sr59 provides an additional asset for wheat improvement to mitigate yield losses caused by stem rust.

Susceptibility of the Tomato Mutant High Pigment-2dg (hp-2dg) to Orobanche spp. Infection

NARCIS (Netherlands)

Lopez Raez, J.A.; Charnikhova, T.; Mulder, P.P.J.; Kohlen, W.; Bino, R.J.; Levin, I.; Bouwmeester, H.J.

2008-01-01

The consumption of natural products with potential health benefits has been continuously growing, and enhanced pigmentation is of major economic importance in fruits and vegetables. The tomato hp-2dg is an important mutant line that has been introgressed into commercial tomato cultivars marketed as

Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice.

Science.gov (United States)

Thalapati, Sudhakar; Batchu, Anil K; Neelamraju, Sarla; Ramanan, Rajeshwari

2012-06-01

Chromosomal segments from wild rice species Oryza rufipogon, introgressed into an elite indica rice restorer line (KMR3) using molecular markers, resulted in significant increase in yield. Here we report the transcriptome analysis of flag leaves and fully emerged young panicles of one of the high yielding introgression lines IL50-7 in comparison to KMR3. A 66-fold upregulated gene Os11Gsk, which showed no transcript in KMR3 was highly expressed in O. rufipogon and IL50-7. A 5-kb genomic region including Os11Gsk and its flanking regions could be PCR amplified only from IL50-7, O. rufipogon, japonica varieties of rice-Nipponbare and Kitaake but not from the indica varieties, KMR3 and Taichung Native-1. Three sister lines of IL50-7 yielding higher than KMR3 showed presence of Os11Gsk, whereas the gene was absent in three other ILs from the same cross having lower yield than KMR3, indicating an association of the presence of Os11Gsk with high yield. Southern analysis showed additional bands in the genomic DNA of O. rufipogon and IL50-7 with Os11Gsk probe. Genomic sequence analysis of ten highly co-expressed differentially regulated genes revealed that two upregulated genes in IL50-7 were derived from O. rufipogon and most of the downregulated genes were either from KMR3 or common to KMR3, IL50-7, and O. rufipogon. Thus, we show that Os11Gsk is a wild rice-derived gene introduced in KMR3 background and increases yield either by regulating expression of functional genes sharing homology with it or by causing epigenetic modifications in the introgression line.

Suitability of a selected set of simple sequence repeats (SSR ...

African Journals Online (AJOL)

Jane

2011-07-13

Jul 13, 2011 ... and lodging susceptibility, O. glaberrima is being ... grown in deep water, including coastal mangrove areas .... Rice genotypes used in the study, species, country of origin and ecosystem as referenced in .... South America.

A Hypersensitivity-Like Response to Meloidogyne graminicola in Rice (Oryza sativa).

Science.gov (United States)

Phan, Ngan Thi; De Waele, Dirk; Lorieux, Mathias; Xiong, Lizhong; Bellafiore, Stephane

2018-04-01

Meloidogyne graminicola is a major plant-parasitic nematode affecting rice cultivation in Asia. Resistance to this nematode was found in the African rice genotypes Oryza glaberrima and O. longistaminata; however, due to interspecific hybrid sterility, the introgression of resistance genes in the widely consumed O. sativa varieties remains challenging. Recently, resistance was found in O. sativa and, here, we report for the first time the histological and genetic characterization of the resistance to M. graminicola in Zhonghua 11, an O. sativa variety. Bright-light microscopy and fluorescence observations of the root tissue of this variety revealed that the root cells surrounding the nematode displayed a hypersensitivity-like reaction with necrotic cells at early stages of infection when nematodes are migrating in the root's mesoderm. An accumulation of presumably phenolic compounds in the nematodes' neighboring root cells was also observed. In addition, at a later stage of infection, not only were few feeding sites observed but also the giant cells were underdeveloped, underlining an incompatible interaction. Furthermore, we generated a hybrid O. sativa population by crossing Zhonghua 11 with the susceptible O. sativa variety IR64 in order to describe the genetic background of this resistance. Our data suggested that the resistance to M. graminicola infection was qualitative rather than quantitative and, therefore, major resistance genes must be involved in this infection process. The full characterization of the defense mechanism and the preliminary study of the genetic inheritance of novel sources of resistance to Meloidogyne spp. in rice constitute a major step toward their use in crop breeding.

African Journal of Biotechnology - Vol 7, No 23 (2008)

African Journals Online (AJOL)

Oryza sativa) and Tog5681 (Oryza glaberrima) · EMAIL FREE FULL TEXT EMAIL ... Perceptions and attitudes of geography teachers to biotechnology: A study focusing on genetically modified (GM) foods · EMAIL FREE FULL TEXT EMAIL FREE ...

Mitochondrial introgression via ancient hybridization, and systematics of the Australian endemic pygopodid gecko genus Delma.

Science.gov (United States)

Brennan, Ian G; Bauer, Aaron M; Jackman, Todd R

2016-01-01

Of the more than 1500 species of geckos found across six continents, few remain as unfamiliar as the pygopodids - Family Pygopodidae (Gray, 1845). These gekkotans are limited to Australia (44 species) and New Guinea (2 species), but have diverged extensively into the most ecologically diverse limbless radiation save Serpentes. Current phylogenetic understanding of the family has relied almost exclusively on two works, which have produced and synthesized an immense amount of morphological, geographical, and molecular data. However, current interspecific relationships within the largest genus Delma Gray 1831 are based chiefly upon data from two mitochondrial loci (16s, ND2). Here, we reevaluate the interspecific relationships within the genus Delma using two mitochondrial and four nuclear loci (RAG1, MXRA5, MOS, DYNLL1), and identify points of strong conflict between nuclear and mitochondrial genomic data. We address mito-nuclear discordance, and remedy this conflict by recognizing several points of mitochondrial introgression as the result of ancient hybridization events. Owing to the legacy value and intraspecific informativeness, we suggest the continued use of ND2 as a phylogenetic marker. Results identify strong support for species groups, but relationships among these clades, and the placement of several enigmatic taxa remain uncertain. We suggest a more careful review of Delma australis and the 'northwest Australia' clade. Accurately assessing and addressing species richness and relationships within this endemic Australian Gekkotan genus is relevant for understanding patterns of squamate speciation across the region. Copyright © 2015 Elsevier Inc. All rights reserved.

New insight into hybridization and unidirectional introgression between Ammodytes japonicus and Ammodytes heian (Trachiniformes, Ammodytidae).

Science.gov (United States)

Kim, Jin-Koo; Bae, Seung Eun; Lee, Soo Jeong; Yoon, Moon Geun

2017-01-01

Based on northern (NOL) and southern (SOL) mitochondrial lineages, recently, it proposed the new species Ammodytes heian and revived the species name Ammodytes japonicus to describe sand lances from the northwestern Pacific Ocean. This study used molecular methods to investigate genetic relationships between the two sand lance species in Korea and Japan. In total, 154 specimens were collected from four locations in Korea (Baengnyeongdo in the Yellow Sea, Tongyeong in the Korean Strait, and Jumunjin and Gijang in the East Sea), and 50 specimens were collected from a single location in Japan (Wakkanai in the Okhotsk Sea). Mitochondrial DNA analysis demonstrated that the individuals from Baengnyeongdo and Tongyeong all belonged to the SOL, whereas those from Gijang, Jumunjin, and Wakkanai included individuals from both the NOL and SOL (over 75% NOL). Population structure analyses were performed on the same individuals using seven microsatellite DNA markers. The population structure analysis based on 201 specimens identified two clusters (named as northern group and southern group), with the admixture proportion (q) of heian. However, the admixture proportion in the Jumunjin and Gijang sand lances was 0.71-0.75 for the southern group, indicating that hybridization and unidirectional introgression from SOL to NOL occurs in southwestern margin of the East Sea. Our findings illustrate the speciation process based on different patterns of gene flow between Korean and Japanese sand lance, which is strongly influenced by both the paleo-climatic change and the contemporary local oceanic current pattern.

Characterizing haploinsufficiency of SHELL gene to improve fruit form prediction in introgressive hybrids of oil palm.

Science.gov (United States)

Teh, Chee-Keng; Muaz, Siti Dalila; Tangaya, Praveena; Fong, Po-Yee; Ong, Ai-Ling; Mayes, Sean; Chew, Fook-Tim; Kulaveerasingam, Harikrishna; Appleton, David

2017-06-08

The fundamental trait in selective breeding of oil palm (Eleais guineensis Jacq.) is the shell thickness surrounding the kernel. The monogenic shell thickness is inversely correlated to mesocarp thickness, where the crude palm oil accumulates. Commercial thin-shelled tenera derived from thick-shelled dura × shell-less pisifera generally contain 30% higher oil per bunch. Two mutations, sh MPOB (M1) and sh AVROS (M2) in the SHELL gene - a type II MADS-box transcription factor mainly present in AVROS and Nigerian origins, were reported to be responsible for different fruit forms. In this study, we have tested 1,339 samples maintained in Sime Darby Plantation using both mutations. Five genotype-phenotype discrepancies and eight controls were then re-tested with all five reported mutations (sh AVROS , sh MPOB , sh MPOB2 , sh MPOB3 and sh MPOB4 ) within the same gene. The integration of genotypic data, pedigree records and shell formation model further explained the haploinsufficiency effect on the SHELL gene with different number of functional copies. Some rare mutations were also identified, suggesting a need to further confirm the existence of cis-compound mutations in the gene. With this, the prediction accuracy of fruit forms can be further improved, especially in introgressive hybrids of oil palm. Understanding causative variant segregation is extremely important, even for monogenic traits such as shell thickness in oil palm.

African Journal of Biotechnology - Vol 11, No 33 (2012)

African Journals Online (AJOL)

Introgression of bacterial blight (BB) resistance genes Xa7 and Xa21 into popular restorer line and their hybrids by molecular marker-assisted backcross (MABC) selection scheme ... Concentration of selected heavy metals in water of the Juru River, Penang, Malaysia · EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT

Genetics and mapping of a novel downy mildew resistance gene, Pl(18), introgressed from wild Helianthus argophyllus into cultivated sunflower (Helianthus annuus L.).

Science.gov (United States)

Qi, L L; Foley, M E; Cai, X W; Gulya, T J

2016-04-01

A novel downy mildew resistance gene, Pl(18), was introgressed from wild Helianthus argophyllus into cultivated sunflower and genetically mapped to linkage group 2 of the sunflower genome. The new germplasm, HA-DM1, carrying Pl(18) has been released to the public. Sunflower downy mildew (DM) is considered to be the most destructive foliar disease that has spread to every major sunflower-growing country of the world, except Australia. A new dominant downy mildew resistance gene (Pl 18) transferred from wild Helianthus argophyllus (PI 494573) into cultivated sunflower was mapped to linkage group (LG) 2 of the sunflower genome using bulked segregant analysis with 869 simple sequence repeat (SSR) markers. Phenotyping 142 BC1F2:3 families derived from the cross of HA 89 and H. argophyllus confirmed the single gene inheritance of resistance. Since no other Pl gene has been mapped to LG2, this gene was novel and designated as Pl (18). SSR markers CRT214 and ORS203 flanked Pl(18) at a genetic distance of 1.1 and 0.4 cM, respectively. Forty-six single nucleotide polymorphism (SNP) markers that cover the Pl(18) region were surveyed for saturation mapping of the region. Six co-segregating SNP markers were 1.2 cM distal to Pl(18), and another four co-segregating SNP markers were 0.9 cM proximal to Pl(18). The new BC2F4-derived germplasm, HA-DM1, carrying Pl(18) has been released to the public. This new line is highly resistant to all Plasmopara halstedii races identified in the USA providing breeders with an effective new source of resistance against downy mildew in sunflower. The molecular markers that were developed will be especially useful in marker-assisted selection and pyramiding of Pl resistance genes because of their close proximity to the gene and the availability of high-throughput SNP detection assays.

Ancestral QTL alleles from wild emmer wheat improve drought resistance and productivity in modern wheat cultivars

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Lianne eMerchuk-Ovnat

2016-04-01

Full Text Available Wild emmer wheat (Triticum turgidum ssp. dicoccoides is considered a promising source for improving stress resistances in domesticated wheat. Here we explored the potential of selected quantitative trait loci (QTLs from wild emmer wheat, introgressed via marker-assisted selection, to enhance drought resistance in elite durum (T. turgidum ssp. durum and bread (T. aestivum wheat cultivars. The resultant near-isogenic lines (BC3F3 and BC3F4 were genotyped using SNP array to confirm the introgressed genomic regions and evaluated in two consecutive years under well-watered (690–710 mm and water-limited (290–320 mm conditions. Three of the introgressed QTLs were successfully validated, two in the background of durum wheat cv. Uzan (on chromosomes 1BL and 2BS, and one in the background of bread wheat cvs. Bar Nir and Zahir (chromosome 7AS. In most cases, the QTL x environment interaction was validated in terms of improved grain yield and biomass - specifically under drought (7AS QTL in cv. Bar Nir background, under both treatments (2BS QTL, and a greater stability across treatments (1BL QTL. The results provide a first demonstration that introgression of wild emmer QTL alleles can enhance productivity and yield stability across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of drought resistance.

Variability and performance evaluation of introgressed Nigerian dura x Deli dura oil palm progenies.

Science.gov (United States)

Noh, A; Rafii, M Y; Mohd Din, A; Kushairi, A; Norziha, A; Rajanaidu, N; Latif, M A; Malek, M A

2014-04-03

Twelve introgressed oil palm (Elaeis guineensis) progenies of Nigerian dura x Deli dura were evaluated for bunch yield, yield attributes, bunch quality components and vegetative characters at the Malaysian Palm Oil Board Research Station, in Keratong, Pahang, Malaysia. Analysis of variance revealed significant to highly significant genotypic differences, indicating sufficient genetic variability among the progenies for bunch yield and its attributes, vegetative characters and bunch quality components, except fruit to bunch ratio. Fresh fruit bunch yield ranged from 167 kg·palm(-1)·year(-1) in PK1330 to 212 kg·palm(-1)·year(-1) in PK1351, with a mean yield of 192 kg·palm(-1)·year(-1). Among the progeny, PK1313 had the highest oil to bunch ratio (19.36%), due to its high mesocarp to fruit ratio, fruit to bunch ratio and low shell to fruit ratio. Among the progenies, PK1313 produced the highest oil yield of 31.4 kg·palm(-1)·year(-1), due to a high mesocarp to fruit ratio (61.2%) and a low shell to fruit ratio (30.7%), coupled with high fruit to bunch ratio (65.6%). PK1330 was found promising for selection, as it had desirable vegetative characters, including smaller petiole cross section (27.15 cm2), short rachis length (4.83 m), short palm height (1.85 m), and the lowest leaf number (164.6), as these vegetative characters are prerequisites for selecting palms for high density planting and high yield per hectare. The genetic variability among the progenies was found to be high, indicating ample scope for further breeding, followed by selection.

Tissue culture-induced alteration in cytosine methylation in new rice ...

African Journals Online (AJOL)

Zizania DNA introgression could induce a large number of genetic and epigenetic changes of the new rice recombinant inbred lines genome. In this present study, we employed inter-simple sequence repeat (ISSR) to further study the genetic and epigenetic changes that are induced by tissue culture. Changes induced by ...

seed storage proteins arl2 and its variants from the apa locus of wild ...

African Journals Online (AJOL)

sion of arcelin and ARL2 tepary bean proteins. Furthermore, a reduction in size and weight of emerged adult insects to almost half was observed. This work demonstrates the superior resistance common bean backcross lines to A. obtectus conferred by the presence of the APA proteins introgressed from tepary bean.

Management of rice seed during insurgency : a case study in Sierra Leone

NARCIS (Netherlands)

Mokuwa, G.A.

2015-01-01

Keywords: Technography, Oryza glaberrima, Oryza sativa, farmer hybrids, sub-optimal agriculture, farmer adaptive management, plant genetic resources, peace and extreme (wartime) conditions, local seed channels, selection for robustness, Sierra Leone, West Africa.

Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea.

Science.gov (United States)

Ravago-Gotanco, Rachel; de la Cruz, Talna Lorena; Pante, Ma Josefa; Borsa, Philippe

2018-01-01

The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.

Characterization of susceptibility and resistance responses to potato cyst nematode (Globodera spp.) infection of tomato lines in the absence and presence of the broad-spectrum nematode resistance Hero gene.

Science.gov (United States)

Sobczak, Miroslaw; Avrova, Anna; Jupowicz, Justyna; Phillips, Mark S; Ernst, Karin; Kumar, Amar

2005-02-01

The tomato Hero A gene is the only member of a multigene family that confers a high level (>80%) of resistance to all the economically important pathotypes of potato cyst nematode (PCN) species Globodera rostochiensis and G. pallida. Although the resistance levels of transgenic tomato lines were similar to those of the tomato line LA1792 containing the introgressed Hero multigene family, transgenic potato plants expressing the tomato Hero A gene are not resistant to PCNs. Comparative microscopy studies of in vitro infected roots of PCN-susceptible tomato cv. Money Maker, the resistant breeding line LA1792, and transgenic line L10 with Ro1 pathotype have revealed no statistically significant difference in the number of juveniles invading roots. However, syncytia (specialized feeding cells) induced in LA1792 and L10 roots mostly were found to have degenerated a few days after their induction, and a few surviving syncytia were able to support only the development of males rather than females. Thus, the ratio between males and females was biased towards males on LA1792 and L10 roots. A series of changes occur in resistant plants leading to formation of a layer of necrotic cells separating the syncytium from stellar conductive tissues and this is followed by degradation of the syncytium. Although the Hero A gene is expressed in all tissues, including roots, stems, leaves, and flower buds, its expression is upregulated in roots in response to PCN infection. Moreover, the expression profiles of the Hero A correlates with the timing of death of the syncytium.

AFLPs reveal genomic regions not detected by RFLPs: a case study in tomato

NARCIS (Netherlands)

Bonnema, G.; Berg, van den P.; Lindhout, P.

2002-01-01

A set of three tomato chromosome 7 introgression lines (ILs) containing overlapping segments of Lycopersicon pennellii DNA was screened with a set of 10 EcoRI–MseI and 10 PstI–MseI AFLP primer combinations. A large number of markers were identified that mapped to one of the four regions of

Evidence for the Emergence of New Rice Types of Interspecific Hybrid Origin in West African Farmers' Fields

NARCIS (Netherlands)

Nuijten, H.A.C.P.; Treuren, van R.; Struik, P.C.; Mokuwa, G.A.; Okry, F.; Teeken, B.W.E.; Richards, P.

2009-01-01

In West Africa two rice species (Oryza glaberrima Steud. and Oryza sativa L.) co-exist. Although originally it was thought that interspecific hybridization is impossible without biotechnological methods, progenies of hybridization appear to occur in farmer fields. AFLP analysis was used to assess

Introgression of ivermectin resistance genes into a susceptible Haemonchus contortus strain by multiple backcrossing.

Directory of Open Access Journals (Sweden)

Elizabeth Redman

2012-02-01

Full Text Available Anthelmintic drug resistance in livestock parasites is already widespread and in recent years there has been an increasing level of anthelmintic drug selection pressure applied to parasitic nematode populations in humans leading to concerns regarding the emergence of resistance. However, most parasitic nematodes, particularly those of humans, are difficult experimental subjects making mechanistic studies of drug resistance extremely difficult. The small ruminant parasitic nematode Haemonchus contortus is a more amenable model system to study many aspects of parasite biology and investigate the basic mechanisms and genetics of anthelmintic drug resistance. Here we report the successful introgression of ivermectin resistance genes from two independent ivermectin resistant strains, MHco4(WRS and MHco10(CAVR, into the susceptible genome reference strain MHco3(ISE using a backcrossing approach. A panel of microsatellite markers were used to monitor the procedure. We demonstrated that after four rounds of backcrossing, worms that were phenotypically resistant to ivermectin had a similar genetic background to the susceptible reference strain based on the bulk genotyping with 18 microsatellite loci and individual genotyping with a sub-panel of 9 microsatellite loci. In addition, a single marker, Hcms8a20, showed evidence of genetic linkage to an ivermectin resistance-conferring locus providing a starting point for more detailed studies of this genomic region to identify the causal mutation(s. This work presents a novel genetic approach to study anthelmintic resistance and provides a "proof-of-concept" of the use of forward genetics in an important model strongylid parasite of relevance to human hookworms. The resulting strains provide valuable resources for candidate gene studies, whole genome approaches and for further genetic analysis to identify ivermectin resistance loci.

1772-IJBCS-Article-Abolade Adekunle

African Journals Online (AJOL)

hp

A hybrid swarm involving O. sativa, O. glaberrima and O. longistaminata occuring in Jebba, Nigeria was studied to investigate the processes involved in the population dynamics. Reproductive parameters such as pollen stainability, pollen size, anther structure, seed set were investigated. The chromosomes of the hybrid.

Acetylated starch of Ofada rice as a sustained polymer in ...

African Journals Online (AJOL)

Objectives: To formulate and evaluate repaglinide microspheres using acetylated starch of the indigenous rice species Oryza glaberrima Steud (Ofada) as polymer. Materials and Methods: Ofada rice starch was acetylated with acetic anhydride in pyridine (DS 2.68) and characterized for morphology (Scanning electron ...

A new premna (Verbenaceae) from New Guinea

NARCIS (Netherlands)

Lam, H.J.

1954-01-01

Premna brongersmai, nov. spec. — Frutex? Ramuli teretes conspicue subdistanter lenticellati 0.3—0.5 cm crassi, internodia in specimine 7—11 cm longa. Folia coriacea subrigida, decussatim opposita glaberrima petiolata, ovata vel oblongo-ovata vel subovata vel oblongo-lanceolata, basi plus minusve

Evidence for hybridization and introgression within a species-rich oak (Quercus spp. community

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Finkeldey Reiner

2007-11-01

Full Text Available Abstract Background Analysis of interspecific gene flow is crucial for the understanding of speciation processes and maintenance of species integrity. Oaks (genus Quercus, Fagaceae are among the model species for the study of hybridization. Natural co-occurrence of four closely related oak species is a very rare case in the temperate forests of Europe. We used both morphological characters and genetic markers to characterize hybridization in a natural community situated in west-central Romania and which consists of Quercus robur, Q. petraea, Q. pubescens, and Q. frainetto, respectively. Results On the basis of pubescence and leaf morphological characters ~94% of the sampled individuals were assigned to pure species. Only 16 (~6% individual trees exhibited intermediate morphologies or a combination of characters of different species. Four chloroplast DNA haplotypes were identified in the study area. The distribution of haplotypes within the white oak complex showed substantial differences among species. However, the most common haplotypes were present in all four species. Furthermore, based on a set of 7 isozyme and 6 microsatellite markers and using a Bayesian admixture analysis without any a priori information on morphology we found that four genetic clusters best fit the data. There was a very good correspondence of each species with one of the inferred genetic clusters. The estimated introgression level varied markedly between pairs of species ranging from 1.7% between Q. robur and Q. frainetto to 16.2% between Q. pubescens and Q. frainetto. Only nine individuals (3.4% appeared to be first-generation hybrids. Conclusion Our data indicate that natural hybridization has occurred at relatively low rates. The different levels of gene flow among species might be explained by differences in flowering time and spatial position within the stand. In addition, a partial congruence between phenotypically and genetically intermediate individuals was

Performance and feeding behaviour of two biotypes of the black currant-lettuce aphid, Nasonovia ribisnigri, on resistant and susceptible Lactuca sativa near-isogenic lines

NARCIS (Netherlands)

Broeke, ten C.J.M.; Dicke, M.; Loon, van J.J.A.

2013-01-01

The black currant-lettuce aphid, Nasonovia ribisnigri, is an important pest of cultivated lettuce, Lactuca sativa. Since 1982, the control of this aphid on lettuce is largely based on host plant resistance, conferred by the Nr gene, introgressed from Lactuca virosa. The resistance mechanism remains

Development and Molecular Cytogenetic Identification of a Novel Wheat-Leymus mollis Lm#7Ns (7D Disomic Substitution Line with Stripe Rust Resistance.

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Xiaofei Yang

Full Text Available Leymus mollis (2n = 4x = 28, NsNsXmXm possesses novel and important genes for resistance against multi-fungal diseases. The development of new wheat-L. mollis introgression lines is of great significance for wheat disease resistance breeding. M11003-3-1-15-8, a novel disomic substitution line of common wheat cv. 7182 -L. mollis, developed and selected from the BC1F5 progeny between wheat cv. 7182 and octoploid Tritileymus M47 (2n = 8x = 56, AABBDDNsNs, was characterized by morphological and cytogenetic identification, analysis of functional molecular markers, genomic in situ hybridization (GISH, sequential fluorescence in situ hybridization (FISH-genomic in situ hybridization (GISH and disease resistance evaluation. Cytological observations suggested that M11003-3-1-15-8 contained 42 chromosomes and formed 21 bivalents at meiotic metaphase I. The GISH investigations showed that line contained 40 wheat chromosomes and a pair of L. mollis chromosomes. EST-STS multiple loci markers and PLUG (PCR-based Landmark Unique Gene markers confirmed that the introduced L. mollis chromosomes belonged to homoeologous group 7, it was designated as Lm#7Ns. While nulli-tetrasomic and sequential FISH-GISH analysis using the oligonucleotide Oligo-pSc119.2 and Oligo-pTa535 as probes revealed that the wheat 7D chromosomes were absent in M11003-3-1-15-8. Therefore, it was deduced that M11003-3-1-15-8 was a wheat-L. mollis Lm#7Ns (7D disomic substitution line. Field disease resistance demonstrated that the introduced L. mollis chromosomes Lm#7Ns were responsible for the stripe rust resistance at the adult stage. Moreover, M11003-3-1-15-8 had a superior numbers of florets. The novel disomic substitution line M11003-3-1-15-8, could be exploited as an important genetic material in wheat resistance breeding programs and genetic resources.

