Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

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Ward Judson A

2013-01-01

Full Text Available Abstract Background Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry. Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputation require a reference genome and thus are not an option for most species. Results Genotyping by Sequencing (GBS was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs linked these results to published maps for cross-validation and map comparison. Conclusions GBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation

Kinetics of methane fermentation yield in biogas reactors: Genetic variation and association with chemical composition in maize

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Grieder, Christoph; Mittweg, Greta; Dhillon, Baldev S.; Montes, Juan M.; Orsini, Elena; Melchinger, Albrecht E.

2012-01-01

Maize (Zea mays L.) is the most competitive crop for methane production in Germany. Methane fermentation yield per unit of dry matter (MFY) is a determinant of methane yield, but little information is available on this trait. Our objectives were to investigate the kinetics of MFY during fermentation of maize, estimate quantitative-genetic parameters for different traits related to MFY and examine the relationship of MFY with chemical composition and silage quality. Whole-plant material of 16 inbreds and their 32 testcrosses was analyzed for MFY over 35 days of fermentation using a discontinuous laboratory assay. Data were also generated on chemical composition and in vitro digestible organic matter (IVDOM). Significant genotypic variances and high heritabilities were observed for MFY at early fermentation stages (up to 5 days) probably due to different concentrations of easily degradable chemical components. However, genotypic variances and heritability of MFY reduced as fermentation progressed, because of complete or partial degradation of all chemical components. Further, there were strong correlations of MFY with chemical components at early fermentation stages but not at later stages. Therefore, MFY at later stages, which is closer to potential MFY, does not seem to be amenable to selection. High heritability of IVDOM and its strong correlation with MFY in testcrosses indicated its possible use for preliminary or indirect selection. Keeping in view the magnitude of genetic variance that was low for MFY and high for dry matter yield (DMY), the other component of methane yield, more emphasis on breeding for DMY seems appropriate. -- Highlights: ► We investigated methane fermentation yield (MFY) of diverse germplasm of maize. ► The kinetics of MFY and its correlations with chemical composition were examined. ► Genetic variance and heritability for MFY decreased with fermentation time. ► Complete fermentation (35 d) reduced correlations of MFY with chemical

Heritable effect of plant water availability conditions on restoration of male fertility in the ‘9E’ CMS-inducing cytoplasm of sorghum

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Lev Aleksandrovich Elkonin

2012-05-01

Full Text Available Heritable changes of phenotype arising in plant ontogenesis by the influence of environmental factors belong to the most intriguing genetic phenomena. Studying restoration of male fertility in the ‘9E’ type of CMS-inducing cytoplasm of sorghum and related CMS-inducing cytoplasms, A4 and M35-1A, in some hybrid combinations, we found an unusual inheritance pattern: the Rf-genes functioned in the self-pollinated progenies of F1 hybrids (up to F10 but did not or poorly expressed in backcrosses of these hybrids to CMS-lines with the same cytoplasm type. In experiments on parallel growing of the same F1 hybrid combinations in the ‘dry plot’ and in the ‘irrigated plot’, it was found that high level of plant water availability during panicle and pollen developmental stages significantly increased male fertility of F1 and testcross hybrid populations, in which fertility-restoring genes were in heterozygote state, whereas in F2 populations the influences of water availability conditions cause less pronounce effects. Similarly, male-sterile F1 plants, being transferred from the ‘dry plot’ to greenhouse, produced male-fertile panicles. In addition, male-sterile plants from F2 families, which segregated-out as recessives, being transferred to greenhouse also produced male-fertile panicles. In the progenies of these revertants that were grown in field conditions and in the ‘dry plot’, stable inheritance of male fertility for 3 cycles of self-pollination was observed, and a number of stable fertile lines in the ‘9E’ cytoplasm were obtained. However, in test-crosses of these fertile lines to CMS-lines with the ‘9E’ cytoplasm restoration of male fertility was not observed, except the progeny of one revertant that behaved as fertility-restorer line. These data suggest that the functional state of fertility-restoring genes for the ‘9E’ sorghum cytoplasm is epigenetically-regulated trait established by the influence of environmental

RELATIONSHIP BETWEEN DIFFERENT ALLOGAMIC ASSOCIATED TRAIT CHARACTERISTICS OF THE FIVE NEWLY DEVELOPED CYTOPLASMIC MALE STERILE (CMS LINES IN RICE

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Nematzadeh GHORBAN ALI

2006-10-01

Full Text Available Five suitable maintainer varieties were identifi ed through testcrosses with IR58025A and the transfer of wild abortive cytoplasm was carried out by seven successive backcrosses. Five new CMS lines were developed by this approach in well adapted high yielding improved varietal background such as ‘Nemat’, ‘Neda’, ‘Dasht’, ‘Amol3’ and ‘Champa’. Agronomical characterization and allogamy-associated traits of the fi ve newly developed CMS lines were studied for their interrelationship. Anther length had a signifi cant positive correlation with the duration of glume opening (0.759 and high correlation of (0.698 with the angle between lemma and palea. The results indicated that ‘Nemat’ A, ‘Neda’ A, ‘Dasht’ A are more suitable as parents for hybrid seed production due to their favorable and superior fl oral characteristics in comparison to IR58025A.

Accuracy of genomic selection in European maize elite breeding populations.

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Zhao, Yusheng; Gowda, Manje; Liu, Wenxin; Würschum, Tobias; Maurer, Hans P; Longin, Friedrich H; Ranc, Nicolas; Reif, Jochen C

2012-03-01

Genomic selection is a promising breeding strategy for rapid improvement of complex traits. The objective of our study was to investigate the prediction accuracy of genomic breeding values through cross validation. The study was based on experimental data of six segregating populations from a half-diallel mating design with 788 testcross progenies from an elite maize breeding program. The plants were intensively phenotyped in multi-location field trials and fingerprinted with 960 SNP markers. We used random regression best linear unbiased prediction in combination with fivefold cross validation. The prediction accuracy across populations was higher for grain moisture (0.90) than for grain yield (0.58). The accuracy of genomic selection realized for grain yield corresponds to the precision of phenotyping at unreplicated field trials in 3-4 locations. As for maize up to three generations are feasible per year, selection gain per unit time is high and, consequently, genomic selection holds great promise for maize breeding programs.

Development of a novel Sinapis arvensis disomic addition line in Brassica napus containing the restorer gene for Nsa CMS and improved resistance to Sclerotinia sclerotiorum and pod shattering.