Amplified fragment length polymorphism (AFLP) and genealogy ...

African Journals Online (AJOL)

STORAGESEVER

2010-06-07

Jun 7, 2010 ... Pang CY, Du XM, Ma ZY (2006). Evaluation of the introgressed lines and screening for elite germplasm in Gossypium, Chin. Sci. Bull. 51(1):. 304-312. Pieter V, Rene H, Marjo B (1995). AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23(21): 4407-4414. Qian SY, Huang JQ, Zhou BL, Peng ...

The occurence of a hybrid swarm involving O. longistaminata A ...

African Journals Online (AJOL)

A hybrid swarm involving Oryza longistaminata, O. glaberrima and O. sativa was discovered at Jebba in Nigeria. A preliminary study in 2000 paved the way for this study which used extensive morphological and anatomical markers to identify and characterise putative hybrids and their advanced generation segregants.

Dissecting a QTL into Candidate Genes Highlighted the Key Role of Pectinesterases in Regulating the Ascorbic Acid Content in Tomato Fruit

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Valentino Ruggieri

2015-07-01

Full Text Available Tomato ( is a crucial component of the human diet because of its high nutritional value and the antioxidant content of its fruit. As a member of the Solanaceae family, it is considered a model species for genomic studies in this family, especially since its genome has been completely sequenced. Among genomic resources available, introgression lines represent a valuable tool to mine the genetic diversity present in wild species. One introgression line, IL12-4, was previously selected for high ascorbic acid (AsA content, and a transcriptomic analysis indicated the involvement of genes controlling pectin degradation in AsA accumulation. In this study the integration of data from different “omics” platforms has been exploited to identify candidate genes that increase AsA belonging to the wild region 12-4. Thirty-two genes potentially involved in pathways controlling AsA levels were analyzed with bioinformatic tools. Two hundred-fifty nonsynonymous polymorphisms were detected in their coding regions, and 11.6% revealed deleterious effects on predicted protein function. To reduce the number of genes that had to be functionally validated, introgression sublines of the region 12–4 were selected using species-specific polymorphic markers between the two species. Four sublines were obtained and we demonstrated that a subregion of around 1 Mbp includes 12 candidate genes potentially involved in AsA accumulation. Among these, only five exhibited structural deleterious variants, and one of the 12 was differentially expressed between the two species. We have highlighted the role of three polymorphic pectinesterases and inhibitors of pectinesterases that merit further investigation.

Non-Destructive Assessment of Aroma Volatiles from a Climacteric Near-Isogenic Line of Melon Obtained by Headspace Stir-Bar Sorptive Extraction

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Juan Pablo Fernández-Trujillo

2013-08-01

Full Text Available A climacteric aromatic near-isogenic line (NIL of melon (Cucumis melo L. SC3-5-1 contained an introgression of the non-climacteric Korean cultivar “Shongwan Charmi” accession PI 161375 (SC in the genetic background of the non-climacteric cultivar “Piel de Sapo” (PS. The aroma production was monitored during ripening at 21 °C in intact fruit using headspace sorptive bar extraction (HSSE. Bars were composed of polydimethylsiloxane (PDMS and aromas were desorbed and analyzed by gas-chromatography mass-spectrometry. The aromatic profile was composed of 70 aromatic compounds plus 21 alkanes with a predominance of esters, particularly acetate (2-methylbutyl acetate, 2-methylpropyl acetate, hexyl acetate, and phenylmethyl acetate. Some compounds were severely affected by postharvest time. The acetate esters (3-methylbutyl acetate, butan-2-yl acetate and phenylmethyl acetate decreased with ripening and sulfur-derived compounds (S-methyl butanethioate and S-methyl 3-methylbutanethioate increased gradually with ripening. A few compounds increased at the senescence phase (propyl ethanoate. Other compounds such as hexadecanoic acid showed a marked decrease after harvest, some decreasing from a relative maximum at harvest (2-methylpropyl hexanoate; n-hexanoic acid; nonanoic acid.

New insight into hybridization and unidirectional introgression between Ammodytes japonicus and Ammodytes heian (Trachiniformes, Ammodytidae.

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Jin-Koo Kim

Full Text Available Based on northern (NOL and southern (SOL mitochondrial lineages, recently, it proposed the new species Ammodytes heian and revived the species name Ammodytes japonicus to describe sand lances from the northwestern Pacific Ocean. This study used molecular methods to investigate genetic relationships between the two sand lance species in Korea and Japan. In total, 154 specimens were collected from four locations in Korea (Baengnyeongdo in the Yellow Sea, Tongyeong in the Korean Strait, and Jumunjin and Gijang in the East Sea, and 50 specimens were collected from a single location in Japan (Wakkanai in the Okhotsk Sea. Mitochondrial DNA analysis demonstrated that the individuals from Baengnyeongdo and Tongyeong all belonged to the SOL, whereas those from Gijang, Jumunjin, and Wakkanai included individuals from both the NOL and SOL (over 75% NOL. Population structure analyses were performed on the same individuals using seven microsatellite DNA markers. The population structure analysis based on 201 specimens identified two clusters (named as northern group and southern group, with the admixture proportion (q of < 0.1 for the northern group in the Backyeongdo and Tongyeong sand lances and < 0.1 for the southern group in the Wakkanai sand lances. The high heterogeneity indicated that the former was probably A. japonicus and the latter probably A. heian. However, the admixture proportion in the Jumunjin and Gijang sand lances was 0.71-0.75 for the southern group, indicating that hybridization and unidirectional introgression from SOL to NOL occurs in southwestern margin of the East Sea. Our findings illustrate the speciation process based on different patterns of gene flow between Korean and Japanese sand lance, which is strongly influenced by both the paleo-climatic change and the contemporary local oceanic current pattern.

Rice as commodity and anti-commodity

NARCIS (Netherlands)

Richards, P.

2016-01-01

On the Upper West Africa coast rice belongs to two species — African rice (Oryza glaberrima Steud.) and Asian rice (Oryza sativa L.). African rice was domesticated in the region, perhaps three millennia ago, from a presumed wild ancestor, O. barthii. Asian rice was introduced via trans-Saharan

GUEI G. R.-1.mdi

African Journals Online (AJOL)

lara

interspecific progenies possess characters that cover the range of both their parents. Cluster analysis amalgamated some as possessing the adaptive morphological traits of their O.glaberrima parents, and the panicle and yield attributes of improved O. sativa parents. O. sativa of temperate origin, but of tropical japonica ...

QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

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Zaidi, Pervez Haider; Rashid, Zerka; Vinayan, Madhumal Thayil; Almeida, Gustavo Dias; Phagna, Ramesh Kumar; Babu, Raman

2015-01-01

Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate

Biological effects of rice harbouring Bph14 and Bph15 on brown planthopper, Nilaparvata lugens.

Science.gov (United States)

Li, Jie; Chen, Qiuhong; Wang, Liangquan; Liu, Jia; Shang, Keke; Hua, Hongxia

2011-05-01

Brown planthopper (Nilaparvata lugens Stål; BPH) resistance genes Bph14 and Bph15 have been introgressed singly or pyramided into rice variety Minghui 63 (MH63). The antibiosis and antixenosis effects of these rice lines on BPH and the expression of five P450 genes of BPH regulated by these rice lines were investigated in this study. The resistance level of rice lines harbouring resistance genes was improved compared with MH63. MH63::14 (carrying Bph14) had negative effects on the development of males, honeydew excretion of females, the female ratio and the copulation rate compared with MH63. MH63::14 also exhibited antixenosis action against BPH nymphs, female adults and oviposition. Besides these negative effects, MH63::15 (carrying Bph15) could also retard the development of females, lower the fecundity and shorten the lifespan of females. The antixenosis action of MH63::15 was stronger than that of MH63::14. When Bph14 and Bph15 were pyramided, antibiosis and antixenosis effects were significantly enhanced relative to single-introgression lines. Among the five P450 genes of BPH, expression of three genes was upregulated, one gene was downregulated and one gene was unchanged by resistant hosts. Both Bph14 and Bph15 could improve resistance levels of MH63. MH63::15 and MH63::14&15 had greater potential to control BPH infestations than MH63::14. Copyright © 2011 Society of Chemical Industry.

Molecular Diversity Analysis and Genetic Mapping of Pod Shatter Resistance Loci in Brassica carinata L.

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Rosy Raman

2017-11-01

Full Text Available Seed lost due to easy pod dehiscence at maturity (pod shatter is a major problem in several members of Brassicaceae family. We investigated the level of pod shatter resistance in Ethiopian mustard (Brassica carinata and identified quantitative trait loci (QTL for targeted introgression of this trait in Ethiopian mustard and its close relatives of the genus Brassica. A set of 83 accessions of B. carinata, collected from the Australian Grains Genebank, was evaluated for pod shatter resistance based on pod rupture energy (RE. In comparison to B. napus (RE = 2.16 mJ, B. carinata accessions had higher RE values (2.53 to 20.82 mJ. A genetic linkage map of an F2 population from two contrasting B. carinata selections, BC73526 (shatter resistant with high RE and BC73524 (shatter prone with low RE comprising 300 individuals, was constructed using a set of 6,464 high quality DArTseq markers and subsequently used for QTL analysis. Genetic analysis of the F2 and F2:3 derived lines revealed five statistically significant QTL (LOD ≥ 3 that are linked with pod shatter resistance on chromosomes B1, B3, B8, and C5. Herein, we report for the first time, identification of genetic loci associated with pod shatter resistance in B. carinata. These characterized accessions would be useful in Brassica breeding programs for introgression of pod shatter resistance alleles in to elite breeding lines. Molecular markers would assist marker-assisted selection for tracing the introgression of resistant alleles. Our results suggest that the value of the germplasm collections can be harnessed through genetic and genomics tools.

The U-line line balancing problem

NARCIS (Netherlands)

Miltenburg, G.J.; Wijngaard, J.

1994-01-01

The traditional line balancing (LB) problem considers a production line in which stations are arranged consecutively in a line. A balance is determined by grouping tasks into stations while moving forward (or backward) through a precedence network. Recently many production lines are being arranged

High-throughput phenotyping to detect drought tolerance QTL in wild barley introgression lines

KAUST Repository

Honsdorf, Nora; March, Timothy John; Berger, Bettina; Tester, Mark A.; Pillen, Klaus

2014-01-01

and well watered treatments. High correlation (r = 0.98) between image based biomass estimates and actual biomass was demonstrated, and the suitability of the system to accurately and non-destructively estimate biomass was validated. Subsequently

Radiocarbon Based Ages and Growth Rates: Hawaiian Deep Sea Corals

Energy Technology Data Exchange (ETDEWEB)

Roark, E B; Guilderson, T P; Dunbar, R B; Ingram, B L

2006-01-13

The radial growth rates and ages of three different groups of Hawaiian deep-sea 'corals' were determined using radiocarbon measurements. Specimens of Corallium secundum, Gerardia sp., and Leiopathes glaberrima, were collected from 450 {+-} 40 m at the Makapuu deep-sea coral bed using a submersible (PISCES V). Specimens of Antipathes dichotoma were collected at 50 m off Lahaina, Maui. The primary source of carbon to the calcitic C. secundum skeleton is in situ dissolved inorganic carbon (DIC). Using bomb {sup 14}C time markers we calculate radial growth rates of {approx} 170 {micro}m y{sup -1} and ages of 68-75 years on specimens as tall as 28 cm of C. secundum. Gerardia sp., A. dichotoma, and L. glaberrima have proteinaceous skeletons and labile particulate organic carbon (POC) is their primary source of architectural carbon. Using {sup 14}C we calculate a radial growth rate of 15 {micro}m y{sup -1} and an age of 807 {+-} 30 years for a live collected Gerardia sp., showing that these organisms are extremely long lived. Inner and outer {sup 14}C measurements on four sub-fossil Gerardia spp. samples produce similar growth rate estimates (range 14-45 {micro}m y{sup -1}) and ages (range 450-2742 years) as observed for the live collected sample. Similarly, with a growth rate of < 10 {micro}m y{sup -1} and an age of {approx}2377 years, L. glaberrima at the Makapuu coral bed, is also extremely long lived. In contrast, the shallow-collected A. dichotoma samples yield growth rates ranging from 130 to 1,140 {micro}m y{sup -1}. These results show that Hawaiian deep-sea corals grow more slowly and are older than previously thought.

High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population

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Yi Yang

2017-09-01

Full Text Available Seeds per silique (SS, seed weight (SW, and silique length (SL are important determinant traits of seed yield potential in rapeseed (Brassica napus L., and are controlled by naturally occurring quantitative trait loci (QTLs. Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses (B. rapa ssp. chinesis × O. violaceus × B. napus. In present study, a doubled haploid (DH population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0–34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs (cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09, and cqSL.C09 were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique

Author Details

African Journals Online (AJOL)

Bolaji, A. O.. Vol 14, No 2 (2012) - Articles The occurence of a hybrid swarm involving O. longistaminata A. Chev. et Roehr., Oryza glaberrima Steud. and Oryza sativa Linn. in Jebba, Nigeria Abstract PDF. ISSN: 0794-4896. AJOL African Journals Online. HOW TO USE AJOL... for Researchers · for Librarians · for Authors ...

Marker Assisted Transfer of Two Powdery Mildew Resistance Genes PmTb7A.1 and PmTb7A.2 from Triticum boeoticum (Boiss.) to Triticum aestivum (L.).

Science.gov (United States)

Elkot, Ahmed Fawzy Abdelnaby; Chhuneja, Parveen; Kaur, Satinder; Saluja, Manny; Keller, Beat; Singh, Kuldeep

2015-01-01

Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici, is one of the important wheat diseases, worldwide. Two PM resistance genes, designated as PmTb7A.1 and PmTb7A.2, were identified in T. boeoticum acc. pau5088 and mapped on chromosome 7AL approximately 48cM apart. Two resistance gene analogue (RGA)-STS markers Ta7AL-4556232 and 7AL-4426363 were identified to be linked to the PmTb7A.1 and PmTb7A.2, at a distance of 0.6cM and 6.0cM, respectively. In the present study, following marker assisted selection (MAS), the two genes were transferred to T. aestivum using T. durum as bridging species. As many as 12,317 florets of F1 of the cross T. durum /T. boeoticum were pollinated with T. aestivum lines PBW343-IL and PBW621 to produce 61 and 65 seeds, respectively, of three-way F1. The resulting F1s of the cross T. durum/T. boeoticum//T. aestivum were screened with marker flanking both the PM resistance genes PmTb7A.1 and PmTb7A.2 (foreground selection) and the selected plants were backcrossed to generate BC1F1. Marker assisted selection was carried both in BC1F1 and the BC2F1 generations. Introgression of alien chromatin in BC2F1 plants varied from 15.4-62.9 percent. Out of more than 110 BC2F1 plants showing introgression for markers linked to the two PM resistance genes, 40 agronomically desirable plants were selected for background selection for the carrier chromosome to identify the plants with minimum of the alien introgression. Cytological analysis showed that most plants have chromosome number ranging from 40-42. The BC2F2 plants homozygous for the two genes have been identified. These will be crossed to generate lines combining both the PM resistance genes but with minimal of the alien introgression. The PM resistance gene PmTb7A.1 maps in a region very close to Sr22, a stem rust resistance gene effective against the race Ug99. Analysis of selected plants with markers linked to Sr22 showed introgression of Sr22 from T. boeoticum in several BC2F1 plants

Marker Assisted Transfer of Two Powdery Mildew Resistance Genes PmTb7A.1 and PmTb7A.2 from Triticum boeoticum (Boiss. to Triticum aestivum (L..

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Ahmed Fawzy Abdelnaby Elkot

Full Text Available Powdery mildew (PM, caused by Blumeria graminis f. sp. tritici, is one of the important wheat diseases, worldwide. Two PM resistance genes, designated as PmTb7A.1 and PmTb7A.2, were identified in T. boeoticum acc. pau5088 and mapped on chromosome 7AL approximately 48cM apart. Two resistance gene analogue (RGA-STS markers Ta7AL-4556232 and 7AL-4426363 were identified to be linked to the PmTb7A.1 and PmTb7A.2, at a distance of 0.6cM and 6.0cM, respectively. In the present study, following marker assisted selection (MAS, the two genes were transferred to T. aestivum using T. durum as bridging species. As many as 12,317 florets of F1 of the cross T. durum /T. boeoticum were pollinated with T. aestivum lines PBW343-IL and PBW621 to produce 61 and 65 seeds, respectively, of three-way F1. The resulting F1s of the cross T. durum/T. boeoticum//T. aestivum were screened with marker flanking both the PM resistance genes PmTb7A.1 and PmTb7A.2 (foreground selection and the selected plants were backcrossed to generate BC1F1. Marker assisted selection was carried both in BC1F1 and the BC2F1 generations. Introgression of alien chromatin in BC2F1 plants varied from 15.4-62.9 percent. Out of more than 110 BC2F1 plants showing introgression for markers linked to the two PM resistance genes, 40 agronomically desirable plants were selected for background selection for the carrier chromosome to identify the plants with minimum of the alien introgression. Cytological analysis showed that most plants have chromosome number ranging from 40-42. The BC2F2 plants homozygous for the two genes have been identified. These will be crossed to generate lines combining both the PM resistance genes but with minimal of the alien introgression. The PM resistance gene PmTb7A.1 maps in a region very close to Sr22, a stem rust resistance gene effective against the race Ug99. Analysis of selected plants with markers linked to Sr22 showed introgression of Sr22 from T. boeoticum in

comportement des nouveaux riz africains face a la pyriculariose

African Journals Online (AJOL)

AISA

Key words : Riz, NERICA variety, blast, inoculation, resistance, Côte d'Ivoire. INTRODUCTION. Les nouveaux riz africains ou NERICA (New Rice for Africa) sont des hybrides interspécifiques. (Oryza glaberrima X O. sativa) mises au point par l'ADRAO (actuellement dénommé Centre. Africain pour le Riz) dans les années 90.

Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.

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Jie Qiu

Full Text Available Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou and a wild line (Lanxi 1 collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1 no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2 besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3 high heterozygous rates (0.19-0.49 were observed in several semi-wild lines; and (4 over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.

Morphological and Phylogenetic Characterization of New Gephyrocapsa Isolates Suggests Introgressive Hybridization in the Emiliania/Gephyrocapsa Complex (Haptophyta).

Science.gov (United States)

Bendif, El Mahdi; Probert, Ian; Young, Jeremy R; von Dassow, Peter

2015-07-01

The coccolithophore genus Gephyrocapsa contains a cosmopolitan assemblage of pelagic species, including the bloom-forming Gephyrocapsa oceanica, and is closely related to the emblematic coccolithophore Emiliania huxleyi within the Noëlaerhabdaceae. These two species have been extensively studied and are well represented in culture collections, whereas cultures of other species of this family are lacking. We report on three new strains of Gephyrocapsa isolated into culture from samples from the Chilean coastal upwelling zone using a novel flow cytometric single-cell sorting technique. The strains were characterized by morphological analysis using scanning electron microscopy and phylogenetic analysis of 6 genes (nuclear 18S and 28S rDNA, plastidial 16S and tufA, and mitochondrial cox1 and cox3 genes). Morphometric features of the coccoliths indicate that these isolates are distinct from G. oceanica and best correspond to G. muellerae. Surprisingly, both plastidial and mitochondrial gene phylogenies placed these strains within the E. huxleyi clade and well separated from G. oceanica isolates, making Emiliania appear polyphyletic. The only nuclear sequence difference, 1bp in the 28S rDNA region, also grouped E. huxleyi with the new Gephyrocapsa isolates and apart from G. oceanica. Specifically, the G. muellerae morphotype strains clustered with the mitochondrial β clade of E. huxleyi, which, like G. muellerae, has been associated with cold (temperate and sub-polar) waters. Among putative evolutionary scenarios that could explain these results we discuss the possibility that E. huxleyi is not a valid taxonomic unit, or, alternatively the possibility of past hybridization and introgression between each E. huxleyi clade and older Gephyrocapsa clades. In either case, the results support the transfer of Emiliania to Gephyrocapsa. These results have important implications for relating morphological species concepts to ecological and evolutionary units of diversity

Introgression of Black Rot Resistance from Brassica carinata to Cauliflower (Brassica oleracea botrytis Group) through Embryo Rescue.

Science.gov (United States)

Sharma, Brij B; Kalia, Pritam; Singh, Dinesh; Sharma, Tilak R

2017-01-01

Black rot caused by Xanthomonas campestris pv. campestris ( Xcc ) is a very important disease of cauliflower ( Brassica oleracea botrytis group) resulting into 10-50% yield losses every year. Since there is a dearth of availability of resistance to black rot disease in B. oleracea (C genome), therefore exploration of A and B genomes was inevitable as they have been reported to be potential reservoirs of gene(s) for resistance to black rot. To utilize these sources, interspecific hybrid and backcross progeny (B 1 ) were generated between cauliflower "Pusa Sharad" and Ethiopian mustard "NPC-9" employing in vitro embryo rescue technique. Direct ovule culture method was better than siliqua culture under different temperature regime periods. Hybridity testing of F 1 inter-specific plants was carried out using co-dominant SSR marker and Brassica B and C genome-specific (DB and DC) primers. Meiosis in the di-genomic (BCC) interspecific hybrid of B. oleracea botrytis group (2 n = 18, CC) × B. carinata (2 n = 4x = 34, BBCC) was higly disorganized and cytological analysis of pollen mother cells revealed chromosomes 2 n = 26 at metaphase-I. Fertile giant pollen grain formation was observed frequently in interspecific F 1 hybrid and BC 1 plants. The F 1 inter-specific plants were found to be resistant to Xcc race 1. Segregation distortion was observed in BC 1 generation for black rot resistance and different morphological traits. The At1g70610 marker analysis confirmed successful introgression of black rot resistance in interspecific BC 1 population. This effort will go a long way in pyramiding gene(s) for resistance against black rot in Cole crops, especially cauliflower and cabbage for developing durable resistance, thus minimize dependency on bactericides.

Introgression of Black Rot Resistance from Brassica carinata to Cauliflower (Brassica oleracea botrytis Group) through Embryo Rescue

Science.gov (United States)

Sharma, Brij B.; Kalia, Pritam; Singh, Dinesh; Sharma, Tilak R.

2017-01-01

Black rot caused by Xanthomonas campestris pv. campestris (Xcc) is a very important disease of cauliflower (Brassica oleracea botrytis group) resulting into 10–50% yield losses every year. Since there is a dearth of availability of resistance to black rot disease in B. oleracea (C genome), therefore exploration of A and B genomes was inevitable as they have been reported to be potential reservoirs of gene(s) for resistance to black rot. To utilize these sources, interspecific hybrid and backcross progeny (B1) were generated between cauliflower “Pusa Sharad” and Ethiopian mustard “NPC-9” employing in vitro embryo rescue technique. Direct ovule culture method was better than siliqua culture under different temperature regime periods. Hybridity testing of F1 inter-specific plants was carried out using co-dominant SSR marker and Brassica B and C genome-specific (DB and DC) primers. Meiosis in the di-genomic (BCC) interspecific hybrid of B. oleracea botrytis group (2n = 18, CC) × B. carinata (2n = 4x = 34, BBCC) was higly disorganized and cytological analysis of pollen mother cells revealed chromosomes 2n = 26 at metaphase-I. Fertile giant pollen grain formation was observed frequently in interspecific F1 hybrid and BC1 plants. The F1 inter-specific plants were found to be resistant to Xcc race 1. Segregation distortion was observed in BC1 generation for black rot resistance and different morphological traits. The At1g70610 marker analysis confirmed successful introgression of black rot resistance in interspecific BC1 population. This effort will go a long way in pyramiding gene(s) for resistance against black rot in Cole crops, especially cauliflower and cabbage for developing durable resistance, thus minimize dependency on bactericides. PMID:28769959

Introgression of Black Rot Resistance from Brassica carinata to Cauliflower (Brassica oleracea botrytis Group through Embryo Rescue

Directory of Open Access Journals (Sweden)

Brij B. Sharma

2017-07-01

Full Text Available Black rot caused by Xanthomonas campestris pv. campestris (Xcc is a very important disease of cauliflower (Brassica oleracea botrytis group resulting into 10–50% yield losses every year. Since there is a dearth of availability of resistance to black rot disease in B. oleracea (C genome, therefore exploration of A and B genomes was inevitable as they have been reported to be potential reservoirs of gene(s for resistance to black rot. To utilize these sources, interspecific hybrid and backcross progeny (B1 were generated between cauliflower “Pusa Sharad” and Ethiopian mustard “NPC-9” employing in vitro embryo rescue technique. Direct ovule culture method was better than siliqua culture under different temperature regime periods. Hybridity testing of F1 inter-specific plants was carried out using co-dominant SSR marker and Brassica B and C genome-specific (DB and DC primers. Meiosis in the di-genomic (BCC interspecific hybrid of B. oleracea botrytis group (2n = 18, CC × B. carinata (2n = 4x = 34, BBCC was higly disorganized and cytological analysis of pollen mother cells revealed chromosomes 2n = 26 at metaphase-I. Fertile giant pollen grain formation was observed frequently in interspecific F1 hybrid and BC1 plants. The F1 inter-specific plants were found to be resistant to Xcc race 1. Segregation distortion was observed in BC1 generation for black rot resistance and different morphological traits. The At1g70610 marker analysis confirmed successful introgression of black rot resistance in interspecific BC1 population. This effort will go a long way in pyramiding gene(s for resistance against black rot in Cole crops, especially cauliflower and cabbage for developing durable resistance, thus minimize dependency on bactericides.

Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton

Directory of Open Access Journals (Sweden)

Michael A. Gore

2014-03-01

Full Text Available The superior fiber properties of L. serve as a source of novel variation for improving fiber quality in Upland cotton ( L., but introgression from has been largely unsuccessful due to hybrid breakdown and a lack of genetic and genomic resources. In an effort to overcome these limitations, we constructed a linkage map and conducted a quantitative trait locus (QTL analysis of 10 agronomic and fiber quality traits in a recombinant inbred mapping population derived from a cross between TM-1, an Upland cotton line, and NM24016, an elite line with stabilized introgression from . The linkage map consisted of 429 simple-sequence repeat (SSR and 412 genotyping-by-sequencing (GBS-based single-nucleotide polymorphism (SNP marker loci that covered half of the tetraploid cotton genome. Notably, the 841 marker loci were unevenly distributed among the 26 chromosomes of tetraploid cotton. The 10 traits evaluated on the TM-1 × NM24016 population in a multienvironment trial were highly heritable, and most of the fiber traits showed considerable transgressive variation. Through the QTL analysis, we identified a total of 28 QTLs associated with the 10 traits. Our study provides a novel resource that can be used by breeders and geneticists for the genetic improvement of agronomic and fiber quality traits in Upland cotton.

A hairy-leaf gene, BLANKET LEAF, of wild Oryza nivara increases photosynthetic water use efficiency in rice.

Science.gov (United States)

Hamaoka, Norimitsu; Yasui, Hideshi; Yamagata, Yoshiyuki; Inoue, Yoko; Furuya, Naruto; Araki, Takuya; Ueno, Osamu; Yoshimura, Atsushi

2017-12-01

High water use efficiency is essential to water-saving cropping. Morphological traits that affect photosynthetic water use efficiency are not well known. We examined whether leaf hairiness improves photosynthetic water use efficiency in rice. A chromosome segment introgression line (IL-hairy) of wild Oryza nivara (Acc. IRGC105715) with the genetic background of Oryza sativa cultivar 'IR24' had high leaf pubescence (hair). The leaf hairs developed along small vascular bundles. Linkage analysis in BC 5 F 2 and F 3 populations showed that the trait was governed by a single gene, designated BLANKET LEAF (BKL), on chromosome 6. IL-hairy plants had a warmer leaf surface in sunlight, probably due to increased boundary layer resistance. They had a lower transpiration rate under moderate and high light intensities, resulting in higher photosynthetic water use efficiency. Introgression of BKL on chromosome 6 from O. nivara improved photosynthetic water use efficiency in the genetic background of IR24.

Gene transfer from wild Helianthus to sunflower: topicalities and limits

Directory of Open Access Journals (Sweden)

Breton Catherine

2010-03-01

Full Text Available Sunflower (2n=17 belongs to the Helianthus genus (Asteraceae. Wild Helianthus species display morphological variation for branching and stem number, for architecture and seed size, and for resistance to abiotic and biotic stresses due to which they thrive in different environments in North America. The genus is divided into botanical sections, two for annual as sunflower, and two for perennial species as Jerusalem artichoke that produces rhizomes (tubers. We explain the difficulties and successes obtained by crossing sunflower with these species to improve the agronomic traits of the sunflower crop. It is easier to cross the annual species than the perennials’ with sunflower. Several traits such as Cytoplasmic male sterility and restorer Rf-PET1 genes, Downy mildew resistance, Phomopsis resistance, Sclerotinia resistance, Rust resistance, and Orobanche resistance have already been introduced from annual species into sunflower crop, but the complex genomic organization of these species compared to sunflower limits their important potential. Perennial species are much more diverse, and their genomes display 2n, 4n, or 6n chromosomes for n 17. The realities of inter-specific hybridization are relatively disappointing due to the introgression lines that have low oil and low seed yield. We report here several attempts to introgress agronomic traits from these species to sunflower, and we present as a case study, an introgressed progenies from H. mollis, a diploid species with sessile small leaves. We constructed a preliminary genetic map with AFLP markers in 21 BC1 plants, and we then showed that some progenies display 6 to 44% of introgression from H. mollis. Although this study is promising due to the novel compact architecture of the progenies, we cannot estimate the transferability from H. mollis to other perennial Helianthus to improve sunflower.

Line facilities outline

International Nuclear Information System (INIS)

1998-08-01

This book deals with line facilities. The contents of this book are outline line of wire telecommunication ; development of line, classification of section of line and theory of transmission of line, cable line ; structure of line, line of cable in town, line out of town, domestic cable and other lines, Optical communication ; line of optical cable, transmission method, measurement of optical communication and cable of the sea bottom, Equipment of telecommunication line ; telecommunication line facilities and telecommunication of public works, construction of cable line and maintenance and Regulation of line equipment ; regulation on technique, construction and maintenance.

Evidence of Natural Hybridization and Introgression between Vasconcellea Species (Caricaceae) from Southern Ecuador Revealed by Chloroplast, Mitochondrial and Nuclear DNA Markers

Science.gov (United States)

VAN DROOGENBROECK, B.; KYNDT, T.; ROMEIJN-PEETERS, E.; VAN THUYNE, W.; GOETGHEBEUR, P.; ROMERO-MOTOCHI, J. P.; GHEYSEN, G.

2006-01-01

• Background and Aims Vasconcellea × heilbornii is believed to be of natural hybrid origin between V. cundinamarcensis and V. stipulata, and is often difficult to discriminate from V. stipulata on morphological grounds. The aim of this paper is to examine individuals of these three taxa and of individuals from the closely related species V. parviflora and V. weberbaueri, which all inhabit a hybrid zone in southern Ecuador. • Methods Molecular data from mitochondrial, chloroplast and nuclear DNA from 61 individuals were analysed. • Key Results Molecular analysis confirmed occasional contemporary hybridization between V. stipulata, V. cundinamarcensis and V. × heilbornii and suggested the possible involvement of V. weberbaueri in the origin of V. × heilbornii. In addition, the molecular data indicated unidirectional introgression of the V. cundinamarcensis nuclear genome into that of V. stipulata. Several of the individuals examined with morphology similar to that of V. stipulata had genetic traces of hybridization with V. cundinamarcensis, which only seems to act as pollen donor in interspecific hybridization events. Molecular analyses also strongly suggested that most of the V. × heilbornii individuals are not F1 hybrids but instead are progeny of repeated backcrosses with V. stipulata. • Conclusions The results of the present study point to the need for re-evaluation of natural populations of V. stipulata and V. × heilbornii. In general, this analysis demonstrates the complex patterns of genetic and morphological diversity found in natural plant hybrid zones. PMID:16500954

Similarity law for Widom lines and coexistence lines.

Science.gov (United States)

Banuti, D T; Raju, M; Ihme, M

2017-05-01

The coexistence line of a fluid separates liquid and gaseous states at subcritical pressures, ending at the critical point. Only recently, it became clear that the supercritical state space can likewise be divided into regions with liquidlike and gaslike properties, separated by an extension to the coexistence line. This crossover line is commonly referred to as the Widom line, and is characterized by large changes in density or enthalpy, manifesting as maxima in the thermodynamic response functions. Thus, a reliable representation of the coexistence line and the Widom line is important for sub- and supercritical applications that depend on an accurate prediction of fluid properties. While it is known for subcritical pressures that nondimensionalization with the respective species critical pressures p_{cr} and temperatures T_{cr} only collapses coexistence line data for simple fluids, this approach is used for Widom lines of all fluids. However, we show here that the Widom line does not adhere to the corresponding states principle, but instead to the extended corresponding states principle. We resolve this problem in two steps. First, we propose a Widom line functional based on the Clapeyron equation and derive an analytical, species specific expression for the only parameter from the Soave-Redlich-Kwong equation of state. This parameter is a function of the acentric factor ω and compares well with experimental data. Second, we introduce the scaled reduced pressure p_{r}^{*} to replace the previously used reduced pressure p_{r}=p/p_{cr}. We show that p_{r}^{*} is a function of the acentric factor only and can thus be readily determined from fluid property tables. It collapses both subcritical coexistence line and supercritical Widom line data over a wide range of species with acentric factors ranging from -0.38 (helium) to 0.34 (water), including alkanes up to n-hexane. By using p_{r}^{*}, the extended corresponding states principle can be applied within

A new mathematical formulation of the line-by-line method in case of weak line overlapping

Science.gov (United States)

Ishov, Alexander G.; Krymova, Natalie V.

1994-01-01

A rigorous mathematical proof is presented for multiline representation on the equivalent width of a molecular band which consists in the general case of n overlapping spectral lines. The multiline representation includes a principal term and terms of minor significance. The principal term is the equivalent width of the molecular band consisting of the same n nonoverlapping spectral lines. The terms of minor significance take into consideration the overlapping of two, three and more spectral lines. They are small in case of the weak overlapping of spectral lines in the molecular band. The multiline representation can be easily generalized for optically inhomogeneous gas media and holds true for combinations of molecular bands. If the band lines overlap weakly the standard formulation of line-by-line method becomes too labor-consuming. In this case the multiline representation permits line-by-line calculations to be performed more effectively. Other useful properties of the multiline representation are pointed out.

76 FR 51367 - China Shipping Container Lines Co., Ltd.; COSCO Container Lines Company Limited; Evergreen Line A...

Science.gov (United States)

2011-08-18

... FEDERAL MARITIME COMMISSION [Docket No. 11-12] China Shipping Container Lines Co., Ltd.; COSCO Container Lines Company Limited; Evergreen Line A Joint Service Agreement; Hanjin Shipping Co., Ltd... Maritime Commission (Commission) by China Shipping Container Lines Co., Ltd.; COSCO Container Lines Company...

Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis.

Directory of Open Access Journals (Sweden)

Brian R Barber

Full Text Available BACKGROUND: Multiple loci and population genetic methods were employed to study the phylogeographic history of the Patagonian freshwater crab Aegla neuquensis (Aeglidae: Decopoda. This taxon occurs in two large river systems in the Patagonian Steppe, from the foothills of the Andes Mountains east to the Atlantic Ocean. METHODOLOGY/PRINCIPAL FINDINGS: A nuclear phylogeny and multilocus nested clade phylogeographic analysis detected a fragmentation event between the Negro and Chico-Chubut river systems. This event occurred approximately 137 thousand years ago. An isolation-with-migration analysis and maximum-likelihood estimates of gene flow showed asymmetrical exchange of genetic material between these two river systems exclusively in their headwaters. We used information theory to determine the best-fit demographic history between these two river systems under an isolation-with-migration model. The best-fit model suggests that the Negro and the ancestral populations have the same effective population sizes; whereas the Chico-Chubut population is smaller and shows that gene flow from the Chico-Chubut into the Negro is four times higher than in the reverse direction. Much of the Chico-Chubut system appears to have only been recently colonized while the Negro populations appear to have been in place for most of the evolutionary history of this taxon. CONCLUSIONS/SIGNIFICANCE: Due to mitochondrial introgression, three nuclear loci provided different phylogeographic resolution than the three mitochondrial genes for an ancient fragmentation event observed in the nuclear phylogeny. However, the mitochondrial locus provided greater resolution on more recent evolutionary events. Our study, therefore, demonstrates the need to include both nuclear and mitochondrial loci for a more complete understanding of evolutionary histories and associated phylogeographic events. Our results suggest that gene flow between these systems, before and after fragmentation

From Off-line to On-line Handwriting Recognition

NARCIS (Netherlands)

Lallican, P.; Viard-Gaudin, C.; Knerr, S.

2004-01-01

On-line handwriting includes more information on time order of the writing signal and on the dynamics of the writing process than off-line handwriting. Therefore, on-line recognition systems achieve higher recognition rates. This can be concluded from results reported in the literature, and has been

Cytogenetic analysis and mapping of leaf rust resistance in Aegilops speltoides Tausch derived bread wheat line Selection2427 carrying putative gametocidal gene(s).

Science.gov (United States)

Niranjana, M; Vinod; Sharma, J B; Mallick, Niharika; Tomar, S M S; Jha, S K

2017-12-01

Leaf rust (Puccinia triticina) is a major biotic stress affecting wheat yields worldwide. Host-plant resistance is the best method for controlling leaf rust. Aegilops speltoides is a good source of resistance against wheat rusts. To date, five Lr genes, Lr28, Lr35, Lr36, Lr47, and Lr51, have been transferred from Ae. speltoides to bread wheat. In Selection2427, a bread wheat introgresed line with Ae. speltoides as the donor parent, a dominant gene for leaf rust resistance was mapped to the long arm of chromosome 3B (LrS2427). None of the Lr genes introgressed from Ae. speltoides have been mapped to chromosome 3B. Since none of the designated seedling leaf rust resistance genes have been located on chromosome 3B, LrS2427 seems to be a novel gene. Selection2427 showed a unique property typical of gametocidal genes, that when crossed to other bread wheat cultivars, the F 1 showed partial pollen sterility and poor seed setting, whilst Selection2427 showed reasonable male and female fertility. Accidental co-transfer of gametocidal genes with LrS2427 may have occurred in Selection2427. Though LrS2427 did not show any segregation distortion and assorted independently of putative gametocidal gene(s), its utilization will be difficult due to the selfish behavior of gametocidal genes.

VT Digital Line Graph Miscellaneous Transmission Lines

Data.gov (United States)

Vermont Center for Geographic Information — (Link to Metadata) This datalayer is comprised of Miscellaineous Transmission Lines. Digital line graph (DLG) data are digital representations of cartographic...

Efficient algorithm for generating spectra using line-by-line methods

International Nuclear Information System (INIS)

Sonnad, V.; Iglesias, C.A.

2011-01-01

A method is presented for efficient generation of spectra using line-by-line approaches. The only approximation is replacing the line shape function with an interpolation procedure, which makes the method independent of the line profile functional form. The resulting computational savings for large number of lines is proportional to the number of frequency points in the spectral range. Therefore, for large-scale problems the method can provide speedups of two orders of magnitude or more. A method was presented to generate line-by-line spectra efficiently. The first step was to replace the explicit calculation of the profile by the Newton divided-differences interpolating polynomial. The second step is to accumulate the lines effectively reducing their number to the number of frequency points. The final step is recognizing the resulting expression as a convolution and amenable to FFT methods. The reduction in computational effort for a configuration-to-configuration transition array with large number of lines is proportional to the number of frequency points. The method involves no approximations except for replacing the explicit profile evaluation by interpolation. Specifically, the line accumulation and convolution are exact given the interpolation procedure. Furthermore, the interpolation makes the method independent of the line profile functional form contrary to other schemes using FFT methods to generate line-by-line spectra but relying on the analytic form of the profile Fourier transform. Finally, the method relies on a uniform frequency mesh. For non-uniform frequency meshes, however, the method can be applied by using a suitable temporary uniform mesh and the results interpolated onto the final mesh with little additional cost.

Analysis of some coplanar transmission lines: coplanar coupled lines, coplanar coupled striplines, and coplanar coupled lines with rectangular microshield

Science.gov (United States)

Yuan, Naichang; He, Jianguo; Yao, Demiao; Dai, Qin; Lin, Weigan

1995-06-01

Two types of coplanar transmission lines, rectangular microshield coplanar coupled lines (RMCCL) and coplanar coupled rectangular microshield lines (CCRML), are proposed for MMIC applications. These are developed from coplanar coupled lines (CCL) and coplanar coupled strip lines (CCS). Analytic formulas are presented for calculating the quasistatic TEM parameters of these coupled lines by means of exact conformal mapping techniques. Numerical results are also presented to illustrate the properties of these coplanar transmission lines.

Genetic dissection of nonhost resistance of wild lettuce, Lactuca saligna, to downy mildew

OpenAIRE

Zhang, N.

2008-01-01

Lettuce downy mildew is the most destructive disease in lettuce (Lactuca spp.) cultivation and is caused by Bremia lactucae. The successful cross between its host L. sativa and the nonhost, L. saligna, and offers a rare chance to study the genetics of the nonhost resistance. From a set of 29 Backcross Inbred Lines (BILs) representing in total 96% of the L. saligna genome, 15 introgressions were identified to contribute to this resistance at one to four tested lettuce developmental stages and ...

Optimization of line configuration and balancing for flexible machining lines

Science.gov (United States)

Liu, Xuemei; Li, Aiping; Chen, Zurui

2016-05-01

Line configuration and balancing is to select the type of line and allot a given set of operations as well as machines to a sequence of workstations to realize high-efficiency production. Most of the current researches for machining line configuration and balancing problems are related to dedicated transfer lines with dedicated machine workstations. With growing trends towards great product variety and fluctuations in market demand, dedicated transfer lines are being replaced with flexible machining line composed of identical CNC machines. This paper deals with the line configuration and balancing problem for flexible machining lines. The objective is to assign operations to workstations and find the sequence of execution, specify the number of machines in each workstation while minimizing the line cycle time and total number of machines. This problem is subject to precedence, clustering, accessibility and capacity constraints among the features, operations, setups and workstations. The mathematical model and heuristic algorithm based on feature group strategy and polychromatic sets theory are presented to find an optimal solution. The feature group strategy and polychromatic sets theory are used to establish constraint model. A heuristic operations sequencing and assignment algorithm is given. An industrial case study is carried out, and multiple optimal solutions in different line configurations are obtained. The case studying results show that the solutions with shorter cycle time and higher line balancing rate demonstrate the feasibility and effectiveness of the proposed algorithm. This research proposes a heuristic line configuration and balancing algorithm based on feature group strategy and polychromatic sets theory which is able to provide better solutions while achieving an improvement in computing time.

Molecular and genetic characterization of the Ry adg locus on chromosome XI from Andigena potatoes conferring extreme resistance to potato virus Y.

Science.gov (United States)

Herrera, María Del Rosario; Vidalon, Laura Jara; Montenegro, Juan D; Riccio, Cinzia; Guzman, Frank; Bartolini, Ida; Ghislain, Marc

2018-05-31

We have elucidated the Andigena origin of the potato Ry adg gene on chromosome XI of CIP breeding lines and developed two marker assays to facilitate its introgression in potato by marker-assisted selection. Potato virus Y (PVY) is causing yield and quality losses forcing farmers to renew periodically their seeds from clean stocks. Two loci for extreme resistance to PVY, one on chromosome XI and the other on XII, have been identified and used in breeding. The latter corresponds to a well-known source of resistance (Solanum stoloniferum), whereas the one on chromosome XI was reported from S. stoloniferum and S. tuberosum group Andigena as well. To elucidate its taxonomic origin in our breeding lines, we analyzed the nucleotide sequences of tightly linked markers (M45, M6) and screened 251 landraces of S. tuberosum group Andigena for the presence of this gene. Our results indicate that the PVY resistance allele on chromosome XI in our breeding lines originated from S. tuberosum group Andigena. We have developed two marker assays to accelerate the introgression of Ry adg gene into breeding lines by marker-assisted selection (MAS). First, we have multiplexed RYSC3, M6 and M45 DNA markers flanking the Ry adg gene and validated it on potato varieties with known presence/absence of the Ry adg gene and a progeny of 6,521 individuals. Secondly, we developed an allele-dosage assay particularly useful to identify multiplex Ry adg progenitors. The assay based on high-resolution melting analysis at the M6 marker confirmed Ry adg plex level as nulliplex, simplex and duplex progenitors and few triplex progenies. These marker assays have been validated and can be used to facilitate MAS in potato breeding.

LINE FUSION GENES: a database of LINE expression in human genes

Directory of Open Access Journals (Sweden)

Park Hong-Seog

2006-06-01

Full Text Available Abstract Background Long Interspersed Nuclear Elements (LINEs are the most abundant retrotransposons in humans. About 79% of human genes are estimated to contain at least one segment of LINE per transcription unit. Recent studies have shown that LINE elements can affect protein sequences, splicing patterns and expression of human genes. Description We have developed a database, LINE FUSION GENES, for elucidating LINE expression throughout the human gene database. We searched the 28,171 genes listed in the NCBI database for LINE elements and analyzed their structures and expression patterns. The results show that the mRNA sequences of 1,329 genes were affected by LINE expression. The LINE expression types were classified on the basis of LINEs in the 5' UTR, exon or 3' UTR sequences of the mRNAs. Our database provides further information, such as the tissue distribution and chromosomal location of the genes, and the domain structure that is changed by LINE integration. We have linked all the accession numbers to the NCBI data bank to provide mRNA sequences for subsequent users. Conclusion We believe that our work will interest genome scientists and might help them to gain insight into the implications of LINE expression for human evolution and disease. Availability http://www.primate.or.kr/line

Cable line engineering

International Nuclear Information System (INIS)

Jang, Hak Sin; Kim, Sin Yeong

1998-02-01

This book is about cable line engineering. It is comprised of nine chapters, which deals with summary of cable communication such as way, process of cable communication and optical communication, Line constant of transmission on primary constant, reflection and crosstalk, communication cable line of types like flat cable, coaxial cable and loaded cable, Install of communication line with types and facility of aerial line, construction method of communication line facility, Measurement of communication line, Carrier communication of summary, PCM communication with Introduction, regeneration relay system sampling and quantization and Electric communication service and general information network with mobile communication technique and satellite communication system.

Adaptive consequences of human-mediated introgression for indigenous tree species: the case of a relict Pinus pinaster population.

Science.gov (United States)

Ramírez-Valiente, José Alberto; Robledo-Arnuncio, Juan José

2014-12-01

, a potential early selective advantage of exotic and hybrid genotypes would enhance initial steps of introgression of non-native genes into the study relict population of P. pinaster. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Cereal cyst nematode resistance conferred by the Cre7 gene from Aegilops triuncialis and its relationship with Cre genes from Australian wheat cultivars

OpenAIRE

Montes, Maria Jesus; Andrés, María Fe; Sin, E.; Lopez Braña, Isidoro; Martín-Sánchez, J.A.; Romero, M.D.; Delibes Castro, Angeles

2008-01-01

Cereal cyst nematode (CCN; Heterodera avenae Woll.) is a root pathogen of cereal crops that can cause severe yield losses in wheat (Triticum aestivum). Differential host–nematode interactions occur in wheat cultivars carrying different CCN resistance (Cre) genes. The objective of this study was to determine the CCN resistance conferred by the Cre7 gene from Aegilops triuncialis in a 42-chromosome introgression line and to assess the effects of the Cre1, Cre3, Cre4, and Cre8 genes present in A...

A haplotype specific to North European wheat (Triticum aestivum L.)

Czech Academy of Sciences Publication Activity Database

Tsombalova, J.; Karafiátová, Miroslava; Vrána, Jan; Kubaláková, Marie; Peusa, H.; Jakobson, I.; Jarve, M.; Valárik, Miroslav; Doležel, Jaroslav; Jarve, K.

2017-01-01

Roč. 64, č. 4 (2017), s. 653-664 ISSN 0925-9864 R&D Projects: GA MŠk(CZ) LO1204; GA ČR(CZ) GA14-07164S Institutional support: RVO:61389030 Keywords : bread wheat * genetic diversity * polyploid wheat * introgression lines * molecular analysis * tetraploid wheat * hexaploid wheat * powdery mildew * spelta l. * map * Common wheat * Triticum aestivum L * Spelt * Triticum spelta L * Chromosome 4A * Zero alleles * Haplotype * Linkage disequilibrium Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 1.294, year: 2016

Transmission Line Ampacity Improvements of AltaLink Wind Plant Overhead Tie-Lines Using Weather-Based Dynamic Line Rating

Energy Technology Data Exchange (ETDEWEB)

Bhattarai, Bishnu P.; Gentle, Jake P.; Hill, Porter; McJunkin, Tim; Myers, Kurt S.; Abbound, Alex; Renwick, Rodger; Hengst, David

2017-07-01

Abstract—Overhead transmission lines (TLs) are conventionally given seasonal ratings based on conservative environmental assumptions. Such an approach often results in underutilization of the line ampacity as the worst conditions prevail only for a short period over a year/season. We presents dynamic line rating (DLR) as an enabling smart grid technology that adaptively computes ratings of TLs based on local weather conditions to utilize additional headroom of existing lines. In particular, general line ampacity state solver utilizes measured weather data for computing the real-time thermal rating of the TLs. The performance of the presented method is demonstrated from a field study of DLR technology implementation on four TL segments at AltaLink, Canada. The performance is evaluated and quantified by comparing the existing static and proposed dynamic line ratings, and the potential benefits of DLR for enhanced transmission assets utilization. For the given line segments, the proposed DLR results in real-time ratings above the seasonal static ratings for most of the time; up to 95.1% of the time, with a mean increase of 72% over static rating.

Directed line liquids

International Nuclear Information System (INIS)

Kamien, R.D.

1992-01-01

This thesis is devoted to the study of ensembles of dense directed lines. These lines are principally to be thought of as polymers, though they also have the morphology of flux lines in high temperature superconductors, strings of colloidal spheres in electrorheological fluids and the world lines of quantum mechanical bosons. The authors discuss how directed polymer melts, string-like formations in electrorheological and ferro-fluids, flux lines in high temperature superconductors and the world lines of quantum mechanical bosons all share similar descriptions. They study a continuous transition in all of these systems, and then study the critical mixing properties of binary mixtures of directed polymers through the renormalization group. They predict the exponents for a directed polymer blend consolute point and a novel two-phase superfluid liquid-gas critical point

Application of a high-speed breeding technology to apple (Malus × domestica) based on transgenic early flowering plants and marker-assisted selection.