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Wei, Wenhui; Li, Yunchang; Wang, Lijun; Liu, Shengyi; Yan, Xiaohong; Mei, Desheng; Li, Yinde; Xu, Yusong; Peng, Pengfei; Hu, Qiong

2010-04-01

An allo-cytoplasmic male sterile line, which was developed through somatic hybridization between Brassica napus and Sinapis arvensis (thus designated as Nsa CMS line), possesses high potential for hybrid production of rapeseed. In order to select for restorer lines, fertile plants derived from the same somatic hybridization combination were self-pollinated and testcrossed with the parental Nsa CMS line for six generations. A novel disomic alien addition line, B. napus-S. arvensis, has been successfully developed. GISH analysis showed that it contains one pair of chromosomes from S. arvensis and 19 pairs from B. napus, and retains stable and regular mitotic and meiotic processes. The addition line displays very strong restoration ability to Nsa CMS line, high resistance to Sclerotinia sclerotiorum and a low incidence of pod shattering. Because the addition line shares these very important agricultural characters, it is a valuable restorer to Nsa CMS line, and is named NR1 here (Nsa restorer no. 1).

A novel Capsicum gene inhibits host-specific disease resistance to Phytophthora capsici.

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Reeves, Gregory; Monroy-Barbosa, Ariadna; Bosland, Paul W

2013-05-01

A novel disease resistance inhibitor gene (inhibitor of P. capsici resistance [Ipcr]), found in the chile pepper (Capsicum annuum) variety 'New Mexico Capsicum Accession 10399' (NMCA10399), inhibits resistance to Phytophthora capsici but not to other species of Phytophthora. When a highly P. capsici-resistant variety was hybridized with NMCA10399, the resultant F1 populations, when screened, were completely susceptible to P. capsici for root rot and foliar blight disease syndromes, despite the dominance inheritance of P. capsici resistance in chile pepper. The F2 population displayed a 3:13 resistant-to-susceptible (R:S) ratio. The testcross population displayed a 1:1 R:S ratio, and a backcross population to NMCA10399 displayed complete susceptibility. These results demonstrate the presence of a single dominant inhibitor gene affecting P. capsici resistance in chile pepper. Moreover, when lines carrying the Ipcr gene were challenged against six Phytophthora spp., the nonhost resistance was not overcome. Therefore, the Ipcr gene is interfering with host-specific resistance but not the pathogen- or microbe-associated molecular pattern nonhost responses.

Development of Novel Cytoplasmic Male Sterile Source from Dongxiang Wild Rice (Oryza rufipogon

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Xian-hua SHEN

2013-09-01

Full Text Available This study was conducted to develop and characterize a novel cytoplasmic male sterile (CMS source which was identified from Dongxiang wild rice (Oryza rufipogon by crossing Dongxiang wild rice as female with Zhongzao 35, an indica inbred variety, as male and continuous backcrossing with Zhongzao 35. Observation under optical microscope manifested that this novel CMS belonged to typical abortion type with less pollen compared with wild abortive type cytoplasm (CMS-WA. Sequential planting showed that this novel CMS has complete and stable male sterility. Testcross experiment showed that all the 24 tested materials including maintainer and restorer lines of CMS-WA and Honglian type cytoplasm (CMS-HL and other indica inbred varieties are the maintainers with complete maintaining ability, suggesting that this novel CMS has fertility restoration totally different from CMS-WA and CMS-HL and belongs to a novel type of CMS. So far, we only discovered a unique fertility restoration source for this novel CMS. Inheritance analysis showed that the fertility restoration of this CMS was governed by three pairs of independent dominant genes. Prospect for application of this novel CMS system in hybrid rice breeding was also discussed.

Development and identification of a wheat-Roegneria kamoji translocation line T7A/1Rk no.1

International Nuclear Information System (INIS)

Bie Tongde; Feng Yigao; Chen Peidu; Xu Chuanmei

2009-01-01

Pollen of Triticum aestivum-Roegneria kamoji del1Rk No.1L disomic addition line, treated with 10 Gy 6 0C o γ-rays, was pollinated to T · aestivum cv. Chinese Spring. A reciprocal chromosomal translocation line involving wheat 7A and R.kamoji 1Rk No.1 was identified in M 2 generation using the techniques including C-banding, GISH, sequential C-banding/45S rDNA-FISH, and sequential GISH/45S rDNA-FISH. A 45S rDNA locus and its corresponding red band in GISH pattern were observed specific to the short arm of 1Rk No.1 and could be used as a marker of 1Rk No.1 chromosome. Analyses of chromosome constitution of M 2 population and test-crosses showed that the reciprocal translocation chromosomes were co-segregated in offspring, and the transmitting ratios were both higher through female gametes than through male ones. The results of scab resistance identification in 2004, 2005 and 2006 showed that the translocation line conveyed scab resistance that varied in different years in different district. The experiment also showed that pollen irradiation was an effective method to induce wheat-alien chromosome translocations. (authors)

The Genetic Variability of Floral and Agronomic Characteristics of Newly-Bred Cytoplasmic Male Sterile Rice

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Raafat El-Namaky

2018-05-01

Full Text Available Male sterility enabled commercialization of heterosis in rice but low seed set remains a constraint on hybrid dissemination. We evaluated 216 F6 maintainer lines for agronomic and floral characteristics in augmented design and selected 15 maintainer lines, which were testcrossed with IR58025A. Five backcrosses were conducted to transfer cytoplasmic male sterility (CMS to select maintainer lines. Newly-bred BC5:6 CMS lines were evaluated for outcrossing rates and agronomic characteristics. There were highly significant differences among 216 F6 maintainer lines for characteristics whose genotypic variance was higher than environmental variance. The phenotypic coefficient of variation was almost the same as the genotypic coefficient of variation, indicating that most phenotypic variation was due to genetics. There were highly significant differences among CMS lines for number of days to 50% flowering and maturity; stigma exertion; panicle exertion, length and weight; spikelet fertility; tillers per plant; plant height; grains per panicle; grain yield per plant; and 1000-grain weight, but not for pollen and panicle sterility during dry and wet seasons. Three CMS lines (CMS3, CMS12, and CMS14, exhibited high outcrossing rates (56.17%, 51.42% and 48.44%, respectively, which had a highly significant, positive correlation with stigma exertion (0.97, spikelet opening angle (0.82, and panicle exertion (0.95.