Science.gov (United States)

Flachowsky, Henryk; Le Roux, Pierre-Marie; Peil, Andreas; Patocchi, Andrea; Richter, Klaus; Hanke, Magda-Viola

2011-10-01

Breeding of apple (Malus × domestica) remains a slow process because of protracted generation cycles. Shortening the juvenile phase to achieve the introgression of traits from wild species into prebreeding material within a reasonable time frame is a great challenge. In this study, we evaluated early flowering transgenic apple lines overexpressing the BpMADS4 gene of silver birch with regard to tree morphology in glasshouse conditions. Based on the results obtained, line T1190 was selected for further analysis and application to fast breeding. The DNA sequences flanking the T-DNA were isolated and the T-DNA integration site was mapped on linkage group 4. The inheritance and correctness of the T-DNA integration were confirmed after meiosis. A crossbred breeding programme was initiated by crossing T1190 with the fire blight-resistant wild species Malus fusca. Transgenic early flowering F(1) seedlings were selected and backcrossed with 'Regia' and 98/6-10 in order to introgress the apple scab Rvi2, Rvi4 and powdery mildew Pl-1, Pl-2 resistance genes and the fire blight resistance quantitative trait locus FB-F7 present in 'Regia'. Three transgenic BC'1 seedlings pyramiding Rvi2, Rvi4 and FB-F7, as well as three other BC'1 seedlings combining Pl-1 and Pl-2, were identified. Thus, the first transgenic early flowering-based apple breeding programme combined with marker-assisted selection was established. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

Performance and feeding behaviour of two biotypes of the black currant-lettuce aphid, Nasonovia ribisnigri, on resistant and susceptible Lactuca sativa near-isogenic lines.

Science.gov (United States)

ten Broeke, Cindy J M; Dicke, Marcel; van Loon, Joop J A

2013-10-01

The black currant-lettuce aphid, Nasonovia ribisnigri, is an important pest of cultivated lettuce, Lactuca sativa. Since 1982, the control of this aphid on lettuce is largely based on host plant resistance, conferred by the Nr gene, introgressed from Lactuca virosa. The resistance mechanism remains to be identified. N. ribisnigri populations virulent on the Nr-based resistance in lettuce have emerged in several locations in Europe since 2007. The objective of this study was to investigate the resistance mechanism mediated by the Nr gene in lettuce by detailed studies of aphid feeding behaviour and performance. Both avirulent (Nr:0) and virulent (Nr:1)biotypes of N. ribisnigri were studied on five resistant and two susceptible near isogenic lines (NILs). In addition, survival and colony development were quantified.Nr:0 aphids showed a strong decrease in sieve element ingestion and took longer to accept a sieve element on resistant NILs compared with susceptible NILs, and no aphids survived on the resistant NIL. Nr:1 aphids fed and performed equally well on the resistant and susceptible NILs. The resistance mechanism against Nr:0 aphids encoded by the Nr gene seems to be located in the phloem, although we also observed differences in feeding behaviour during the pathway phase to the phloem. Nr:1 aphids were highly virulent to the resistance conferred by the Nr gene. The consequences of the appearance of Nr:1 aphids for control of N. ribisnigri are discussed.

MICROLENSING OF QUASAR BROAD EMISSION LINES: CONSTRAINTS ON BROAD LINE REGION SIZE

Energy Technology Data Exchange (ETDEWEB)

Guerras, E.; Mediavilla, E. [Instituto de Astrofisica de Canarias, Via Lactea S/N, La Laguna E-38200, Tenerife (Spain); Jimenez-Vicente, J. [Departamento de Fisica Teorica y del Cosmos, Universidad de Granada, Campus de Fuentenueva, E-18071 Granada (Spain); Kochanek, C. S. [Department of Astronomy and the Center for Cosmology and Astroparticle Physics, The Ohio State University, 4055 McPherson Lab, 140 West 18th Avenue, Columbus, OH 43221 (United States); Munoz, J. A. [Departamento de Astronomia y Astrofisica, Universidad de Valencia, E-46100 Burjassot, Valencia (Spain); Falco, E. [Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Motta, V. [Departamento de Fisica y Astronomia, Universidad de Valparaiso, Avda. Gran Bretana 1111, Valparaiso (Chile)

2013-02-20

We measure the differential microlensing of the broad emission lines between 18 quasar image pairs in 16 gravitational lenses. We find that the broad emission lines are in general weakly microlensed. The results show, at a modest level of confidence (1.8{sigma}), that high ionization lines such as C IV are more strongly microlensed than low ionization lines such as H{beta}, indicating that the high ionization line emission regions are more compact. If we statistically model the distribution of microlensing magnifications, we obtain estimates for the broad line region size of r{sub s} = 24{sup +22} {sub -15} and r{sub s} = 55{sup +150} {sub -35} lt-day (90% confidence) for the high and low ionization lines, respectively. When the samples are divided into higher and lower luminosity quasars, we find that the line emission regions of more luminous quasars are larger, with a slope consistent with the expected scaling from photoionization models. Our estimates also agree well with the results from local reveberation mapping studies.

Lining seam elimination algorithm and surface crack detection in concrete tunnel lining

Science.gov (United States)

Qu, Zhong; Bai, Ling; An, Shi-Quan; Ju, Fang-Rong; Liu, Ling

2016-11-01

Due to the particularity of the surface of concrete tunnel lining and the diversity of detection environments such as uneven illumination, smudges, localized rock falls, water leakage, and the inherent seams of the lining structure, existing crack detection algorithms cannot detect real cracks accurately. This paper proposed an algorithm that combines lining seam elimination with the improved percolation detection algorithm based on grid cell analysis for surface crack detection in concrete tunnel lining. First, check the characteristics of pixels within the overlapping grid to remove the background noise and generate the percolation seed map (PSM). Second, cracks are detected based on the PSM by the accelerated percolation algorithm so that the fracture unit areas can be scanned and connected. Finally, the real surface cracks in concrete tunnel lining can be obtained by removing the lining seam and performing percolation denoising. Experimental results show that the proposed algorithm can accurately, quickly, and effectively detect the real surface cracks. Furthermore, it can fill the gap in the existing concrete tunnel lining surface crack detection by removing the lining seam.

High Line

DEFF Research Database (Denmark)

Kiib, Hans

2015-01-01

At just over 10 meters above street level, the High Line extends three kilometers through three districts of Southwestern Manhattan in New York. It consists of simple steel construction, and previously served as an elevated rail line connection between Penn Station on 34th Street and the many....... The High Line project has been carried out as part of an open conversion strategy. The result is a remarkable urban architectural project, which works as a catalyst for the urban development of Western Manhattan. The greater project includes the restoration and reuse of many old industrial buildings...

Both Hd1 and Ehd1 are important for artificial selection of flowering time in cultivated rice.

Science.gov (United States)

Wei, Fu-Jin; Tsai, Yuan-Ching; Wu, Hshin-Ping; Huang, Lin-Tzu; Chen, Yu-Chi; Chen, Yi-Fang; Wu, Cheng-Chieh; Tseng, Yi-Tzu; Hsing, Yue-Ie C

2016-01-01

Rice is a facultative short-day plant, and it requires a photoperiod shorter than the critical day length to get flowering. Sensitivity to photoperiod has been suggested as a major selection target in cultivated or weedy rice. The modern rice varieties in Taiwan may be cultivated twice a year. These varieties contain loss-of-function of two important flowering-time related genes, Heading date 1 (Hd1) and Early heading date 1 (Ehd1), and are mainly from a mega variety, Taichung 65. However, the parental lines of this variety were sensitive to photoperiod, thus, how Taichung 65 loss its sensitivity is a mystery. In this study, we used accession-specific single nucleotide polymorphism analysis to reveal the gene flow that occurred between different rice accessions decades ago and demonstrate that two landraces introgressed during the breeding process, which led to the loss of photoperiod sensitivity. Both Hd1 and Ehd1 may be important during artificial selection for flowering time, especially in a subtropical region such as Taiwan. This is a good example of introgression playing important roles during rice domestication. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Advanced Backcross QTL Analysis for the Whole Plant Growth Duration Salt Tolerance in Rice (Oryza sativa L.)

Institute of Scientific and Technical Information of China (English)

CHAI Lu; LI Zhi-kang; ZHANG Jian; PAN Xiao-biao; ZHANG Fan; ZHENG Tian-qing; ZHAO Xiu-qing; WANG Wen-sheng; Ali Jauhar; XU Jian-long

2014-01-01

Salinity is a major factor limiting rice yield in coastal areas of Asia. To facilitate breeding salt tolerant rice varieties, the whole-plant growth duration salt tolerance (ST) was genetically dissected by phenotyping two sets of BC2F5 introgression lines (ILs) for four yield traits under severe natural salt stress and non-stress ifled conditions using SSR markers and the methods of advanced backcross QTL (AB-QTL) analysis and selective introgression. Many QTLs affecting four yield traits under salt stress and non-stress conditions were identiifed, most (>90%) of which were clustered in 13 genomic regions of the rice genome and involved in complex epistasis. Most QTLs affecting yield traits were differentially expressed under salt stress and non-stress conditions. Our results suggested that genetics complementarily provides an adequate explanation for the hidden genetic diversity for ST observed in both IL populations. Some promising Huanghuazhan (HHZ) ILs with favorable donor alleles at multiple QTLs and signiifcantly improved yield traits under salt stress and non-stress conditions were identiifed, providing excellent materials and relevant genetic information for improving rice ST by marker-assisted selection (MAS) or genome selection.

An ultrafast line-by-line algorithm for calculating spectral transmittance and radiance

International Nuclear Information System (INIS)

Tan, X.

2013-01-01

An ultrafast line-by-line algorithm for calculating spectral transmittance and radiance of gases is presented. The algorithm is based on fast convolution of the Voigt line profile using Fourier transform and a binning technique. The algorithm breaks a radiative transfer calculation into two steps: a one-time pre-computation step in which a set of pressure independent coefficients are computed using the spectral line information; a normal calculation step in which the Fourier transform coefficients of the optical depth are calculated using the line of sight information and the coefficients pre-computed in the first step, the optical depth is then calculated using an inverse Fourier transform and the spectral transmittance and radiance are calculated. The algorithm is significantly faster than line-by-line algorithms that do not employ special speedup techniques by a factor of 10 3 –10 6 . A case study of the 2.7 μm band of H 2 O vapor is presented. -- Highlights: •An ultrafast line-by-line model based on FFT and a binning technique is presented. •Computationally expensive calculations are factored out into a pre-computation step. •It is 10 3 –10 8 times faster than LBL algorithms that do not employ speedup techniques. •Good agreement with experimental data for the 2.7 μm band of H 2 O

Covariant electromagnetic field lines

Science.gov (United States)

Hadad, Y.; Cohen, E.; Kaminer, I.; Elitzur, A. C.

2017-08-01

Faraday introduced electric field lines as a powerful tool for understanding the electric force, and these field lines are still used today in classrooms and textbooks teaching the basics of electromagnetism within the electrostatic limit. However, despite attempts at generalizing this concept beyond the electrostatic limit, such a fully relativistic field line theory still appears to be missing. In this work, we propose such a theory and define covariant electromagnetic field lines that naturally extend electric field lines to relativistic systems and general electromagnetic fields. We derive a closed-form formula for the field lines curvature in the vicinity of a charge, and show that it is related to the world line of the charge. This demonstrates how the kinematics of a charge can be derived from the geometry of the electromagnetic field lines. Such a theory may also provide new tools in modeling and analyzing electromagnetic phenomena, and may entail new insights regarding long-standing problems such as radiation-reaction and self-force. In particular, the electromagnetic field lines curvature has the attractive property of being non-singular everywhere, thus eliminating all self-field singularities without using renormalization techniques.

The End of the Lines for OX 169: No Binary Broad-Line Region

Science.gov (United States)

Halpern, J. P.; Eracleous, M.

2000-03-01

We show that unusual Balmer emission-line profiles of the quasar OX 169, frequently described as either self-absorbed or double peaked, are actually neither. The effect is an illusion resulting from two coincidences. First, the forbidden lines are quite strong and broad. Consequently, the [N II] λ6583 line and the associated narrow-line component of Hα present the appearance of twin Hα peaks. Second, the redshift of 0.2110 brings Hβ into coincidence with Na I D at zero redshift, and ISM absorption in Na I D divides the Hβ emission line. In spectra obtained over the past decade, we see no substantial change in the character of the line profiles and no indication of intrinsic double-peaked structure. The Hγ, Mg II, and Lyα emission lines are single peaked, and all of the emission-line redshifts are consistent once they are correctly attributed to their permitted and forbidden-line identifications. A systematic shift of up to 700 km s-1 between broad and narrow lines is seen, but such differences are common and could be due to gravitational and transverse redshift in a low-inclination disk. Stockton & Farnham had called attention to an apparent tidal tail in the host galaxy of OX 169 and speculated that a recent merger had supplied the nucleus with a coalescing pair of black holes that was now revealing its existence in the form of two physically distinct broad-line regions. Although there is no longer any evidence for two broad emission-line regions in OX 169, binary black holes should form frequently in galaxy mergers, and it is still worthwhile to monitor the radial velocities of emission lines that could supply evidence of their existence in certain objects.

Nasca Lines, Peru

Science.gov (United States)

2001-01-01

The Nasca Lines are located in the Pampa region of Peru, the desolate plain of the Peruvian coast 400 km south of Lima. The Lines were first spotted when commercial airlines began flying across the Peruvian desert in the 1920's. Passengers reported seeing 'primitive landing strips' on the ground below. The Lines were made by removing the iron-oxide coated pebbles which cover the surface of the desert. When the gravel is removed, they contrast with the light color underneath. In this way the lines were drawn as furrows of a lighter color. On the pampa, south of the Nasca Lines, archaeologists have now uncovered the lost city of the line-builders, Cahuachi. It was built nearly two thousand years ago and was mysteriously abandoned 500 years later. This ASTER sub-image covers an area of 14 x 18 km, was acquired on December 22, 2000, and is located at 14.7 degrees south latitude and 75.1 degrees west longitude. The U.S. science team is located at NASA's Jet Propulsion Laboratory, Pasadena, Calif. The Terra mission is part of NASA's Science Mission Directorate.

Increased Mycoplasma hyopneumoniae Disease Prevalence in Domestic Hybrids Among Free-Living Wild Boar.

Science.gov (United States)

Goedbloed, Daniel J; van Hooft, Pim; Lutz, Walburga; Megens, Hendrik-Jan; van Wieren, Sip E; Ydenberg, Ron C; Prins, Herbert H T

2015-12-01

Wildlife immune genes are subject to natural selection exerted by pathogens. In contrast, domestic immune genes are largely protected from pathogen selection by veterinary care. Introgression of domestic alleles into the wild could lead to increased disease susceptibility, but observations are scarce due to low introgression rates, low disease prevalence and reduced survival of domestic hybrids. Here we report the first observation of a deleterious effect of domestic introgression on disease prevalence in a free-living large mammal. A fraction of 462 randomly sampled free-living European wild boar (Sus scrofa) was genetically identified as recent wild boar-domestic pig hybrids based on 351 SNP data. Analysis of antibody prevalence against the bacterial pathogen Mycoplasma hyopneumoniae (Mhyo) showed an increased Mhyo prevalence in wild-domestic hybrids. We argue that the most likely mechanism explaining the observed association between domestic hybrid status and Mhyo antibody prevalence would be introgression of deleterious domestic alleles. We hypothesise that large-scale use of antibiotics in the swine breeding sector may have played a role in shaping the relatively deleterious properties of domestic swine immune genes and that domestic introgression may also lead to increased wildlife disease susceptibility in the case of other species.

An OCD perspective of line edge and line width roughness metrology

Science.gov (United States)

Bonam, Ravi; Muthinti, Raja; Breton, Mary; Liu, Chi-Chun; Sieg, Stuart; Seshadri, Indira; Saulnier, Nicole; Shearer, Jeffrey; Patlolla, Raghuveer; Huang, Huai

2017-03-01

Metrology of nanoscale patterns poses multiple challenges that range from measurement noise, metrology errors, probe size etc. Optical Metrology has gained a lot of significance in the semiconductor industry due to its fast turn around and reliable accuracy, particularly to monitor in-line process variations. Apart from monitoring critical dimension, thickness of films, there are multiple parameters that can be extracted from Optical Metrology models3. Sidewall angles, material compositions etc., can also be modeled to acceptable accuracy. Line edge and Line Width roughness are much sought of metrology following critical dimension and its uniformity, although there has not been much development in them with optical metrology. Scanning Electron Microscopy is still used as a standard metrology technique for assessment of Line Edge and Line Width roughness. In this work we present an assessment of Optical Metrology and its ability to model roughness from a set of structures with intentional jogs to simulate both Line edge and Line width roughness at multiple amplitudes and frequencies. We also present multiple models to represent roughness and extract relevant parameters from Optical metrology. Another critical aspect of optical metrology setup is correlation of measurement to a complementary technique to calibrate models. In this work, we also present comparison of roughness parameters extracted and measured with variation of image processing conditions on a commercially available CD-SEM tool.

Modification of the U-line of the RHIC injection line

International Nuclear Information System (INIS)

Xu, Jianming.

1991-09-01

The parameters of the U-line of the RHIC injection line with low β waist are described. In that lattice, the location of SA is not dispersion free and 14 quadrupoles are needed. This line has been modified to move SA to a dispersion free region (after the 8-degree bend), the length and maximum gradient of quadrupoles have been adjusted to fit the existing quadrupole parameters and the number of quadrupoles is reduced to 12. 2 refs., 3 tabs

Difference in membrane repair capacity between cancer cell lines and a normal cell line

DEFF Research Database (Denmark)

Frandsen, Stine Krog; McNeil, Anna K.; Novak, Ivana

2016-01-01

repair was investigated by disrupting the plasma membrane using laser followed by monitoring fluorescent dye entry over time in seven cancer cell lines, an immortalized cell line, and a normal primary cell line. The kinetics of repair in living cells can be directly recorded using this technique...... cancer cell lines (p immortalized cell line (p

Molecular and cytogenetic characterization of wheat introgression lines carrying the stem rust resistance gene Sr39.

Science.gov (United States)

Stem rust, caused by Puccinia graminis Pers.:Pers. f.sp. tritici Eriks. and Henn., poses a serious threat to global wheat production because of the emergence of Pgt-TTKSK (Ug99). The TTKSK resistant gene Sr39 was derived from Aegilops speltoides through chromosome translocation. In this study, we ch...

Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of featherless chickens

Directory of Open Access Journals (Sweden)

Wells Kirsty L

2012-06-01

map genes based on genotyping of DNA samples from pooled whole blood. The identification of the sc mutation has important implications for the future breeding of this potentially useful trait for the poultry industry, and our genotyping assay can facilitate its rapid introgression into production lines.

Purity, adulteration and price of drugs bought on-line versus off-line in the Netherlands.

Science.gov (United States)

van der Gouwe, Daan; Brunt, Tibor M; van Laar, Margriet; van der Pol, Peggy

2017-04-01

On-line drug markets flourish and consumers have high expectations of on-line quality and drug value. The aim of this study was to (i) describe on-line drug purchases and (ii) compare on-line with off-line purchased drugs regarding purity, adulteration and price. Comparison of laboratory analyses of 32 663 drug consumer samples (stimulants and hallucinogens) purchased between January 2013 and January 2016, 928 of which were bought on-line. The Netherlands. Primary outcome measures were (i) the percentage of samples purchased on-line and (ii) the chemical purity of powders (or dosage per tablet); adulteration; and the price per gram, blotter or tablet of drugs bought on-line compared with drugs bought off-line. The proportion of drug samples purchased on-line increased from 1.4% in 2013 to 4.1% in 2015. The frequency varied widely, from a maximum of 6% for controlled, traditional substances [ecstasy tablets, 3,4-methylenedioxy-methamphetamine (MDMA) powder, amphetamine powder, cocaine powder, 4-bromo-2,5-dimethoxyphenethylamine (2C-B) and lysergic acid diethylamide (LSD)] to more than a third for new psychoactive substances (NPS) [4-fluoroamphetamine (4-FA), 5/6-(2-aminopropyl)benzofuran (5/6-APB) and methoxetamine (MXE)]. There were no large differences in drug purity, yet small but statistically significant differences were found for 4-FA (on-line 59% versus off-line 52% purity for 4-FA on average, P = 0.001), MDMA powders (45 versus 61% purity for MDMA, P = 0.02), 2C-B tablets (21 versus 10 mg 2C-B/tablet dosage, P = 0.49) and ecstasy tablets (131 versus 121 mg MDMA/tablet dosage, P = 0.05). The proportion of adulterated samples purchased on-line and off-line did not differ, except for 4-FA powder, being less adulterated on-line (χ 2  = 8.3; P < 0.02). Drug prices were mainly higher on-line, ranging for various drugs from 10 to 23% higher than that of drugs purchased off-line (six of 10 substances: P < 0.05). Dutch drug users increasingly

Low-molecular-weight glutenin subunits from the 1U genome of Aegilops umbellulata confer superior dough rheological properties and improve breadmaking quality of bread wheat.

Science.gov (United States)

Wang, Jian; Wang, Chang; Zhen, Shoumin; Li, Xiaohui; Yan, Yueming

2018-04-01

Wheat-related genomes may carry new glutenin genes with the potential for quality improvement of breadmaking. In this study, we estimated the gluten quality properties of the wheat line CNU609 derived from crossing between Chinese Spring (CS, Triticum aestivum L., 2n = 6x = 42, AABBDD) and the wheat Aegilops umbellulata (2n = 2x = 14, UU) 1U(1B) substitution line, and investigated the function of 1U-encoded low-molecular-weight glutenin subunits (LMW-GS). The main quality parameters of CNU609 were significantly improved due to introgression of the 1U genome, including dough development time, stability time, farinograph quality number, gluten index, loaf size and inner structure. Glutenin analysis showed that CNU609 and CS had the same high-molecular-weight glutenin subunit (HMW-GS) composition, but CNU609 carried eight specific 1U genome-encoded LMW-GS. The introgression of the 1U-encoded LMW-GS led to more and larger protein body formation in the CNU609 endosperm. Two new LMW-m type genes from the 1U genome, designated Glu-U3a and Glu-U3b, were cloned and characterized. Secondary structure prediction implied that both Glu-U3a and Glu-U3b encode subunits with high α-helix and β-strand content that could benefit the formation of superior gluten structure. Our results indicate that the 1U genome has superior LMW-GS that can be used as new gene resources for wheat gluten quality improvement. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Crossing the LINE toward genomic instability: LINE-1 retrotransposition in cancer

Science.gov (United States)

Kemp, Jacqueline; Longworth, Michelle

2015-12-01

Retrotransposons are repetitive DNA sequences that are positioned throughout the human genome. Retrotransposons are capable of copying themselves and mobilizing new copies to novel genomic locations in a process called retrotransposition. While most retrotransposon sequences in the human genome are incomplete and incapable of mobilization, the LINE-1 retrotransposon, which comprises approximately 17% of the human genome, remains active. The disruption of cellular mechanisms that suppress retrotransposon activity is linked to the generation of aneuploidy, a potential driver of tumor development. When retrotransposons insert into a novel genomic region, they have the potential to disrupt the coding sequence of endogenous genes and alter gene expression, which can lead to deleterious consequences for the organism. Additionally, increased LINE-1 copy numbers provide more chances for recombination events to occur between retrotransposons, which can lead to chromosomal breaks and rearrangements. LINE-1 activity is increased in various cancer cell lines and in patient tissues resected from primary tumors. LINE-1 activity also correlates with increased cancer metastasis. This review aims to give a brief overview of the connections between LINE-1 retrotransposition and the loss of genome stability. We will also discuss the mechanisms that repress retrotransposition in human cells and their links to cancer.

Locus-dependent selection in crop-wild hybrids of lettuce under field conditions and its implication for GM crop development

NARCIS (Netherlands)

Hooftman, D.A.P.; Flavell, A.J.; Jansen, H.; den Nijs, H.C.M.; Syed, N.H.; Sørensen, A.P.; Orozco-ter Wengel, P.; van de Wiel, C.C.M.

2011-01-01

Gene escape from crops has gained much attention in the last two decades, as transgenes introgressing into wild populations could affect the latter’s ecological characteristics. However, different genes have different likelihoods of introgression. The mixture of selective forces provided by natural

Theoretical Atomic Physics code development IV: LINES, A code for computing atomic line spectra

International Nuclear Information System (INIS)

Abdallah, J. Jr.; Clark, R.E.H.

1988-12-01

A new computer program, LINES, has been developed for simulating atomic line emission and absorption spectra using the accurate fine structure energy levels and transition strengths calculated by the (CATS) Cowan Atomic Structure code. Population distributions for the ion stages are obtained in LINES by using the Local Thermodynamic Equilibrium (LTE) model. LINES is also useful for displaying the pertinent atomic data generated by CATS. This report describes the use of LINES. Both CATS and LINES are part of the Theoretical Atomic PhysicS (TAPS) code development effort at Los Alamos. 11 refs., 9 figs., 1 tab

Major Co-localized QTL for Plant Height, Branch Initiation Height, Stem Diameter, and Flowering Time in an Alien Introgression Derived Brassica napus DH Population

Directory of Open Access Journals (Sweden)

Yusen Shen

2018-03-01

Full Text Available Plant height (PH, branch initiation height (BIH, and stem diameter (SD are three stem-related traits that play crucial roles in plant architecture and lodging resistance. Herein, we show one doubled haploid (DH population obtained from a cross between Y689 (one Capsella bursa-pastoris derived Brassica napus intertribal introgression and Westar (B. napus cultivar that these traits were significantly positively correlated with one another and with flowering time (FT. Based on a high-density SNP map, a total of 102 additive quantitative trait loci (QTL were identified across six environments. Seventy-two consensus QTL and 49 unique QTL were identified using a two-round strategy of QTL meta-analysis. Notably, a total of 19 major QTL, including 11 novel ones, were detected for these traits, which comprised two QTL clusters on chromosomes A02 and A07. Conditional QTL mapping was performed to preliminarily evaluate the genetic basis (pleiotropy or tight linkage of the co-localized QTL. In addition, QTL by environment interactions (QEI mapping was performed to verify the additive QTL and estimate the QEI effect. In the genomic regions of all major QTL, orthologs of the genes involved in phytohormone biosynthesis, phytohormone signaling, flower development, and cell differentiation in Arabidopsis were proposed as candidate genes. Of these, BnaA02g02560, an ortholog of Arabidopsis GASA4, was suggested as a candidate gene for PH, SD, and FT; and BnaA02g08490, an ortholog of Arabidopsis GNL, was associated with PH, BIH and FT. These results provide useful information for further genetic studies on stem-related traits and plant growth adaptation.