Genetic analysis in maize foundation parents with mapping population and testcross population: Ye478 carried more favorable alleles and using QTL information could improve foundation parents

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Yinghong Liu

2016-09-01

Full Text Available The development of maize foundation parents is an important part of genetics and breeding research, and applying new genetic information to produce foundation parents has been challenging. In this study, we focused on quantitative trait loci (QTLs and general combining ability (GCA of Ye478, a widely used foundation parent in China. We developed three sets of populations for QTL mapping and to analyze the GCA for some agronomic traits. The assessment of 15 traits resulted in the detection of 251 QTLs in six tested environments, with 119 QTLs identified through a joint analysis across all environments. Further analyses revealed that most favorable alleles for plant type-related traits were from Ye478, and more than half of the favorable alleles for yield-related traits were from R08, another foundation parent used in southwestern China, suggesting that different types of foundation parents carried different favorable alleles. We observed that the GCA for most traits (e.g., plant height and 100-kernel weight was maintained in the inbred lines descended from the foundation parents. Additionally, the continuous improvement in the GCA of the descendants of the foundation parents was consistent with the main trend in maize breeding programs. We identified three significant genomic regions that were highly conserved in three Ye478 descendants, including the stable QTL for plant height. The GCA for the traits in the F7 generation revealed that the QTLs for the given traits per se were affected by additive effects in the same way in different populations.

A first linkage map of globe artichoke (Cynara cardunculus var. scolymus L.) based on AFLP, S-SAP, M-AFLP and microsatellite markers.

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Lanteri, S; Acquadro, A; Comino, C; Mauro, R; Mauromicale, G; Portis, E

2006-05-01

We present the first genetic maps of globe artichoke (Cynara cardunculus var. scolymus L. 2n=2x=34), constructed with a two-way pseudo-testcross strategy. A F1 mapping population of 94 individuals was generated between a late-maturing, non-spiny type and an early-maturing spiny type. The 30 AFLP, 13 M-AFLP and 9 S-SAP primer combinations chosen identified, respectively, 352, 38 and 41 polymorphic markers. Of 32 microsatellite primer pairs tested, 12 identified heterozygous loci in one or other parent, and 7 were fully informative as they segregated in both parents. The female parent map comprised 204 loci, spread over 18 linkage groups and spanned 1330.5 cM with a mean marker density of 6.5 cM. The equivalent figures for the male parent map were 180 loci, 17 linkage groups, 1239.4 and 6.9 cM. About 3% of the AFLP and AFLP-derived markers displayed segregation distortion with a P value below 0.01, and were not used for map construction. All the SSR loci were included in the linkage analysis, although one locus did show some segregation distortion. The presence of 78 markers in common to both maps allowed the alignment of 16 linkage groups. The maps generated provide a firm basis for the mapping of agriculturally relevant traits, which will then open the way for the application of a marker-assisted selection breeding strategy in this species.

Strain Specific Factors Control Effector Gene Silencing in Phytophthora sojae.

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Sirjana Devi Shrestha

Full Text Available The Phytophthora sojae avirulence gene Avr3a encodes an effector that is capable of triggering immunity on soybean plants carrying the resistance gene Rps3a. P. sojae strains that express Avr3a are avirulent to Rps3a plants, while strains that do not are virulent. To study the inheritance of Avr3a expression and virulence towards Rps3a, genetic crosses and self-fertilizations were performed. A cross between P. sojae strains ACR10 X P7076 causes transgenerational gene silencing of Avr3a allele, and this effect is meiotically stable up to the F5 generation. However, test-crosses of F1 progeny (ACR10 X P7076 with strain P6497 result in the release of silencing of Avr3a. Expression of Avr3a in the progeny is variable and correlates with the phenotypic penetrance of the avirulence trait. The F1 progeny from a direct cross of P6497 X ACR10 segregate for inheritance for Avr3a expression, a result that could not be explained by parental imprinting or heterozygosity. Analysis of small RNA arising from the Avr3a gene sequence in the parental strains and hybrid progeny suggests that the presence of small RNA is necessary but not sufficient for gene silencing. Overall, we conclude that inheritance of the Avr3a gene silenced phenotype relies on factors that are variable among P. sojae strains.

Genetic linkage map and QTL identification for adventitious rooting traits in red gum eucalypts.

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Sumathi, Murugan; Bachpai, Vijaya Kumar Waman; Mayavel, A; Dasgupta, Modhumita Ghosh; Nagarajan, Binai; Rajasugunasekar, D; Sivakumar, Veerasamy; Yasodha, Ramasamy

2018-05-01

The eucalypt species, Eucalyptus tereticornis and Eucalyptus camaldulensis , show tolerance to drought and salinity conditions, respectively, and are widely cultivated in arid and semiarid regions of tropical countries. In this study, genetic linkage map was developed for interspecific cross E. tereticornis  ×  E. camaldulensis using pseudo-testcross strategy with simple sequence repeats (SSRs), intersimple sequence repeats (ISSRs), and sequence-related amplified polymorphism (SRAP) markers. The consensus genetic map comprised totally 283 markers with 84 SSRs, 94 ISSRs, and 105 SRAP markers on 11 linkage groups spanning 1163.4 cM genetic distance. Blasting the SSR sequences against E. grandis sequences allowed an alignment of 64% and the average ratio of genetic-to-physical distance was 1.7 Mbp/cM, which strengths the evidence that high amount of synteny and colinearity exists among eucalypts genome. Blast searches also revealed that 37% of SSRs had homologies with genes, which could potentially be used in the variety of downstream applications including candidate gene polymorphism. Quantitative trait loci (QTL) analysis for adventitious rooting traits revealed six QTL for rooting percent and root length on five chromosomes with interval and composite interval mapping. All the QTL explained 12.0-14.7% of the phenotypic variance, showing the involvement of major effect QTL on adventitious rooting traits. Increasing the density of markers would facilitate the detection of more number of small-effect QTL and also underpinning the genes involved in rooting process.

Construction of a SSR-Based Genetic Map and Identification of QTLs for Catechins Content in Tea Plant (Camellia sinensis)

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Ma, Chun-Lei; Wang, Xin-Chao; Jin, Ji-Qiang; Wang, Xue-Min; Chen, Liang

2014-01-01

Catechins are the most important bioactive compounds in tea, and have been demonstrated to possess a wide variety of pharmacological activities. To characterize quantitative trait loci (QTLs) for catechins content in the tender shoots of tea plant, we constructed a moderately saturated genetic map using 406 simple sequence repeat (SSR) markers, based on a pseudo-testcross population of 183 individuals derived from an intraspecific cross of two Camellia sinensis varieties with diverse catechins composition. The map consisted of fifteen linkage groups (LGs), corresponding to the haploid chromosome number of tea plant (2n = 2x = 30). The total map length was 1,143.5 cM, with an average locus spacing of 2.9 cM. A total of 25 QTLs associated with catechins content were identified over two measurement years. Of these, nine stable QTLs were validated across years, and clustered into four main chromosome regions on LG03, LG11, LG12 and LG15. The population variability explained by each QTL was predominantly at moderate-to-high levels and ranged from 2.4% to 71.0%, with an average of 17.7%. The total number of QTL for each trait varied from four to eight, while the total population variability explained by all QTLs for a trait ranged between 38.4% and 79.7%. This is the first report on the identification of QTL for catechins content in tea plant. The results of this study provide a foundation for further cloning and functional characterization of catechin QTLs for utilization in improvement of tea plant. PMID:24676054

Arbitrarily amplified DNA: New molecular approaches to plant breeding, ecology and evolution

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Caetano-Anolles, G [Department of Biology, University of Oslo, Oslo (Norway)

2001-11-01

Several DNA fingerprinting techniques that use arbitrary primers to characterize, scan and tag genomic DNA were optimized and used to study plants and microbial pathogens. The generated arbitrarily amplified DNA (AAD) profiles could be tailored in their complexity and polymorphic content, allowing analysis of closely related organisms, such as vegetatively-propagated horticultural crops or clonal fungal populations. AAD markers were used in cultivar and strain identification, map-based cloning, and marker-assisted breeding, sometimes as sequence-tagged sites. Phenetic analysis using parsimony, cluster, and numerical methods was applied successfully to the identification of genetic relationships in turfgrass species such as bermudagrass, woody plants such as dogwoods, and floricultural species such as petunia and chrysanthemum. AAD profiles were used to measure for the first time a genome-wide mutation rate, directly in a plant. Mutation rates in vegetatively propagated bermudagrass were comparable to those in human, mice, fruit flies, and worms. In combination with established tools used in molecular systematics (e.g. rDNA sequence analysis), AAD markers tracked the introduction of exotic dogwood anthracnose-causing fungi in North America. As part of a breeding effort to combat dogwood diseases, AAD was used in pseudo-testcross mapping of the tree at the intra-specific level. Markers were efficiently generated despite the close relatedness of parental dogwood material. Finally, DNA markers and tags were also generated in soybean, and were used to construct high density maps and walk towards defined genomic regions in the positional cloning of the supernodulation nts-1 symbiotic gene. (author)

Arbitrarily amplified DNA: New molecular approaches to plant breeding, ecology and evolution

International Nuclear Information System (INIS)

Caetano-Anolles, G.

2001-01-01

Several DNA fingerprinting techniques that use arbitrary primers to characterize, scan and tag genomic DNA were optimized and used to study plants and microbial pathogens. The generated arbitrarily amplified DNA (AAD) profiles could be tailored in their complexity and polymorphic content, allowing analysis of closely related organisms, such as vegetatively-propagated horticultural crops or clonal fungal populations. AAD markers were used in cultivar and strain identification, map-based cloning, and marker-assisted breeding, sometimes as sequence-tagged sites. Phenetic analysis using parsimony, cluster, and numerical methods was applied successfully to the identification of genetic relationships in turfgrass species such as bermudagrass, woody plants such as dogwoods, and floricultural species such as petunia and chrysanthemum. AAD profiles were used to measure for the first time a genome-wide mutation rate, directly in a plant. Mutation rates in vegetatively propagated bermudagrass were comparable to those in human, mice, fruit flies, and worms. In combination with established tools used in molecular systematics (e.g. rDNA sequence analysis), AAD markers tracked the introduction of exotic dogwood anthracnose-causing fungi in North America. As part of a breeding effort to combat dogwood diseases, AAD was used in pseudo-testcross mapping of the tree at the intra-specific level. Markers were efficiently generated despite the close relatedness of parental dogwood material. Finally, DNA markers and tags were also generated in soybean, and were used to construct high density maps and walk towards defined genomic regions in the positional cloning of the supernodulation nts-1 symbiotic gene. (author)

Exploring new alleles for frost tolerance in winter rye.

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Erath, Wiltrud; Bauer, Eva; Fowler, D Brian; Gordillo, Andres; Korzun, Viktor; Ponomareva, Mira; Schmidt, Malthe; Schmiedchen, Brigitta; Wilde, Peer; Schön, Chris-Carolin

2017-10-01

Rye genetic resources provide a valuable source of new alleles for the improvement of frost tolerance in rye breeding programs. Frost tolerance is a must-have trait for winter cereal production in northern and continental cropping areas. Genetic resources should harbor promising alleles for the improvement of frost tolerance of winter rye elite lines. For frost tolerance breeding, the identification of quantitative trait loci (QTL) and the choice of optimum genome-based selection methods are essential. We identified genomic regions involved in frost tolerance of winter rye by QTL mapping in a biparental population derived from a highly frost tolerant selection from the Canadian cultivar Puma and the European elite line Lo157. Lines per se and their testcrosses were phenotyped in a controlled freeze test and in multi-location field trials in Russia and Canada. Three QTL on chromosomes 4R, 5R, and 7R were consistently detected across environments. The QTL on 5R is congruent with the genomic region harboring the Frost resistance locus 2 (Fr-2) in Triticeae. The Puma allele at the Fr-R2 locus was found to significantly increase frost tolerance. A comparison of predictive ability obtained from the QTL-based model with different whole-genome prediction models revealed that besides a few large, also small QTL effects contribute to the genomic variance of frost tolerance in rye. Genomic prediction models assigning a high weight to the Fr-R2 locus allow increasing the selection intensity for frost tolerance by genome-based pre-selection of promising candidates.

Development of a possible nonmammalian test system for radiation-induced germ-cell mutagenesis using a fish, the Japanese medaka (Oryzias latipes)

International Nuclear Information System (INIS)

Shima, A.; Shimada, A.

1991-01-01

To develop a specific-locus test (SLT) system for environmental mutagenesis using vertebrate species other than the mouse, we first established a tester stock of the fish medaka (Oryzias latipes) that is homozygous recessive at three loci. The phenotypic expression of these loci can be easily recognized early in embryonic development by observation through the transparent egg membrane. We irradiated wild-type males with 137Cs gamma-rays to determine the dose-response relationships for dominant lethal and specific-locus mutations induced in sperm, spermatids, and spermatogonia. Through observation of 322,666 loci in control offspring and 374,026 loci in offspring obtained from 0.64-, 4.75-, or 9.50-Gy-irradiated gametes, specific-locus mutations were phenotypically detected during early development. These putative mutations, designated total mutation, can be recognized only in embryos of oviparous animals. The developmental fate of these mutant embryos was precisely followed. During subsequent embryonic development, a large fraction died and thus was unavailable for test-crossing, which was used to identify viable mutations. Our medaka SLT system demonstrates that the vast majority of total mutations is associated with dominant lethal mutations. Thus far only one spontaneous viable mutation has been observed, so that all doubling calculations involving this endpoint carry a large error. With these reservations, however, we conclude that the quantitative data so far obtained from the medaka SLT are quite comparable to those from the mouse SLT and, hence, indicate the validity of the medaka SLT as a possible nonmammalian test system

Exocrine Dysfunction Correlates with Endocrinal Impairment of Pancreas in Type 2 Diabetes Mellitus.