Second-line failure and first experience with third-line antiretroviral therapy in Mumbai, India

Directory of Open Access Journals (Sweden)

Samsuddin Khan

2014-07-01

Full Text Available Background: There are limited data on the failure of second-line antiretroviral therapy (ART and the use of third-line ART in people living with HIV in resource-limited settings. Since 2011, the Médecins Sans Frontières (MSF HIV/tuberculosis programme in Mumbai, India, has been providing third-line ART to patients in care. Objective: To describe the experiences and programmatic challenges during management of suspected second-line ART failure and third-line ART therapy for patients living with HIV, including the use of HIV viral load (VL testing. Design: This was a retrospective, observational cohort study of patients with suspected second-line ART treatment failure, who were followed for at least 12 months between January 2011 and March 2014. Results: A total of 47 patients with suspected second-line failure met the inclusion criteria during the study period. Twenty-nine of them (62% responded to enhanced adherence support, had a subsequent undetectable VL after a median duration of 3 months and remained on second-line ART. The other 18 patients had to be initiated on a third-line ART regimen, which consisted of darunavir–ritonavir, raltegravir, and one or more appropriate nucleoside or nucleotide reverse transcriptase inhibitors, based on the results of HIV genotype testing. Of the 13 patients for whom follow-up VL results were available, 11 achieved virological suppression after a median duration of 3 months on third-line ART (interquartile range: 2.5–3.0. No serious treatment-related adverse events were recorded. Conclusions: With intensive counselling and adherence support in those suspected of failing second-line ART, unnecessary switching to more expensive third-line ART can be averted in the majority of cases. However, there is an increasing need for access to third-line ART medications such as darunavir and raltegravir, for which national ART programmes should be prepared. The cost of such medications and inadequate access to VL

Survey of transmission line corridors. [Data on delays in transmission line construction

Energy Technology Data Exchange (ETDEWEB)

1979-01-05

The intent of this study is to determine the extent of delays experienced in planning and constructing transmission lines in the continental United States. The reasons for the delays are identified for each line studied and their effect on the total electrical system is sought. Data was collected for 136 different lines either recently built or currently under study. Statistics were developed for each line in several categories and comparisons of lines delayed were made by company, area served and generation capacity. From the study presented here it was found that: right-of-way acquisition procedures including condemnation and easement negotiation practices delay more projects than local, state and federal regulatory requirements combined; load growth reductions particularly in the east have reduced the impact of regulatory delays; the south, southeast and southwestern areas of the country experience fewer delays in constructing transmission lines than the more populated states, and the cost for corridor delays was responded to for only 17 of the 142 projects surveyed. By far the most costly delay is the expense of condemning land for transmission right-of-way.

LINES

Directory of Open Access Journals (Sweden)

Minas Bakalchev

2015-10-01

Full Text Available The perception of elements in a system often creates their interdependence, interconditionality, and suppression. The lines from a basic geometrical element have become the model of a reductive world based on isolation according to certain criteria such as function, structure, and social organization. Their traces are experienced in the contemporary world as fragments or ruins of a system of domination of an assumed hierarchical unity. How can one release oneself from such dependence or determinism? How can the lines become less “systematic” and forms more autonomous, and less reductive? How is a form released from modernistic determinism on the new controversial ground? How can these elements or forms of representation become forms of action in the present complex world? In this paper, the meaning of lines through the ideas of Le Corbusier, Leonidov, Picasso, and Hitchcock is presented. Spatial research was made through a series of examples arising from the projects of the architectural studio “Residential Transformations”, which was a backbone for mapping the possibilities ranging from playfulness to exactness, as tactics of transformation in the different contexts of the contemporary world.

Discovery of Point Mutations in the Voltage-Gated Sodium Channel from African Aedes aegypti Populations: Potential Phylogenetic Reasons for Gene Introgression

Science.gov (United States)

Muranami, Yuto; Kawashima, Emiko; Osei, Joseph H. N.; Sakyi, Kojo Yirenkyi; Dadzie, Samuel; de Souza, Dziedzom K.; Appawu, Maxwell; Ohta, Nobuo; Minakawa, Noboru

2016-01-01

Background Yellow fever is endemic in some countries in Africa, and Aedes aegpyti is one of the most important vectors implicated in the outbreak. The mapping of the nation-wide distribution and the detection of insecticide resistance of vector mosquitoes will provide the beneficial information for forecasting of dengue and yellow fever outbreaks and effective control measures. Methodology/Principal Findings High resistance to DDT was observed in all mosquito colonies collected in Ghana. The resistance and the possible existence of resistance or tolerance to permethrin were suspected in some colonies. High frequencies of point mutations at the voltage-gated sodium channel (F1534C) and one heterozygote of the other mutation (V1016I) were detected, and this is the first detection on the African continent. The frequency of F1534C allele and the ratio of F1534C homozygotes in Ae. aegypti aegypti (Aaa) were significantly higher than those in Ae. aegypti formosus (Aaf). We could detect the two types of introns between exon 20 and 21, and the F1534C mutations were strongly linked with one type of intron, which was commonly found in South East Asian and South and Central American countries, suggesting the possibility that this mutation was introduced from other continents or convergently selected after the introgression of Aaa genes from the above area. Conclusions/Significance The worldwide eradication programs in 1940s and 1950s might have caused high selection pressure on the mosquito populations and expanded the distribution of insecticide-resistant Ae. aegypti populations. Selection of the F1534C point mutation could be hypothesized to have taken place during this period. The selection of the resistant population of Ae. aegypti with the point mutation of F1534C, and the worldwide transportation of vector mosquitoes in accordance with human activity such as trading of used tires, might result in the widespread distribution of F1534C point mutation in tropical countries

Transmission Lines or Poles, Electric - VOLUSIA COUNTY MAJOR POWER LINES (Arcs)

Data.gov (United States)

NSGIC Local Govt | GIS Inventory — Volusia County Power Line data was aggregated by using parcel data and visual inspection of 2005 aerial photography to determine centerline of Power Lines Right of...

Flow lines and export lines of Sabalo Gas Field - the engineering of a complex job; Flow lines e export lines de Sabalo - a engenharia da complexidade

Energy Technology Data Exchange (ETDEWEB)

Serodio, Conrado Jose Morbach [GDK Engenharia, Salvador, BA (Brazil)

2003-07-01

The construction of the natural gas flow lines and export lines system of the Sabalo field, in the far South of Bolivia is an unique job in the pipeline construction area. Its execution is a turning point in terms of engineering and construction technology in this industry. Among the Aguarague Cordillera (mountains), it runs across rocky canyons for more than 5 km, a 2.100 mt long narrow tunnel to overcome the mountains and steep hills along all the ROW length, with a total extension of 70 km, in line pipes ranging from 10'' and 12'' for the flow lines, 28'' for the gas export line and 8' for the condensate line. An integrated construction work plan was settled in order to face and overcome the complex construction situations found in every feet of the pipeline. Four simultaneous work sites were mobilized, 8 independent work fronts, 700 professionals and more than 150 pieces of heavy construction equipment, brought from 3 different countries. Special techniques were adopted also to handle the challenging detail engineering . All in all, the correct conjunction of a sound engineering work, planning, human resources and equipment and the managing flexibility to create alternatives and solutions at the fast pace required by a dynamic work schedule were essential to succeed, in a job with no room for mistakes. The successfully job completion open new possibilities to other challenging projects alike.(author)

Alternate Double Single Track Lines

Energy Technology Data Exchange (ETDEWEB)

Moraga Contreras, P.; Grande Andrade, Z.; Castillo Ron, E.

2016-07-01

The paper discusses the advantages and shortcomings of alternate double single track (ADST) lines with respect to double track lines for high speed lines. ADST lines consists of sequences of double and single track segments optimally selected in order to reduce the construction and maintenance costs of railway lines and to optimize the timetables used to satisfy a given demand. The single tracks are selected to coincide with expensive segments (tunnels and viaducts) and the double tracks are chosen to coincide with flat areas and only where they are necessary. At the same time, departure times are adjusted for trains to cross at the cheap double track segments. This alternative can be used for new lines and also for existing conventional lines where some new tracks are to be constructed to reduce travel time (increase speed). The ADST proposal is illustrated with some examples of both types (new lines and where conventional lines exist), including the Palencia-Santander, the Santiago-Valparaíso-Viña del Mar and the Dublin-Belfast lines, where very important reductions (90 %) are obtained, especially where a railway infrastructure already exist. (Author)

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs.

Science.gov (United States)

Bosse, Mirte; Lopes, Marcos S; Madsen, Ole; Megens, Hendrik-Jan; Crooijmans, Richard P M A; Frantz, Laurent A F; Harlizius, Barbara; Bastiaansen, John W M; Groenen, Martien A M

2015-12-22

Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs. © 2015 The Author(s).

Determinants of durability of first-line antiretroviral therapy regimen and time from first-line failure to second-line antiretroviral therapy initiation

DEFF Research Database (Denmark)

Desmonde, Sophie; Eboua, François T; Malateste, Karen

2015-01-01

BACKGROUND: We described reasons for switching to second-line antiretroviral treatment (ART) and time to switch in HIV-infected children failing first-line ART in West Africa. METHODS: We included all children aged 15 years or less, starting ART (at least three drugs) in the paediatric Ie...... post-ART initiation, 188 (7%) had switched to second-line. The most frequent reasons were drug stock outs (20%), toxicity (18%), treatment failure (16%) and poor adherence (8%). Over the 24-month follow-up period, 322 (12%) children failed first-line ART after a median time of 7 months...... rare and switches after an immunological failure were insufficient. These gaps reveal that it is crucial to advocate for both sustainable access to first-line and alternative regimens to provide adequate roll-out of paediatric ART programmes....

Recent progress on the genetics and molecular breeding of brown planthopper resistance in rice.

Science.gov (United States)

Hu, Jie; Xiao, Cong; He, Yuqing

2016-12-01

Brown planthopper (BPH) is the most devastating pest of rice. Host-plant resistance is the most desirable and economic strategy in the management of BPH. To date, 29 major BPH resistance genes have been identified from indica cultivars and wild rice species, and more than ten genes have been fine mapped to chromosome regions of less than 200 kb. Four genes (Bph14, Bph26, Bph17 and bph29) have been cloned. The increasing number of fine-mapped and cloned genes provide a solid foundation for development of functional markers for use in breeding. Several BPH resistant introgression lines (ILs), near-isogenic lines (NILs) and pyramided lines (PLs) carrying single or multiple resistance genes were developed by marker assisted backcross breeding (MABC). Here we review recent progress on the genetics and molecular breeding of BPH resistance in rice. Prospect for developing cultivars with durable, broad-spectrum BPH resistance are discussed.

Homotopic Polygonal Line Simplification

DEFF Research Database (Denmark)

Deleuran, Lasse Kosetski

This thesis presents three contributions to the area of polygonal line simplification, or simply line simplification. A polygonal path, or simply a path is a list of points with line segments between the points. A path can be simplified by morphing it in order to minimize some objective function...

On-line adaptive line frequency noise cancellation from a nuclear power measuring channel

Directory of Open Access Journals (Sweden)

Qadir Javed

2011-01-01

Full Text Available On-line software for adaptively canceling 50 Hz line frequency noise has been designed and tested at Pakistan Research Reactor 1. Line frequency noise causes much problem in weak signals acquisition. Sometimes this noise is so dominant that original signal is totally corrupted. Although notch filter can be used for eliminating this noise, but if signal of interest is in close vicinity of 50 Hz, then original signal is also attenuated and hence overall performance is degraded. Adaptive noise removal is a technique which could be employed for removing line frequency without degrading the desired signal. In this paper line frequency noise has been eliminated on-line from a nuclear power measuring channel. The adaptive LMS algorithm has been used to cancel 50 Hz noise. The algorithm has been implemented in labVIEW with NI 6024 data acquisition card. The quality of the acquired signal has been improved much as can be seen in experimental results.

Radiosensitivity of mesothelioma cell lines

International Nuclear Information System (INIS)

Haekkinen, A.M.; Laasonen, A.; Linnainmaa, K.; Mattson, K.; Pyrhoenen, S.

1996-01-01

The present study was carried out in order to examine the radiosensitivity of malignant pleural mesothelioma cell lines. Cell kinetics, radiation-induced delay of the cell cycle and DNA ploidy of the cell lines were also determined. For comparison an HeLa and a human foetal fibroblast cell line were simultaneously explored. Six previously cytogenetically and histologically characterized mesothelioma tumor cell lines were applied. A rapid tiazolyl blue microtiter (MTT) assay was used to analyze radiosensitivity and cell kinetics and DNA ploidy of the cultured cells were determined by flow cytometry. The survival fraction after a dose of 2 Gy (SF2), parameters α and β of the linear quadratic model (LQ-model) and mean inactivation dose (D MID ) were also estimated. The DNA index of four cell lines equaled 1.0 and two cell lines equaled 1.5 and 1.6. Different mesothelioma cell lines showed a great variation in radiosensitivity. Mean survival fraction after a radiation dose of 2 Gy (SF2) was 0.60 and ranged from 0.36 to 0.81 and mean α value was 0.26 (range 0.48-0.083). The SF2 of the most sensitive diploid mesothelioma cell line was 0.36: Less than that of the foetal fibroblast cell line (0.49). The survival fractions (0.81 and 0.74) of the two most resistant cell lines, which also were aneuploid, were equal to that of the HeLa cell line (0.78). The α/β ratios of the most sensitive cell lines were almost an order of magnitude greater than those of the two most resistant cell lines. Radiation-induced delay of the most resistant aneuploid cell line was similar to that of HeLa cells but in the most sensitive (diploid cells) there was practically no entry into the G1 phase following the 2 Gy radiation dose during 36 h. (orig.)

Radiosensitivity of mesothelioma cell lines

Energy Technology Data Exchange (ETDEWEB)

Haekkinen, A.M. [Dept. of Oncology, Univ. Central Hospital, Helsinki (Finland); Laasonen, A. [Dept. of Pathology, Central Hospital of Etelae-Pohjanmaa, Seinaejoki (Finland); Linnainmaa, K. [Dept. of Industrial Hygiene and Toxicology, Inst. of Occupational Health, Helsinki (Finland); Mattson, K. [Dept. Pulmonary Medicine, Univ. Central Hospital, Helsinki (Finland); Pyrhoenen, S. [Dept. of Oncology, Univ. Central Hospital, Helsinki (Finland)

1996-10-01

The present study was carried out in order to examine the radiosensitivity of malignant pleural mesothelioma cell lines. Cell kinetics, radiation-induced delay of the cell cycle and DNA ploidy of the cell lines were also determined. For comparison an HeLa and a human foetal fibroblast cell line were simultaneously explored. Six previously cytogenetically and histologically characterized mesothelioma tumor cell lines were applied. A rapid tiazolyl blue microtiter (MTT) assay was used to analyze radiosensitivity and cell kinetics and DNA ploidy of the cultured cells were determined by flow cytometry. The survival fraction after a dose of 2 Gy (SF2), parameters {alpha} and {beta} of the linear quadratic model (LQ-model) and mean inactivation dose (D{sub MID}) were also estimated. The DNA index of four cell lines equaled 1.0 and two cell lines equaled 1.5 and 1.6. Different mesothelioma cell lines showed a great variation in radiosensitivity. Mean survival fraction after a radiation dose of 2 Gy (SF2) was 0.60 and ranged from 0.36 to 0.81 and mean {alpha} value was 0.26 (range 0.48-0.083). The SF2 of the most sensitive diploid mesothelioma cell line was 0.36: Less than that of the foetal fibroblast cell line (0.49). The survival fractions (0.81 and 0.74) of the two most resistant cell lines, which also were aneuploid, were equal to that of the HeLa cell line (0.78). The {alpha}/{beta} ratios of the most sensitive cell lines were almost an order of magnitude greater than those of the two most resistant cell lines. Radiation-induced delay of the most resistant aneuploid cell line was similar to that of HeLa cells but in the most sensitive (diploid cells) there was practically no entry into the G1 phase following the 2 Gy radiation dose during 36 h. (orig.).

World lines.

OpenAIRE

Waser Jürgen; Fuchs Raphael; Ribicic Hrvoje; Schindler Benjamin; Blöschl Günther; Gröller Eduard

2010-01-01

In this paper we present World Lines as a novel interactive visualization that provides complete control over multiple heterogeneous simulation runs. In many application areas decisions can only be made by exploring alternative scenarios. The goal of the suggested approach is to support users in this decision making process. In this setting the data domain is extended to a set of alternative worlds where only one outcome will actually happen. World Lines integrate simulation visualization and...

Research for the Influence of Distribution Network Line Reclosing Current on Line Protection

Directory of Open Access Journals (Sweden)

Yu Kansheng

2016-01-01

Full Text Available According to the distribution network line structure and reclosing control strategy, the system simulation model of distribution network lines has established based on the real-time digital simulation RTDS. Based on this, distribution network switching impulse current characteristic has researched with different capacity, different distribution and different load power factor under the different voltage switching angles. The results of the study provide a scientific basis for distribution network line protection setting, in order to further lay the foundation for improvement the validity and reliability of distribution network line protection action.

The last line effect explained

NARCIS (Netherlands)

Beller, M. (Moritz); Zaidman, A. (Andy); Karpov, A. (Andrey); R.A. Zwaan (Rolf)

2017-01-01

textabstractMicro-clones are tiny duplicated pieces of code; they typically comprise only few statements or lines. In this paper, we study the “Last Line Effect,” the phenomenon that the last line or statement in a micro-clone is much more likely to contain an error than the previous lines or

Dynamic Line Rating - Technologies and Challenges of PMU on Overhead Lines

DEFF Research Database (Denmark)

Alvarez, David; Rosero, Javier; Silva, Filipe Miguel Faria da

2016-01-01

for line rating computation and monitoring are identified, these are: sensors, communications, management information system and information analysis tools, which are part of integral dynamic line rating systems. Finally, the benefits and challenges of using phasor measurement units for real time capacity...

The last line effect explained

NARCIS (Netherlands)

Beller, M.M.; Zaidman, A.E.; Karpov, Andrey; Zwaan, Rolf A.

Micro-clones are tiny duplicated pieces of code; they typically comprise only few statements or lines. In this paper, we study the “Last Line Effect,” the phenomenon that the last line or statement in a micro-clone is much more likely to contain an error than the previous lines or statements. We do

Assessing the impact of stocking northern-origin hatchery brook trout on the genetics of wild populations in North Carolina

Science.gov (United States)

Kazyak, David C.; Rash, Jacob; Lubinski, Barbara A.; King, Tim L.

2018-01-01

The release of hatchery-origin fish into streams with endemics can degrade the genetics of wild populations if interbreeding occurs. Starting in the 1800s, brook trout descendent from wild populations in the northeastern United States were stocked from hatcheries into streams across broad areas of North America to create and enhance fishery resources. Across the southeastern United States, many millions of hatchery-origin brook trout have been released into hundreds of streams, but the extent of introgression with native populations is not well resolved despite large phylogeographic distances between these groups. We used three assessment approaches based on 12 microsatellite loci to examine the extent of hatchery introgression in 406 wild brook trout populations in North Carolina. We found high levels of differentiation among most collections (mean F′ST = 0.718), and among most wild collections and hatchery strains (mean F′ST = 0.732). Our assessment of hatchery introgression was consistent across the three metrics, and indicated that most wild populations have not been strongly influenced by supplemental stocking. However, a small proportion of wild populations in North Carolina appear to have been strongly influenced by stocked conspecifics, or in some cases, may have been founded entirely by hatchery lineages. In addition, we found significant differences in the apparent extent of hatchery introgression among major watersheds, with the Savannah River being the most strongly impacted. Conversely, populations in the Pee Dee River watershed showed little to no evidence of hatchery introgression. Our study represents the first large-scale effort to quantify the extent of hatchery introgression across brook trout populations in the southern Appalachians using highly polymorphic microsatellite markers.

Genetics of hybrid male sterility between drosophila sibling species: a complex web of epistasis is revealed in interspecific studies.

Science.gov (United States)

Palopoli, M F; Wu, C I

1994-10-01

To study the genetic differences responsible for the sterility of their male hybrids, we introgressed small segments of an X chromosome from Drosophila simulans into a pure Drosophila mauritiana genetic background, then assessed the fertility of males carrying heterospecific introgressions of varying size. Although this analysis examined less than 20% of the X chromosome (roughly 5% of the euchromatic portion of the D. simulans genome), and the segments were introgressed in only one direction, a minimum of four factors that contribute to hybrid male sterility were revealed. At least two of the factors exhibited strong epistasis: males carrying either factor alone were consistently fertile, whereas males carrying both factors together were always sterile. Distinct spermatogenic phenotypes were observed for sterile introgressions of different lengths, and it appeared that an interaction between introgressed segments also influenced the stage of spermatogenic defect. Males with one category of introgression often produced large quantities of motile sperm and were observed copulating, but never inseminated females. Evidently these two species have diverged at a large number of loci which have varied effects on hybrid male fertility. By extrapolation, we estimate that there are at least 40 such loci on the X chromosome alone. Because these species exhibit little DNA-sequence divergence at arbitrarily chosen loci, it seems unlikely that the extensive functional divergence observed could be due mainly to random genetic drift. Significant epistasis between conspecific genes appears to be a common component of hybrid sterility between recently diverged species of Drosophila. The linkage relationships of interacting factors could shed light on the role played by epistatic selection in the dynamics of the allele substitutions responsible for reproductive barriers between species.

Primeiro relato de ocorrência de Anastrepha serpentina e Anastrepha leptozona (Dip.: Tephritidae em abiu (Pouteria caimito no Estado de São Paulo

Directory of Open Access Journals (Sweden)

Raga Adalton

2003-01-01

Full Text Available Foi registrada pela primeira vez a infestação das moscas-das-frutas Anastrepha serpentina (Wied. e Anastrepha leptozona Hendel (Dip.: Tephritidae em abiu Pouteria caimito (Sapotaceae no Estado de São Paulo. Os frutos coletados foram oriundos da Coleção de Fruteiras Nativas e Exóticas, localizada na sede do Pólo Regional de Desenvolvimento Tecnológico do Vale do Ribeira (SP, município de Pariquera-Açu. Também emergiram espécimens de Neosilba glaberrima (Wied. (Lonchaeidae.

Numerical simulations of sheared magnetic lines at the solar null line

Science.gov (United States)

Kuźma, B.; Murawski, K.; Solov'ev, A.

2015-05-01

Aims: We perform numerical simulations of sheared magnetic lines at the magnetic null line configuration of two magnetic arcades that are settled in a gravitationally stratified and magnetically confined solar corona. Methods: We developed a general analytical model of a 2.5D solar atmospheric structure. As a particular application of this model, we adopted it for the curved magnetic field lines with an inverted Y shape that compose the null line above two magnetic arcades, which are embedded in the solar atmosphere that is specified by the realistic temperature distribution. The physical system is described by 2.5D magnetohydrodynamic equations that are numerically solved by the FLASH code. Results: The magnetic field line shearing, implemented about 200 km below the transition region, results in Alfvén and magnetoacoustic waves that are able to penetrate solar coronal regions above the magnetic null line. As a result of the coupling of these waves, partial reflection from the transition region and scattering from inhomogeneous regions the Alfvén waves experience fast attenuation on time scales comparable to their wave periods, and the physical system relaxes in time. The attenuation time grows with the large amplitude and characteristic growing time of the shearing. Conclusions: By having chosen a different magnetic flux function, the analytical model we devised can be adopted to derive equilibrium conditions for a diversity of 2.5D magnetic structures in the solar atmosphere. Movie associated to Fig. 5 is available in electronic form at http://www.aanda.org

Incentive-Compatible Robust Line Planning

Science.gov (United States)

Bessas, Apostolos; Kontogiannis, Spyros; Zaroliagis, Christos

The problem of robust line planning requests for a set of origin-destination paths (lines) along with their frequencies in an underlying railway network infrastructure, which are robust to fluctuations of real-time parameters of the solution. In this work, we investigate a variant of robust line planning stemming from recent regulations in the railway sector that introduce competition and free railway markets, and set up a new application scenario: there is a (potentially large) number of line operators that have their lines fixed and operate as competing entities issuing frequency requests, while the management of the infrastructure itself remains the responsibility of a single entity, the network operator. The line operators are typically unwilling to reveal their true incentives, while the network operator strives to ensure a fair (or socially optimal) usage of the infrastructure, e.g., by maximizing the (unknown to him) aggregate incentives of the line operators.

Growth, morphology, and developmental instability of rainbow trout, Yellowstone cutthroat trout, and four hybrid generations

Science.gov (United States)

Ostberg, C.O.; Duda, J.J.; Graham, J.H.; Zhang, S.; Haywood, K. P.; Miller, B.; Lerud, T.L.