Science.gov (United States)

Prasanna Kumar, H R; Gowdappa, H Basavana; Hosmani, Tejashwi; Urs, Tejashri

2018-01-01

Diabetes mellitus (DM) is a chronic abnormal metabolic condition, which manifests elevated blood sugar level over a prolonged period. The pancreatic endocrine system generally gets affected during diabetes, but often abnormal exocrine functions are also manifested due to its proximity to the endocrine system. Fecal elastase-1 (FE-1) is found to be an ideal biomarker to reflect the exocrine insufficiency of the pancreas. The aim of this study was conducted to assess exocrine dysfunction of the pancreas in patients with type-2 DM (T2DM) by measuring FE levels and to associate the level of hyperglycemia with exocrine pancreatic dysfunction. A prospective, cross-sectional comparative study was conducted on both T2DM patients and healthy nondiabetic volunteers. FE-1 levels were measured using a commercial kit (Human Pancreatic Elastase ELISA BS 86-01 from Bioserv Diagnostics). Data analysis was performed based on the important statistical parameters such as mean, standard deviation, standard error, t -test-independent samples, and Chi-square test/cross tabulation using SPSS for Windows version 20.0. Statistically nonsignificant ( P = 0.5051) relationship between FE-1 deficiency and age was obtained, which implied age as a noncontributing factor toward exocrine pancreatic insufficiency among diabetic patients. Statistically significant correlation ( P = 0.003) between glycated hemoglobin and FE-1 levels was also noted. The association between retinopathy ( P = 0.001) and peripheral pulses ( P = 0.001) with FE-1 levels were found to be statistically significant. This study validates the benefit of FE-1 estimation, as a surrogate marker of exocrine pancreatic insufficiency, which remains unmanifest and subclinical.

Genetic analysis and identification of SSR markers associated with rice blast disease in a BC2F1 backcross population.

Science.gov (United States)

Hasan, N; Rafii, M Y; Abdul Rahim, H; Nusaibah, S A; Mazlan, N; Abdullah, S

2017-01-23

Rice (Oryza sativa L.) blast disease is one of the most destructive rice diseases in the world. The fungal pathogen, Magnaporthe oryzae, is the causal agent of rice blast disease. Development of resistant cultivars is the most preferred method to achieve sustainable rice production. However, the effectiveness of resistant cultivars is hindered by the genetic plasticity of the pathogen genome. Therefore, information on genetic resistance and virulence stability are vital to increase our understanding of the molecular basis of blast disease resistance. The present study set out to elucidate the resistance pattern and identify potential simple sequence repeat markers linked with rice blast disease. A backcross population (BC 2 F 1 ), derived from crossing MR264 and Pongsu Seribu 2 (PS2), was developed using marker-assisted backcross breeding. Twelve microsatellite markers carrying the blast resistance gene clearly demonstrated a polymorphic pattern between both parental lines. Among these, two markers, RM206 and RM5961, located on chromosome 11 exhibited the expected 1:1 testcross ratio in the BC 2 F 1 population. The 195 BC 2 F 1 plants inoculated against M. oryzae pathotype P7.2 showed a significantly different distribution in the backcrossed generation and followed Mendelian segregation based on a single-gene model. This indicates that blast resistance in PS2 is governed by a single dominant gene, which is linked to RM206 and RM5961 on chromosome 11. The findings presented in this study could be useful for future blast resistance studies in rice breeding programs.

Gamma radiation-induced mutant of NSIC RC144 with broad-spectrum resistance to bacterial blight

International Nuclear Information System (INIS)

Alfonso, A.A.; Avellanoza, E.S.; Miranda, R.T.; Espejo, E.O.; Garcia, N.S.

2014-01-01

Mutant lines derived from gamma radiation-treated commercial variety NSIC RC144 were produced and screened for novel resistance to bacterial blight, one of the most serious diseases of rice. Preliminary screening of a bulk M2 population through induced method using race 3 of the pathogen Xanthomonas oryzae pv. oryzae (Xoo) resulted in the selection of 89 resistant plants. Subsequent repeated bacterial blight screenings and generation advance for five seasons resulted in the selection of two highly resistant M7 sister lines whose origin can be traced to a single M2 plant. DNA fingerprinting using 63 genome-wide simple sequence repeat (SSR) markers revealed an identical pattern in these lines. Using the same set of markers, they also exhibited 98% similarity to wild type NSIC RC144 indicating that the resistance is due to mutation and not due to genetic admixture or seed impurity. Two seasons of bacterial blight screening using 14 local isolates representing ten races of Xoo revealed an identical reaction pattern in these lines. The reaction pattern was observed to be unique compared to known patterns in four IRBB isolines (IRBB 4, 5, 7 and 21) with strong resistant reaction to bacterial blight suggesting possible novel resistance. The susceptible reaction in F1 testcrosses using Xoo race 6 and the segregation patterns in two F2 populations that fit with the expected 3 susceptible: 1 resistant ratio (P = 0.4, ns) suggest a single-gene recessive mutation in these lines. These mutants are now being used as resistance donor in the breeding program while further molecular characterization to map and characterize the mutated gene is being pursued

Exocrine dysfunction correlates with endocrinal impairment of pancreas in Type 2 diabetes mellitus

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H R Prasanna Kumar

2018-01-01

Full Text Available Background: Diabetes mellitus (DM is a chronic abnormal metabolic condition, which manifests elevated blood sugar level over a prolonged period. The pancreatic endocrine system generally gets affected during diabetes, but often abnormal exocrine functions are also manifested due to its proximity to the endocrine system. Fecal elastase-1 (FE-1 is found to be an ideal biomarker to reflect the exocrine insufficiency of the pancreas. Aim: The aim of this study was conducted to assess exocrine dysfunction of the pancreas in patients with type-2 DM (T2DM by measuring FE levels and to associate the level of hyperglycemia with exocrine pancreatic dysfunction. Methodology: A prospective, cross-sectional comparative study was conducted on both T2DM patients and healthy nondiabetic volunteers. FE-1 levels were measured using a commercial kit (Human Pancreatic Elastase ELISA BS 86-01 from Bioserv Diagnostics. Data analysis was performed based on the important statistical parameters such as mean, standard deviation, standard error, t-test-independent samples, and Chi-square test/cross tabulation using SPSS for Windows version 20.0. Results: Statistically nonsignificant (P = 0.5051 relationship between FE-1 deficiency and age was obtained, which implied age as a noncontributing factor toward exocrine pancreatic insufficiency among diabetic patients. Statistically significant correlation (P = 0.003 between glycated hemoglobin and FE-1 levels was also noted. The association between retinopathy (P = 0.001 and peripheral pulses (P = 0.001 with FE-1 levels were found to be statistically significant. Conclusion: This study validates the benefit of FE-1 estimation, as a surrogate marker of exocrine pancreatic insufficiency, which remains unmanifest and subclinical.

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps.

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Teh, Soon Li; Fresnedo-Ramírez, Jonathan; Clark, Matthew D; Gadoury, David M; Sun, Qi; Cadle-Davidson, Lance; Luby, James J

2017-01-01

Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis ) breeding program, although experimental families are typically unreplicated, the genetic backgrounds may contain similar progenitors previously selected due to their contribution of favorable alleles. In this study, we investigated the utility of joint QTL identification provided by analyzing half-sib families. The genetic control of powdery mildew was studied using two half-sib F 1 families, namely GE0711/1009 (MN1264 × MN1214; N  = 147) and GE1025 (MN1264 × MN1246; N  = 125) with multiple species in their ancestry. Maternal genetic maps consisting of 1077 and 1641 single nucleotide polymorphism (SNP) markers, respectively, were constructed using a pseudo-testcross strategy. Ratings of field resistance to powdery mildew were obtained based on whole-plant evaluation of disease severity. This 2-year analysis uncovered two QTLs that were validated on a consensus map in these half-sib families with improved precision relative to the parental maps. Examination of haplotype combinations based on the two QTL regions identified strong association of haplotypes inherited from 'Seyval blanc', through MN1264, with powdery mildew resistance. This investigation also encompassed the use of microsatellite markers to establish a correlation between 206-bp (UDV-015b) and 357-bp (VViv67) fragment sizes with resistance-carrying haplotypes. Our work is one of the first reports in grapevine demonstrating the use of SNP-based maps and haplotypes for QTL identification and tagging of powdery mildew resistance in half-sib families.

Studies on combining ability and heritability of milling and physical properties in indica hybrid rice

International Nuclear Information System (INIS)

Zhang Lihua; Wang Linyou; Wang Jianjun

2003-01-01

14 different qualities parents of indica hybrid rice, including 7 CMS lines and 7 restorers, were chosen to analyze the combining ability of milling property and physical property by way of p x q incomplete diallel cross (NC II) design. The results showed that: 1) Both general combining ability (gca) and specific combining ability (sca) were highly significant in all 12 characters; the genetic additive effects was principal in brown rice length (BRL), brown rice width (BRW), ratio of length to width of brown rice (RLWBR), milled rice length (MRL), milled rice width (MRW), ratio of length to width of milled rice (RLWMR) and chalkyness (CN); while the nonadditive effects were greater in brown rice rate (BRR), milled rice rate (MRR), head rice rate (HRR), chalky rice percentage (CRP) and area of chalky rice (ACR). 2) Through the analysis of the contribution ratio of the male, female and their interaction to the total variance of the quality characters in F 1 hybrids, the results showed that BRR, MRR, BRL, MRL and ACR were influenced more greatly by restorer line than by CMS line, but the others were influenced more greatly by CMS line than by restorer line. 3) The gca and sca effects were independent each other, which suggests that it is essential to make widely testcrosses in the selection of hybrid combinations. There existed a positive correlation between gca and phenotypic value of parents, which indicates that great attention must be paid to the improvement of parent own characters in hybrid rice breeding. 4) BRL, BRW, RLWBR, MRL, MRW and RLWMR had higher narrow heritabilities (h N 2 ), and these characters may be used as indirect traits in early breeding generation

QTL mapping of combining ability and heterosis of agronomic traits in rice backcross recombinant inbred lines and hybrid crosses.

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Zhen Qu

Full Text Available BACKGROUND: Combining ability effects are very effective genetic parameters in deciding the next phase of breeding programs. Although some breeding strategies on the basis of evaluating combining ability have been utilized extensively in hybrid breeding, little is known about the genetic basis of combining ability. Combining ability is a complex trait that is controlled by polygenes. With the advent and development of molecular markers, it is feasible to evaluate the genetic bases of combining ability and heterosis of elite rice hybrids through QTL analysis. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we first developed a QTL-mapping method for dissecting combining ability and heterosis of agronomic traits. With three testcross populations and a BCRIL population in rice, biometric and QTL analyses were conducted for ten agronomic traits. The significance of general combining ability and special combining ability for most of the traits indicated the importance of both additive and non-additive effects on expression levels. A large number of additive effect QTLs associated with performance per se of BCRIL and general combining ability, and dominant effect QTLs associated with special combining ability and heterosis were identified for the ten traits. CONCLUSIONS/SIGNIFICANCE: The combining ability of agronomic traits could be analyzed by the QTL mapping method. The characteristics revealed by the QTLs for combining ability of agronomic traits were similar with those by multitudinous QTLs for agronomic traits with performance per se of BCRIL. Several QTLs (1-6 in this study were identified for each trait for combining ability. It demonstrated that some of the QTLs were pleiotropic or linked tightly with each other. The identification of QTLs responsible for combining ability and heterosis in the present study provides valuable information for dissecting genetic basis of combining ability.

Model training across multiple breeding cycles significantly improves genomic prediction accuracy in rye (Secale cereale L.).

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Auinger, Hans-Jürgen; Schönleben, Manfred; Lehermeier, Christina; Schmidt, Malthe; Korzun, Viktor; Geiger, Hartwig H; Piepho, Hans-Peter; Gordillo, Andres; Wilde, Peer; Bauer, Eva; Schön, Chris-Carolin

2016-11-01

Genomic prediction accuracy can be significantly increased by model calibration across multiple breeding cycles as long as selection cycles are connected by common ancestors. In hybrid rye breeding, application of genome-based prediction is expected to increase selection gain because of long selection cycles in population improvement and development of hybrid components. Essentially two prediction scenarios arise: (1) prediction of the genetic value of lines from the same breeding cycle in which model training is performed and (2) prediction of lines from subsequent cycles. It is the latter from which a reduction in cycle length and consequently the strongest impact on selection gain is expected. We empirically investigated genome-based prediction of grain yield, plant height and thousand kernel weight within and across four selection cycles of a hybrid rye breeding program. Prediction performance was assessed using genomic and pedigree-based best linear unbiased prediction (GBLUP and PBLUP). A total of 1040 S 2 lines were genotyped with 16 k SNPs and each year testcrosses of 260 S 2 lines were phenotyped in seven or eight locations. The performance gap between GBLUP and PBLUP increased significantly for all traits when model calibration was performed on aggregated data from several cycles. Prediction accuracies obtained from cross-validation were in the order of 0.70 for all traits when data from all cycles (N CS  = 832) were used for model training and exceeded within-cycle accuracies in all cases. As long as selection cycles are connected by a sufficient number of common ancestors and prediction accuracy has not reached a plateau when increasing sample size, aggregating data from several preceding cycles is recommended for predicting genetic values in subsequent cycles despite decreasing relatedness over time.