2011-01-01

Hybridization of cutthroat trout Oncorhynchus clarkii with nonindigenous rainbow trout O. mykiss contributes to the decline of cutthroat trout subspecies throughout their native range. Introgression by rainbow trout can swamp the gene pools of cutthroat trout populations, especially if there is little selection against hybrids. We used rainbow trout, Yellowstone cutthroat trout O. clarkii bouvieri, and rainbow trout × Yellowstone cutthroat trout F1 hybrids as parents to construct seven different line crosses: F1 hybrids (both reciprocal crosses), F2 hybrids, first-generation backcrosses (both rainbow trout and Yellowstone cutthroat trout), and both parental taxa. We compared growth, morphology, and developmental instability among these seven crosses reared at two different temperatures. Growth was related to the proportion of rainbow trout genome present within the crosses. Meristic traits were influenced by maternal, additive, dominant, overdominant, and (probably) epistatic genetic effects. Developmental stability, however, was not disturbed in F1 hybrids, F2 hybrids, or backcrosses. Backcrosses were morphologically similar to their recurrent parent. The lack of developmental instability in hybrids suggests that there are few genetic incompatibilities preventing introgression. Our findings suggest that hybrids are not equal: that is, growth, development, character traits, and morphology differ depending on the genomic contribution from each parental species as well as the hybrid generation.

Development of a Handheld Line Information Reader and Generator for Efficient Management of Optical Communication Lines.

Science.gov (United States)

Lee, Jaeyul; Kwon, Hyungwoo; Song, Jaewon; Jeon, Mansik; Kim, Jeehyun

2017-08-24

A handheld line information reader and a line information generator were developed for the efficient management of optical communication lines. The line information reader consists of a photo diode, trans-impedance amplifier, voltage amplifier, microcontroller unit, display panel, and communication modules. The line information generator consists of a laser diode, laser driving circuits, microcontroller unit, and communication modules. The line information reader can detect the optical radiation field of the test line by bending the optical fiber. To enhance the sensitivity of the line information reader, an additional lens was used with a focal length of 4.51 mm. Moreover, the simulation results obtained through BeamPROP ® software from Synopsys, Inc. demonstrated a stronger optical radiation field of the fiber due to a longer transmission wavelength and larger bending angle of the fiber. Therefore, the developed devices can be considered as useful tools for the efficient management of optical communication lines.

GOSAT-2014 methane spectral line list

International Nuclear Information System (INIS)

Nikitin, A.V.; Lyulin, O.M.; Mikhailenko, S.N.; Perevalov, V.I.; Filippov, N.N.; Grigoriev, I.M.; Morino, I.; Yoshida, Y.; Matsunaga, T.

2015-01-01

The updated methane spectral line list GOSAT-2014 for the 5550–6240 cm −1 region with the intensity cutoff of 5×10 –25 cm/molecule at 296 K is presented. The line list is based on the extensive measurements of the methane spectral line parameters performed at different temperatures and pressures of methane without and with buffer gases N 2 , O 2 and air. It contains the following spectral line parameters of about 12150 transitions: line position, line intensity, energy of lower state, air-induced and self-pressure-induced broadening and shift coefficients and temperature exponent of air-broadening coefficient. The accuracy of the line positions and intensities are considerably improved in comparison with the previous version GOSAT-2009. The improvement of the line list is done mainly due to the involving to the line position and intensity retrieval of six new spectra recorded with short path way (8.75 cm). The air-broadening and air-shift coefficients for the J-manifolds of the 2ν 3 (F 2 ) band are refitted using the new more precise values of the line positions and intensities. The line assignment is considerably extended. The lower state J-value was assigned to 6397 lines representing 94.4% of integrated intensity of the considering wavenumber region. The complete assignment was done for 2750 lines. - Highlights: • The upgrade of the GOSAT methane line list in the 5550–6240 cm −1 region is done. • 12,146 experimental methane line positions and intensities are retrieved. • 6376 lower energy levels for methane lines are determined

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Introgressive hybridization facilitates incorporation of genes from one species into the gene pool of another. Studies on long-term effects of introgressive hybridization in animal systems are sparse. Drosophila nasuta ( 2 n = 8 ) and D. albomicans ( 2 n = 6 )—a pair of allopatric, morphologically almost identical, cross-fertile ...

Rapid line scan MR angiography

International Nuclear Information System (INIS)

Frahm, J.; Merboldt, K.D.; Hanicke, W.; Bruhn, H.

1987-01-01

Direct MR angiography may be performed using line scan imaging techniques combined with presaturation of stationary spins. Thus, a single line scan echo yields a projection of vessels due to the signal from reflowing unsaturated spins. Reconstruction of an angiographic image is performed line by line at slightly incremented positions. In particular, line scan angiography is direct and fast without a sensitivity to artifacts even for high flow rates. Image resolution and field of view may be chosen without restrictions, and zoom images using enhanced gradients may be recorded without aliasing artifacts. The method is robust with respect to eddy currents and pulsatile flow. Line scan MR angiograms of phantoms, animals, and human volunteers have been recorded using 90 0 radio frequency pulses and gradient-recalled echoes

Spotting Separator Points at Line Terminals in Compressed Document Images for Text-line Segmentation

OpenAIRE

R, Amarnath; Nagabhushan, P.

2017-01-01

Line separators are used to segregate text-lines from one another in document image analysis. Finding the separator points at every line terminal in a document image would enable text-line segmentation. In particular, identifying the separators in handwritten text could be a thrilling exercise. Obviously it would be challenging to perform this in the compressed version of a document image and that is the proposed objective in this research. Such an effort would prevent the computational burde...

VT Electric Transmission Line Corridors - corridor lines

Data.gov (United States)

Vermont Center for Geographic Information — (Link to Metadata) The ELTRN layer depicts electric transmission line corridors in Vermont. Various methods have been used to digitize features. The data layer...

High-resolution Laboratory Measurements of Coronal Lines near the Fe IX Line at 171 Å

Science.gov (United States)

Beiersdorfer, Peter; Träbert, Elmar

2018-02-01

We present high-resolution laboratory measurements in the spectral region between 165 and 175 Å that focus on the emission from various ions of C, O, F, Ne, S, Ar, Fe, and Ni. This wavelength region is centered on the λ171 Fe IX channel of the Atmospheric Imaging Assembly on the Solar Dynamics Observatory, and we place special emphasis on the weaker emission lines of Fe IX predicted in this region. In general, our measurements show a multitude of weak lines missing in the current databases, where the emission lines of Ni are probably most in need of further identification and reclassification. We also find that the wavelengths of some of the known lines need updating. Using the multi-reference Møller–Plesset method for wavelength predictions and collisional-radiative modeling of the line intensities, we have made tentative assignments of more than a dozen lines to the spectrum of Fe IX, some of which have formerly been identified as Fe VII, Fe XIV, or Fe XVI lines. Several Fe features remain unassigned, although they appear to be either Fe VII or Fe X lines. Further work will be needed to complete and correct the spectral line lists in this wavelength region.

Fine mapping of a quantitative resistance gene for gray leaf spot of maize (Zea mays L.) derived from teosinte (Z. mays ssp. parviglumis).

Science.gov (United States)

Zhang, Xinye; Yang, Qin; Rucker, Elizabeth; Thomason, Wade; Balint-Kurti, Peter

2017-06-01

In this study we mapped the QTL Qgls8 for gray leaf spot (GLS) resistance in maize to a ~130 kb region on chromosome 8 including five predicted genes. In previous work, using near isogenic line (NIL) populations in which segments of the teosinte (Zea mays ssp. parviglumis) genome had been introgressed into the background of the maize line B73, we had identified a QTL on chromosome 8, here called Qgls8, for gray leaf spot (GLS) resistance. We identified alternate teosinte alleles at this QTL, one conferring increased GLS resistance and one increased susceptibility relative to the B73 allele. Using segregating populations derived from NIL parents carrying these contrasting alleles, we were able to delimit the QTL region to a ~130 kb (based on the B73 genome) which encompassed five predicted genes.

VT Digital Line Graph Railroads

Data.gov (United States)

Vermont Center for Geographic Information — (Link to Metadata) This datalayer is comprised of major railroad lines for the state of Vermont. These railroad lines line up well along quadrangle boundaries, but...

The line makes the difference: line managers as effective HRM partners

NARCIS (Netherlands)

Bos-Nehles, Anna Christina

2010-01-01

The HR role of line managers is highly discussed and criticized but little empirically researched. It is argued that line managers are not able to effectively implement HR practices because they do not have the desire, capacity and competences needed to perform well and lack support and policies &

Power line communications theory and applications for narrowband and broadband communications over power lines

CERN Document Server

Ferreira, Hendrik C; Newbury, John; Swart, Theo G

2010-01-01

Power Line Communications (PLC) is a promising emerging technology, which has attracted much attention due to the wide availability of power distribution lines. This book provides a thorough introduction to the use of power lines for communication purposes, ranging from channel characterization, communications on the physical layer and electromagnetic interference, through to protocols, networks, standards and up to systems and implementations. With contributions from many of the most prominent international PLC experts from academia and industry, Power Line Communications brings togeth

Optical Variability of Narrow-line and Broad-line Seyfert 1 Galaxies

Science.gov (United States)

Rakshit, Suvendu; Stalin, C. S.

2017-06-01

We studied the optical variability (OV) of a large sample of narrow-line Seyfert 1 (NLSy1) and broad-line Seyfert 1 (BLSy1) galaxies with z anti-correlated with Fe II strength but correlated with the width of the Hβ line. The well-known anti-correlation of variability-luminosity and the variability-Eddington ratio is present in our data. Among the radio-loud sample, variability amplitude is found to be correlated with radio-loudness and radio-power, suggesting that jets also play an important role in the OV in radio-loud objects, in addition to the Eddington ratio, which is the main driving factor of OV in radio-quiet sources.

Molecular Mapping of PMR1, a Novel Locus Conferring Resistance to Powdery Mildew in Pepper (Capsicum annuum).

Science.gov (United States)

Jo, Jinkwan; Venkatesh, Jelli; Han, Koeun; Lee, Hea-Young; Choi, Gyung Ja; Lee, Hee Jae; Choi, Doil; Kang, Byoung-Cheorl

2017-01-01

Powdery mildew, caused by Leveillula taurica , is a major fungal disease affecting greenhouse-grown pepper ( Capsicum annuum ). Powdery mildew resistance has a complex mode of inheritance. In the present study, we investigated a novel powdery mildew resistance locus, PMR1 , using two mapping populations: 102 'VK515' F 2:3 families (derived from a cross between resistant parental line 'VK515R' and susceptible parental line 'VK515S') and 80 'PM Singang' F 2 plants (derived from the F 1 'PM Singang' commercial hybrid). Genetic analysis of the F 2:3 'VK515' and F 2 'PM Singang' populations revealed a single dominant locus for inheritance of the powdery mildew resistance trait. Genetic mapping showed that the PMR1 locus is located on syntenic regions of pepper chromosome 4 in a 4-Mb region between markers CZ2_11628 and HRM4.1.6 in 'VK515R'. Six molecular markers including one SCAR marker and five SNP markers were localized to a region 0 cM from the PMR1 locus. Two putative nucleotide-binding site leucine-rich repeat (NBS-LRR)-type disease resistance genes were identified in this PMR1 region. Genotyping-by-sequencing (GBS) and genetic mapping analysis revealed suppressed recombination in the PMR1 region, perhaps due to alien introgression. In addition, a comparison of species-specific InDel markers as well as GBS-derived SNP markers indicated that C. baccatum represents a possible source of such alien introgression of powdery mildew resistance into 'VK515R'. The molecular markers developed in this study will be especially helpful for marker-assisted selection in pepper breeding programs for powdery mildew resistance.

Line Shape Variability in a Sample of AGN with Broad Lines

Indian Academy of Sciences (India)

2016-01-27

Jan 27, 2016 ... We give here a comparative review of the line shape variability in a sample of five type 1 AGNs, those with broad emission lines in their spectra, of the data obtained from the international long-term optical monitoring campaign coordinated by the Special Astrophysical Observatory of the Russian Academy ...

Atlas transmission line breakdown analysis

CERN Document Server

Nielsen, K E; Ballard, E O; Elizondo, J M; Gribble, R F; McCuistian, B T; Parsons, W M

1999-01-01

The Atlas facility will use 24 radially converging, vertically oriented and tapered, oil insulated, triplate transmission lines between the Marx generators and the central load region. Among the requirements of the transmission lines are low inductance and high reliability. The inter-conductor gap is nominally 2 cm and the lines taper from a height of 1.75 m at the Marx end to 0.32 m at the output end. The aluminum conductors, held together by 20 insulating spacers, are assembled and inserted as a unit into radial oil-filled steel tanks. The negative, high-voltage, center conductor is 2.54-cm thick and the outer ground conductors are 1.59-cm thick. All 24 triplate transmission lines connect to a transition section at near 1 m radius that couples the transmission lines to a disk/conical solid- dielectric-insulated power flow channel transmission line terminating at the load. Peak operating voltage on the lines can be as high as 240 kV with an effective stress time of 0.8 mu s. Testing of small sections of the ...

Genetic characterisation of novel resistance alleles to stem rust and stripe rust in wheat-alien introgression lines

OpenAIRE

Rahmatov, Mahbubjon

2016-01-01

Bread wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) is one of the most important food crops world-wide, but is attacked by many diseases and pests that cause significant yield losses. Globally, stem rust (Sr) (Puccinia graminis f. sp. tritici Erikss & E. Henning), stripe rust (Yr) (Puccinia striiformis Westend. f. sp. tritici Eriks) and leaf rust (Lr) (Puccinia triticina Eriks) are a great threat to wheat production. The majority of the Sr, Yr and Lr resistance genes are already defeated...

Optimization of antibody immobilization for on-line or off-line immunoaffinity chromatography

DEFF Research Database (Denmark)

Beyer, Natascha Helena; Schou, Christian; Højrup, Peter

2009-01-01

-POROS. Protein G-based matrices are very stable showing essentially no decline in performance after 50 application-wash-elution-reequilibration cycles and being easily prepared within 2-3 h of working time with a typical antibody coupling yield of above 80%. In off-line applications where constant flow....... A systematic study was conducted to determine the most versatile antibody immobilization method for use in on-line and off-line IA chromatography applications using commonly accessible immobilization methods. Four chemistries were examined using polyclonal and monoclonal antibodies and antibody fragments. We...

Line-shape asymmetry of water vapor absorption lines in the 720-nm wavelength region

Science.gov (United States)

Grossmann, Benoist E.; Browell, Edward V.

1991-01-01

Spectral line-shape analyses were performed for water vapor lines broadened by argon, oxygen, and xenon in the 720-nm wavelength region. A line-shape asymmetry was observed, which is attributed to statistical dependence or correlation between velocity- and state-changing collisions. The generalized (asymmetric) Galatry profile, which results from the soft-collision profile and includes correlation between velocity- and state-changing collisions, was fitted to the observed line shapes and was found to compare favorably with the observed data. The most prominent asymmetries were observed with xenon as the buffer gas.

China's Bilateral Currency Swap Lines

OpenAIRE

Zhitao, Lin; Wenjie, Zhan; Cheung, Yin-Wong

2016-01-01

We study the determinants of China’s bilateral local currency swap lines that were established since the recent global finance crisis. It is found that economic factors, political considerations, and institutional characteristics including trade intensity, economic size, strategic partnership, free trade agreement, corruption, and stability affect the decision of signing a swap line agreement. Once a swap line agreement decision is made, the size of the swap line is then mainly affected by tr...

Series Transmission Line Transformer

Science.gov (United States)

Buckles, Robert A.; Booth, Rex; Yen, Boris T.

2004-06-29

A series transmission line transformer is set forth which includes two or more of impedance matched sets of at least two transmissions lines such as shielded cables, connected in parallel at one end ans series at the other in a cascading fashion. The cables are wound about a magnetic core. The series transmission line transformer (STLT) which can provide for higher impedance ratios and bandwidths, which is scalable, and which is of simpler design and construction.

Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines.

Science.gov (United States)

Romano, Paolo; Manniello, Assunta; Aresu, Ottavia; Armento, Massimiliano; Cesaro, Michela; Parodi, Barbara

2009-01-01

The Cell Line Data Base (CLDB) is a well-known reference information source on human and animal cell lines including information on more than 6000 cell lines. Main biological features are coded according to controlled vocabularies derived from international lists and taxonomies. HyperCLDB (http://bioinformatics.istge.it/hypercldb/) is a hypertext version of CLDB that improves data accessibility by also allowing information retrieval through web spiders. Access to HyperCLDB is provided through indexes of biological characteristics and navigation in the hypertext is granted by many internal links. HyperCLDB also includes links to external resources. Recently, an interest was raised for a reference nomenclature for cell lines and CLDB was seen as an authoritative system. Furthermore, to overcome the cell line misidentification problem, molecular authentication methods, such as fingerprinting, single-locus short tandem repeat (STR) profile and single nucleotide polymorphisms validation, were proposed. Since this data is distributed, a reference portal on authentication of human cell lines is needed. We present here the architecture and contents of CLDB, its recent enhancements and perspectives. We also present a new related database, the Cell Line Integrated Molecular Authentication (CLIMA) database (http://bioinformatics.istge.it/clima/), that allows to link authentication data to actual cell lines.

Cell lines authentication and mycoplasma detection as minimun quality control of cell lines in biobanking.

Science.gov (United States)

Corral-Vázquez, C; Aguilar-Quesada, R; Catalina, P; Lucena-Aguilar, G; Ligero, G; Miranda, B; Carrillo-Ávila, J A

2017-06-01

Establishment of continuous cell lines from human normal and tumor tissues is an extended and useful methodology for molecular characterization of cancer pathophysiology and drug development in research laboratories. The exchange of these cell lines between different labs is a common practice that can compromise assays reliability due to contamination with microorganism such as mycoplasma or cells from different flasks that compromise experiment reproducibility and reliability. Great proportions of cell lines are contaminated with mycoplasma and/or are replaced by cells derived for a different origin during processing or distribution process. The scientific community has underestimated this problem and thousand of research experiment has been done with cell lines that are incorrectly identified and wrong scientific conclusions have been published. Regular contamination and authentication tests are necessary in order to avoid negative consequences of widespread misidentified and contaminated cell lines. Cell banks generate, store and distribute cell lines for research, being mandatory a consistent and continuous quality program. Methods implementation for guaranteeing both, the absence of mycoplasma and authentication in the supplied cell lines, has been performed in the Andalusian Health System Biobank. Specifically, precise results were obtained using real time PCR detection for mycoplasma and 10 STRs identification by capillary electrophoresis for cell line authentication. Advantages and disadvantages of these protocols are discussed.

An analysis model of the secondary tunnel lining considering ground-primary support-secondary lining interaction

Energy Technology Data Exchange (ETDEWEB)

Seo, Seong-Ho; Chang, Seok-Bue [Yooshin Engineering Corporation, Seoul(Korea); Lee, Sang-Duk [Ajou University, Suwon(Korea)

2002-06-30

It is the common practice to over design the reinforcement for the secondary tunnel lining due to the lack of rational insight into the ground loosening loads, and due to the conservative application of the empirical design methods. The main loads of the secondary lining are the ground loosening loads and the ground water pressure, and the ground load is critical in the reinforcement design of the secondary lining in the case of drained tunnel. If the external load is absent around a tunnel. the reasons of the load for secondary tunnel lining are the deterioration of the primary supports such as shotcrete, steel rib, and rock bolts. Accordingly, the analysis method considering the ground-primary supports-secondary lining interaction should be required for the rational design of the secondary tunnel lining. In this paper, the interaction was conceptually described by the simple mass-spring model and the load transfer from the ground and primary supports to the secondary lining is showed by the ground-primary supports-secondary lining reaction curves for the theoretical solution of a circular tunnel, And also, the application of this proposed model to numerical analysis is verified in order to check the potential for the tunnel with the complex analysis conditions. (author). 8 refs., 2 tabs., 7 figs.

Stokes line width

International Nuclear Information System (INIS)

Nikiskov, A.I.; Ritus, V.I.

1993-01-01

The concept of Stokes line width is introduced for the asymptotic expansions of functions near an essential singularity. Explicit expressions are found for functions (switching functions) that switch on the exponentially small terms for the Dawson integral, Airy function, and the gamma function. A different, more natural representation of a function, not associated with expansion in an asymptotic series, in the form of dominant and recessive terms is obtained by a special division of the contour integral which represents the function into contributions of higher and lower saddle points. This division leads to a narrower, natural Stokes line width and a switching function of an argument that depends on the topology of the lines of steepest descent from the saddle point

Comparisons on Genetic Diversity among the Isonuclear-Alloplasmic Male Sterile Lines and Their Maintainer Lines in Rice

Directory of Open Access Journals (Sweden)

Jin-quan LI

2007-06-01

Full Text Available Four sets of rice isonuclear-alloplasmic lines including 16 male sterile lines and their maintainer lines were analyzed by using 91 pairs of SSR primers to study the genetic diversity of nuclear genome and their relative relationships. A total of 169 alleles were detected in the 16 lines, with a frequency of polymorphic loci of 53.85% and an average number of alleles per locus of 1.8, and the average gene diversity was 0.228. Four sets of the isonuclear-alloplasmic male sterile lines shared 146 identical alleles, corresponding to 86.39% of the total alleles; meanwhile, there are 23 different alleles among the tested materials, being 13.61% of the total alleles. On average, 78.70% identical alleles and 21.30% different alleles of the total alleles were detected between the isonuclear-alloplasmic male sterile lines and their maintainer lines. There were 53.85% identical alleles and 46.15% different alleles of the total alleles among the homozygous allonucleus male sterile lines. The fingerprints were established for some male sterile lines and maintainer lines. All the materials tested were divided into three groups at the 0.2 genetic distance based on the cluster analysis. Eight lines of Huanong A and Huayu A (including Huanong B and Huayu B were in the first group, four lines of Kezhen A (including Kezhen B in the second group, and four lines of Zhenshan 97A (including Zhenshan 97B in the third group. For the isonuclear-alloplasmic male sterile lines, the similarity coefficient between Y (Yegong type and WA (wild abortive type or between CW (Raoping wild rice and WA type reached 87–98%.

Interspecific and interploidal gene flow in Central European Arabidopsis (Brassicaceae

Directory of Open Access Journals (Sweden)

Jørgensen Marte H

2011-11-01

Full Text Available Abstract Background Effects of polyploidisation on gene flow between natural populations are little known. Central European diploid and tetraploid populations of Arabidopsis arenosa and A. lyrata are here used to study interspecific and interploidal gene flow, using a combination of nuclear and plastid markers. Results Ploidal levels were confirmed by flow cytometry. Network analyses clearly separated diploids according to species. Tetraploids and diploids were highly intermingled within species, and some tetraploids intermingled with the other species, as well. Isolation with migration analyses suggested interspecific introgression from tetraploid A. arenosa to tetraploid A. lyrata and vice versa, and some interploidal gene flow, which was unidirectional from diploid to tetraploid in A. arenosa and bidirectional in A. lyrata. Conclusions Interspecific genetic isolation at diploid level combined with introgression at tetraploid level indicates that polyploidy may buffer against negative consequences of interspecific hybridisation. The role of introgression in polyploid systems may, however, differ between plant species, and even within the small genus Arabidopsis, we find very different evolutionary fates when it comes to introgression.

Evolution of postmating reproductive isolation: measuring the fitness effects of chromosomal regions containing hybrid male sterility factors.

Science.gov (United States)

Johnson, N A; Wu, C I

1993-08-01

At least six regions of the X chromosome can cause male sterility when introgressed from Drosophila mauritiana into Drosophila simulans. In this article, we present the results of the other fitness effects caused by two X-linked regions that contain hybrid male sterility factors. In both regions, females that are heterozygous for an introgression with such a sterility factor produce substantially-fewer offspring than females heterozygous for an introgression that lacks the sterility factor. Thus, the hybrid male sterility factors, or other genes nearby, have substantial effects on female productivity. In contrast, hybrid male sterility factors have little or no effect on the relative viabilities of either sex. The evolutionary implications of these findings are discussed.

A new technique for on-line and off-line high speed computation

International Nuclear Information System (INIS)

Hartouni, E.P.; Jensen, D.A.; Klima, B.; Kreisler, M.N.; Rabin, M.S.Z.; Uribe, J.; Gottschalk, E.; Gara, A.; Knapp, B.C.

1989-01-01

A new technique for both on-line and off-line computation has been developed. With this technique, a reconstruction analysis in Elementary Particle Physics, otherwise prohibitively long, has been accomplished. It will be used on-line in an upcoming Fermilab experiment to reconstruct more than 100,000 events per second and to trigger on the basis of that information. The technique delivers 40 Giga operations per second, has a bandwidth on the order of Gigabytes per second and has a modest cost. An overview of the program, details of the system, and performance measurements are presented in this paper

Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability

Directory of Open Access Journals (Sweden)

Xu Chunming

2009-05-01

Full Text Available Abstract Background Inter-specific hybridization occurs frequently in plants, which may induce genetic and epigenetic instabilities in the resultant hybrids, allopolyploids and introgressants. It remains unclear however whether pollination by alien pollens of an incompatible species may impose a "biological stress" even in the absence of genome-merger or genetic introgression, whereby genetic and/or epigenetic instability of the maternal recipient genome might be provoked. Results We report here the identification of a rice mutator-phenotype from a set of rice plants derived from a crossing experiment involving two remote and apparently incompatible species, Oryza sativa L. and Oenothera biennis L. The mutator-phenotype (named Tong211-LP showed distinct alteration in several traits, with the most striking being substantially enlarged panicles. Expectably, gel-blotting by total genomic DNA of the pollen-donor showed no evidence for introgression. Characterization of Tong211-LP (S0 and its selfed progenies (S1 ruled out contamination (via seed or pollen or polyploidy as a cause for its dramatic phenotypic changes, but revealed transgenerational mobilization of several previously characterized transposable elements (TEs, including a MITE (mPing, and three LTR retrotransposons (Osr7, Osr23 and Tos17. AFLP and MSAP fingerprinting revealed extensive, transgenerational alterations in cytosine methylation and to a less extent also genetic variation in Tong211-LP and its immediate progenies. mPing mobility was found to correlate with cytosine methylation alteration detected by MSAP but not with genetic variation detected by AFLP. Assay by q-RT-PCR of the steady-state transcript abundance of a set of genes encoding for the various putative DNA methyltransferases, 5-methylcytosine DNA glycosylases, and small interference RNA (siRNA pathway-related proteins showed that, relative to the rice parental line, heritable perturbation in expression of 12 out of

CLO : The cell line ontology

NARCIS (Netherlands)

Sarntivijai, Sirarat; Lin, Yu; Xiang, Zuoshuang; Meehan, Terrence F.; Diehl, Alexander D.; Vempati, Uma D.; Schuerer, Stephan C.; Pang, Chao; Malone, James; Parkinson, Helen; Liu, Yue; Takatsuki, Terue; Saijo, Kaoru; Masuya, Hiroshi; Nakamura, Yukio; Brush, Matthew H.; Haendel, Melissa A.; Zheng, Jie; Stoeckert, Christian J.; Peters, Bjoern; Mungall, Christopher J.; Carey, Thomas E.; States, David J.; Athey, Brian D.; He, Yongqun

2014-01-01

Background: Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO

Microwave transmission-line impedance data

CERN Document Server

Gunston, M A R

1996-01-01

A compendium of data for computing the characteristic impedance of transmission lines based on physical dimensions. Covers both conventional structures and unusual geometries, including coaxial, eccentric and elliptic coaxial, twin-wire, wire-above-ground, microstrip and derivatives, stripline, slabline and trough line. Also details numerous configurations of coupled lines.

Parallel plate transmission line transformer

NARCIS (Netherlands)

Voeten, S.J.; Brussaard, G.J.H.; Pemen, A.J.M.

2011-01-01

A Transmission Line Transformer (TLT) can be used to transform high-voltage nanosecond pulses. These transformers rely on the fact that the length of the pulse is shorter than the transmission lines used. This allows connecting the transmission lines in parallel at the input and in series at the

Wood pole overhead lines

CERN Document Server

Wareing, Brian

2005-01-01

This new book concentrates on the mechanical aspects of distribution wood pole lines, including live line working, environmental influences, climate change and international standards. Other topics include statutory requirements, safety, profiling, traditional and probabilistic design, weather loads, bare and covered conductors, different types of overhead systems, conductor choice, construction and maintenance. A section has also been devoted to the topic of lightning, which is one of the major sources of faults on overhead lines. The book focuses on the effects of this problem and the strate

Parallel field line and stream line tracing algorithms for space physics applications

Science.gov (United States)

Toth, G.; de Zeeuw, D.; Monostori, G.

2004-05-01

Field line and stream line tracing is required in various space physics applications, such as the coupling of the global magnetosphere and inner magnetosphere models, the coupling of the solar energetic particle and heliosphere models, or the modeling of comets, where the multispecies chemical equations are solved along stream lines of a steady state solution obtained with single fluid MHD model. Tracing a vector field is an inherently serial process, which is difficult to parallelize. This is especially true when the data corresponding to the vector field is distributed over a large number of processors. We designed algorithms for the various applications, which scale well to a large number of processors. In the first algorithm the computational domain is divided into blocks. Each block is on a single processor. The algorithm folows the vector field inside the blocks, and calculates a mapping of the block surfaces. The blocks communicate the values at the coinciding surfaces, and the results are interpolated. Finally all block surfaces are defined and values inside the blocks are obtained. In the second algorithm all processors start integrating along the vector field inside the accessible volume. When the field line leaves the local subdomain, the position and other information is stored in a buffer. Periodically the processors exchange the buffers, and continue integration of the field lines until they reach a boundary. At that point the results are sent back to the originating processor. Efficiency is achieved by a careful phasing of computation and communication. In the third algorithm the results of a steady state simulation are stored on a hard drive. The vector field is contained in blocks. All processors read in all the grid and vector field data and the stream lines are integrated in parallel. If a stream line enters a block, which has already been integrated, the results can be interpolated. By a clever ordering of the blocks the execution speed can be

Minnesota County Boundaries - lines

Data.gov (United States)

Minnesota Department of Natural Resources — Minnesota county boundaries derived from a combination of 1:24,000 scale PLS lines, 1:100,000 scale TIGER, 1:100,000 scale DLG, and 1:24,000 scale hydrography lines....

A tangent subsolar merging line

International Nuclear Information System (INIS)

Crooker, N.U.; Siscoe, G.L.; Toffoletto, F.R.

1990-01-01

The authors describe a global magnetospheric model with a single subsolar merging line whose position is determined neither locally by the relative orientations and strengths of the merging fields nor globally by the orientation of a separator line--the governing parameters of most previous models--but by the condition of tangential contact between the external field and the magnetopause. As in previous models, the tilt of the merging line varies with IMF orientation, but here it also depends upon the ratio of Earth's magnetic flux that leaks out of the magnetopause to IMF flux that penetrates in. In the limiting case treated by Alekseyev and Belen'kaya, with no leakage of Earth's field and total IMF penetration, the merging line forms a great circle around a spherical magnetosphere where undeviated IMF lines lie tangent to its surface. This tangent merging line lies perpendicular to the IMF. They extend their work to the case of finite leakage and partial penetration, which distort the IMF into a draped pattern, thus changing the locus of tangency to the sphere. In the special case where the penetrating IMF flux is balanced by an equal amount of Earth flux leakage, the tangent merging line bisects the angle between the IMF and Earth's northward subsolar field. This result is identical to the local merging line model result for merging fields with equal magnitude. Here a global flux balance condition replaces the local equal magnitude condition

Transmission line capital costs

International Nuclear Information System (INIS)

Hughes, K.R.; Brown, D.R.

1995-05-01

The displacement or deferral of conventional AC transmission line installation is a key benefit associated with several technologies being developed with the support of the U.S. Department of Energy's Office of Energy Management (OEM). Previous benefits assessments conducted within OEM have been based on significantly different assumptions for the average cost per mile of AC transmission line. In response to this uncertainty, an investigation of transmission line capital cost data was initiated. The objective of this study was to develop a database for preparing preliminary estimates of transmission line costs. An extensive search of potential data sources identified databases maintained by the Bonneville Power Administration (BPA) and the Western Area Power Administration (WAPA) as superior sources of transmission line cost data. The BPA and WAPA data were adjusted to a common basis and combined together. The composite database covers voltage levels from 13.8 to 765 W, with cost estimates for a given voltage level varying depending on conductor size, tower material type, tower frame type, and number of circuits. Reported transmission line costs vary significantly, even for a given voltage level. This can usually be explained by variation in the design factors noted above and variation in environmental and land (right-of-way) costs, which are extremely site-specific. Cost estimates prepared from the composite database were compared to cost data collected by the Federal Energy Regulatory Commission (FERC) for investor-owned utilities from across the United States. The comparison was hampered because the only design specifications included with the FERC data were voltage level and line length. Working within this limitation, the FERC data were not found to differ significantly from the composite database. Therefore, the composite database was judged to be a reasonable proxy for estimating national average costs

MEMS-based transmission lines for microwave applications

Science.gov (United States)

Wu, Qun; Fu, Jiahui; Gu, Xuemai; Shi, Huajuan; Lee, Jongchul

2003-04-01

This paper mainly presents a briefly review for recent progress in MEMS-based transmission lines for use in microwave and millimeterwave range. MEMS-based transmission lines including different transmission line structure such as membrane-supported microstrip line microstrip line, coplanar microshield transmission line, LIGA micromachined planar transmission line, micromachined waveguides and coplanar waveguide are discussed. MEMS-based transmission lines are characterized by low propagation loss, wide operation frequency band, low dispersion and high quality factor, in addition, the fabrication is compatible with traditional processing of integrated circuits (IC"s). The emergence of MEMS-based transmission lines provided a solution for miniaturizing microwave system and monolithic microwave integrated circuits.

Silver linings.

Science.gov (United States)

Bultas, Margaret W; Pohlman, Shawn

2014-01-01

The purpose of this interpretive phenomenological study was to gain a better understanding of the experiences of 11 mothers of preschool children with autism spectrum disorder (ASD). Mothers were interviewed three times over a 6 week period. Interviews were analyzed using interpretive methods. This manuscript highlights one particular theme-a positive perspective mothers described as the "silver lining." This "silver lining" represents optimism despite the adversities associated with parenting a child with ASD. A deeper understanding of this side of mothering children with ASD may help health care providers improve rapport, communication, and result in more authentic family centered care. Copyright © 2014 Elsevier Inc. All rights reserved.

Constancy of spectral-line bisectors

International Nuclear Information System (INIS)

Gray, D.F.

1983-01-01

Bisectors of spectral line profiles in cool stars indicate the strength of convection in the photospheres of these objects. The present investigation is concerned with the feasibility of studying time variations in line bisectors, the reality of apparent line-to-line differences within the same stellar spectrum, and bisector differences between stars of identical spectral types. The differences considered pertain to the shape of the bisector. The material used in the investigation was acquired at the McDonald Observatory using a 1728 diode Reticon array at the coudefocus of the 2.1-m telescope. Observed bisector errors are discussed. It is established that different lines in the same star show significantly different bisectors. The observed error bands are shown by the shaded regions. The slope and curvature are unique for each case

Intra lines uniformity and inter lines variation of rice mutants resulting from irradiation of South Kalimantan local varieties

International Nuclear Information System (INIS)

Raihani Wahdah; Gusti Rumayadi; Rahmi Zulhidiani

2016-01-01

The preference of farmer in tidal swamp on local rice varieties are quite high, but local varieties have a long life and low yield characters, so it needs to be improved for the trait. This study is part of activities of the local rice varieties improvement to generate promising lines were short-moderate aged, but the slimming and pera (high amylose content) grains maintained. The aims of this study were to determine the intra lines uniformity and the inter lines variation of M5 generation of rice mutant lines. The experiment was carried out in the Experimental Station of Agriculture Faculty, Lambung Mangkurat University from March to September 2014. The experiment used 150 earliest flowering lines of 300 M5 mutant lines that were planted. Intra lines uniformity were analysed by comparing the variance of each mutant lines with variance of its parent, while the variation among lines were analyzed by comparing the variance of all lines with variance of its parent. More than 85 % M5 mutant lines from Siam Harli as parent and > 79 % of Siam Kuatek as parent are uniform. The uniform character at all M5 mutant lines, both of Siam Harli or Siam Kuatek parent are the harvest age, the filled grains number, and the empty grains number. There is no variability between M5 mutant lines, but some of M5 mutant lines from Siam Harli and Siam Kuatek have some better characters than their parents, so there is an opportunity for selection. (author)

Mjollnir Rotational Line Scan Diagnostics.

Science.gov (United States)

1981-05-19

using long cavity. M8 Removable Pellicle Beam Splitter for He-Ne Lineup Beam. Removed before HF or DF laser is turned on. 27 A 27 * A r of the chopper...three probe laser lines, however three lines were sequentially measured to verify the diagnostic equipment. Two of the three lines have been monitored

QSOs with narrow emission lines

International Nuclear Information System (INIS)

Baldwin, J.A.; Mcmahon, R.; Hazard, C.; Williams, R.E.

1988-01-01

Observations of two new high-redshift, narrow-lined QSOs (NLQSOs) are presented and discussed together with observations of similar objects reported in the literature. Gravitational lensing is ruled out as a possible means of amplifying the luminosity for one of these objects. It is found that the NLQSOs have broad bases on their emission lines as well as the prominent narrow cores which define this class. Thus, these are not pole-on QSOs. The FWHM of the emission lines fits onto the smoothly falling tail of the lower end of the line-width distribution for complete QSO samples. The equivalent widths of the combined broad and narrow components of the lines are normal for QSOs of the luminosity range under study. However, the NLQSOs do show ionization differences from broader-lined QSOs; most significant, the semiforbidden C III/C IV intensity ratio is unusually low. The N/C abundance ratio in these objects is found to be normal; the Al/C abundance ratio may be quite high. 38 references

Teaching Braille Line Tracking Using Stimulus Fading

Science.gov (United States)

Scheithauer, Mindy C.; Tiger, Jeffrey H.

2014-01-01

Line tracking is a prerequisite skill for braille literacy that involves moving one's finger horizontally across a line of braille text and identifying when a line ends so the reader may reset his or her finger on the subsequent line. Current procedures for teaching line tracking are incomplete, because they focus on tracking lines with only…

Line ratios and wavelengths of helium-like argon n=2 satellite transitions and resonance lines

International Nuclear Information System (INIS)

Biedermann, C.; Radtke, R.; Fournier, K.

2003-01-01

The characteristic X-ray emission from helium-like argon was investigated as a mean to diagnose hot plasmas. We have measured the radiation from n=2-1 parent lines and from KLn dielectronic recombination satellites with high wavelength resolution as function of the excitation energy using the Berlin Electron Beam Ion Trap. Values of wavelength relative to the resonance and forbidden line are tabulated and compared with references. The line intensity observed over a wide range of excitation energies is weighted with a Maxwellian electron-energy distribution to analyze line ratios as function of plasma temperature. Line ratios (j+z)/w and k/w compare nicely with theoretical predictions and demonstrate their applicability as temperature diagnostic. The ratio z/(x+y) shows not to depend on the electron density

LED-Based High-Voltage Lines Warning System

Directory of Open Access Journals (Sweden)

Eldar MUSA

2013-04-01

Full Text Available LED-based system, running with the current of high-voltage lines and converting the current flowing through the line into the light by using a toroid transformer, has been developed. The transformer’s primary winding is constituted by the high voltage power line. Toroidal core consists of two equal parts and the secondary windings are evenly placed on these two parts. The system is mounted on the high-voltage lines as a clamp. The secondary winding ends are connected in series by the connector on the clamp. LEDs are supplied by the voltage at the ends of secondary. Current flowing through highvoltage transmission lines is converted to voltage by the toroidal transformer and the light emitting LEDs are supplied with this voltage. The theory of the conversion of the current flowing through the line into the light is given. The system, running with the current of the line and converting the current into the light, has been developed. System has many application areas such as warning high voltage lines (warning winches to not hinder the high-voltage lines when working under the lines, warning planes to not touch the high-voltage lines, remote measurement of high-voltage line currents, and local illumination of the line area

Effect of splitting a mixed-model line on shortening the line length under open- and closed-boundary working area settings

Science.gov (United States)

Zhang, Donghao; Matsuura, Haruki; Asada, Akiko

2017-04-01

Some automobile factories have segmented mixed-model production lines into shorter sub-lines according to part group, such as engine, trim, and powertrain. The effects of splitting a line into sub-lines have been reported from the standpoints of worker motivation, productivity improvement, and autonomy based on risk spreading. There has been no mention of the possibility of shortening the line length by altering the product sequence using sub-lines. The purpose of the present paper is to determine the conditions under which sub-lines reduce the line length and the degree to which the line length may be shortened. The line lengths for a non-split line and a line that has been split into sub-lines are compared using three methods for determining the working area, the standard closed boundary, the optimized open boundary, and real-life constant-length stations. The results are discussed by analyzing the upper and lower bounds of the line length. Based on these results, a procedure for deciding whether or not to split a production line is proposed.

Development of Elite BPH-Resistant Wide-Spectrum Restorer Lines for Three and Two Line Hybrid Rice.

Science.gov (United States)

Fan, Fengfeng; Li, Nengwu; Chen, Yunping; Liu, Xingdan; Sun, Heng; Wang, Jie; He, Guangcun; Zhu, Yingguo; Li, Shaoqing

2017-01-01

Hybrid rice has contributed significantly to the world food security. Breeding of elite high-yield, strong-resistant broad-spectrum restorer line is an important strategy for hybrid rice in commercial breeding programs. Here, we developed three elite brown planthopper (BPH)-resistant wide-spectrum restorer lines by pyramiding big-panicle gene Gn8.1 , BPH-resistant genes Bph6 and Bph9 , fertility restorer genes Rf3, Rf4, Rf5 , and Rf6 through molecular marker assisted selection. Resistance analysis revealed that the newly developed restorer lines showed stronger BPH-resistance than any of the single-gene donor parent Luoyang-6 and Luoyang-9. Moreover, the three new restorer lines had broad spectrum recovery capabilities for Honglian CMS, Wild abortive CMS and two-line GMS sterile lines, and higher grain yields than that of the recurrent parent 9,311 under nature field conditions. Importantly, the hybrid crosses also showed good performance for grain yield and BPH-resistance. Thus, the development of elite BPH-resistant wide-spectrum restorer lines has a promising future for breeding of broad spectrum BPH-resistant high-yield varieties.

Genetic variability in local Brazilian horse lines using microsatellite markers.

Science.gov (United States)

Silva, A C M; Paiva, S R; Albuquerque, M S M; Egito, A A; Santos, S A; Lima, F C; Castro, S T; Mariante, A S; Correa, P S; McManus, C M

2012-04-10

Genetic variability at 11 microsatellite markers was analyzed in five naturalized/local Brazilian horse breeds or genetic groups. Blood samples were collected from 328 animals of the breeds Campeira (Santa Catarina State), Lavradeira (Roraima State), Pantaneira (Pantanal Mato-Grossense), Mangalarga Marchador (Minas Gerais State), as well as the genetic group Baixadeiro (Maranhão State), and the exotic breeds English Thoroughbred and Arab. We found significant genetic variability within evaluated microsatellite loci, with observed heterozygosis varying between 0.426 and 0.768 and polymorphism information content values of 0.751 to 0.914. All breeds showed high inbreeding coefficients and were not in Hardy-Weinberg equilibrium. The smallest genetic distance was seen between the Pantaneira and Arab breeds. The principal component analyzes and Bayesian approach demonstrated that the exotic breeds have had a significant influence on the genetic formation of the local breeds, with introgression of English Throroughbred in Pantaneira and Lavradeira, as well as genetic proximity between the Arab, Pantaneira and Mangalarga Marchador populations. This study shows the need to conserve traits acquired by naturalized horse breeds over centuries of natural selection in Brazil due to the genetic uniqueness of each group, suggesting a reduced gene flow between them. These results reinforce the need to include these herds in animal genetic resource conservation programs to maximize the genetic variability and conserve useful allele combinations.

Cluster Analysis of Maize Inbred Lines

Directory of Open Access Journals (Sweden)

Jiban Shrestha

2016-12-01

Full Text Available The determination of diversity among inbred lines is important for heterosis breeding. Sixty maize inbred lines were evaluated for their eight agro morphological traits during winter season of 2011 to analyze their genetic diversity. Clustering was done by average linkage method. The inbred lines were grouped into six clusters. Inbred lines grouped into Clusters II had taller plants with maximum number of leaves. The cluster III was characterized with shorter plants with minimum number of leaves. The inbred lines categorized into cluster V had early flowering whereas the group into cluster VI had late flowering time. The inbred lines grouped into the cluster III were characterized by higher value of anthesis silking interval (ASI and those of cluster VI had lower value of ASI. These results showed that the inbred lines having widely divergent clusters can be utilized in hybrid breeding programme.

Authentication of M14 melanoma cell line proves misidentification of MDA‐MB‐435 breast cancer cell line

Science.gov (United States)

Korch, Christopher; Hall, Erin M.; Dirks, Wilhelm G.; Ewing, Margaret; Faries, Mark; Varella‐Garcia, Marileila; Robinson, Steven; Storts, Douglas; Turner, Jacqueline A.; Wang, Ying; Burnett, Edward C.; Healy, Lyn; Kniss, Douglas; Neve, Richard M.; Nims, Raymond W.; Reid, Yvonne A.; Robinson, William A.

2017-01-01

A variety of analytical approaches have indicated that melanoma cell line UCLA‐SO‐M14 (M14) and breast carcinoma cell line MDA‐MB‐435 originate from a common donor. This indicates that at some point in the past, one of these cell lines became misidentified, meaning that it ceased to correspond to the reported donor and instead became falsely identified (through cross‐contamination or other means) as a cell line from a different donor. Initial studies concluded that MDA‐MB‐435 was the misidentified cell line and M14 was the authentic cell line, although contradictory evidence has been published, resulting in further confusion. To address this question, we obtained early samples of the melanoma cell line (M14), a lymphoblastoid cell line from the same donor (ML14), and donor serum preserved at the originator's institution. M14 samples were cryopreserved in December 1975, before MDA‐MB‐435 cells were established in culture. Through a series of molecular characterizations, including short tandem repeat (STR) profiling and cytogenetic analysis, we demonstrated that later samples of M14 and MDA‐MB‐435 correspond to samples of M14 frozen in 1975, to the lymphoblastoid cell line ML14, and to the melanoma donor's STR profile, sex and blood type. This work demonstrates conclusively that M14 is the authentic cell line and MDA‐MB‐435 is misidentified. With clear provenance information and authentication testing of early samples, it is possible to resolve debates regarding the origins of problematic cell lines that are widely used in cancer research. PMID:28940260

Line lessons: Enbridge's Northern Line provides valuable information

Energy Technology Data Exchange (ETDEWEB)

Ross, E.

2000-02-01

Experiences gained from the 14-year old Norman Wells crude oil pipeline in the Northwest Territories may provide operators with valuable insights in natural gas pipeline developments in northern Canada. The Norman Wells line is the first and only long-distance pipeline in North America buried in permafrost and has proven to be a veritable laboratory on pipeline behaviour in extremely cold climates which also happen to be discontinuous at the same time. The line was built by Enbridge with a 'limit state' design, i e. it was built to move within the permafrost within certain limits, the amount of movement depending upon the area in which the line was built. This technology, which is still cutting edge, allows the pipeline to react to the freeze-thaw cycle without being affected by the heaving and resettling. The knowledge gained from the Norman Wells Line has come in very useful in the more recent AltaGas Services project transporting natural gas from a nearby well into the the town of Inuvik. Enbridge also contributed to the development of various pipeline inspection tools such as the 'Geopig' which travels within the pipeline and can pinpoint the location of problems practically within a matter of inches, and the 'Rolligon' an amphibious vehicle with five-foot diameter rubber tires that displaces only two pounds per square inch, leaving barely a track as it travels along the right-of-way during times other than winter.

Development of 25 near-isogenic lines (NILs) with ten BPH resistance genes in rice (Oryza sativa L.): production, resistance spectrum, and molecular analysis.

Science.gov (United States)

Jena, Kshirod K; Hechanova, Sherry Lou; Verdeprado, Holden; Prahalada, G D; Kim, Sung-Ryul

2017-11-01

A first set of 25 NILs carrying ten BPH resistance genes and their pyramids was developed in the background of indica variety IR24 for insect resistance breeding in rice. Brown planthopper (Nilaparvata lugens Stal.) is one of the most destructive insect pests in rice. Development of near-isogenic lines (NILs) is an important strategy for genetic analysis of brown planthopper (BPH) resistance (R) genes and their deployment against diverse BPH populations. A set of 25 NILs with 9 single R genes and 16 multiple R gene combinations consisting of 11 two-gene pyramids and 5 three-gene pyramids in the genetic background of the susceptible indica rice cultivar IR24 was developed through marker-assisted selection. The linked DNA markers for each of the R genes were used for foreground selection and confirming the introgressed regions of the BPH R genes. Modified seed box screening and feeding rate of BPH were used to evaluate the spectrum of resistance. BPH reaction of each of the NILs carrying different single genes was variable at the antibiosis level with the four BPH populations of the Philippines. The NILs with two- to three-pyramided genes showed a stronger level of antibiosis (49.3-99.0%) against BPH populations compared with NILs with a single R gene NILs (42.0-83.5%) and IR24 (10.0%). Background genotyping by high-density SNPs markers revealed that most of the chromosome regions of the NILs (BC 3 F 5 ) had IR24 genome recovery of 82.0-94.2%. Six major agronomic data of the NILs showed a phenotypically comparable agronomic performance with IR24. These newly developed NILs will be useful as new genetic resources for BPH resistance breeding and are valuable sources of genes in monitoring against the emerging BPH biotypes in different rice-growing countries.

Line width and line shape analysis in the inductively coupled plasma by high resolution Fourier transform spectrometry

International Nuclear Information System (INIS)

Faires, L.M.; Palmer, B.A.; Brault, J.W.

1984-01-01

High resolution Fourier transform spectrometry has been used to perform line width and line shape analysis of eighty-one iron I emision lines in the spectral range 290 to 390nm originating in the normal analytical zone of an inductively coupled plasma. Computer programs using non-linear least squares fitting techniques for line shape analysis were applied to the fully resolved spectra to determine Gaussian and Lorentzian components of the total observed line width. The effect of noise in the spectrum on the precision of the line fitting technique was assessed, and the importance of signal to noise ratio for line shape analysis is discussed. Translational (Doppler) temperatures were calculated from the Gaussian components of the line width and were found to be on the order of 6300 0 K. The excitation temperature of iron I was also determined from the same spectral data by the spectroscopic slope method based on the Einstein-Boltzmann expression for spectral intensity and was found to be on the order of 4700 0 K. 31 references

Nuclear gamma ray lines from supernovae

International Nuclear Information System (INIS)

Jardim, J.O.D.