Use of Genomic Estimated Breeding Values Results in Rapid Genetic Gains for Drought Tolerance in Maize

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B.S. Vivek

2017-03-01

Full Text Available More than 80% of the 19 million ha of maize ( L. in tropical Asia is rainfed and prone to drought. The breeding methods for improving drought tolerance (DT, including genomic selection (GS, are geared to increase the frequency of favorable alleles. Two biparental populations (CIMMYT-Asia Population 1 [CAP1] and CAP2 were generated by crossing elite Asian-adapted yellow inbreds (CML470 and VL1012767 with an African white drought-tolerant line, CML444. Marker effects of polymorphic single-nucleotide polymorphisms (SNPs were determined from testcross (TC performance of F families under drought and optimal conditions. Cycle 1 (C1 was formed by recombining the top 10% of the F families based on TC data. Subsequently, (i C2[PerSe_PS] was derived by recombining those C1 plants that exhibited superior per se phenotypes (phenotype-only selection, and (ii C2[TC-GS] was derived by recombining a second set of C1 plants with high genomic estimated breeding values (GEBVs derived from TC phenotypes of F families (marker-only selection. All the generations and their top crosses to testers were evaluated under drought and optimal conditions. Per se grain yields (GYs of C2[PerSe_PS] and that of C2[TC-GS] were 23 to 39 and 31 to 53% better, respectively, than that of the corresponding F population. The C2[TC-GS] populations showed superiority of 10 to 20% over C2[PerSe-PS] of respective populations. Top crosses of C2[TC-GS] showed 4 to 43% superiority of GY over that of C2[PerSe_PS] of respective populations. Thus, GEBV-enabled selection of superior phenotypes (without the target stress resulted in rapid genetic gains for DT.

Optimizing the allocation of resources for genomic selection in one breeding cycle.

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Riedelsheimer, Christian; Melchinger, Albrecht E

2013-11-01

We developed a universally applicable planning tool for optimizing the allocation of resources for one cycle of genomic selection in a biparental population. The framework combines selection theory with constraint numerical optimization and considers genotype  ×  environment interactions. Genomic selection (GS) is increasingly implemented in plant breeding programs to increase selection gain but little is known how to optimally allocate the resources under a given budget. We investigated this problem with model calculations by combining quantitative genetic selection theory with constraint numerical optimization. We assumed one selection cycle where both the training and prediction sets comprised double haploid (DH) lines from the same biparental population. Grain yield for testcrosses of maize DH lines was used as a model trait but all parameters can be adjusted in a freely available software implementation. An extension of the expected selection accuracy given by Daetwyler et al. (2008) was developed to correctly balance between the number of environments for phenotyping the training set and its population size in the presence of genotype × environment interactions. Under small budget, genotyping costs mainly determine whether GS is superior over phenotypic selection. With increasing budget, flexibility in resource allocation increases greatly but selection gain leveled off quickly requiring balancing the number of populations with the budget spent for each population. The use of an index combining phenotypic and GS predicted values in the training set was especially beneficial under limited resources and large genotype × environment interactions. Once a sufficiently high selection accuracy is achieved in the prediction set, further selection gain can be achieved most efficiently by massively expanding its size. Thus, with increasing budget, reducing the costs for producing a DH line becomes increasingly crucial for successfully exploiting the

Rapid Cycling Genomic Selection in a Multiparental Tropical Maize Population.

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Zhang, Xuecai; Pérez-Rodríguez, Paulino; Burgueño, Juan; Olsen, Michael; Buckler, Edward; Atlin, Gary; Prasanna, Boddupalli M; Vargas, Mateo; San Vicente, Félix; Crossa, José

2017-07-05

Genomic selection (GS) increases genetic gain by reducing the length of the selection cycle, as has been exemplified in maize using rapid cycling recombination of biparental populations. However, no results of GS applied to maize multi-parental populations have been reported so far. This study is the first to show realized genetic gains of rapid cycling genomic selection (RCGS) for four recombination cycles in a multi-parental tropical maize population. Eighteen elite tropical maize lines were intercrossed twice, and self-pollinated once, to form the cycle 0 (C 0 ) training population. A total of 1000 ear-to-row C 0 families was genotyped with 955,690 genotyping-by-sequencing SNP markers; their testcrosses were phenotyped at four optimal locations in Mexico to form the training population. Individuals from families with the best plant types, maturity, and grain yield were selected and intermated to form RCGS cycle 1 (C 1 ). Predictions of the genotyped individuals forming cycle C 1 were made, and the best predicted grain yielders were selected as parents of C 2 ; this was repeated for more cycles (C 2 , C 3 , and C 4 ), thereby achieving two cycles per year. Multi-environment trials of individuals from populations C 0, C 1 , C 2 , C 3 , and C 4 , together with four benchmark checks were evaluated at two locations in Mexico. Results indicated that realized grain yield from C 1 to C 4 reached 0.225 ton ha -1 per cycle, which is equivalent to 0.100 ton ha -1  yr -1 over a 4.5-yr breeding period from the initial cross to the last cycle. Compared with the original 18 parents used to form cycle 0 (C 0 ), genetic diversity narrowed only slightly during the last GS cycles (C 3 and C 4 ). Results indicate that, in tropical maize multi-parental breeding populations, RCGS can be an effective breeding strategy for simultaneously conserving genetic diversity and achieving high genetic gains in a short period of time. Copyright © 2017 Zhang et al.