1980-01-01

From theoretical considerations of the behaviour of gamma ray line fluxes occurring after a supernova explosion, the 1.156 and 0.847 MeV lines are seen to be the most likely to be observed. The 1.156 MeV line has been previously observed by other investigators. Observations of the 0.847 MeV line, and 1.332, 1.173 and 0.059 MeV lines using a Ge(Li) telescope aboard a stratospheric balloon which was flown in Brazil in 1977 are reported. The observation using a NaI(Tl) detector of a line in the energy interval 1.5 - 1.6 MeV, which may be due to 0 18 (p,p') 0 18 sup (*) reaction is also reported. (Author) [pt

Line profile variations in selected Seyfert galaxies

International Nuclear Information System (INIS)

Kollatschny, W; Zetzl, M; Ulbrich, K

2010-01-01

Continua as well as the broad emission lines in Seyfert 1 galaxies vary in different galaxies with different amplitudes on typical timescales of days to years. We present the results of two independent variability campaigns taken with the Hobby-Eberly Telescope. We studied in detail the integrated line and continuum variations in the optical spectra of the narrow-line Seyfert galaxy Mrk 110 and the very broad-line Seyfert galaxy Mrk 926. The broad-line emitting region in Mrk 110 has radii of four to 33 light-days as a function of the ionization degree of the emission lines. The line-profile variations are matched by Keplerian disk models with some accretion disk wind. The broad-line region in Mrk 926 is very small showing an extension of two to three light-days only. We could detect a structure in the rms line-profiles as well as in the response of the line profile segments of Mrk 926 indicating the BLR is structured.

Second-Line Therapy for Advanced NSCLC.

Science.gov (United States)

Weiss, Jared M; Stinchcombe, Thomas E

2013-01-01

Most patients with lung cancer have non-small cell lung cancer (NSCLC) subtype and have advanced disease at the time of diagnosis. Improvements in both first-line and subsequent therapies are allowing longer survival and enhanced quality of life for these patients. The median overall survival observed in many second-line trials is approximately 9 months, and many patients receive further therapy after second-line therapy. The cytotoxic agents pemetrexed and docetaxel and the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) erlotinib and gefitinib are standard second-line therapies. For patients with EGFR mutation, a TKI is the favored second-line therapy if not already used in first-line therapy. For patients without the EGFR mutation, TKIs are an option, but many oncologists favor cytotoxic therapy. The inhibitor of the EML4/ALK fusion protein, crizotinib, has recently become a standard second-line treatment for patients with the gene rearrangement and has promise for patients with the ROS1 rearrangement.

PIXE analysis of U and Pu from hot particles: K-lines vs L-lines

DEFF Research Database (Denmark)

Jiménez-Ramos, M.C.; García López, J.; Eriksson, M.

2012-01-01

. (2007) [1] and Jiménez-Ramos et al. (2010) [2], radioactive particles from aircraft accidents in Palomares and Thule have been characterized. Using micro-Proton Induced X-ray Emission (μ-PIXE) and confocal X-ray fluorescence microprobe (μ-XRF), the L-lines of the main components in these particles, U......-lines present not overlapping between the main peaks in the spectra and the X-ray absorption in the sample is much lower than for L-lines....

Transmission Line Security Monitor: Final Report

Energy Technology Data Exchange (ETDEWEB)

John Svoboda

2011-04-01

The Electric Power Transmission Line Security Monitor System Operational Test is a project funded by the Technical Support Working Group (TSWG). TSWG operates under the Combating Terrorism Technical Support Office that functions under the Department of Defense. The Transmission Line Security Monitor System is based on technology developed by Idaho National Laboratory. The technology provides a means for real-time monitoring of physical threats and/or damage to electrical transmission line towers and conductors as well as providing operational parameters to transmission line operators to optimize transmission line operation. The end use is for monitoring long stretches of transmission lines that deliver electrical power from remote generating stations to cities and industry. These transmission lines are generally located in remote transmission line corridors where security infrastructure may not exist. Security and operational sensors in the sensor platform on the conductors take power from the transmission line and relay security and operational information to operations personnel hundreds of miles away without relying on existing infrastructure. Initiated on May 25, 2007, this project resulted in pre-production units tested in realistic operational environments during 2010. A technology licensee, Lindsey Manufacturing of Azusa California, is assisting in design, testing, and ultimately production. The platform was originally designed for a security monitoring mission, but it has been enhanced to include important operational features desired by electrical utilities.

Successful Wide Hybridization and Introgression Breeding in a Diverse Set of Common Peppers (Capsicum annuum) Using Different Cultivated Ají (C. baccatum) Accessions as Donor Parents

Science.gov (United States)

2015-01-01

Capsicum baccatum, commonly known as ají, has been reported as a source of variation for many different traits to improve common pepper (C. annuum), one of the most important vegetables in the world. However, strong interspecific hybridization barriers exist between them. A comparative study of two wide hybridization approaches for introgressing C. baccatum genes into C. annuum was performed: i) genetic bridge (GB) using C. chinense and C. frutescens as bridge species; and, ii) direct cross between C. annuum and C. baccatum combined with in vitro embryo rescue (ER). A diverse and representative collection of 18 accessions from four cultivated species of Capsicum was used, including C. annuum (12), C. baccatum (3), C. chinense (2), and C. frutescens (1). More than 5000 crosses were made and over 1000 embryos were rescued in the present study. C. chinense performed as a good bridge species between C. annuum and C. baccatum, with the best results being obtained with the cross combination [C. baccatum (♀) × C. chinense (♂)] (♀) × C. annuum (♂), while C. frutescens gave poor results as bridge species due to strong prezygotic and postzygotic barriers. Virus-like-syndrome or dwarfism was observed in F1 hybrids when both C. chinense and C. frutescens were used as female parents. Regarding the ER strategy, the best response was found in C. annuum (♀) × C. baccatum (♂) crosses. First backcrosses to C. annuum (BC1s) were obtained according to the crossing scheme [C. annuum (♀) × C. baccatum (♂)] (♀) × C. annuum (♂) using ER. Advantages and disadvantages of each strategy are discussed in relation to their application to breeding programmes. These results provide breeders with useful practical information for the regular utilization of the C. baccatum gene pool in C. annuum breeding. PMID:26642059

Reduction of the visual impact of overhead transmission line systems through utilisation of line surge arresters as lightning protection

DEFF Research Database (Denmark)

Sørensen, Thomas Kjærsgaard; Holbøll, Joachim

2008-01-01

with the Technical University of Denmark, on how to lessen the visual impact of 400 kV overhead line transmission systems. In this paper omission of shield wires combined with installation of a suitable number of line surge arresters is investigated as a possible alternative to transmission lines equipped...... with shielding wires thereby reducing tower height, allowing more compact designs of towers thus minimizing the visual environment impact of the lines. Omission of shield wires in the system and instead utilizing a larger number of surge arresters in the (upper) phases of an overhead line without reduction...... will be investigated by transient simulations on a 400 kV line with either shield wires or line surge arresters. These simulations will also be used to estimate number and location of the line surge arresters in the line to ensure a satisfactory performance of the line when omitting shield wires in the tower top...

Transmission of radioiodine through sampling lines

International Nuclear Information System (INIS)

Unrein, P.J.; Pelletier, C.A.; Cline, J.E.; Voilleque, P.G.

1985-01-01

An experimental program to measure radioiodine transmission through sampling lines is described. The transmission depends upon both deposition on and resuspension from the walls of the line. The deposition and resuspension processes are themselves controlled by the length, diameter, and material of the line and the conditions under which it is operated. The operating conditions under study are sampling flow rate, temperature and relative humidity. Measurement results have been interpreted in terms of a four-compartment model of radioiodine deposition and resuspension. The model is applied to each of twenty or more segments of the line. Experimental measurements of short-term transmission fractions and the deposition velocities derived from them are presented for six lines. Data on resuspension rates for the same lines were obtained and are also discussed

Introgression of leaf rust and stripe rust resistance from Sharon goatgrass (Aegilops sharonensis Eig) into bread wheat (Triticum aestivum L.).

Science.gov (United States)

Millet, E; Manisterski, J; Ben-Yehuda, P; Distelfeld, A; Deek, J; Wan, A; Chen, X; Steffenson, B J

2014-06-01

Leaf rust and stripe rust are devastating wheat diseases, causing significant yield losses in many regions of the world. The use of resistant varieties is the most efficient way to protect wheat crops from these diseases. Sharon goatgrass (Aegilops sharonensis or AES), which is a diploid wild relative of wheat, exhibits a high frequency of leaf and stripe rust resistance. We used the resistant AES accession TH548 and induced homoeologous recombination by the ph1b allele to obtain resistant wheat recombinant lines carrying AES chromosome segments in the genetic background of the spring wheat cultivar Galil. The gametocidal effect from AES was overcome by using an "anti-gametocidal" wheat mutant. These recombinant lines were found resistant to highly virulent races of the leaf and stripe rust pathogens in Israel and the United States. Molecular DArT analysis of the different recombinant lines revealed different lengths of AES segments on wheat chromosome 6B, which indicates the location of both resistance genes.

DETECTION OF REST-FRAME OPTICAL LINES FROM X-SHOOTER SPECTROSCOPY OF WEAK EMISSION-LINE QUASARS

International Nuclear Information System (INIS)

Plotkin, Richard M.; Gallo, Elena; Shemmer, Ohad; Trakhtenbrot, Benny; Anderson, Scott F.; Brandt, W. N.; Luo, Bin; Schneider, Donald P.; Fan, Xiaohui; Lira, Paulina; Richards, Gordon T.; Strauss, Michael A.; Wu, Jianfeng

2015-01-01

Over the past 15 yr, examples of exotic radio-quiet quasars with intrinsically weak or absent broad emission line regions (BELRs) have emerged from large-scale spectroscopic sky surveys. Here, we present spectroscopy of seven such weak emission line quasars (WLQs) at moderate redshifts (z = 1.4–1.7) using the X-shooter spectrograph, which provides simultaneous optical and near-infrared spectroscopy covering the rest-frame ultraviolet (UV) through optical. These new observations effectively double the number of WLQs with spectroscopy in the optical rest-frame, and they allow us to compare the strengths of (weak) high-ionization emission lines (e.g., C iv) to low-ionization lines (e.g., Mg ii, Hβ, Hα) in individual objects. We detect broad Hβ and Hα emission in all objects, and these lines are generally toward the weaker end of the distribution expected for typical quasars (e.g., Hβ has rest-frame equivalent widths ranging from 15–40 Å). However, these low-ionization lines are not exceptionally weak, as is the case for high-ionization lines in WLQs. The X-shooter spectra also display relatively strong optical Fe ii emission, Hβ FWHM ≲ 4000 km s −1 , and significant C iv blueshifts (≈1000–5500 km s −1 ) relative to the systemic redshift; two spectra also show elevated UV Fe ii emission, and an outflowing component to their (weak) Mg ii emission lines. These properties suggest that WLQs are exotic versions of “wind-dominated” quasars. Their BELRs either have unusual high-ionization components, or their BELRs are in an atypical photoionization state because of an unusually soft continuum

Spectral Line Shapes. Proceedings

International Nuclear Information System (INIS)

Zoppi, M.; Ulivi, L.

1997-01-01

These proceedings represent papers presented at the 13th International Conference on Spectral Line Shapes which was held in Firenze,Italy from June 16-21, 1996. The topics covered a wide range of subjects emphasizing the physical processes associated with the formation of line profiles: high and low density plasma; atoms and molecules in strong laser fields, Dopple-free and ultra-fine spectroscopy; the line shapes generated by the interaction of neutrals, atoms and molecules, where the relavant quantities are single particle properties, and the interaction-induced spectroscopy. There were 131 papers presented at the conference, out of these, 6 have been abstracted for the Energy Science and Technology database

Database of emission lines

Science.gov (United States)

Binette, L.; Ortiz, P.; Joguet, B.; Rola, C.

1998-11-01

A widely accessible data bank (available through Netscape) and consiting of all (or most) of the emission lines reported in the litterature is being built. It will comprise objects as diverse as HII regions, PN, AGN, HHO. One of its use will be to define/refine existing diagnostic emission line diagrams.

APOBEC3DE Inhibits LINE-1 Retrotransposition by Interacting with ORF1p and Influencing LINE Reverse Transcriptase Activity.

Directory of Open Access Journals (Sweden)

Weizi Liang

Full Text Available Human long interspersed elements 1 (LINE-1 or L1 is the only autonomous non-LTR retroelement in humans and has been associated with genome instability, inherited genetic diseases, and the development of cancer. Certain human APOBEC3 family proteins are known to have LINE-1 restriction activity. The mechanisms by which APOBEC3 affects LINE-1 retrotransposition are not all well characterized; here, we confirm that both A3B and A3DE have a strong ability to inhibit LINE-1 retrotransposition. A3DE interacts with LINE-1 ORF1p to target LINE-1 ribonucleoprotein particles in an RNA-dependent manner. Moreover, A3DE binds to LINE-1 RNA and ORF1 protein in cell culture system. Fluorescence microscopy demonstrated that A3DE co-localizes with ORF1p in cytoplasm. Furthermore, A3DE inhibits LINE-1 reverse transcriptase activity in LINE-1 ribonucleoprotein particles in a cytidine deaminase-independent manner. In contrast, A3B has less inhibitory effects on LINE-1 reverse transcriptase activity despite its strong inhibition of LINE-1 retrotransposition. This study demonstrates that different A3 proteins have been evolved to inhibit LINE-1 activity through distinct mechanisms.

Building Bridges One Line at a Time

Science.gov (United States)

Grigsby, Cathy Murray

2012-01-01

In this article, first-grade students were taught the different kinds of lines that were part of the construction of various bridges--the curved lines of the arches of stone bridges, straight lines connecting the cables of a suspension bridge, vertical lines, horizontal lines, and so on. They gained practice in drawing structures and in fine brush…

Along the line

DEFF Research Database (Denmark)

Dinesen, Cort Ross

2011-01-01

Embarking on a work of art constitutes a reduction of information – because we grasp the diversity and plurality of the manifestations we encounter by abstracting them and transforming them into manageable concepts; as we do when we draw contour lines on the landscape – they are imaginary...... and invisible but an abstraction essential for noting a difference or marking a place on a map. In the same way, a stroke in a sketch or a line in the sand is a manifestation of our ability to draw a boundary that both includes and excludes information. Where the line makes the birth of an idea visible......, it expresses through movement our tendency to mark a difference by drawing attention to and enclosing a whole series of relations that confront our preconceived notions. It is in the process of transformation in which we reduce the complexity of how we work, and rethink our ideas anew by refining the very same...

The identification of a gene (Cwp1), silenced during Solanum evolution, which causes cuticle microfissuring and dehydration when expressed in tomato fruit.

Science.gov (United States)

Hovav, Ran; Chehanovsky, Noam; Moy, Michal; Jetter, Reinhard; Schaffer, Arthur A

2007-11-01

One of the most intriguing phenomena of fleshy fruit is the ability to maintain high water content at maturity, even following harvest. This is accomplished by a fruit cuticle that is highly impermeable to water diffusion. In this paper, we report on a novel genotype of tomato, developed via introgression from the wild species Solanum habrochaites, which is characterized by microfissuring of the fruit cuticle and dehydration of the mature fruit. The microfissure/dehydration phenotype is inherited as a single gene, termed Cwp1 (cuticular water permeability). The gene was fine mapped, and its identity was determined by map-based cloning and differential expression analysis in near-isogenic lines. Causality of the Cwp1 gene was shown by the heterologous transgenic expression of the gene in the cultivated tomato, which caused a microfissured fruit cuticle leading to dehydrated fruit. Cwp1 encodes for a protein of unidentified function in the DUF833 domain family. The gene is expressed in the fruit epidermis of the dehydrating genotype harbouring the wild-species introgression, but not in the cultivated tomato. It is expressed only in the primitive green-fruited wild tomato species, but is not expressed in the cultivated Solanum lycopersicum and the closely related Solanum cheesmaniae and Solanum pimpinellifolium, indicating a pre-adaptive role for Cwp1 silencing in the evolution and domestication of the cultivated tomato.

Program of telluric lines monitoring

Directory of Open Access Journals (Sweden)

Vince I.

2006-01-01

Full Text Available A new observational program of telluric lines monitoring was introduced at Belgrade Astronomical Observatory. The ultimate goal of this program is to investigate the properties of Earth’s atmosphere through modeling the observed profiles of telluric lines. The program is intend to observe infrared molecular oxygen lines that were selected according to spectral sensitivity of the available CCD camera. In this paper we give the initial and the final selection criteria for spectral lines included in the program the description of equipment and procedures used for observations and reduction, a review of preliminary observational results with the estimated precision, and a short discussion on the comparison of the theoretical predictions and the measurements.

[The smile line, a literature search].

Science.gov (United States)

van der Geld, P A; van Waas, M A

2003-09-01

Beautiful teeth, visible when smiling, are in line with the present ideal of beauty. The display of teeth when smiling is determined by the smile line: the projection of the lower border of the upper lip on the maxillary teeth when smiling. On the basis of a literature search the determining methods of the smile line are discussed, demographic data of the position of the smile line are given, and factors of influence are examined. There is no unequivocal method for determining the position of the smile line. A rough distinction can be made between qualitative and (semi)-quantitative methods. The (semi)-quantitative methods have clear advantages for research purposes, but their reliability is unknown. It was demonstrated that among minimally 40% of subjects the maxillary gingiva was not visible when smiling. The mandibular gingiva was not visible when smiling among more than 90% of subjects. Furthermore, it appeared that among women the smile line was on average higher situated than among men and that it has not yet been proven that the smile line will be situated lower when growing older.

A specialized bioengineering ion beam line

International Nuclear Information System (INIS)

Yu, L.D.; Sangyuenyongpipat, S.; Sriprom, C.; Thongleurm, C.; Suwanksum, R.; Tondee, N.; Prakrajang, K.; Vilaithong, T.; Brown, I.G.; Wiedemann, H.

2007-01-01

A specialized bioengineering ion beam line has recently been completed at Chiang Mai University to meet rapidly growing needs of research and application development in low-energy ion beam biotechnology. This beam line possesses special features: vertical main beam line, low-energy (30 keV) ion beams, double swerve of the beam, a fast pumped target chamber, and an in-situ atomic force microscope (AFM) system chamber. The whole beam line is situated in a bioclean environment, occupying two stories. The quality of the ion beam has been studied. It has proved that this beam line has significantly contributed to our research work on low-energy ion beam biotechnology

Molecular Mapping of PMR1, a Novel Locus Conferring Resistance to Powdery Mildew in Pepper (Capsicum annuum

Directory of Open Access Journals (Sweden)

Jinkwan Jo

2017-12-01

Full Text Available Powdery mildew, caused by Leveillula taurica, is a major fungal disease affecting greenhouse-grown pepper (Capsicum annuum. Powdery mildew resistance has a complex mode of inheritance. In the present study, we investigated a novel powdery mildew resistance locus, PMR1, using two mapping populations: 102 ‘VK515' F2:3 families (derived from a cross between resistant parental line ‘VK515R' and susceptible parental line ‘VK515S' and 80 ‘PM Singang' F2 plants (derived from the F1 ‘PM Singang' commercial hybrid. Genetic analysis of the F2:3 ‘VK515' and F2 ‘PM Singang' populations revealed a single dominant locus for inheritance of the powdery mildew resistance trait. Genetic mapping showed that the PMR1 locus is located on syntenic regions of pepper chromosome 4 in a 4-Mb region between markers CZ2_11628 and HRM4.1.6 in ‘VK515R'. Six molecular markers including one SCAR marker and five SNP markers were localized to a region 0 cM from the PMR1 locus. Two putative nucleotide-binding site leucine-rich repeat (NBS-LRR-type disease resistance genes were identified in this PMR1 region. Genotyping-by-sequencing (GBS and genetic mapping analysis revealed suppressed recombination in the PMR1 region, perhaps due to alien introgression. In addition, a comparison of species-specific InDel markers as well as GBS-derived SNP markers indicated that C. baccatum represents a possible source of such alien introgression of powdery mildew resistance into ‘VK515R'. The molecular markers developed in this study will be especially helpful for marker-assisted selection in pepper breeding programs for powdery mildew resistance.

Illustrative Line Styles for Flow Visualization

NARCIS (Netherlands)

Everts, Maarten H.; Bekker, Hendrik; Roerdink, Jos B. T. M.; Isenberg, Tobias

2011-01-01

We present a flexible illustrative line style model for the visualization of streamline data. Our model partitions view-oriented line strips into parallel bands whose basic visual properties can be controlled independently. We thus extend previous line stylization techniques specifically for

Flow Visualization using Illustrative Line Styles

NARCIS (Netherlands)

Everts, Maarten H.; Bekker, Hendrik; Roerdink, Jos B. T. M.; Isenberg, Tobias; Bekker, Paulus

2011-01-01

We present a flexible illustrative line style model for the visualization of streamline data. Our model partitions view- oriented line strips into parallel bands whose basic visual properties can be controlled independently. We thus extend previous line stylization techniques specifically for

Computer-based mechanical design of overhead lines

Science.gov (United States)

Rusinaru, D.; Bratu, C.; Dinu, R. C.; Manescu, L. G.

2016-02-01

Beside the performance, the safety level according to the actual standards is a compulsory condition for distribution grids’ operation. Some of the measures leading to improvement of the overhead lines reliability ask for installations’ modernization. The constraints imposed to the new lines components refer to the technical aspects as thermal stress or voltage drop, and look for economic efficiency, too. The mechanical sizing of the overhead lines is after all an optimization problem. More precisely, the task in designing of the overhead line profile is to size poles, cross-arms and stays and locate poles along a line route so that the total costs of the line's structure to be minimized and the technical and safety constraints to be fulfilled.The authors present in this paper an application for the Computer-Based Mechanical Design of the Overhead Lines and the features of the corresponding Visual Basic program, adjusted to the distribution lines. The constraints of the optimization problem are adjusted to the existing weather and loading conditions of Romania. The outputs of the software application for mechanical design of overhead lines are: the list of components chosen for the line: poles, cross-arms, stays; the list of conductor tension and forces for each pole, cross-arm and stay for different weather conditions; the line profile drawings.The main features of the mechanical overhead lines design software are interactivity, local optimization function and high-level user-interface

Veterans Crisis Line: 1-800-273-8255

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Veterans Crisis Line Skip to Main Content SuicidePreventionLifeline.org Get Help Materials Get Involved Crisis Centers About Be There ... Line FAQs Veteran Suicide Welcome to the Veterans Crisis Line Website The Veterans Crisis Line connects Veterans ...

Reddening and He i{sup ∗} λ 10830 Absorption Lines in Three Narrow-line Seyfert 1 Galaxies

Energy Technology Data Exchange (ETDEWEB)

Zhang, Shaohua; Zhou, Hongyan; Shi, Xiheng; Pan, Xiang; Ji, Tuo; Jiang, Peng; Wang, Shufen [Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136 (China); Liu, Wenjuan [Key Laboratory for the Structure and Evolution of Celestial Objects, Yunnan Observatories, Chinese Academy of Sciences, Kunming, Yunnan 650011 (China); Jiang, Ning, E-mail: zhangshaohua@pric.org.cn, E-mail: zhouhongyan@pric.org.cn [Key Laboratory for Researches in Galaxies and Cosmology, Department of Astronomy, University of Sciences and Technology of China, Chinese Academy of Sciences, Hefei, Anhui, 230026 (China)

2017-08-20

We report the detection of heavy reddening and the He i* λ 10830 absorption lines at the active galactic nucleus (AGN) redshift in three narrow-line Seyfert 1 galaxies: SDSS J091848.61+211717.0, SDSS J111354.66+124439.0, and SDSS J122749.13+321458.9. They exhibit very red optical to near-infrared colors, narrow Balmer/Paschen broad emission lines and He i* λ 10830 absorption lines. The ultraviolet-optical-infrared nucleus continua are reddened by the SMC extinction law of E ( B − V ) ∼ 0.74, 1.17, and 1.24 mag for three objects, which are highly consistent with the values obtained from the broad-line Balmer decrements, but larger than those of narrow emission lines. The reddening analysis suggests that the extinction dust simultaneously obscures the accretion disk, the broad emission-line region, and the hot dust from the inner edge of the torus. It is possible that the dust obscuring the AGN structures is the dusty torus itself. Furthermore, the Cloudy analysis of the He i* λ 10830 absorption lines proposes the distance of the absorption materials to be the extend scale of the torus, which greatly increases probabilities of the obscure and absorption materials being the dusty torus.

Are both sympatric species Ilex perado and Ilex canariensis secretly hybridizing? Indication from nuclear markers collected in Tenerife

Directory of Open Access Journals (Sweden)

Manen Jean-François

2004-11-01

Full Text Available Abstract Background Intra-specific and intra-individual polymorphism is frequently observed in nuclear markers of Ilex (Aquifoliaceae and discrepancy between plastid and nuclear phylogenies is the rule in this genus. These observations suggest that inter-specific plastid or/and nuclear introgression played an important role in the process of evolution of Ilex. With the aim of a precise understanding of the evolution of this genus, two distantly related sympatric species collected in Tenerife (Canary Islands, I. perado and I. canariensis, were studied in detail. Introgression between these two species was previously never reported. One plastid marker (the atpB-rbcL spacer and two nuclear markers, the ribosomal internal transcribed spacer (ITS and the nuclear encoded plastid glutamine synthetase (nepGS were analyzed for 13 and 27 individuals of I. perado and I. canariensis, respectively. Results The plastid marker is intra-specifically constant and correlated with species identity. On the other hand, whereas the nuclear markers are conserved in I. perado, they are highly polymorphic in I. canariensis. The presence of pseudogenes and recombination in ITS sequences of I. canariensis explain this polymorphism. Ancestral sequence polymorphism with incomplete lineage sorting, or past or recent hybridization with an unknown species could explain this polymorphism, not resolved by concerted evolution. However, as already reported for many other plants, past or recent introgression of an alien genotype seem the most probable explanation for such a tremendous polymorphism. Conclusions Data do not allow the determination with certitude of the putative species introgressing I. canariensis, but I. perado is suspected. The introgression would be unilateral, with I. perado as the male donor, and the paternal sequences would be rapidly converted in highly divergent and consequently unidentifiable pseudogenes. At least, this study allows the establishment of

Magnetic pulse sharpener and delay-line