KASPTM genotyping technology and its use in gene­tic-breeding programs (a study of maize

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Н. Е. Волкова

2017-06-01

Full Text Available Purpose. To review publications relating to the key point of the genotyping technology that is competitive allele-specific polymerase chain reaction (which is called now Kompetitive Allele Specific PCR, KASPTM and its use in various genetic-breeding researching (a study of maize. Results. The essence of KASP-genotyping, its advantages are highlighted. The requirements for matrix DNA are presented, since the success of the KASP-analysis depends on its qua­lity and quantity. Examples of global projects of plant breeding for increasing crop yields using the KASP genoty­ping technology are given. The results of KASP genotyping and their introduction into breeding and seed production, in particular, for determining genetic identity, genetic purity, origin check, marker-assisted selection, etc. are presented using maize as an example. It is demonstrated how geno­mic selection according to KASP genotyping technology can lead to rapid genetic enhancement of drought resistance in maize. Comparison of the effectiveness of creating lines with certain traits (for example, combination of high grain yield and drought resistance using traditional breeding approaches (phenotype selection and molecular genetic methods (selection by markers was proved that it takes four seasons (two years in case of greenhouses in order to unlock the potential of the plant genotype using traditional self-pollination, test-crossing and definitions, while using markers, the population was enriched with target alleles during one season. At the same time, there was no need for a stress factor. Conclusions. KASP genotyping technology is a high-precision and effective tool for modern genetics and breeding, which is successfully used to study genetic diversity, genetic relationship, population structure, gene­tic identity, genetic purity, origin check, quantitative locus mapping, allele mapping, marker-assisted selection, marker-assisted breeding. It is expedient and timely to

Genetic Gains in Grain Yield of a Maize Population Improved through Marker Assisted Recurrent Selection under Stress and Non-stress Conditions in West Africa

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Rekiya O. Abdulmalik

2017-05-01

Full Text Available Marker-assisted recurrent selection (MARS is a breeding method used to accumulate favorable alleles that for example confer tolerance to drought in inbred lines from several genomic regions within a single population. A bi-parental cross formed from two parents that combine resistance to Striga hermonthica with drought tolerance, which was improved through MARS, was used to assess changes in the frequency of favorable alleles and its impact on inbred line improvement. A total of 200 testcrosses of randomly selected S1 lines derived from the original (C0 and advanced selection cycles of this bi-parental population, were evaluated under drought stress (DS and well-watered (WW conditions at Ikenne and under artificial Striga infestation at Abuja and Mokwa in Nigeria in 2014 and 2015. Also, 60 randomly selected S1 lines each derived from the four cycles (C0, C1, C2, C3 were genotyped with 233 SNP markers using KASP assay. The results showed that the frequency of favorable alleles increased with MARS in the bi-parental population with none of the markers showing fixation. The gain in grain yield was not significant under DS condition due to the combined effect of DS and armyworm infestation in 2015. Because the parents used for developing the bi-parental cross combined tolerance to drought with resistance to Striga, improvement in grain yield under DS did not result in undesirable changes in resistance to the parasite in the bi-parental maize population improved through MARS. MARS increased the mean number of combinations of favorable alleles in S1 lines from 114 in C0 to 124 in C3. The level of heterozygosity decreased by 15%, while homozygosity increased by 13% due to the loss of some genotypes in the population. This study demonstrated the effectiveness of MARS in increasing the frequency of favorable alleles for tolerance to drought without disrupting the level of resistance to Striga in a bi-parental population targeted as a source of improved

Genetic Gains in Grain Yield of a Maize Population Improved through Marker Assisted Recurrent Selection under Stress and Non-stress Conditions in West Africa.

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Abdulmalik, Rekiya O; Menkir, Abebe; Meseka, Silvestro K; Unachukwu, Nnanna; Ado, Shehu G; Olarewaju, Joseph D; Aba, Daniel A; Hearne, Sarah; Crossa, Jose; Gedil, Melaku

2017-01-01

Marker-assisted recurrent selection (MARS) is a breeding method used to accumulate favorable alleles that for example confer tolerance to drought in inbred lines from several genomic regions within a single population. A bi-parental cross formed from two parents that combine resistance to Striga hermonthica with drought tolerance, which was improved through MARS, was used to assess changes in the frequency of favorable alleles and its impact on inbred line improvement. A total of 200 testcrosses of randomly selected S 1 lines derived from the original (C 0 ) and advanced selection cycles of this bi-parental population, were evaluated under drought stress (DS) and well-watered (WW) conditions at Ikenne and under artificial Striga infestation at Abuja and Mokwa in Nigeria in 2014 and 2015. Also, 60 randomly selected S 1 lines each derived from the four cycles (C 0 , C 1 , C 2 , C 3 ) were genotyped with 233 SNP markers using KASP assay. The results showed that the frequency of favorable alleles increased with MARS in the bi-parental population with none of the markers showing fixation. The gain in grain yield was not significant under DS condition due to the combined effect of DS and armyworm infestation in 2015. Because the parents used for developing the bi-parental cross combined tolerance to drought with resistance to Striga , improvement in grain yield under DS did not result in undesirable changes in resistance to the parasite in the bi-parental maize population improved through MARS. MARS increased the mean number of combinations of favorable alleles in S 1 lines from 114 in C 0 to 124 in C 3 . The level of heterozygosity decreased by 15%, while homozygosity increased by 13% due to the loss of some genotypes in the population. This study demonstrated the effectiveness of MARS in increasing the frequency of favorable alleles for tolerance to drought without disrupting the level of resistance to Striga in a bi-parental population targeted as a source of improved

The accuracy of prediction of genomic selection in elite hybrid rye populations surpasses the accuracy of marker-assisted selection and is equally augmented by multiple field evaluation locations and test years.

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Wang, Yu; Mette, Michael Florian; Miedaner, Thomas; Gottwald, Marlen; Wilde, Peer; Reif, Jochen C; Zhao, Yusheng

2014-07-04

Marker-assisted selection (MAS) and genomic selection (GS) based on genome-wide marker data provide powerful tools to predict the genotypic value of selection material in plant breeding. However, case-to-case optimization of these approaches is required to achieve maximum accuracy of prediction with reasonable input. Based on extended field evaluation data for grain yield, plant height, starch content and total pentosan content of elite hybrid rye derived from testcrosses involving two bi-parental populations that were genotyped with 1048 molecular markers, we compared the accuracy of prediction of MAS and GS in a cross-validation approach. MAS delivered generally lower and in addition potentially over-estimated accuracies of prediction than GS by ridge regression best linear unbiased prediction (RR-BLUP). The grade of relatedness of the plant material included in the estimation and test sets clearly affected the accuracy of prediction of GS. Within each of the two bi-parental populations, accuracies differed depending on the relatedness of the respective parental lines. Across populations, accuracy increased when both populations contributed to estimation and test set. In contrast, accuracy of prediction based on an estimation set from one population to a test set from the other population was low despite that the two bi-parental segregating populations under scrutiny shared one parental line. Limiting the number of locations or years in field testing reduced the accuracy of prediction of GS equally, supporting the view that to establish robust GS calibration models a sufficient number of test locations is of similar importance as extended testing for more than one year. In hybrid rye, genomic selection is superior to marker-assisted selection. However, it achieves high accuracies of prediction only for selection candidates closely related to the plant material evaluated in field trials, resulting in a rather pessimistic prognosis for distantly related material

A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus

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2011-01-01

Background Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers. Results SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome. Conclusions The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping