Prediction of maize phenotype based on whole-genome single nucleotide polymorphisms using deep belief networks

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Rachmatia, H.; Kusuma, W. A.; Hasibuan, L. S.

2017-05-01

Selection in plant breeding could be more effective and more efficient if it is based on genomic data. Genomic selection (GS) is a new approach for plant-breeding selection that exploits genomic data through a mechanism called genomic prediction (GP). Most of GP models used linear methods that ignore effects of interaction among genes and effects of higher order nonlinearities. Deep belief network (DBN), one of the architectural in deep learning methods, is able to model data in high level of abstraction that involves nonlinearities effects of the data. This study implemented DBN for developing a GP model utilizing whole-genome Single Nucleotide Polymorphisms (SNPs) as data for training and testing. The case study was a set of traits in maize. The maize dataset was acquisitioned from CIMMYT’s (International Maize and Wheat Improvement Center) Global Maize program. Based on Pearson correlation, DBN is outperformed than other methods, kernel Hilbert space (RKHS) regression, Bayesian LASSO (BL), best linear unbiased predictor (BLUP), in case allegedly non-additive traits. DBN achieves correlation of 0.579 within -1 to 1 range.

Genome sequence of a 5,310-year-old maize cob provides insights into the early stages of maize domestication

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Ramos Madrigal, Jazmin; Smith, Bruce D.; Moreno Mayar, José Victor

2016-01-01

The complex evolutionary history of maize (Zea mays L. ssp. mays) has been clarified with genomic-level data from modern landraces and wild teosinte grasses [1, 2], augmenting archaeological findings that suggest domestication occurred between 10,000 and 6,250 years ago in southern Mexico [3, 4......]. Maize rapidly evolved under human selection, leading to conspicuous phenotypic transformations, as well as adaptations to varied environments [5]. Still, many questions about the domestication process remain unanswered because modern specimens do not represent the full range of past diversity due...... to abandonment of unproductive lineages, genetic drift, on-going natural selection, and recent breeding activity. To more fully understand the history and spread of maize, we characterized the draft genome of a 5,310-year-old archaeological cob excavated in the Tehuacan Valley of Mexico. We compare this ancient...

Characterization and distribution of repetitive elements in association with genes in the human genome.

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Liang, Kai-Chiang; Tseng, Joseph T; Tsai, Shaw-Jenq; Sun, H Sunny

2015-08-01

Repetitive elements constitute more than 50% of the human genome. Recent studies implied that the complexity of living organisms is not just a direct outcome of a number of coding sequences; the repetitive elements, which do not encode proteins, may also play a significant role. Though scattered studies showed that repetitive elements in the regulatory regions of a gene control gene expression, no systematic survey has been done to report the characterization and distribution of various types of these repetitive elements in the human genome. Sequences from 5' and 3' untranslated regions and upstream and downstream of a gene were downloaded from the Ensembl database. The repetitive elements in the neighboring of each gene were identified and classified using cross-matching implemented in the RepeatMasker. The annotation and distribution of distinct classes of repetitive elements associated with individual gene were collected to characterize genes in association with different types of repetitive elements using systems biology program. We identified a total of 1,068,400 repetitive elements which belong to 37-class families and 1235 subclasses that are associated with 33,761 genes and 57,365 transcripts. In addition, we found that the tandem repeats preferentially locate proximal to the transcription start site (TSS) of genes and the major function of these genes are involved in developmental processes. On the other hand, interspersed repetitive elements showed a tendency to be accumulated at distal region from the TSS and the function of interspersed repeat-containing genes took part in the catabolic/metabolic processes. Results from the distribution analysis were collected and used to construct a gene-based repetitive element database (GBRED; http://www.binfo.ncku.edu.tw/GBRED/index.html). A user-friendly web interface was designed to provide the information of repetitive elements associated with any particular gene(s). This is the first study focusing on the gene

A genome-wide characterization of microRNA genes in maize.

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Lifang Zhang

2009-11-01

Full Text Available MicroRNAs (miRNAs are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with approximately 35% of ancestral sites retained as duplicate homoeologous miRNA genes. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.

Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet (Acipenser ruthenus).

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Biltueva, Larisa S; Prokopov, Dimitry Y; Makunin, Alexey I; Komissarov, Alexey S; Kudryavtseva, Anna V; Lemskaya, Natalya A; Vorobieva, Nadezhda V; Serdyukova, Natalia A; Romanenko, Svetlana A; Gladkikh, Olga L; Graphodatsky, Alexander S; Trifonov, Vladimir A

2017-01-01

Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (Acipenser ruthenus) repetitive DNA. Using FISH, we mapped 16 tandemly arranged sequences on sterlet chromosomes and found them to be unevenly distributed in the genome with a tendency to cluster in particular regions. Some of the satellite DNAs might be used as specific markers to identify individual chromosomes and their paralogs, resulting in the unequivocal identification of at least 18 chromosome pairs. Our results provide an insight into the characteristic genomic distribution of the most common sterlet repetitive sequences. Biased accumulation of repetitive DNAs in particular chromosomes makes them especially interesting for further search for cryptic sex chromosomes. Future studies of these sequences in other acipenserid species will provide new perspectives regarding the evolution of repetitive DNA within the genomes of this fish order. © 2017 S. Karger AG, Basel.

Refining borders of genome-rearrangements including repetitions

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JA Arjona-Medina

2016-10-01

Full Text Available Abstract Background DNA rearrangement events have been widely studied in comparative genomic for many years. The importance of these events resides not only in the study about relatedness among different species, but also to determine the mechanisms behind evolution. Although there are many methods to identify genome-rearrangements (GR, the refinement of their borders has become a huge challenge. Until now no accepted method exists to achieve accurate fine-tuning: i.e. the notion of breakpoint (BP is still an open issue, and despite repeated regions are vital to understand evolution they are not taken into account in most of the GR detection and refinement methods. Methods and results We propose a method to refine the borders of GR including repeated regions. Instead of removing these repetitions to facilitate computation, we take advantage of them using a consensus alignment sequence of the repeated region in between two blocks. Using the concept of identity vectors for Synteny Blocks (SB and repetitions, a Finite State Machine is designed to detect transition points in the difference between such vectors. The method does not force the BP to be a region or a point but depends on the alignment transitions within the SBs and repetitions. Conclusion The accurate definition of the borders of SB and repeated genomic regions and consequently the detection of BP might help to understand the evolutionary model of species. In this manuscript we present a new proposal for such a refinement. Features of the SBs borders and BPs are different and fit with what is expected. SBs with more diversity in annotations and BPs short and richer in DNA replication and stress response, which are strongly linked with rearrangements.

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

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Yandell Mark

2010-07-01

Full Text Available Abstract Background In today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24. The size and complexity of these genomes have prompted much speculation as to the feasibility of completing a conifer genome sequence. Conifer genomes are reputed to be highly repetitive, but there is little information available on the nature and identity of repetitive units in gymnosperms. The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda. Results We present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS sequences representing 7.5% of the genome. Computational annotation of ten BACs predicts three putative protein-coding genes and at least fifteen likely pseudogenes in nearly one megabase of sequence. We found three conifer-specific LTR retroelements in the BACs, and tentatively identified at least 15 others based on evidence from the distantly related angiosperms. Alignment of WGS sequences to the BACs indicates that 80% of BAC sequences have similar copies (≥ 75% nucleotide identity elsewhere in the genome, but only 23% have identical copies (99% identity. The three most common repetitive elements in the genome were identified and, when combined, represent less than 5% of the genome. Conclusions This study indicates that the majority of repeats in the P. taeda genome are 'novel' and will therefore require additional BAC or genomic sequencing for accurate characterization. The pine genome contains a very large number of diverged and probably defunct repetitive elements. This study also provides new evidence that sequencing a pine genome using a WGS approach is

Mixing of maize and wheat genomic DNA by somatic hybridization in regenerated sterile maize plants.

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Szarka, B.; Göntér, I.; Molnár-Láng, M.; Mórocz, S.; Dudits, D.

2002-07-01

Intergeneric somatic hybridization was performed between albino maize ( Zea mays L.) protoplasts and mesophyll protoplasts of wheat ( Triticum aestivum L.) by polyethylene glycol (PEG) treatments. None of the parental protoplasts were able to produce green plants without fusion. The maize cells regenerated only rudimentary albino plantlets of limited viability, and the wheat mesophyll protoplasts were unable to divide. PEG-mediated fusion treatments resulted in hybrid cells with mixed cytoplasm. Six months after fusion green embryogenic calli were selected as putative hybrids. The first-regenerates were discovered as aborted embryos. Regeneration of intact, green, maize-like plants needed 6 months of further subcultures on hormone-free medium. These plants were sterile, although had both male and female flowers. The cytological analysis of cells from callus tissues and root tips revealed 56 chromosomes, but intact wheat chromosomes were not observed. Using total DNA from hybrid plants, three RAPD primer combinations produced bands resembling the wheat profile. Genomic in situ hybridization (GISH) using total wheat DNA as a probe revealed the presence of wheat DNA islands in the maize chromosomal background. The increased viability and the restored green color were the most-significant new traits as compared to the original maize parent. Other intermediate morphological traits of plants with hybrid origin were not found.

Structurally Complex Organization of Repetitive DNAs in the Genome of Cobia (Rachycentron canadum).

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Costa, Gideão W W F; Cioffi, Marcelo de B; Bertollo, Luiz A C; Molina, Wagner F

2015-06-01

Repetitive DNAs comprise the largest fraction of the eukaryotic genome. They include microsatellites or simple sequence repeats (SSRs), which play an important role in the chromosome differentiation among fishes. Rachycentron canadum is the only representative of the family Rachycentridae. This species has been focused on several multidisciplinary studies in view of its important potential for marine fish farming. In the present study, distinct classes of repetitive DNAs, with emphasis on SSRs, were mapped in the chromosomes of this species to improve the knowledge of its genome organization. Microsatellites exhibited a diversified distribution, both dispersed in euchromatin and clustered in the heterochromatin. The multilocus location of SSRs strengthened the heterochromatin heterogeneity in this species, as suggested by some previous studies. The colocalization of SSRs with retrotransposons and transposons pointed to a close evolutionary relationship between these repetitive sequences. A number of heterochromatic regions highlighted a greater complex organization than previously supposed, harboring a diversity of repetitive elements. In this sense, there was also evidence of colocalization of active genetic regions and different classes of repetitive DNAs in a common heterochromatic region, which offers a potential opportunity for further researches regarding the interaction of these distinct fractions in fish genomes.

Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome.

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Regina S Baucom

2009-11-01

Full Text Available Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75% of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR retrotransposon class of retroelements, with >400 families (>350 newly discovered contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families and LINEs (at least 30 families, were observed to contribute 1,991 and approximately 35,000 copies, respectively, or a combined approximately 1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to

Functional role of a highly repetitive DNA sequence in anchorage of the mouse genome.

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Neuer-Nitsche, B; Lu, X N; Werner, D

1988-09-12

The major portion of the eukaryotic genome consists of various categories of repetitive DNA sequences which have been studied with respect to their base compositions, organizations, copy numbers, transcription and species specificities; their biological roles, however, are still unclear. A novel quality of a highly repetitive mouse DNA sequence is described which points to a functional role: All copies (approximately 50,000 per haploid genome) of this DNA sequence reside on genomic Alu I DNA fragments each associated with nuclear polypeptides that are not released from DNA by proteinase K, SDS and phenol extraction. By this quality the repetitive DNA sequence is classified as a member of the sub-set of DNA sequences involved in tight DNA-polypeptide complexes which have been previously shown to be components of the subnuclear structure termed 'nuclear matrix'. From these results it has to be concluded that the repetitive DNA sequence characterized in this report represents or comprises a signal for a large number of site specific attachment points of the mouse genome in the nuclear matrix.

Repetitive elements may comprise over two-thirds of the human genome.

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A P Jason de Koning

2011-12-01

Full Text Available Transposable elements (TEs are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously identified as TEs and low-complexity repeats. We recently developed a highly sensitive alternative de novo strategy, P-clouds, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo "clouds". We show here that P-clouds predicts >840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66%-69% of the human genome is repetitive or repeat-derived. To investigate this remarkable difference, we conducted detailed analyses of the ability of both P-clouds and a commonly used conventional approach, RepeatMasker (RM, to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have surprisingly low sensitivity for even moderately long fragments, in contrast to P-clouds, which has good sensitivity down to small fragment sizes (∼25 bp. Although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. We further developed "element-specific" P-clouds (ESPs to identify novel Alu and MIR SINE elements, and using it we identified ∼100 Mb of previously unannotated human elements. ESP estimates of new MIR sequences are in good agreement with RM-based predictions of the amount that RM missed. These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed.

Zygotic Genome Activation Occurs Shortly after Fertilization in Maize.

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Chen, Junyi; Strieder, Nicholas; Krohn, Nadia G; Cyprys, Philipp; Sprunck, Stefanie; Engelmann, Julia C; Dresselhaus, Thomas

2017-09-01

The formation of a zygote via the fusion of an egg and sperm cell and its subsequent asymmetric division herald the start of the plant's life cycle. Zygotic genome activation (ZGA) is thought to occur gradually, with the initial steps of zygote and embryo development being primarily maternally controlled, and subsequent steps being governed by the zygotic genome. Here, using maize ( Zea mays ) as a model plant system, we determined the timing of zygote development and generated RNA-seq transcriptome profiles of gametes, zygotes, and apical and basal daughter cells. ZGA occurs shortly after fertilization and involves ∼10% of the genome being activated in a highly dynamic pattern. In particular, genes encoding transcriptional regulators of various families are activated shortly after fertilization. Further analyses suggested that chromatin assembly is strongly modified after fertilization, that the egg cell is primed to activate the translational machinery, and that hormones likely play a minor role in the initial steps of early embryo development in maize. Our findings provide important insights into gamete and zygote activity in plants, and our RNA-seq transcriptome profiles represent a comprehensive, unique RNA-seq data set that can be used by the research community. © 2017 American Society of Plant Biologists. All rights reserved.

Next-generation sequencing detects repetitive elements expansion in giant genomes of annual killifish genus Austrolebias (Cyprinodontiformes, Rivulidae).

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García, G; Ríos, N; Gutiérrez, V

2015-06-01

Among Neotropical fish fauna, the South American killifish genus Austrolebias (Cyprinodontiformes: Rivulidae) constitutes an excellent model to study the genomic evolutionary processes underlying speciation events. Recently, unusually large genome size has been described in 16 species of this genus, with an average DNA content of about 5.95 ± 0.45 pg per diploid cell (mean C-value of about 2.98 pg). In the present paper we explore the possible origin of this unparallel genomic increase by means of comparative analysis of the repetitive components using NGS (454-Roche) technology in the lowest and highest Rivulidae genomes. Here, we provide the first annotated Rivulidae-repeated sequences composition and their relative repetitive fraction in both genomes. Remarkably, the genomic proportion of the moderately repetitive DNA in Austrolebias charrua genome represents approximately twice (45%) of the repetitive components of the highly related rivulinae taxon Cynopoecilus melanotaenia (25%). Present work provides evidence about the impact of the repeat families that could be distinctly proliferated among sublineages within Rivulidae fish group, explaining the great genome size differences encompassing the differentiation and speciation events in this family.

Genomic Selection for Drought Tolerance Using Genome-Wide SNPs in Maize

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Thirunavukkarasu Nepolean

2017-04-01

Full Text Available Traditional breeding strategies for selecting superior genotypes depending on phenotypic traits have proven to be of limited success, as this direct selection is hindered by low heritability, genetic interactions such as epistasis, environmental-genotype interactions, and polygenic effects. With the advent of new genomic tools, breeders have paved a way for selecting superior breeds. Genomic selection (GS has emerged as one of the most important approaches for predicting genotype performance. Here, we tested the breeding values of 240 maize subtropical lines phenotyped for drought at different environments using 29,619 cured SNPs. Prediction accuracies of seven genomic selection models (ridge regression, LASSO, elastic net, random forest, reproducing kernel Hilbert space, Bayes A and Bayes B were tested for their agronomic traits. Though prediction accuracies of Bayes B, Bayes A and RKHS were comparable, Bayes B outperformed the other models by predicting highest Pearson correlation coefficient in all three environments. From Bayes B, a set of the top 1053 significant SNPs with higher marker effects was selected across all datasets to validate the genes and QTLs. Out of these 1053 SNPs, 77 SNPs associated with 10 drought-responsive transcription factors. These transcription factors were associated with different physiological and molecular functions (stomatal closure, root development, hormonal signaling and photosynthesis. Of several models, Bayes B has been shown to have the highest level of prediction accuracy for our data sets. Our experiments also highlighted several SNPs based on their performance and relative importance to drought tolerance. The result of our experiments is important for the selection of superior genotypes and candidate genes for breeding drought-tolerant maize hybrids.

Computational prediction and molecular confirmation of Helitron transposons in the maize genome

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He Limei

2008-01-01

Full Text Available Abstract Background Helitrons represent a new class of transposable elements recently uncovered in plants and animals. One remarkable feature of Helitrons is their ability to capture gene sequences, which makes them of considerable potential evolutionary importance. However, because Helitrons lack the typical structural features of other DNA transposable elements, identifying them is a challenge. Currently, most researchers identify Helitrons manually by comparing sequences. With the maize whole genome sequencing project underway, an automated computational Helitron searching tool is needed. The characterization of Helitron activities in maize needs to be addressed in order to better understand the impact of Helitrons on the organization of the genome. Results We developed and implemented a heuristic searching algorithm in PERL for identifying Helitrons. Our HelitronFinder program will (i take FASTA-formatted DNA sequences as input and identify the hairpin looping patterns, and (ii exploit the consensus 5' and 3' end sequences of known Helitrons to identify putative ends. We randomly selected five predicted Helitrons from the program's high quality output for molecular verification. Four out of the five predicted Helitrons were confirmed by PCR assays and DNA sequencing in different maize inbred lines. The HelitronFinder program identified two head-to-head dissimilar Helitrons in a maize BAC sequence. Conclusion We have identified 140 new Helitron candidates in maize with our computational tool HelitronFinder by searching maize DNA sequences currently available in GenBank. Four out of five candidates were confirmed to be real by empirical methods, thus validating the predictions of HelitronFinder. Additional points to emerge from our study are that Helitrons do not always insert at an AT dinucleotide in the host sequences, that they can insert immediately adjacent to an existing Helitron, and that their movement may cause changes in the flanking

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.

Diversity in non-repetitive human sequences not found in the reference genome.

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Kehr, Birte; Helgadottir, Anna; Melsted, Pall; Jonsson, Hakon; Helgason, Hannes; Jonasdottir, Adalbjörg; Jonasdottir, Aslaug; Sigurdsson, Asgeir; Gylfason, Arnaldur; Halldorsson, Gisli H; Kristmundsdottir, Snaedis; Thorgeirsson, Gudmundur; Olafsson, Isleifur; Holm, Hilma; Thorsteinsdottir, Unnur; Sulem, Patrick; Helgason, Agnar; Gudbjartsson, Daniel F; Halldorsson, Bjarni V; Stefansson, Kari

2017-04-01

Genomes usually contain some non-repetitive sequences that are missing from the reference genome and occur only in a population subset. Such non-repetitive, non-reference (NRNR) sequences have remained largely unexplored in terms of their characterization and downstream analyses. Here we describe 3,791 breakpoint-resolved NRNR sequence variants called using PopIns from whole-genome sequence data of 15,219 Icelanders. We found that over 95% of the 244 NRNR sequences that are 200 bp or longer are present in chimpanzees, indicating that they are ancestral. Furthermore, 149 variant loci are in linkage disequilibrium (r 2 > 0.8) with a genome-wide association study (GWAS) catalog marker, suggesting disease relevance. Additionally, we report an association (P = 3.8 × 10 -8 , odds ratio (OR) = 0.92) with myocardial infarction (23,360 cases, 300,771 controls) for a 766-bp NRNR sequence variant. Our results underline the importance of including variation of all complexity levels when searching for variants that associate with disease.

Completed sequence and corrected annotation of the genome of maize Iranian mosaic virus.

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Ghorbani, Abozar; Izadpanah, Keramatollah; Dietzgen, Ralf G

2018-03-01

Maize Iranian mosaic virus (MIMV) is a negative-sense single-stranded RNA virus that is classified in the genus Nucleorhabdovirus, family Rhabdoviridae. The MIMV genome contains six open reading frames (ORFs) that encode in 3΄ to 5΄ order the nucleocapsid protein (N), phosphoprotein (P), putative movement protein (P3), matrix protein (M), glycoprotein (G) and RNA-dependent RNA polymerase (L). In this study, we determined the first complete genome sequence of MIMV using Illumina RNA-Seq and 3'/5' RACE. MIMV genome ('Fars' isolate) is 12,426 nucleotides in length. Unexpectedly, the predicted N gene ORF of this isolate and of four other Iranian isolates is 143 nucleotides shorter than that of the MIMV coding-complete reference isolate 'Shiraz 1' (Genbank NC_011542), possibly due to a minor error in the previous sequence. Genetic variability among the N, P, P3 and G ORFs of Iranian MIMV isolates was limited, but highest in the G gene ORF. Phylogenetic analysis of complete nucleorhabdovirus genomes demonstrated a close evolutionary relationship between MIMV, maize mosaic virus and taro vein chlorosis virus.

Genome-wide recombination dynamics are associated with phenotypic variation in maize.

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Pan, Qingchun; Li, Lin; Yang, Xiaohong; Tong, Hao; Xu, Shutu; Li, Zhigang; Li, Weiya; Muehlbauer, Gary J; Li, Jiansheng; Yan, Jianbing

2016-05-01

Meiotic recombination is a major driver of genetic diversity, species evolution, and agricultural improvement. Thus, an understanding of the genetic recombination landscape across the maize (Zea mays) genome will provide insight and tools for further study of maize evolution and improvement. Here, we used c. 50 000 single nucleotide polymorphisms to precisely map recombination events in 12 artificial maize segregating populations. We observed substantial variation in the recombination frequency and distribution along the ten maize chromosomes among the 12 populations and identified 143 recombination hot regions. Recombination breakpoints were partitioned into intragenic and intergenic events. Interestingly, an increase in the number of genes containing recombination events was accompanied by a decrease in the number of recombination events per gene. This kept the overall number of intragenic recombination events nearly invariable in a given population, suggesting that the recombination variation observed among populations was largely attributed to intergenic recombination. However, significant associations between intragenic recombination events and variation in gene expression and agronomic traits were observed, suggesting potential roles for intragenic recombination in plant phenotypic diversity. Our results provide a comprehensive view of the maize recombination landscape, and show an association between recombination, gene expression and phenotypic variation, which may enhance crop genetic improvement. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE

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Lavrov Dennis V

2009-12-01

Full Text Available Abstract Background The mitochondrial (mt genomes of sponges possess a variety of features, which appear to be intermediate between those of Eumetazoa and non-metazoan opisthokonts. Among these features is the presence of long intergenic regions, which are common in other eukaryotes, but generally absent in Eumetazoa. Here we analyse poriferan mitochondrial intergenic regions, paying particular attention to repetitive sequences within them. In this context we introduce the mitochondrial genome of Ircinia strobilina (Lamarck, 1816; Demospongiae: Dictyoceratida and compare it with mtDNA of other sponges. Results Mt genomes of dictyoceratid sponges are identical in gene order and content but display major differences in size and organization of intergenic regions. An even higher degree of diversity in the structure of intergenic regions was found among different orders of demosponges. One interesting observation made from such comparisons was of what appears to be recurrent invasions of sponge mitochondrial genomes by repetitive hairpin-forming elements, which cause large genome size differences even among closely related taxa. These repetitive hairpin-forming elements are structurally and compositionally divergent and display a scattered distribution throughout various groups of demosponges. Conclusion Large intergenic regions of poriferan mt genomes are targets for insertions of repetitive hairpin- forming elements, similar to the ones found in non-metazoan opisthokonts. Such elements were likely present in some lineages early in animal mitochondrial genome evolution but were subsequently lost during the reduction of intergenic regions, which occurred in the Eumetazoa lineage after the split of Porifera. Porifera acquired their elements in several independent events. Patterns of their intra-genomic dispersal can be seen in the mt genome of Vaceletia sp.

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

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Macas, Jiří; Novák, Petr; Pellicer, Jaume; Čížková, Jana; Koblížková, Andrea; Neumann, Pavel; Fuková, Iva; Doležel, Jaroslav; Kelly, Laura J; Leitch, Ilia J

2015-01-01

The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

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Jiří Macas

Full Text Available The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57% of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%. Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm

Energy Technology Data Exchange (ETDEWEB)

Seaver, Samuel M. D.; Bradbury, Louis M. T.; Frelin, Océane; Zarecki, Raphy; Ruppin, Eytan; Hanson, Andrew D.; Henry, Christopher S.

2015-03-10

There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes.

Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

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Saha, Rajib; Suthers, Patrick F.; Maranas, Costas D.

2011-01-01

The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species. PMID:21755001

Selection for silage yield and composition did not affect genomic diversity within the Wisconsin Quality Synthetic maize population.

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Lorenz, Aaron J; Beissinger, Timothy M; Silva, Renato Rodrigues; de Leon, Natalia

2015-02-02

Maize silage is forage of high quality and yield, and represents the second most important use of maize in the United States. The Wisconsin Quality Synthetic (WQS) maize population has undergone five cycles of recurrent selection for silage yield and composition, resulting in a genetically improved population. The application of high-density molecular markers allows breeders and geneticists to identify important loci through association analysis and selection mapping, as well as to monitor changes in the distribution of genetic diversity across the genome. The objectives of this study were to identify loci controlling variation for maize silage traits through association analysis and the assessment of selection signatures and to describe changes in the genomic distribution of gene diversity through selection and genetic drift in the WQS recurrent selection program. We failed to find any significant marker-trait associations using the historical phenotypic data from WQS breeding trials combined with 17,719 high-quality, informative single nucleotide polymorphisms. Likewise, no strong genomic signatures were left by selection on silage yield and quality in the WQS despite genetic gain for these traits. These results could be due to the genetic complexity underlying these traits, or the role of selection on standing genetic variation. Variation in loss of diversity through drift was observed across the genome. Some large regions experienced much greater loss in diversity than what is expected, suggesting limited recombination combined with small populations in recurrent selection programs could easily lead to fixation of large swaths of the genome. Copyright © 2015 Lorenz et al.

Genome-wide identification, classification and expression profiling of nicotianamine synthase (NAS) gene family in maize

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Zhou, Xiaojin; Li, Suzhen; Zhao, Qianqian; Liu, Xiaoqing; Zhang, Shaojun; Sun, Cheng; Fan, Yunliu; Zhang, Chunyi; Chen, Rumei

2013-01-01

Background Nicotianamine (NA), a ubiquitous molecule in plants, is an important metal ion chelator and the main precursor for phytosiderophores biosynthesis. Considerable progress has been achieved in cloning and characterizing the functions of nicotianamine synthase (NAS) in plants including barley, Arabidopsis and rice. Maize is not only an important cereal crop, but also a model plant for genetics and evolutionary study. The genome sequencing of maize was completed, and many gene families ...

Roles of repetitive sequences

Energy Technology Data Exchange (ETDEWEB)

Bell, G.I.

1991-12-31

The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays

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Berg, Jeremy J.; Birchler, James A.; Grote, Mark N.; Lorant, Anne; Quezada, Juvenal

2018-01-01

While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes. PMID:29746459

Dispersed repetitive sequences in eukaryotic genomes and their possible biological significance

International Nuclear Information System (INIS)

Georgiev, G.P.; Kramerov, D.A.; Ryskov, A.P.; Skryabin, K.G.; Lukanidin, E.M.

1983-01-01

In this paper is described the properties of a novel mouse mdg-like element, the A2 sequence, which is the most abundant repetitive sequence. We also characterized an ubiquitous B2 sequence that represents, after B1, the dominant family among the short interspersed repeats of the mouse genome. The existence of some putative transposition intermediates was shown for repeats of both A and B types of the mouse genome. These are closed circular DNA of the A type and small polyadenylated B + RNAs. The fundamental question that arises is whether these sequences are simply selfish DNA capable of transpositions or do they fulfill some useful biological functions within the genome. 66 references, 11 figures, 1 table

Novel porcine repetitive elements

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Nonneman Dan J

2006-12-01

Full Text Available Abstract Background Repetitive elements comprise ~45% of mammalian genomes and are increasingly known to impact genomic function by contributing to the genomic architecture, by direct regulation of gene expression and by affecting genomic size, diversity and evolution. The ubiquity and increasingly understood importance of repetitive elements contribute to the need to identify and annotate them. We set out to identify previously uncharacterized repetitive DNA in the porcine genome. Once found, we characterized the prevalence of these repeats in other mammals. Results We discovered 27 repetitive elements in 220 BACs covering 1% of the porcine genome (Comparative Vertebrate Sequencing Initiative; CVSI. These repeats varied in length from 55 to 1059 nucleotides. To estimate copy numbers, we went to an independent source of data, the BAC-end sequences (Wellcome Trust Sanger Institute, covering approximately 15% of the porcine genome. Copy numbers in BAC-ends were less than one hundred for 6 repeat elements, between 100 and 1000 for 16 and between 1,000 and 10,000 for 5. Several of the repeat elements were found in the bovine genome and we have identified two with orthologous sites, indicating that these elements were present in their common ancestor. None of the repeat elements were found in primate, rodent or dog genomes. We were unable to identify any of the replication machinery common to active transposable elements in these newly identified repeats. Conclusion The presence of both orthologous and non-orthologous sites indicates that some sites existed prior to speciation and some were generated later. The identification of low to moderate copy number repetitive DNA that is specific to artiodactyls will be critical in the assembly of livestock genomes and studies of comparative genomics.

Contributions of Zea mays subspecies mexicana haplotypes to modern maize.

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Yang, Ning; Xu, Xi-Wen; Wang, Rui-Ru; Peng, Wen-Lei; Cai, Lichun; Song, Jia-Ming; Li, Wenqiang; Luo, Xin; Niu, Luyao; Wang, Yuebin; Jin, Min; Chen, Lu; Luo, Jingyun; Deng, Min; Wang, Long; Pan, Qingchun; Liu, Feng; Jackson, David; Yang, Xiaohong; Chen, Ling-Ling; Yan, Jianbing

2017-11-30

Maize was domesticated from lowland teosinte (Zea mays ssp. parviglumis), but the contribution of highland teosinte (Zea mays ssp. mexicana, hereafter mexicana) to modern maize is not clear. Here, two genomes for Mo17 (a modern maize inbred) and mexicana are assembled using a meta-assembly strategy after sequencing of 10 lines derived from a maize-teosinte cross. Comparative analyses reveal a high level of diversity between Mo17, B73, and mexicana, including three Mb-size structural rearrangements. The maize spontaneous mutation rate is estimated to be 2.17 × 10 -8 ~3.87 × 10 -8 per site per generation with a nonrandom distribution across the genome. A higher deleterious mutation rate is observed in the pericentromeric regions, and might be caused by differences in recombination frequency. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Our data offer a rich resource for constructing the pan-genome of Zea mays and genetic improvement of modern maize varieties.

genome-wide association and metabolic pathway analysis of corn earworm resistance in maize

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Marilyn L. Warburton; Erika D. Womack; Juliet D. Tang; Adam Thrash; J. Spencer Smith; Wenwei Xu; Seth C. Murray; W. Paul Williams

2018-01-01

Maize (Zea mays mays L.) is a staple crop of economic, industrial, and food security importance. Damage to the growing ears by corn earworm [Helicoverpa zea (Boddie)] is a major economic burden and increases secondary fungal infections and mycotoxin levels. To identify biochemical pathways associated with native resistance mechanisms, a genome-wide...

Genome-wide identification of VQ motif-containing proteins and their expression profiles under abiotic stresses in maize

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Weibin eSong

2016-01-01

Full Text Available VQ motif-containing proteins play crucial roles in abiotic stress responses in plants. Recent studies have shown that some VQ proteins physically interact with WRKY transcription factors to activate downstream genes. In the present study, we identified and characterized genes encoding VQ motif-containing proteins using the most recent version of the maize genome sequence. In total, 61VQ genes were identified. In a cluster analysis, these genes clustered into nine groups together with their homologous genes in rice and Arabidopsis. Most of the VQ genes (57 out of 61 numbers identified in maize were found to be single-copy genes. Analyses of RNA-seq data obtained using seedlings under long-term drought treatment showed that the expression levels of most ZmVQ genes (41 out of 61 members changed during the drought stress response. Quantitative real-time PCR analyses showed that most of the ZmVQ genes were responsive to NaCl treatment. Also, approximately half of the ZmVQ genes were co-expressed with ZmWRKY genes. The identification of these VQ genes in the maize genome and knowledge of their expression profiles under drought and osmotic stresses will provide a solid foundation for exploring their specific functions in the abiotic stress responses of maize.

A NOR-associated repetitive element present in the genome of two Salmo species (Salmo salar and S. trutta)

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Abuin, M.; Clabby, C.; Martinez, P.; Goswami, U.; Flavin, F.; Wilkins, N.P.; Houghton, J.A.; Powell, R.; Sanchez, L.

, internal repetition, and long direct repeats with deletions and insertions between individual units. The repetitive element was shown to have a tandem unit arrangement and was estimated to occupy between two and three percent of the Atlantic salmon genome...

The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome

International Nuclear Information System (INIS)

Economou, E.P.; Bergen, A.W.; Warren, A.C.; Antonarakis, S.E.

1990-01-01

To identify DNA polymorphisms that are abundant in the human genome and are detectable by polymerase chain reaction amplification of genomic DNA, the authors hypothesize that the polydeoxyadenylate tract of the Alu family of repetitive elements is polymorphic among human chromosomes. Analysis of the 3' ends of three specific Alu sequences showed two occurrences, one in the adenosine deaminase gene and other in the β-globin pseudogene, were polymorphic. This novel class of polymorphism, termed AluVpA [Alu variable poly(A)] may represent one of the most useful and informative group of DNA markers in the human genome

Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae

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Piednoël, Mathieu; Aberer, Andre J.; Schneeweiss, Gerald M.; Macas, Jiri; Novak, Petr; Gundlach, Heidrun; Temsch, Eva M.; Renner, Susanne S.

2013-01-01

We used next-generation sequencing to characterize the genomes of nine species of Orobanchaceae of known phylogenetic relationships, different life forms, and including a polyploid species. The study species are the autotrophic, nonparasitic Lindenbergia philippensis, the hemiparasitic Schwalbea americana, and seven nonphotosynthetic parasitic species of Orobanche (Orobanche crenata, Orobanche cumana, Orobanche gracilis (tetraploid), and Orobanche pancicii) and Phelipanche (Phelipanche lavandulacea, Phelipanche purpurea, and Phelipanche ramosa). Ty3/Gypsy elements comprise 1.93%–28.34% of the nine genomes and Ty1/Copia elements comprise 8.09%–22.83%. When compared with L. philippensis and S. americana, the nonphotosynthetic species contain higher proportions of repetitive DNA sequences, perhaps reflecting relaxed selection on genome size in parasitic organisms. Among the parasitic species, those in the genus Orobanche have smaller genomes but higher proportions of repetitive DNA than those in Phelipanche, mostly due to a diversification of repeats and an accumulation of Ty3/Gypsy elements. Genome downsizing in the tetraploid O. gracilis probably led to sequence loss across most repeat types. PMID:22723303

Genome-Wide Identification, Phylogenetic and Expression Analyses of the Ubiquitin-Conjugating Enzyme Gene Family in Maize

Science.gov (United States)

Jue, Dengwei; Sang, Xuelian; Lu, Shengqiao; Dong, Chen; Zhao, Qiufang; Chen, Hongliang; Jia, Liqiang

2015-01-01

Background Ubiquitination is a post-translation modification where ubiquitin is attached to a substrate. Ubiquitin-conjugating enzymes (E2s) play a major role in the ubiquitin transfer pathway, as well as a variety of functions in plant biological processes. To date, no genome-wide characterization of this gene family has been conducted in maize (Zea mays). Methodology/Principal Findings In the present study, a total of 75 putative ZmUBC genes have been identified and located in the maize genome. Phylogenetic analysis revealed that ZmUBC proteins could be divided into 15 subfamilies, which include 13 ubiquitin-conjugating enzymes (ZmE2s) and two independent ubiquitin-conjugating enzyme variant (UEV) groups. The predicted ZmUBC genes were distributed across 10 chromosomes at different densities. In addition, analysis of exon-intron junctions and sequence motifs in each candidate gene has revealed high levels of conservation within and between phylogenetic groups. Tissue expression analysis indicated that most ZmUBC genes were expressed in at least one of the tissues, indicating that these are involved in various physiological and developmental processes in maize. Moreover, expression profile analyses of ZmUBC genes under different stress treatments (4°C, 20% PEG6000, and 200 mM NaCl) and various expression patterns indicated that these may play crucial roles in the response of plants to stress. Conclusions Genome-wide identification, chromosome organization, gene structure, evolutionary and expression analyses of ZmUBC genes have facilitated in the characterization of this gene family, as well as determined its potential involvement in growth, development, and stress responses. This study provides valuable information for better understanding the classification and putative functions of the UBC-encoding genes of maize. PMID:26606743

Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust.

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Rochi, Lucia; Diéguez, María José; Burguener, Germán; Darino, Martín Alejandro; Pergolesi, María Fernanda; Ingala, Lorena Romina; Cuyeu, Alba Romina; Turjanski, Adrián; Kreff, Enrique Domingo; Sacco, Francisco

2018-03-01

Rust fungi are one of the most devastating pathogens of crop plants. The biotrophic fungus Puccinia sorghi Schwein (Ps) is responsible for maize common rust, an endemic disease of maize (Zea mays L.) in Argentina that causes significant yield losses in corn production. In spite of this, the Ps genomic sequence was not available. We used Illumina sequencing to rapidly produce the 99.6Mbdraft genome sequence of Ps race RO10H11247, derived from a single-uredinial isolate from infected maize leaves collected in the Argentine Corn Belt Region during 2010. High quality reads were obtained from 200bppaired-end and 5000bpmate-paired libraries and assembled in 15,722 scaffolds. A pipeline which combined an ab initio program with homology-based models and homology to in planta enriched ESTs from four cereal pathogenic fungus (the three sequenced wheat rusts and Ustilago maydis) was used to identify 21,087 putative coding sequences, of which 1599 might be part of the Ps RO10H11247 secretome. Among the 458 highly conserved protein families from the euKaryotic Orthologous Groups (KOG) that occur in a wide range of eukaryotic organisms, 97.5% have at least one member with high homology in the Ps assembly (TBlastN, E-value⩽e-10) covering more than 50% of the length of the KOG protein. Comparative studies with the three sequenced wheat rust fungus, and microsynteny analysis involving Puccinia striiformis f. sp. tritici (Pst, wheat stripe rust fungus), support the quality achieved. The results presented here show the effectiveness of the Illumina strategy for sequencing dikaryotic genomes of non-model organisms and provides reliable DNA sequence information for genomic studies, including pathogenic mechanisms of this maize fungus and molecular marker design. Copyright © 2016 Elsevier Inc. All rights reserved.

Genome Wide Association Study for Drought, Aflatoxin Resistance, and Important Agronomic Traits of Maize Hybrids in the Sub-Tropics

Science.gov (United States)

Farfan, Ivan D. Barrero; De La Fuente, Gerald N.; Murray, Seth C.; Isakeit, Thomas; Huang, Pei-Cheng; Warburton, Marilyn; Williams, Paul; Windham, Gary L.; Kolomiets, Mike

2015-01-01

The primary maize (Zea mays L.) production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with Aspergillus flavus and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5–10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines. PMID:25714370

Correlation of Aquaporins and Transmembrane Solute Transporters Revealed by Genome-Wide Analysis in Developing Maize Leaf

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Xun Yue

2012-01-01

Full Text Available Aquaporins are multifunctional membrane channels that facilitate the transmembrane transport of water and solutes. When transmembrane mineral nutrient transporters exhibit the same expression patterns as aquaporins under diverse temporal and physiological conditions, there is a greater probability that they interact. In this study, genome-wide temporal profiling of transcripts analysis and coexpression network-based approaches are used to examine the significant specificity correlation of aquaporins and transmembrane solute transporters in developing maize leaf. The results indicate that specific maize aquaporins are related to specific transmembrane solute transporters. The analysis demonstrates a systems-level correlation between aquaporins, nutrient transporters, and the homeostasis of mineral nutrients in developing maize leaf. Our results provide a resource for further studies into the physiological function of these aquaporins.

Adaptation of maize to temperate climates: mid-density genome-wide association genetics and diversity patterns reveal key genomic regions, with a major contribution of the Vgt2 (ZCN8 locus.

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Sophie Bouchet

Full Text Available The migration of maize from tropical to temperate climates was accompanied by a dramatic evolution in flowering time. To gain insight into the genetic architecture of this adaptive trait, we conducted a 50K SNP-based genome-wide association and diversity investigation on a panel of tropical and temperate American and European representatives. Eighteen genomic regions were associated with flowering time. The number of early alleles cumulated along these regions was highly correlated with flowering time. Polymorphism in the vicinity of the ZCN8 gene, which is the closest maize homologue to Arabidopsis major flowering time (FT gene, had the strongest effect. This polymorphism is in the vicinity of the causal factor of Vgt2 QTL. Diversity was lower, whereas differentiation and LD were higher for associated loci compared to the rest of the genome, which is consistent with selection acting on flowering time during maize migration. Selection tests also revealed supplementary loci that were highly differentiated among groups and not associated with flowering time in our panel, whereas they were in other linkage-based studies. This suggests that allele fixation led to a lack of statistical power when structure and relatedness were taken into account in a linear mixed model. Complementary designs and analysis methods are necessary to unravel the architecture of complex traits. Based on linkage disequilibrium (LD estimates corrected for population structure, we concluded that the number of SNPs genotyped should be at least doubled to capture all QTLs contributing to the genetic architecture of polygenic traits in this panel. These results show that maize flowering time is controlled by numerous QTLs of small additive effect and that strong polygenic selection occurred under cool climatic conditions. They should contribute to more efficient genomic predictions of flowering time and facilitate the dissemination of diverse maize genetic resources under a wide

Genomic Prediction of Single Crosses in the Early Stages of a Maize Hybrid Breeding Pipeline

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Dnyaneshwar C. Kadam

2016-11-01

Full Text Available Prediction of single-cross performance has been a major goal of plant breeders since the beginning of hybrid breeding. Recently, genomic prediction has shown to be a promising approach, but only limited studies have examined the accuracy of predicting single-cross performance. Moreover, no studies have examined the potential of predicting single crosses among random inbreds derived from a series of biparental families, which resembles the structure of germplasm comprising the initial stages of a hybrid maize breeding pipeline. The main objectives of this study were to evaluate the potential of genomic prediction for identifying superior single crosses early in the hybrid breeding pipeline and optimize its application. To accomplish these objectives, we designed and analyzed a novel population of single crosses representing the Iowa Stiff Stalk synthetic/non-Stiff Stalk heterotic pattern commonly used in the development of North American commercial maize hybrids. The performance of single crosses was predicted using parental combining ability and covariance among single crosses. Prediction accuracies were estimated using cross-validation and ranged from 0.28 to 0.77 for grain yield, 0.53 to 0.91 for plant height, and 0.49 to 0.94 for staygreen, depending on the number of tested parents of the single cross and genomic prediction method used. The genomic estimated general and specific combining abilities showed an advantage over genomic covariances among single crosses when one or both parents of the single cross were untested. Overall, our results suggest that genomic prediction of single crosses in the early stages of a hybrid breeding pipeline holds great potential to redesign hybrid breeding and increase its efficiency.

Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome.

Science.gov (United States)

Kolano, B; Gardunia, B W; Michalska, M; Bonifacio, A; Fairbanks, D; Maughan, P J; Coleman, C E; Stevens, M R; Jellen, E N; Maluszynska, J

2011-09-01

The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18-24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18-24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12-13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12-13P was very similar to GISH results, suggesting that the 12-13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

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O'Brien Kimberly

2008-06-01

Full Text Available Abstract Background The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses. Results In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC clone library (87 Mb and sequencing of 22 potato BAC clones (2.9 Mb. The GC content of potato is very similar to Solanum lycopersicon (tomato and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed. Conclusion Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that

Sequencing, assembly, and annotation of Maize B104 : A maize transformation resource

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Maize transformation is complicated. Most lines are not readily cultured and transformed, making the germplasm available for genome engineering extremely limited. Developing a better understanding of the genomic regions responsible for differences in culturability and transformability would be a goo...

Testing the link between genome size and growth rate in maize

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Maud I. Tenaillon

2016-09-01

Full Text Available Little is known about the factors driving within species Genome Size (GS variation. GS may be shaped indirectly by natural selection on development and adaptative traits. Because GS variation is particularly pronounced in maize, we have sampled 83 maize inbred lines from three well described genetic groups adapted to contrasted climate conditions: inbreds of tropical origin, Flint inbreds grown in temperate climates, and Dent inbreds distributed in the Corn Belt. As a proxy for growth rate, we measured the Leaf Elongation Rate maximum during nighttime (LERmax as well as GS in all inbred lines. In addition we combined available and new nucleotide polymorphism data at 29,090 sites to characterize the genetic structure of our panel. We found significant variation for both LERmax and GS among groups defined by our genetic structuring. Tropicals displayed larger GS than Flints while Dents exhibited intermediate values. LERmax followed the opposite trend with greater growth rate in Flints than in Tropicals. In other words, LERmax and GS exhibited a significantly negative correlation (r = − 0.27. However, this correlation was driven by among-group variation rather than within-group variation—it was no longer significant after controlling for structure and kinship among inbreds. Our results indicate that selection on GS may have accompanied ancient maize diffusion from its center of origin, with large DNA content excluded from temperate areas. Whether GS has been targeted by more intense selection during modern breeding within groups remains an open question.

Genome-wide association study identifies candidate genes for starch content regulation in maize kernels

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Na Liu

2016-07-01

Full Text Available Kernel starch content is an important trait in maize (Zea mays L. as it accounts for 65% to 75% of the dry kernel weight and positively correlates with seed yield. A number of starch synthesis-related genes have been identified in maize in recent years. However, many loci underlying variation in starch content among maize inbred lines still remain to be identified. The current study is a genome-wide association study that used a set of 263 maize inbred lines. In this panel, the average kernel starch content was 66.99%, ranging from 60.60% to 71.58% over the three study years. These inbred lines were genotyped with the SNP50 BeadChip maize array, which is comprised of 56,110 evenly spaced, random SNPs. Population structure was controlled by a mixed linear model (MLM as implemented in the software package TASSEL. After the statistical analyses, four SNPs were identified as significantly associated with starch content (P ≤ 0.0001, among which one each are located on chromosomes 1 and 5 and two are on chromosome 2. Furthermore, 77 candidate genes associated with starch synthesis were found within the 100-kb intervals containing these four QTLs, and four highly associated genes were within 20-kb intervals of the associated SNPs. Among the four genes, Glucose-1-phosphate adenylyltransferase (APS1; Gene ID GRMZM2G163437 is known as an important regulator of kernel starch content. The identified SNPs, QTLs, and candidate genes may not only be readily used for germplasm improvement by marker-assisted selection in breeding, but can also elucidate the genetic basis of starch content. Further studies on these identified candidate genes may help determine the molecular mechanisms regulating kernel starch content in maize and other important cereal crops.

Genomic variation in recently collected maize landraces from Mexico

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María Clara Arteaga

2016-03-01

Full Text Available The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE = 0.234 to 0.318 (mean 0.311, while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE = 0.262 and 0.234, respectively. The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law. Keywords: Maize, Teosinte, Maize SNP50K BeadChip, Mexican landraces, Proyecto Global de Maíces Nativos

Biotechnology in maize breeding

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Mladenović-Drinić Snežana

2004-01-01

Full Text Available Maize is one of the most important economic crops and the best studied and most tractable genetic system among monocots. The development of biotechnology has led to a great increase in our knowledge of maize genetics and understanding of the structure and behaviour of maize genomes. Conventional breeding practices can now be complemented by a number of new and powerful techniques. Some of these often referred to as molecular methods, enable scientists to see the layout of the entire genome of any organism and to select plants with preferred characteristics by "reading" at the molecular level, saving precious time and resources. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. Application of molecular markers for genetic studies of maize include: assessment of genetic variability and characterization of germ plasm, identification and fingerprinting of genotypes, estimation of genetic distance, detection of monogamic and quantitative trait loci, marker assisted selection, identification of sequence of useful candidate genes, etc. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible and serve as bases for marker assisted selection. Sequencing of maize genomes would help to elucidate gene function, gene regulation and their expression. Modern biotechnology also includes an array of tools for introducing or deieting a particular gene or genes to produce plants with novel traits. Development of informatics and biotechnology are resulted in bioinformatic as well as in expansion of microarrey technique. Modern biotechnologies could complement and improve the efficiency of traditional selection and breeding techniques to enhance agricultural productivity.

The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome.

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Barghini, Elena; Natali, Lucia; Cossu, Rosa Maria; Giordani, Tommaso; Pindo, Massimo; Cattonaro, Federica; Scalabrin, Simone; Velasco, Riccardo; Morgante, Michele; Cavallini, Andrea

2014-04-01

Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome.

Gene-enriched draft genome of the cattle tick Rhipicephalus microplus: assembly by the hybrid Pacific Biosciences/Illumina approach enabled analysis of the highly repetitive genome.

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Barrero, Roberto A; Guerrero, Felix D; Black, Michael; McCooke, John; Chapman, Brett; Schilkey, Faye; Pérez de León, Adalberto A; Miller, Robert J; Bruns, Sara; Dobry, Jason; Mikhaylenko, Galina; Stormo, Keith; Bell, Callum; Tao, Quanzhou; Bogden, Robert; Moolhuijzen, Paula M; Hunter, Adam; Bellgard, Matthew I

2017-08-01

The genome of the cattle tick Rhipicephalus microplus, an ectoparasite with global distribution, is estimated to be 7.1Gbp in length and consists of approximately 70% repetitive DNA. We report the draft assembly of a tick genome that utilized a hybrid sequencing and assembly approach to capture the repetitive fractions of the genome. Our hybrid approach produced an assembly consisting of 2.0Gbp represented in 195,170 scaffolds with a N50 of 60,284bp. The Rmi v2.0 assembly is 51.46% repetitive with a large fraction of unclassified repeats, short interspersed elements, long interspersed elements and long terminal repeats. We identified 38,827 putative R. microplus gene loci, of which 24,758 were protein coding genes (≥100 amino acids). OrthoMCL comparative analysis against 11 selected species including insects and vertebrates identified 10,835 and 3,423 protein coding gene loci that are unique to R. microplus or common to both R. microplus and Ixodes scapularis ticks, respectively. We identified 191 microRNA loci, of which 168 have similarity to known miRNAs and 23 represent novel miRNA families. We identified the genomic loci of several highly divergent R. microplus esterases with sequence similarity to acetylcholinesterase. Additionally we report the finding of a novel cytochrome P450 CYP41 homolog that shows similar protein folding structures to known CYP41 proteins known to be involved in acaricide resistance. Copyright © 2017 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

A Genome-Wide Association Study Reveals Genes Associated with Fusarium Ear Rot Resistance in a Maize Core Diversity Panel

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Zila, Charles T.; Samayoa, L. Fernando; Santiago, Rogelio; Butrón, Ana; Holland, James B.

2013-01-01

Fusarium ear rot is a common disease of maize that affects food and feed quality globally. Resistance to the disease is highly quantitative, and maize breeders have difficulty incorporating polygenic resistance alleles from unadapted donor sources into elite breeding populations without having a negative impact on agronomic performance. Identification of specific allele variants contributing to improved resistance may be useful to breeders by allowing selection of resistance alleles in coupling phase linkage with favorable agronomic characteristics. We report the results of a genome-wide association study to detect allele variants associated with increased resistance to Fusarium ear rot in a maize core diversity panel of 267 inbred lines evaluated in two sets of environments. We performed association tests with 47,445 single-nucleotide polymorphisms (SNPs) while controlling for background genomic relationships with a mixed model and identified three marker loci significantly associated with disease resistance in at least one subset of environments. Each associated SNP locus had relatively small additive effects on disease resistance (±1.1% on a 0–100% scale), but nevertheless were associated with 3 to 12% of the genotypic variation within or across environment subsets. Two of three identified SNPs colocalized with genes that have been implicated with programmed cell death. An analysis of associated allele frequencies within the major maize subpopulations revealed enrichment for resistance alleles in the tropical/subtropical and popcorn subpopulations compared with other temperate breeding pools. PMID:24048647

Interspersion of highly repetitive DNA with single copy DNA in the genome of the red crab, Geryon quinquedens

Energy Technology Data Exchange (ETDEWEB)

Christie, N.T. (Univ. of Tennessee, Oak Ridge); Skinner, D.M.

1979-02-01

Kinetic analysis of the reassociation of 420 nucleotide (NT) long fragments has shown that essentially all of the repetitive sequences of the DNA of the red crab Geryon quinquedens are highly repetitive. There are negligible amounts of low and intermediate repetitive DNAs. Though atypical of most eukaryotes, this pattern has been observed in al other brachyurans (true crabs) studied. The major repetitive component is subdivided into short runs of 300 NT and longer runs of greater than 1200 NT while the minor component has an average sequence length of 400 NT. Both components reassociate at rates commonly observed for satellite DNAs. Unique among eukaryotes the organization of the genome includes single copy DNA contiguous to short runs (300 NT) of both repetitive components. Although patent satellites are not present, subsets of the repetitive DNA have been isolated by either restriction endonuclease digestion or by centrifugation in Ag/sup +/ or Hg/sup 2 +//Cs/sub 2/SO/sub 4/ density gradients.

Effect of Trait Heritability, Training Population Size and Marker Density on Genomic Prediction Accuracy Estimation in 22 bi-parental Tropical Maize Populations.

Science.gov (United States)

Zhang, Ao; Wang, Hongwu; Beyene, Yoseph; Semagn, Kassa; Liu, Yubo; Cao, Shiliang; Cui, Zhenhai; Ruan, Yanye; Burgueño, Juan; San Vicente, Felix; Olsen, Michael; Prasanna, Boddupalli M; Crossa, José; Yu, Haiqiu; Zhang, Xuecai

2017-01-01

Genomic selection is being used increasingly in plant breeding to accelerate genetic gain per unit time. One of the most important applications of genomic selection in maize breeding is to predict and select the best un-phenotyped lines in bi-parental populations based on genomic estimated breeding values. In the present study, 22 bi-parental tropical maize populations genotyped with low density SNPs were used to evaluate the genomic prediction accuracy ( r MG ) of the six trait-environment combinations under various levels of training population size (TPS) and marker density (MD), and assess the effect of trait heritability ( h 2 ), TPS and MD on r MG estimation. Our results showed that: (1) moderate r MG values were obtained for different trait-environment combinations, when 50% of the total genotypes was used as training population and ~200 SNPs were used for prediction; (2) r MG increased with an increase in h 2 , TPS and MD, both correlation and variance analyses showed that h 2 is the most important factor and MD is the least important factor on r MG estimation for most of the trait-environment combinations; (3) predictions between pairwise half-sib populations showed that the r MG values for all the six trait-environment combinations were centered around zero, 49% predictions had r MG values above zero; (4) the trend observed in r MG differed with the trend observed in r MG / h , and h is the square root of heritability of the predicted trait, it indicated that both r MG and r MG / h values should be presented in GS study to show the accuracy of genomic selection and the relative accuracy of genomic selection compared with phenotypic selection, respectively. This study provides useful information to maize breeders to design genomic selection workflow in their breeding programs.

Effect of Trait Heritability, Training Population Size and Marker Density on Genomic Prediction Accuracy Estimation in 22 bi-parental Tropical Maize Populations

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Ao Zhang

2017-11-01

Full Text Available Genomic selection is being used increasingly in plant breeding to accelerate genetic gain per unit time. One of the most important applications of genomic selection in maize breeding is to predict and select the best un-phenotyped lines in bi-parental populations based on genomic estimated breeding values. In the present study, 22 bi-parental tropical maize populations genotyped with low density SNPs were used to evaluate the genomic prediction accuracy (rMG of the six trait-environment combinations under various levels of training population size (TPS and marker density (MD, and assess the effect of trait heritability (h2, TPS and MD on rMG estimation. Our results showed that: (1 moderate rMG values were obtained for different trait-environment combinations, when 50% of the total genotypes was used as training population and ~200 SNPs were used for prediction; (2 rMG increased with an increase in h2, TPS and MD, both correlation and variance analyses showed that h2 is the most important factor and MD is the least important factor on rMG estimation for most of the trait-environment combinations; (3 predictions between pairwise half-sib populations showed that the rMG values for all the six trait-environment combinations were centered around zero, 49% predictions had rMG values above zero; (4 the trend observed in rMG differed with the trend observed in rMG/h, and h is the square root of heritability of the predicted trait, it indicated that both rMG and rMG/h values should be presented in GS study to show the accuracy of genomic selection and the relative accuracy of genomic selection compared with phenotypic selection, respectively. This study provides useful information to maize breeders to design genomic selection workflow in their breeding programs.

Repetitive sequences: the hidden diversity of heterochromatin in prochilodontid fish

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Maria L. Terencio

2015-08-01

Full Text Available The structure and organization of repetitive elements in fish genomes are still relatively poorly understood, although most of these elements are believed to be located in heterochromatic regions. Repetitive elements are considered essential in evolutionary processes as hotspots for mutations and chromosomal rearrangements, among other functions – thus providing new genomic alternatives and regulatory sites for gene expression. The present study sought to characterize repetitive DNA sequences in the genomes of Semaprochilodus insignis (Jardine & Schomburgk, 1841 and Semaprochilodus taeniurus (Valenciennes, 1817 and identify regions of conserved syntenic blocks in this genome fraction of three species of Prochilodontidae (S. insignis, S. taeniurus, and Prochilodus lineatus (Valenciennes, 1836 by cross-FISH using Cot-1 DNA (renaturation kinetics probes. We found that the repetitive fractions of the genomes of S. insignis and S. taeniurus have significant amounts of conserved syntenic blocks in hybridization sites, but with low degrees of similarity between them and the genome of P. lineatus, especially in relation to B chromosomes. The cloning and sequencing of the repetitive genomic elements of S. insignis and S. taeniurus using Cot-1 DNA identified 48 fragments that displayed high similarity with repetitive sequences deposited in public DNA databases and classified as microsatellites, transposons, and retrotransposons. The repetitive fractions of the S. insignis and S. taeniurus genomes exhibited high degrees of conserved syntenic blocks in terms of both the structures and locations of hybridization sites, but a low degree of similarity with the syntenic blocks of the P. lineatus genome. Future comparative analyses of other prochilodontidae species will be needed to advance our understanding of the organization and evolution of the genomes in this group of fish.

Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes.

Science.gov (United States)

Feschotte, Cédric; Keswani, Umeshkumar; Ranganathan, Nirmal; Guibotsy, Marcel L; Levine, David

2009-07-23

Eukaryotic genomes contain large amount of repetitive DNA, most of which is derived from transposable elements (TEs). Progress has been made to develop computational tools for ab initio identification of repeat families, but there is an urgent need to develop tools to automate the annotation of TEs in genome sequences. Here we introduce REPCLASS, a tool that automates the classification of TE sequences. Using control repeat libraries, we show that the program can classify accurately virtually any known TE types. Combining REPCLASS to ab initio repeat finding in the genomes of Caenorhabditis elegans and Drosophila melanogaster allowed us to recover the contrasting TE landscape characteristic of these species. Unexpectedly, REPCLASS also uncovered several novel TE families in both genomes, augmenting the TE repertoire of these model species. When applied to the genomes of distant Caenorhabditis and Drosophila species, the approach revealed a remarkable conservation of TE composition profile within each genus, despite substantial interspecific covariations in genome size and in the number of TEs and TE families. Lastly, we applied REPCLASS to analyze 10 fungal genomes from a wide taxonomic range, most of which have not been analyzed for TE content previously. The results showed that TE diversity varies widely across the fungi "kingdom" and appears to positively correlate with genome size, in particular for DNA transposons. Together, these data validate REPCLASS as a powerful tool to explore the repetitive DNA landscapes of eukaryotes and to shed light onto the evolutionary forces shaping TE diversity and genome architecture.

Genomic variation in recently collected maize landraces from Mexico

Science.gov (United States)

Arteaga, María Clara; Moreno-Letelier, Alejandra; Mastretta-Yanes, Alicia; Vázquez-Lobo, Alejandra; Breña-Ochoa, Alejandra; Moreno-Estrada, Andrés; Eguiarte, Luis E.; Piñero, Daniel

2015-01-01

The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE = 0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE = 0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law. PMID:26981357

MaizeGDB: enabling access to basic, translational, and applied research information

Science.gov (United States)

MaizeGDB is the Maize Genetics and Genomics Database (available online at http://www.maizegdb.org). The MaizeGDB project is not simply an online database and website but rather an information service to maize researchers that supports customized data access and analysis needs to individual research...

Human CST Facilitates Genome-wide RAD51 Recruitment to GC-Rich Repetitive Sequences in Response to Replication Stress.

Science.gov (United States)

Chastain, Megan; Zhou, Qing; Shiva, Olga; Fadri-Moskwik, Maria; Whitmore, Leanne; Jia, Pingping; Dai, Xueyu; Huang, Chenhui; Ye, Ping; Chai, Weihang

2016-08-02

The telomeric CTC1/STN1/TEN1 (CST) complex has been implicated in promoting replication recovery under replication stress at genomic regions, yet its precise role is unclear. Here, we report that STN1 is enriched at GC-rich repetitive sequences genome-wide in response to hydroxyurea (HU)-induced replication stress. STN1 deficiency exacerbates the fragility of these sequences under replication stress, resulting in chromosome fragmentation. We find that upon fork stalling, CST proteins form distinct nuclear foci that colocalize with RAD51. Furthermore, replication stress induces physical association of CST with RAD51 in an ATR-dependent manner. Strikingly, CST deficiency diminishes HU-induced RAD51 foci formation and reduces RAD51 recruitment to telomeres and non-telomeric GC-rich fragile sequences. Collectively, our findings establish that CST promotes RAD51 recruitment to GC-rich repetitive sequences in response to replication stress to facilitate replication restart, thereby providing insights into the mechanism underlying genome stability maintenance. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

Science.gov (United States)

Gill, Navdeep; Buti, Matteo; Kane, Nolan; Bellec, Arnaud; Helmstetter, Nicolas; Berges, Hélène; Rieseberg, Loren H.

2014-01-01

Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence. PMID:24833511

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L. Genome

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Navdeep Gill

2014-04-01

Full Text Available Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.

Genomic and phylogenetic evidence that Maize rough dwarf and Rice black-streaked dwarf fijiviruses should be classified as different geographic strains of a single species.

Science.gov (United States)

Xie, L; Lv, M-F; Yang, J; Chen, J-P; Zhang, H-M

Maize rough dwarf disease (MRDD) has long been known as one of the most devastating viral diseases of maize worldwide and is caused by single or complex infection by four fijiviruses: Maize rough dwarf virus (MRDV) in Europe and the Middle East, Mal de Rio Cuarto virus (MRCV) in South America, rice black-streaked dwarf virus (RBSDV), and Southern rice black-streaked dwarf virus (SRBSDV or Rice black-streaked dwarf virus 2, RBSDV-2) in East Asia. These are currently classified as four distinct species in the genus Fijivirus, family Reoviridae, but their taxonomic status has been questioned. To help resolve this, the nucleotide sequences of the ten genomic segments of an Italian isolate of MRDV have been determined, providing the first complete genomic sequence of this virus. Its genome has 29144 nucleotides and is similar in organization to those of RBSDV, SRBSDV, and MRCV. The 13 ORFs always share highest identities (81.3-97.2%) with the corresponding ORFs of RBSDV and phylogenetic analyses of the different genome segments and ORFs all confirm that MRDV clusters most closely with RBSDV and that MRCV and SRBSDV are slightly more distantly related. The results suggest that MRDV and RBSDV should be classified as different geographic strains of the same virus species and we suggest the name cereal black-streaked dwarf fijivirus (CBSDV) for consideration.

Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers

Science.gov (United States)

Understanding the maize genomic features would be useful for the study of genetic diversity and evolution and for maize breeding. Here, we used two maize nested association mapping (NAM) populations separately derived in China (CN-NAM) and the US (US-NAM) to explore the maize genomic features. The t...

Genomic Predictability of Interconnected Biparental Maize Populations

Science.gov (United States)

Riedelsheimer, Christian; Endelman, Jeffrey B.; Stange, Michael; Sorrells, Mark E.; Jannink, Jean-Luc; Melchinger, Albrecht E.

2013-01-01

Intense structuring of plant breeding populations challenges the design of the training set (TS) in genomic selection (GS). An important open question is how the TS should be constructed from multiple related or unrelated small biparental families to predict progeny from individual crosses. Here, we used a set of five interconnected maize (Zea mays L.) populations of doubled-haploid (DH) lines derived from four parents to systematically investigate how the composition of the TS affects the prediction accuracy for lines from individual crosses. A total of 635 DH lines genotyped with 16,741 polymorphic SNPs were evaluated for five traits including Gibberella ear rot severity and three kernel yield component traits. The populations showed a genomic similarity pattern, which reflects the crossing scheme with a clear separation of full sibs, half sibs, and unrelated groups. Prediction accuracies within full-sib families of DH lines followed closely theoretical expectations, accounting for the influence of sample size and heritability of the trait. Prediction accuracies declined by 42% if full-sib DH lines were replaced by half-sib DH lines, but statistically significantly better results could be achieved if half-sib DH lines were available from both instead of only one parent of the validation population. Once both parents of the validation population were represented in the TS, including more crosses with a constant TS size did not increase accuracies. Unrelated crosses showing opposite linkage phases with the validation population resulted in negative or reduced prediction accuracies, if used alone or in combination with related families, respectively. We suggest identifying and excluding such crosses from the TS. Moreover, the observed variability among populations and traits suggests that these uncertainties must be taken into account in models optimizing the allocation of resources in GS. PMID:23535384

Genomic Variability of Haemophilus influenzae Isolated from Mexican Children Determined by Using Enterobacterial Repetitive Intergenic Consensus Sequences and PCR

OpenAIRE

Gomez-De-Leon, Patricia; Santos, Jose I.; Caballero, Javier; Gomez, Demostenes; Espinosa, Luz E.; Moreno, Isabel; Piñero, Daniel; Cravioto, Alejandro

2000-01-01

Genomic fingerprints from 92 capsulated and noncapsulated strains of Haemophilus influenzae from Mexican children with different diseases and healthy carriers were generated by PCR using the enterobacterial repetitive intergenic consensus (ERIC) sequences. A cluster analysis by the unweighted pair-group method with arithmetic averages based on the overall similarity as estimated from the characteristics of the genomic fingerprints, was conducted to group the strains. A total of 69 fingerprint...

Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes

Science.gov (United States)

Ni, Yanxiang; Cao, Bo; Ma, Tszshan; Niu, Gang; Huo, Yingdong; Huang, Jiandong; Chen, Danni; Liu, Yi; Yu, Bin; Zhang, Michael Q; Niu, Hanben

2017-01-01

High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaint probes have enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence. We used three-dimensional stochastic optical reconstruction microscopy (3D-STORM) with optimized imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and only 29–34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in human or mouse genome, respectively. We demonstrated our MB-based FISH method was capable of visualizing the so far shortest non-repetitive genomic sequence in 3D at super-resolution. DOI: http://dx.doi.org/10.7554/eLife.21660.001 PMID:28485713

Genetic Dissection of Maize Embryonic Callus Regenerative Capacity Using Multi-Locus Genome-Wide Association Studies

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Langlang Ma

2018-04-01

Full Text Available The regenerative capacity of the embryonic callus, a complex quantitative trait, is one of the main limiting factors for maize transformation. This trait was decomposed into five traits, namely, green callus rate (GCR, callus differentiating rate (CDR, callus plantlet number (CPN, callus rooting rate (CRR, and callus browning rate (CBR. To dissect the genetic foundation of maize transformation, in this study multi-locus genome-wide association studies (GWAS for the five traits were performed in a population of 144 inbred lines genotyped with 43,427 SNPs. Using the phenotypic values in three environments and best linear unbiased prediction (BLUP values, as a result, a total of 127, 56, 160, and 130 significant quantitative trait nucleotides (QTNs were identified by mrMLM, FASTmrEMMA, ISIS EM-BLASSO, and pLARmEB, respectively. Of these QTNs, 63 QTNs were commonly detected, including 15 across multiple environments and 58 across multiple methods. Allele distribution analysis showed that the proportion of superior alleles for 36 QTNs was <50% in 31 elite inbred lines. Meanwhile, these superior alleles had obviously additive effect on the regenerative capacity. This indicates that the regenerative capacity-related traits can be improved by proper integration of the superior alleles using marker-assisted selection. Moreover, a total of 40 candidate genes were found based on these common QTNs. Some annotated genes were previously reported to relate with auxin transport, cell fate, seed germination, or embryo development, especially, GRMZM2G108933 (WOX2 was found to promote maize transgenic embryonic callus regeneration. These identified candidate genes will contribute to a further understanding of the genetic foundation of maize embryonic callus regeneration.

Haben repetitive DNA-Sequenzen biologische Funktionen?

Science.gov (United States)

John, Maliyakal E.; Knöchel, Walter

1983-05-01

By DNA reassociation kinetics it is known that the eucaryotic genome consists of non-repetitive DNA, middle-repetitive DNA and highly repetitive DNA. Whereas the majority of protein-coding genes is located on non-repetitive DNA, repetitive DNA forms a constitutive part of eucaryotic DNA and its amount in most cases equals or even substantially exceeds that of non-repetitive DNA. During the past years a large body of data on repetitive DNA has accumulated and these have prompted speculations ranging from specific roles in the regulation of gene expression to that of a selfish entity with inconsequential functions. The following article summarizes recent findings on structural, transcriptional and evolutionary aspects and, although by no means being proven, some possible biological functions are discussed.

The Sorghum bicolor genome and the diversification of grasses

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Paterson, Andrew H.; Bowers, John E.; Bruggmann, Remy; dubchak, Inna; Grimwood, Jane; Gundlach, Heidrun; Haberer, Georg; Hellsten, Uffe; Mitros, Therese; Poliakov, Alexander; Schmutz, Jeremy; Spannagl, Manuel; Tang, Haibo; Wang, Xiyin; Wicker, Thomas; Bharti, Arvind K.; Chapman, Jarrod; Feltus, F. Alex; Gowik, Udo; Grigoriev, Igor V.; Lyons, Eric; Maher, Christopher A.; Martis, Mihaela; Marechania, Apurva; Otillar, Robert P.; Penning, Bryan W.; Salamov, Asaf. A.; Wang, Yu; Zhang, Lifang; Carpita, Nicholas C.; Freeling, Michael; Gingle, Alan R.; hash, C. Thomas; Keller, Beat; Klein, Patricia; Kresovich, Stephen; McCann, Maureen C.; Ming, Ray; Peterson, Daniel G.; ur-Rahman, Mehboob-; Ware, Doreen; Westhoff, Peter; Mayer, Klaus F. X.; Messing, Joachim; Rokhsar, Daniel S.

2008-08-20

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approx730-megabase Sorghum bicolor (L.) Moench genome, placing approx98percent of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approx75percent larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approx70 million years ago, most duplicated gene sets lost one member before the sorghum rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24percent of genes are grass-specific and 7percent are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

The use of mycobacterial interspersed repetitive unit typing and whole genome sequencing to inform tuberculosis prevention and control activities.

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Gilbert, Gwendolyn L; Sintchenko, Vitali

2013-07-01

Molecular strain typing of Mycobacterium tuberculosis has been possible for only about 20 years; it has significantly improved our understanding of the evolution and epidemiology of Mycobacterium tuberculosis and tuberculosis disease. Mycobacterial interspersed repetitive unit typing, based on 24 variable number tandem repeat unit loci, is highly discriminatory, relatively easy to perform and interpret and is currently the most widely used molecular typing system for tuberculosis surveillance. Nevertheless, clusters identified by mycobacterial interspersed repetitive unit typing sometimes cannot be confirmed or adequately defined by contact tracing and additional methods are needed. Recently, whole genome sequencing has been used to identify single nucleotide polymorphisms and other mutations, between genotypically indistinguishable isolates from the same cluster, to more accurately trace transmission pathways. Rapidly increasing speed and quality and reduced costs will soon make large scale whole genome sequencing feasible, combined with the use of sophisticated bioinformatics tools, for epidemiological surveillance of tuberculosis.

Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes.

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Wang, Yijun; Deng, Dexiang; Shi, Yating; Miao, Nan; Bian, Yunlong; Yin, Zhitong

2012-03-01

Auxin response factors (ARFs), member of the plant-specific B3 DNA binding superfamily, target specifically to auxin response elements (AuxREs) in promoters of primary auxin-responsive genes and heterodimerize with Aux/IAA proteins in auxin signaling transduction cascade. In previous research, we have isolated and characterized maize Aux/IAA genes in whole-genome scale. Here, we report the comprehensive analysis of ARF genes in maize. A total of 36 ARF genes were identified and validated from the B73 maize genome through an iterative strategy. Thirty-six maize ARF genes are distributed in all maize chromosomes except chromosome 7. Maize ARF genes expansion is mainly due to recent segmental duplications. Maize ARF proteins share one B3 DNA binding domain which consists of seven-stranded β sheets and two short α helixes. Twelve maize ARFs with glutamine-rich middle regions could be as activators in modulating expression of auxin-responsive genes. Eleven maize ARF proteins are lack of homo- and heterodimerization domains. Putative cis-elements involved in phytohormones and light signaling responses, biotic and abiotic stress adaption locate in promoters of maize ARF genes. Expression patterns vary greatly between clades and sister pairs of maize ARF genes. The B3 DNA binding and auxin response factor domains of maize ARF proteins are primarily subjected to negative selection during selective sweep. The mixed selective forces drive the diversification and evolution of genomic regions outside of B3 and ARF domains. Additionally, the dicot-specific proliferation of ARF genes was detected. Comparative genomics analysis indicated that maize, sorghum and rice duplicate chromosomal blocks containing ARF homologs are highly syntenic. This study provides insights into the distribution, phylogeny and evolution of ARF gene family.

Genomic-Enabled Prediction in Maize Using Kernel Models with Genotype × Environment Interaction.

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Bandeira E Sousa, Massaine; Cuevas, Jaime; de Oliveira Couto, Evellyn Giselly; Pérez-Rodríguez, Paulino; Jarquín, Diego; Fritsche-Neto, Roberto; Burgueño, Juan; Crossa, Jose

2017-06-07

Multi-environment trials are routinely conducted in plant breeding to select candidates for the next selection cycle. In this study, we compare the prediction accuracy of four developed genomic-enabled prediction models: (1) single-environment, main genotypic effect model (SM); (2) multi-environment, main genotypic effects model (MM); (3) multi-environment, single variance G×E deviation model (MDs); and (4) multi-environment, environment-specific variance G×E deviation model (MDe). Each of these four models were fitted using two kernel methods: a linear kernel Genomic Best Linear Unbiased Predictor, GBLUP (GB), and a nonlinear kernel Gaussian kernel (GK). The eight model-method combinations were applied to two extensive Brazilian maize data sets (HEL and USP data sets), having different numbers of maize hybrids evaluated in different environments for grain yield (GY), plant height (PH), and ear height (EH). Results show that the MDe and the MDs models fitted with the Gaussian kernel (MDe-GK, and MDs-GK) had the highest prediction accuracy. For GY in the HEL data set, the increase in prediction accuracy of SM-GK over SM-GB ranged from 9 to 32%. For the MM, MDs, and MDe models, the increase in prediction accuracy of GK over GB ranged from 9 to 49%. For GY in the USP data set, the increase in prediction accuracy of SM-GK over SM-GB ranged from 0 to 7%. For the MM, MDs, and MDe models, the increase in prediction accuracy of GK over GB ranged from 34 to 70%. For traits PH and EH, gains in prediction accuracy of models with GK compared to models with GB were smaller than those achieved in GY. Also, these gains in prediction accuracy decreased when a more difficult prediction problem was studied. Copyright © 2017 Bandeira e Sousa et al.

Genomic-Enabled Prediction in Maize Using Kernel Models with Genotype × Environment Interaction

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Massaine Bandeira e Sousa

2017-06-01

Full Text Available Multi-environment trials are routinely conducted in plant breeding to select candidates for the next selection cycle. In this study, we compare the prediction accuracy of four developed genomic-enabled prediction models: (1 single-environment, main genotypic effect model (SM; (2 multi-environment, main genotypic effects model (MM; (3 multi-environment, single variance G×E deviation model (MDs; and (4 multi-environment, environment-specific variance G×E deviation model (MDe. Each of these four models were fitted using two kernel methods: a linear kernel Genomic Best Linear Unbiased Predictor, GBLUP (GB, and a nonlinear kernel Gaussian kernel (GK. The eight model-method combinations were applied to two extensive Brazilian maize data sets (HEL and USP data sets, having different numbers of maize hybrids evaluated in different environments for grain yield (GY, plant height (PH, and ear height (EH. Results show that the MDe and the MDs models fitted with the Gaussian kernel (MDe-GK, and MDs-GK had the highest prediction accuracy. For GY in the HEL data set, the increase in prediction accuracy of SM-GK over SM-GB ranged from 9 to 32%. For the MM, MDs, and MDe models, the increase in prediction accuracy of GK over GB ranged from 9 to 49%. For GY in the USP data set, the increase in prediction accuracy of SM-GK over SM-GB ranged from 0 to 7%. For the MM, MDs, and MDe models, the increase in prediction accuracy of GK over GB ranged from 34 to 70%. For traits PH and EH, gains in prediction accuracy of models with GK compared to models with GB were smaller than those achieved in GY. Also, these gains in prediction accuracy decreased when a more difficult prediction problem was studied.

Deep Investigation of Arabidopsis thaliana Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter

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Maumus, Florian; Quesneville, Hadi

2014-01-01

Eukaryotic genomes contain highly variable amounts of DNA with no apparent function. This so-called junk DNA is composed of two components: repeated and repeat-derived sequences (together referred to as the repeatome), and non-annotated sequences also known as genomic dark matter. Because of their high duplication rates as compared to other genomic features, transposable elements are predominant contributors to the repeatome and the products of their decay is thought to be a major source of genomic dark matter. Determining the origin and composition of junk DNA is thus important to help understanding genome evolution as well as host biology. In this study, we have used a combination of tools enabling to show that the repeatome from the small and reducing A. thaliana genome is significantly larger than previously thought. Furthermore, we present the concepts and results from a series of innovative approaches suggesting that a significant amount of the A. thaliana dark matter is of repetitive origin. As a tentative standard for the community, we propose a deep compendium annotation of the A. thaliana repeatome that may help addressing farther genome evolution as well as transcriptional and epigenetic regulation in this model plant. PMID:24709859

A repetitive elements perspective in Polycomb epigenetics.

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Valentina eCasa

2012-10-01

Full Text Available Repetitive elements comprise over two-thirds of the human genome. For a long time, these elements have received little attention since they were considered non functional. On the contrary, recent evidence indicates that they play central roles in genome integrity, gene expression and disease. Indeed, repeats display meiotic instability associated with disease and are located within common fragile sites, which are hotspots of chromosome rearrangements in tumors. Moreover, a variety of diseases have been associated with aberrant transcription of repetitive elements. Overall this indicates that appropriate regulation of repetitive elements’ activity is fundamental.Polycomb group (PcG proteins are epigenetic regulators that are essential for the normal development of multicellular organisms. Mammalian PcG proteins are involved in fundamental processes, such as cellular memory, cell proliferation, genomic imprinting, X-inactivation, and cancer development. PcG proteins can convey their activity through long-distance interactions also on different chromosomes. This indicates that the 3D organization of PcG proteins contributes significantly to their function. However, it is still unclear how these complex mechanisms are orchestrated and which role PcG proteins play in the multi-level organization of gene regulation. Intriguingly, the greatest proportion of Polycomb-mediated chromatin modifications is located in genomic repeats and it has been suggested that they could provide a binding platform for Polycomb proteins.Here, these lines of evidence are woven together to discuss how repetitive elements could contribute to chromatin organization in the 3D nuclear space.

i-Genome: A database to summarize oligonucleotide data in genomes

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Chang Yu-Chung

2004-10-01

Full Text Available Abstract Background Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Computing the frequencies and the occurrences of a pattern in complete genomes is time-consuming. Results The proposed database provides information about sequence features generated by exhaustively computing the sequences of the complete genome. The repetitive elements in the eukaryotic genomes, such as LINEs, SINEs, Alu and LTR, are obtained from Repbase. The database supports various complete genomes including human, yeast, worm, and 128 microbial genomes. Conclusions This investigation presents and implements an efficiently computational approach to accumulate the occurrences of the oligonucleotides or patterns in complete genomes. A database is established to maintain the information of the sequence features, including the distributions of oligonucleotide, the gene distribution, the distribution of repetitive elements in genomes and the occurrences of the oligonucleotides. The database can provide more effective and efficient way to access the repetitive features in genomes.

Repetitive DNA in the pea (Pisum sativum L. genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula

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Navrátilová Alice

2007-11-01

Full Text Available Abstract Background Extraordinary size variation of higher plant nuclear genomes is in large part caused by differences in accumulation of repetitive DNA. This makes repetitive DNA of great interest for studying the molecular mechanisms shaping architecture and function of complex plant genomes. However, due to methodological constraints of conventional cloning and sequencing, a global description of repeat composition is available for only a very limited number of higher plants. In order to provide further data required for investigating evolutionary patterns of repeated DNA within and between species, we used a novel approach based on massive parallel sequencing which allowed a comprehensive repeat characterization in our model species, garden pea (Pisum sativum. Results Analysis of 33.3 Mb sequence data resulted in quantification and partial sequence reconstruction of major repeat families occurring in the pea genome with at least thousands of copies. Our results showed that the pea genome is dominated by LTR-retrotransposons, estimated at 140,000 copies/1C. Ty3/gypsy elements are less diverse and accumulated to higher copy numbers than Ty1/copia. This is in part due to a large population of Ogre-like retrotransposons which alone make up over 20% of the genome. In addition to numerous types of mobile elements, we have discovered a set of novel satellite repeats and two additional variants of telomeric sequences. Comparative genome analysis revealed that there are only a few repeat sequences conserved between pea and soybean genomes. On the other hand, all major families of pea mobile elements are well represented in M. truncatula. Conclusion We have demonstrated that even in a species with a relatively large genome like pea, where a single 454-sequencing run provided only 0.77% coverage, the generated sequences were sufficient to reconstruct and analyze major repeat families corresponding to a total of 35–48% of the genome. These data

Genetic diversity in South African maize ( Zea mays L.) genotypes as ...

African Journals Online (AJOL)

One thousand and forty three (1043) maize genotypes including white and yellow maize inbred lines as well as hybrids from the public germplasm collection were characterized with 80 microsatellite markers distributed throughout the genome. A total of 1874 alleles were amplified and used in the genetic diversity analysis.

Contrasting insect attraction and herbivore-induced plant volatile production in maize

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Maize inbred line W22 is an important resource for genetic studies due to the availability of the UniformMu mutant population and a complete genome sequence. In this study, we assessed the suitability of W22 as a model for tritrophic interactions between maize, Spodoptera frugiperda (fall armyworm) ...

Genome-Wide Association Mapping of and Aspergillus flavus Aflatoxin Accumulation Resistance in Maize

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Marilyn L. Warburton; Juliet D. Tang; Gary L. Windham; Leigh K. Hawkins; Seth C. Murray; Wenwei Xu; Debbie Boykin; Andy Perkins; W. Paul Williams

2015-01-01

Contamination of maize (Zea mays L.) with aflatoxin, produced by the fungus Aspergillus flavus Link, has severe health and economic consequences. Efforts to reduce aflatoxin accumulation in maize have focused on identifying and selecting germplasm with natural host resistance factors, and several maize lines with significantly...

The 50th Annual Maize Genetics Conference

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Cone, Karen

2014-03-26

The 50th Annual Maize Genetics Conference was held February 27 - March 2, 2008 at the Marriott Wardman Park Hotel in Washington, D.C. As the golden anniversary of the Conference and coinciding with the release of a draft of the maize genome sequence, this was a special meeting. To publicize this unique occasion, meeting organizers hosted a press conference, which was attended by members of the press representing science and non-science publications, and an evening reception at the Smithsonian National Museum of Natural History, where the draft sequence was announced and awards were presented to Dr. Mary Clutter and Senator Kit Bond to thank them for their outstanding contributions to maize genetics and genomics research. As usual, the Conference provided an invigorating forum for exchange of recent research results in many areas of maize genetics, e.g., cytogenetics, development, molecular genetics, transposable element biology, biochemical genetics, and genomics. Results were shared via both oral and poster presentations. Invited talks were given by four distinguished geneticists: Vicki Chandler, University of Arizona; John Doebley, University of Wisconsin; Susan Wessler, University of Georgia; and Richard Wilson, Washington University. There were 46 short talks and 241 poster presentations. The Conference was attended by over 500 participants. This included a large number of first-time participants in the meeting and an increasingly visible presence by individuals from underrepresented groups. Although we do not have concrete counts, there seem to be more African American, African and Hispanic/Latino attendees coming to the meeting than in years past. In addition, this meeting attracted many participants from outside the U.S. Student participation continues to be hallmark of the spirit of free exchange and cooperation characteristic of the maize genetics community. With the generous support provided by DOE, USDA NSF, and corporate/private donors, organizers were

Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing.

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Hribová, Eva; Neumann, Pavel; Matsumoto, Takashi; Roux, Nicolas; Macas, Jirí; Dolezel, Jaroslav

2010-09-16

Bananas and plantains (Musa spp.) are grown in more than a hundred tropical and subtropical countries and provide staple food for hundreds of millions of people. They are seed-sterile crops propagated clonally and this makes them vulnerable to a rapid spread of devastating diseases and at the same time hampers breeding improved cultivars. Although the socio-economic importance of bananas and plantains cannot be overestimated, they remain outside the focus of major research programs. This slows down the study of nuclear genome and the development of molecular tools to facilitate banana improvement. In this work, we report on the first thorough characterization of the repeat component of the banana (M. acuminata cv. 'Calcutta 4') genome. Analysis of almost 100 Mb of sequence data (0.15× genome coverage) permitted partial sequence reconstruction and characterization of repetitive DNA, making up about 30% of the genome. The results showed that the banana repeats are predominantly made of various types of Ty1/copia and Ty3/gypsy retroelements representing 16 and 7% of the genome respectively. On the other hand, DNA transposons were found to be rare. In addition to new families of transposable elements, two new satellite repeats were discovered and found useful as cytogenetic markers. To help in banana sequence annotation, a specific Musa repeat database was created, and its utility was demonstrated by analyzing the repeat composition of 62 genomic BAC clones. A low-depth 454 sequencing of banana nuclear genome provided the largest amount of DNA sequence data available until now for Musa and permitted reconstruction of most of the major types of DNA repeats. The information obtained in this study improves the knowledge of the long-range organization of banana chromosomes, and provides sequence resources needed for repeat masking and annotation during the Musa genome sequencing project. It also provides sequence data for isolation of DNA markers to be used in genetic

Molecular characterization of the genome of Maize rayado fino virus, the type member of the genus Marafivirus.

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Hammond, R W; Ramirez, P

2001-04-10

The complete nucleotide sequence of the single-stranded RNA genome of Maize rayado fino virus (MRFV), the type member of the genus Marafivirus, is 6305 nucleotides (nts) in length and contains two putative open reading frames (ORFs). The largest ORF (nt 97-6180) encodes a polyprotein of 224 kDa with sequence similarities at its N-terminus to the replication-associated proteins of other viruses with positive-strand RNA genomes and to the papainlike protease domain found in tymoviruses. The C-terminus of the 224-kDa ORF also encodes the MRFV capsid protein. A smaller, overlapping ORF (nt 302-1561) encodes a putative protein of 43 kDa with unknown function but with limited sequence similarities to putative movement proteins of tymoviruses. The nucleotide sequence and proposed genome expression strategy of MRFV is most closely related to that of oat blue dwarf virus (OBDV). Unlike OBDV, MRFV RNA does not appear to contain a poly(A) tail, and it encodes a putative second overlapping open reading frame.

Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains

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Bharti Arvind K

2008-12-01

Full Text Available Abstract Background Many plant genomes are resistant to whole-genome assembly due to an abundance of repetitive sequence, leading to the development of gene-rich sequencing techniques. Two such techniques are hypomethylated partial restriction (HMPR and methylation spanning linker libraries (MSLL. These libraries differ from other gene-rich datasets in having larger insert sizes, and the MSLL clones are designed to provide reads localized to "epigenetic boundaries" where methylation begins or ends. Results A large-scale study in maize generated 40,299 HMPR sequences and 80,723 MSLL sequences, including MSLL clones exceeding 100 kb. The paired end reads of MSLL and HMPR clones were shown to be effective in linking existing gene-rich sequences into scaffolds. In addition, it was shown that the MSLL clones can be used for anchoring these scaffolds to a BAC-based physical map. The MSLL end reads effectively identified epigenetic boundaries, as indicated by their preferential alignment to regions upstream and downstream from annotated genes. The ability to precisely map long stretches of fully methylated DNA sequence is a unique outcome of MSLL analysis, and was also shown to provide evidence for errors in gene identification. MSLL clones were observed to be significantly more repeat-rich in their interiors than in their end reads, confirming the correlation between methylation and retroelement content. Both MSLL and HMPR reads were found to be substantially gene-enriched, with the SalI MSLL libraries being the most highly enriched (31% align to an EST contig, while the HMPR clones exhibited exceptional depletion of repetitive DNA (to ~11%. These two techniques were compared with other gene-enrichment methods, and shown to be complementary. Conclusion MSLL technology provides an unparalleled approach for mapping the epigenetic status of repetitive blocks and for identifying sequences mis-identified as genes. Although the types and natures of

Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development.

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Sun, Cheng; Wyngaard, Grace; Walton, D Brian; Wichman, Holly A; Mueller, Rachel Lockridge

2014-03-11

Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two different nuclear genomes. Phylogenetically diverse taxa undergo chromatin diminution--some ciliates, nematodes, copepods, and vertebrates. In cyclopoid copepods, chromatin diminution occurs in taxa with massively expanded germline genomes; depending on species, germline genome sizes range from 15 - 75 Gb, 12-74 Gb of which are lost from pre-somatic cell lineages at germline--soma differentiation. This is more than an order of magnitude more sequence than is lost from other taxa. To date, the sequences excised from copepods have not been analyzed using large-scale genomic datasets, and the processes underlying germline genomic gigantism in this clade, as well as the functional significance of chromatin diminution, have remained unknown. Here, we used high-throughput genomic sequencing and qPCR to characterize the germline and somatic genomes of Mesocyclops edax, a freshwater cyclopoid copepod with a germline genome of ~15 Gb and a somatic genome of ~3 Gb. We show that most of the excised DNA consists of repetitive sequences that are either 1) verifiable transposable elements (TEs), or 2) non-simple repeats of likely TE origin. Repeat elements in both genomes are skewed towards younger (i.e. less divergent) elements. Excised DNA is a non-random sample of the germline repeat element landscape; younger elements, and high frequency DNA transposons and LINEs, are disproportionately eliminated from the somatic genome. Our results suggest that germline genome expansion in M. edax reflects explosive repeat element proliferation, and that billions of base pairs of such repeats are deleted from the somatic genome every generation. Thus, we hypothesize that chromatin diminution is a mechanism that controls repeat element load, and that this load can evolve to be divergent between tissue types within single organisms.

Rhipicephalus (Boophilus) microplus strain Deutsch, whole genome shotgun sequencing project first submission of genome sequence

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The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence difficult. Cot filtration/selection techniques were used to reduce the repetitive fraction of the tick genome and enrich for the fraction of DNA with gene-containing regions. The Cot-selected ...

Comparison of whole-genome prediction models for traits with contrasting genetic architecture in a diversity panel of maize inbred lines

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Riedelsheimer Christian

2012-09-01

Full Text Available Abstract Background There is increasing empirical evidence that whole-genome prediction (WGP is a powerful tool for predicting line and hybrid performance in maize. However, there is a lack of knowledge about the sensitivity of WGP models towards the genetic architecture of the trait. Whereas previous studies exclusively focused on highly polygenic traits, important agronomic traits such as disease resistances, nutrifunctional or climate adaptational traits have a genetic architecture which is either much less complex or unknown. For such cases, information about model robustness and guidelines for model selection are lacking. Here, we compared five WGP models with different assumptions about the distribution of the underlying genetic effects. As contrasting model traits, we chose three highly polygenic agronomic traits and three metabolites each with a major QTL explaining 22 to 30% of the genetic variance in a panel of 289 diverse maize inbred lines genotyped with 56,110 SNPs. Results We found the five WGP models to be remarkable robust towards trait architecture with the largest differences in prediction accuracies ranging between 0.05 and 0.14 for the same trait, most likely as the result of the high level of linkage disequilibrium prevailing in elite maize germplasm. Whereas RR-BLUP performed best for the agronomic traits, it was inferior to LASSO or elastic net for the three metabolites. We found the approach of genome partitioning of genetic variance, first applied in human genetics, as useful in guiding the breeder which model to choose, if prior knowledge of the trait architecture is lacking. Conclusions Our results suggest that in diverse germplasm of elite maize inbred lines with a high level of LD, WGP models differ only slightly in their accuracies, irrespective of the number and effects of QTL found in previous linkage or association mapping studies. However, small gains in prediction accuracies can be achieved if the WGP model is

The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elements

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Raheleh eSheibani-Tezerji

2015-05-01

Full Text Available The seed as a habitat for microorganisms is as yet under-explored and has quite distinct characteristics as compared to other vegetative plant tissues. In this study, we investigated three closely related P. ananatis strains (named S6, S7 and S8, which were isolated from maize seeds of healthy plants. Plant inoculation experiments revealed that each of these strains exhibited a different phenotype ranging from weak pathogenic (S7, commensal (S8, to a beneficial, growth-promoting effect (S6 in maize. We performed a comparative genomics analysis in order to find genetic determinants responsible for the differences observed. Recent studies provided exciting insight into the genetic drivers of niche adaption and functional diversification of the genus Pantoea. However, we report here for the first time on the analysis of P. ananatis strains colonizing the same ecological niche but showing distinct interaction strategies with the host plant. Our comparative analysis revealed that genomes of these three strains are highly similar. However, genomic differences in genes encoding protein secretion systems and putative effectors, and transposase/integrases/phage related genes could be observed.

Making better maize plants for sustainable grain production in a changing climate.

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Gong, Fangping; Wu, Xiaolin; Zhang, Huiyong; Chen, Yanhui; Wang, Wei

2015-01-01

Achieving grain supply security with limited arable land is a major challenge in the twenty-first century, owing to the changing climate and increasing global population. Maize plays an increasingly vital role in global grain production. As a C4 plant, maize has a high yield potential. Maize is predicted to become the number one cereal in the world by 2020. However, maize production has plateaued in many countries, and hybrid and production technologies have been fully exploited. Thus, there is an urgent need to shape maize traits and architectures for increased stress tolerance and higher yield in a changing climate. Recent achievements in genomics, proteomics, and metabolomics have provided an unprecedented opportunity to make better maize. In this paper, we discuss the current challenges and potential of maize production, particularly in China. We also highlight the need for enhancing maize tolerance to drought and heat waves, summarize the elite shoot and root traits and phenotypes, and propose an ideotype for sustainable maize production in a changing climate. This will facilitate targeted maize improvement through a conventional breeding program combined with molecular techniques.

MIPS PlantsDB: a database framework for comparative plant genome research.

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Nussbaumer, Thomas; Martis, Mihaela M; Roessner, Stephan K; Pfeifer, Matthias; Bader, Kai C; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

2013-01-01

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.

Molecular Basis of Resistance to Fusarium Ear Rot in Maize

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Alessandra Lanubile

2017-10-01

Full Text Available The impact of climate change has been identified as an emerging issue for food security and safety, and the increased incidence of mycotoxin contamination in maize over the last two decades is considered a potential emerging hazard. Disease control by chemical and agronomic approaches is often ineffective and increases the cost of production; for this reason the exploitation of genetic resistance is the most sustainable method for reducing contamination. The review focuses on the significant advances that have been made in the development of transcriptomic, genetic and genomic information for maize, Fusarium verticillioides molds, and their interactions, over recent years. Findings from transcriptomic studies have been used to outline a specific model for the intracellular signaling cascade occurring in maize cells against F. verticillioides infection. Several recognition receptors, such as receptor-like kinases and R genes, are involved in pathogen perception, and trigger down-stream signaling networks mediated by mitogen-associated protein kinases. These signals could be orchestrated primarily by hormones, including salicylic acid, auxin, abscisic acid, ethylene, and jasmonic acid, in association with calcium signaling, targeting multiple transcription factors that in turn promote the down-stream activation of defensive response genes, such as those related to detoxification processes, phenylpropanoid, and oxylipin metabolic pathways. At the genetic and genomic levels, several quantitative trait loci (QTL and single-nucleotide polymorphism markers for resistance to Fusarium ear rot deriving from QTL mapping and genome-wide association studies are described, indicating the complexity of this polygenic trait. All these findings will contribute to identifying candidate genes for resistance and to applying genomic technologies for selecting resistant maize genotypes and speeding up a strategy of breeding to contrast disease, through plants

PCR amplification of repetitive sequences as a possible approach in relative species quantification

DEFF Research Database (Denmark)

Ballin, Nicolai Zederkopff; Vogensen, Finn Kvist; Karlsson, Anders H

2012-01-01

Abstract Both relative and absolute quantifications are possible in species quantification when single copy genomic DNA is used. However, amplification of single copy genomic DNA does not allow a limit of detection as low as one obtained from amplification of repetitive sequences. Amplification...... of repetitive sequences is therefore frequently used in absolute quantification but problems occur in relative quantification as the number of repetitive sequences is unknown. A promising approach was developed where data from amplification of repetitive sequences were used in relative quantification of species...... to relatively quantify the amount of chicken DNA in a binary mixture of chicken DNA and pig DNA. However, the designed PCR primers lack the specificity required for regulatory species control....

Construction of a bacterial artificial chromosome library of S-type CMS maize mitochondria

Institute of Scientific and Technical Information of China (English)

无

2000-01-01

In order to isolate mitochondrial genes easily, we have developed a new method to construct S-type CMS maize mitochondrial gene library by means of embedding mitochondria and enzymatic digesting mitochondria in situ, preparing mtDNA by electrophoresis, digesting LMP agarose with β-agarase, using BAC vector and electroporation. About 2 500 white clones of Mo17 CMS-J mitochondrial gene library were obtained with the average size of 18.24 kb, ranging from 5 to 40 kb, 63.6% inserts came from mitochondrial genome and represented 48 ′ mitochondrial genome equivalents. All the probes had detected the positive clones in the gene library. It is helpful to elucidating the maize mitochondrial genome structure and mechanism of S-type CMS, and may give some valuable reference to the construction of other plant mitochondrial genome library.

Successful application of FTA Classic Card technology and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes.

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Owor, Betty E; Shepherd, Dionne N; Taylor, Nigel J; Edema, Richard; Monjane, Adérito L; Thomson, Jennifer A; Martin, Darren P; Varsani, Arvind

2007-03-01

Leaf samples from 155 maize streak virus (MSV)-infected maize plants were collected from 155 farmers' fields in 23 districts in Uganda in May/June 2005 by leaf-pressing infected samples onto FTA Classic Cards. Viral DNA was successfully extracted from cards stored at room temperature for 9 months. The diversity of 127 MSV isolates was analysed by PCR-generated RFLPs. Six representative isolates having different RFLP patterns and causing either severe, moderate or mild disease symptoms, were chosen for amplification from FTA cards by bacteriophage phi29 DNA polymerase using the TempliPhi system. Full-length genomes were inserted into a cloning vector using a unique restriction enzyme site, and sequenced. The 1.3-kb PCR product amplified directly from FTA-eluted DNA and used for RFLP analysis was also cloned and sequenced. Comparison of cloned whole genome sequences with those of the original PCR products indicated that the correct virus genome had been cloned and that no errors were introduced by the phi29 polymerase. This is the first successful large-scale application of FTA card technology to the field, and illustrates the ease with which large numbers of infected samples can be collected and stored for downstream molecular applications such as diversity analysis and cloning of potentially new virus genomes.

Evolution of the Largest Mammalian Genome.

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Evans, Ben J; Upham, Nathan S; Golding, Goeffrey B; Ojeda, Ricardo A; Ojeda, Agustina A

2017-06-01

The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5 Ma. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrerae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared with the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects-including during the evolution of hypersaline dietary tolerance in T. barrerae. ©The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas.

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Liseron-Monfils, Christophe; Lewis, Tim; Ashlock, Daniel; McNicholas, Paul D; Fauteux, François; Strömvik, Martina; Raizada, Manish N

2013-03-15

The discovery of genetic networks and cis-acting DNA motifs underlying their regulation is a major objective of transcriptome studies. The recent release of the maize genome (Zea mays L.) has facilitated in silico searches for regulatory motifs. Several algorithms exist to predict cis-acting elements, but none have been adapted for maize. A benchmark data set was used to evaluate the accuracy of three motif discovery programs: BioProspector, Weeder and MEME. Analysis showed that each motif discovery tool had limited accuracy and appeared to retrieve a distinct set of motifs. Therefore, using the benchmark, statistical filters were optimized to reduce the false discovery ratio, and then remaining motifs from all programs were combined to improve motif prediction. These principles were integrated into a user-friendly pipeline for motif discovery in maize called Promzea, available at http://www.promzea.org and on the Discovery Environment of the iPlant Collaborative website. Promzea was subsequently expanded to include rice and Arabidopsis. Within Promzea, a user enters cDNA sequences or gene IDs; corresponding upstream sequences are retrieved from the maize genome. Predicted motifs are filtered, combined and ranked. Promzea searches the chosen plant genome for genes containing each candidate motif, providing the user with the gene list and corresponding gene annotations. Promzea was validated in silico using a benchmark data set: the Promzea pipeline showed a 22% increase in nucleotide sensitivity compared to the best standalone program tool, Weeder, with equivalent nucleotide specificity. Promzea was also validated by its ability to retrieve the experimentally defined binding sites of transcription factors that regulate the maize anthocyanin and phlobaphene biosynthetic pathways. Promzea predicted additional promoter motifs, and genome-wide motif searches by Promzea identified 127 non-anthocyanin/phlobaphene genes that each contained all five predicted promoter

Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize.

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Riedelsheimer, Christian; Lisec, Jan; Czedik-Eysenberg, Angelika; Sulpice, Ronan; Flis, Anna; Grieder, Christoph; Altmann, Thomas; Stitt, Mark; Willmitzer, Lothar; Melchinger, Albrecht E

2012-06-05

The diversity of metabolites found in plants is by far greater than in most other organisms. Metabolic profiling techniques, which measure many of these compounds simultaneously, enabled investigating the regulation of metabolic networks and proved to be useful for predicting important agronomic traits. However, little is known about the genetic basis of metabolites in crops such as maize. Here, a set of 289 diverse maize inbred lines was genotyped with 56,110 SNPs and assayed for 118 biochemical compounds in the leaves of young plants, as well as for agronomic traits of mature plants in field trials. Metabolite concentrations had on average a repeatability of 0.73 and showed a correlation pattern that largely reflected their functional grouping. Genome-wide association mapping with correction for population structure and cryptic relatedness identified for 26 distinct metabolites strong associations with SNPs, explaining up to 32.0% of the observed genetic variance. On nine chromosomes, we detected 15 distinct SNP-metabolite associations, each of which explained more then 15% of the genetic variance. For lignin precursors, including p-coumaric acid and caffeic acid, we found strong associations (P values to ) with a region on chromosome 9 harboring cinnamoyl-CoA reductase, a key enzyme in monolignol synthesis and a target for improving the quality of lignocellulosic biomass by genetic engineering approaches. Moreover, lignin precursors correlated significantly with lignin content, plant height, and dry matter yield, suggesting that metabolites represent promising connecting links for narrowing the genotype-phenotype gap of complex agronomic traits.

Translational Genomics for the Improvement of Switchgrass

Energy Technology Data Exchange (ETDEWEB)

Carpita, Nicholas; McCann, Maureen

2014-05-07

Our objectives were to apply bioinformatics and high throughput sequencing technologies to identify and classify the genes involved in cell wall formation in maize and switchgrass. Targets for genetic modification were to be identified and cell wall materials isolated and assayed for enhanced performance in bioprocessing. We annotated and assembled over 750 maize genes into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice, and Arabidopsis sequences revealed differences in gene family structure. In addition, differences in expression between gene family members of Arabidopsis, maize and rice underscored the need for a grass-specific genetic model for functional analyses. A forward screen of mature leaves of field-grown maize lines by near-infrared spectroscopy yielded several dozen lines with heritable spectroscopic phenotypes, several of which near-infrared (nir) mutants had altered carbohydrate-lignin compositions. Our contributions to the maize genome sequencing effort built on knowledge of copy number variation showing that uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. For example, although about 25% of all duplicated genes remain genome-wide, all of the cellulose synthase (CesA) homologs were retained. We showed that guaiacyl and syringyl lignin in lignocellulosic cell-wall materials from stems demonstrate a two-fold natural variation in content across a population of maize Intermated B73 x Mo7 (IBM) recombinant inbred lines, a maize Association Panel of 282 inbreds and landraces, and three populations of the maize Nested Association Mapping (NAM) recombinant inbred lines grown in three years. We then defined quantitative trait loci (QTL) for stem lignin content measured using pyrolysis molecular-beam mass spectrometry, and glucose and xylose yield measured using an enzymatic hydrolysis assay. Among five multi-year QTL for lignin

Repetitive elements in parasitic protozoa

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Clayton Christine

2010-05-01

Full Text Available Abstract A recent paper published in BMC Genomics suggests that retrotransposition may be active in the human gut parasite Entamoeba histolytica. This adds to our knowledge of the various types of repetitive elements in parasitic protists and the potential influence of such elements on pathogenicity. See research article http://www.biomedcentral.com/1471-2164/11/321

The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants

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Colasanti Joseph

2006-06-01

Full Text Available Abstract Background The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs. The zinc fingers and surrounding sequence make up the signature ID domain (IDD, which appears to be found in all higher plant genomes. The presence of zinc finger domains and previous biochemical studies showing that ID1 binds to DNA suggests that members of this gene family are involved in transcriptional regulation. Results Comparison of IDD genes identified in Arabidopsis and rice genomes, and all IDD genes discovered in maize EST and genomic databases, suggest that ID1 is a unique member of this gene family. High levels of sequence similarity amongst all IDD genes from maize, rice and Arabidopsis suggest that they are derived from a common ancestor. Several unique features of ID1 suggest that it is a divergent member of the maize IDD family. Although no clear ID1 ortholog was identified in the Arabidopsis genome, highly similar genes that encode proteins with identity extending beyond the ID domain were isolated from rice and sorghum. Phylogenetic comparisons show that these putative orthologs, along with maize ID1, form a group separate from other IDD genes. In contrast to ID1 mRNA, which is detected exclusively in immature leaves, several maize IDD genes showed a broad range of expression in various tissues. Further, Western analysis with an antibody that cross-reacts with ID1 protein and potential orthologs from rice and sorghum shows that all three proteins are detected in immature leaves only. Conclusion Comparative genomic analysis shows that the IDD zinc finger family is highly conserved among both monocots and dicots. The leaf-specific ID1 expression pattern distinguishes it from other maize IDD genes examined. A similar leaf-specific localization pattern was observed for the putative ID1 protein

Somatically segregating clone of apomictic maize-tripsacum hybrid

International Nuclear Information System (INIS)

Yudin, B.F.; Lukina, L.A.

1988-01-01

The results of further study on clone AM-5, isolated in the progeny of γ-irradiated plants of the apomictic hybrid of maize with tripsacum (2n = 38) are reported. The variegated-leaf seedlings of the clone segregate somatically and produce variegated, mottled, green (phenotypically normal) plants in different ratios in the apomictic progenies. The variegated, and to a lesser degree, green segregants segregate further. The mottled apomictics as well as mottled branches of variegated seedlings maintain their phenotype on transplantation, however, these is a progressive enhancement of the characters of vegetative lethality. Lethals of two extra maize genomes to the AM-5 nucleus does not affect significantly the scope and nature of segregation. At the same time, the loss of tripsacum genome restores normal phenotype. Clone AM-5 is an example of hybrid apomictic form causing significant morphological variability, which is, nevertheless, not related with apomictic and reversion to the sexual process

Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties.

Science.gov (United States)

Tian, Hong-Li; Wang, Feng-Ge; Zhao, Jiu-Ran; Yi, Hong-Mei; Wang, Lu; Wang, Rui; Yang, Yang; Song, Wei

2015-01-01

Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed throughout the maize ( Zea mays L.) genome. SNPs have several advantages over simple sequence repeats, such as ease of data comparison and integration, high-throughput processing of loci, and identification of associated phenotypes. SNPs are thus ideal for DNA fingerprinting, genetic diversity analysis, and marker-assisted breeding. Here, we developed a high-throughput and compatible SNP array, maizeSNP3072, containing 3072 SNPs developed from the maizeSNP50 array. To improve genotyping efficiency, a high-quality cluster file, maizeSNP3072_GT.egt, was constructed. All 3072 SNP loci were localized within different genes, where they were distributed in exons (43 %), promoters (21 %), 3' untranslated regions (UTRs; 22 %), 5' UTRs (9 %), and introns (5 %). The average genotyping failure rate using these SNPs was only 6 %, or 3 % using the cluster file to call genotypes. The genotype consistency of repeat sample analysis on Illumina GoldenGate versus Infinium platforms exceeded 96.4 %. The minor allele frequency (MAF) of the SNPs averaged 0.37 based on data from 309 inbred lines. The 3072 SNPs were highly effective for distinguishing among 276 examined hybrids. Comparative analysis using Chinese varieties revealed that the 3072SNP array showed a better marker success rate and higher average MAF values, evaluation scores, and variety-distinguishing efficiency than the maizeSNP50K array. The maizeSNP3072 array thus can be successfully used in DNA fingerprinting identification of Chinese maize varieties and shows potential as a useful tool for germplasm resource evaluation and molecular marker-assisted breeding.

A Foxtail mosaic virus Vector for Virus-Induced Gene Silencing in Maize.

Science.gov (United States)

Mei, Yu; Zhang, Chunquan; Kernodle, Bliss M; Hill, John H; Whitham, Steven A

2016-06-01

Plant viruses have been widely used as vectors for foreign gene expression and virus-induced gene silencing (VIGS). A limited number of viruses have been developed into viral vectors for the purposes of gene expression or VIGS in monocotyledonous plants, and among these, the tripartite viruses Brome mosaic virus and Cucumber mosaic virus have been shown to induce VIGS in maize (Zea mays). We describe here a new DNA-based VIGS system derived from Foxtail mosaic virus (FoMV), a monopartite virus that is able to establish systemic infection and silencing of endogenous maize genes homologous to gene fragments inserted into the FoMV genome. To demonstrate VIGS applications of this FoMV vector system, four genes, phytoene desaturase (functions in carotenoid biosynthesis), lesion mimic22 (encodes a key enzyme of the porphyrin pathway), iojap (functions in plastid development), and brown midrib3 (caffeic acid O-methyltransferase), were silenced and characterized in the sweet corn line Golden × Bantam. Furthermore, we demonstrate that the FoMV infectious clone establishes systemic infection in maize inbred lines, sorghum (Sorghum bicolor), and green foxtail (Setaria viridis), indicating the potential wide applications of this viral vector system for functional genomics studies in maize and other monocots. © 2016 American Society of Plant Biologists. All Rights Reserved.

Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation.

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Amanda Malvessi Cattani

Full Text Available Transcriptional regulation, a multiple-step process, is still poorly understood in the important pig pathogen Mycoplasma hyopneumoniae. Basic motifs like promoters and terminators have already been described, but no other cis-regulatory elements have been found. DNA repeat sequences have been shown to be an interesting potential source of cis-regulatory elements. In this work, a genome-wide search for tandem and palindromic repetitive elements was performed in the intergenic regions of all coding sequences from M. hyopneumoniae strain 7448. Computational analysis demonstrated the presence of 144 tandem repeats and 1,171 palindromic elements. The DNA repeat sequences were distributed within the 5' upstream regions of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct repetitive sequences found in related mycoplasma genomes demonstrated different percentages of conservation among pathogenic and nonpathogenic strains. qPCR assays revealed differential expression among genes showing variable numbers of repetitive elements. In addition, repeats found in 206 genes already described to be differentially regulated under different culture conditions of M. hyopneumoniae strain 232 showed almost 80% conservation in relation to M. hyopneumoniae strain 7448 repeats. Altogether, these findings suggest a potential regulatory role of tandem and palindromic DNA repeats in the M. hyopneumoniae transcriptional profile.

Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation.

Science.gov (United States)

Cattani, Amanda Malvessi; Siqueira, Franciele Maboni; Guedes, Rafael Lucas Muniz; Schrank, Irene Silveira

2016-01-01

Transcriptional regulation, a multiple-step process, is still poorly understood in the important pig pathogen Mycoplasma hyopneumoniae. Basic motifs like promoters and terminators have already been described, but no other cis-regulatory elements have been found. DNA repeat sequences have been shown to be an interesting potential source of cis-regulatory elements. In this work, a genome-wide search for tandem and palindromic repetitive elements was performed in the intergenic regions of all coding sequences from M. hyopneumoniae strain 7448. Computational analysis demonstrated the presence of 144 tandem repeats and 1,171 palindromic elements. The DNA repeat sequences were distributed within the 5' upstream regions of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct repetitive sequences found in related mycoplasma genomes demonstrated different percentages of conservation among pathogenic and nonpathogenic strains. qPCR assays revealed differential expression among genes showing variable numbers of repetitive elements. In addition, repeats found in 206 genes already described to be differentially regulated under different culture conditions of M. hyopneumoniae strain 232 showed almost 80% conservation in relation to M. hyopneumoniae strain 7448 repeats. Altogether, these findings suggest a potential regulatory role of tandem and palindromic DNA repeats in the M. hyopneumoniae transcriptional profile.

Genomic analysis of Fusarium verticillioides.

Science.gov (United States)

Brown, D W; Butchko, R A E; Proctor, R H

2008-09-01

Fusarium verticillioides (teleomorph Gibberella moniliformis) can be either an endophyte of maize, causing no visible disease, or a pathogen-causing disease of ears, stalks, roots and seedlings. At any stage, this fungus can synthesize fumonisins, a family of mycotoxins structurally similar to the sphingolipid sphinganine. Ingestion of fumonisin-contaminated maize has been associated with a number of animal diseases, including cancer in rodents, and exposure has been correlated with human oesophageal cancer in some regions of the world, and some evidence suggests that fumonisins are a risk factor for neural tube defects. A primary goal of the authors' laboratory is to eliminate fumonisin contamination of maize and maize products. Understanding how and why these toxins are made and the F. verticillioides-maize disease process will allow one to develop novel strategies to limit tissue destruction (rot) and fumonisin production. To meet this goal, genomic sequence data, expressed sequence tags (ESTs) and microarrays are being used to identify F. verticillioides genes involved in the biosynthesis of toxins and plant pathogenesis. This paper describes the current status of F. verticillioides genomic resources and three approaches being used to mine microarray data from a wild-type strain cultured in liquid fumonisin production medium for 12, 24, 48, 72, 96 and 120h. Taken together, these approaches demonstrate the power of microarray technology to provide information on different biological processes.

Is there a strategy I iron uptake mechanism in maize?

Science.gov (United States)

Li, Suzhen; Zhou, Xiaojin; Chen, Jingtang; Chen, Rumei

2018-04-03

Iron is a metal micronutrient that is essential for plant growth and development. Graminaceous and nongraminaceous plants have evolved different mechanisms to mediate Fe uptake. Generally, strategy I is used by nongraminaceous plants like Arabidopsis, while graminaceous plants, such as rice, barley, and maize, are considered to use strategy II Fe uptake. Upon the functional characterization of OsIRT1 and OsIRT2 in rice, it was suggested that rice, as an exceptional graminaceous plant, utilizes both strategy I and strategy II Fe uptake systems. Similarly, ZmIRT1 and ZmZIP3 were identified as functional zinc and iron transporters in the maize genome, along with the determination of several genes encoding Zn and Fe transporters, raising the possibility that strategy I Fe uptake also occurs in maize. This mini-review integrates previous reports and recent evidence to obtain a better understanding of the mechanisms of Fe uptake in maize.

Contrasting the Chromosomal Organization of Repetitive DNAs in Two Gryllidae Crickets with Highly Divergent Karyotypes.

Directory of Open Access Journals (Sweden)

Octavio M Palacios-Gimenez

Full Text Available A large percentage of eukaryotic genomes consist of repetitive DNA that plays an important role in the organization, size and evolution. In the case of crickets, chromosomal variability has been found using classical cytogenetics, but almost no information concerning the organization of their repetitive DNAs is available. To better understand the chromosomal organization and diversification of repetitive DNAs in crickets, we studied the chromosomes of two Gryllidae species with highly divergent karyotypes, i.e., 2n(♂ = 29,X0 (Gryllus assimilis and 2n = 9, neo-X1X2Y (Eneoptera surinamensis. The analyses were performed using classical cytogenetic techniques, repetitive DNA mapping and genome-size estimation. Conserved characteristics were observed, such as the occurrence of a small number of clusters of rDNAs and U snDNAs, in contrast to the multiple clusters/dispersal of the H3 histone genes. The positions of U2 snDNA and 18S rDNA are also conserved, being intermingled within the largest autosome. The distribution and base-pair composition of the heterochromatin and repetitive DNA pools of these organisms differed, suggesting reorganization. Although the microsatellite arrays had a similar distribution pattern, being dispersed along entire chromosomes, as has been observed in some grasshopper species, a band-like pattern was also observed in the E. surinamensis chromosomes, putatively due to their amplification and clustering. In addition to these differences, the genome of E. surinamensis is approximately 2.5 times larger than that of G. assimilis, which we hypothesize is due to the amplification of repetitive DNAs. Finally, we discuss the possible involvement of repetitive DNAs in the differentiation of the neo-sex chromosomes of E. surinamensis, as has been reported in other eukaryotic groups. This study provided an opportunity to explore the evolutionary dynamics of repetitive DNAs in two non-model species and will contribute to the

A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize.

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Matt eGeisler

2015-06-01

Full Text Available Interactomes are genome-wide roadmaps of protein-protein interactions. They have been produced for humans, yeast, the fruit fly, and Arabidopsis thaliana and have become invaluable tools for generating and testing hypotheses. A predicted interactome for Zea mays (PiZeaM is presented here as an aid to the research community for this valuable crop species. PiZeaM was built using a proven method of interologs (interacting orthologs that were identified using both one-to-one and many-to-many orthology between genomes of maize and reference species. Where both maize orthologs occurred for an experimentally determined interaction in the reference species, we predicted a likely interaction in maize. A total of 49,026 unique interactions for 6,004 maize proteins were predicted. These interactions are enriched for processes that are evolutionarily conserved, but include many otherwise poorly annotated proteins in maize. The predicted maize interactions were further analyzed by comparing annotation of interacting proteins, including different layers of ontology. A map of pairwise gene co-expression was also generated and compared to predicted interactions. Two global subnetworks were constructed for highly conserved interactions. These subnetworks showed clear clustering of proteins by function. Another subnetwork was created for disease response using a bait and prey strategy to capture interacting partners for proteins that respond to other organisms. Closer examination of this subnetwork revealed the connectivity between biotic and abiotic hormone stress pathways. We believe PiZeaM will provide a useful tool for the prediction of protein function and analysis of pathways for Z. mays researchers and is presented in this paper as a reference tool for the exploration of protein interactions in maize.

Human β satellite DNA: Genomic organization and sequence definition of a class of highly repetitive tandem DNA

International Nuclear Information System (INIS)

Waye, J.S.; Willard, H.F.

1989-01-01

The authors describe a class of human repetitive DNA, called β satellite, that, at a most fundamental level, exists as tandem arrays of diverged ∼68-base-pair monomer repeat units. The monomer units are organized as distinct subsets, each characterized by a multimeric higher-order repeat unit that is tandemly reiterated and represents a recent unit of amplification. They have cloned, characterized, and determined the sequence of two β satellite higher-order repeat units: one located on chromosome 9, the other on the acrocentric chromosomes (13, 14, 15, 21, and 22) and perhaps other sites in the genome. Analysis by pulsed-field gel electrophoresis reveals that these tandem arrays are localized in large domains that are marked by restriction fragment length polymorphisms. In total, β-satellite sequences comprise several million base pairs of DNA in the human genome. Analysis of this DNA family should permit insights into the nature of chromosome-specific and nonspecific modes of satellite DNA evolution and provide useful tools for probing the molecular organization and concerted evolution of the acrocentric chromosomes

Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size.

Science.gov (United States)

Kelly, Laura J; Renny-Byfield, Simon; Pellicer, Jaume; Macas, Jiří; Novák, Petr; Neumann, Pavel; Lysak, Martin A; Day, Peter D; Berger, Madeleine; Fay, Michael F; Nichols, Richard A; Leitch, Andrew R; Leitch, Ilia J

2015-10-01

Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Land management on soil physical properties and maize (Zea mays L. var. BIMA) growth (An adaptation strategy of climate change)

Science.gov (United States)

Zaki, M. K.; Komariah; Pujiasmanto, B.; Noda, K.

2018-03-01

Water deficit is a problem on rainfed maize production but can be solved by proper land management. The objective of the study to determine the soil physical properties and maize yield affected by land management to adapt to drought. The experimental design was a randomized complete block using 5 treatments with 4 repetitions, including: (i) Control (KO), (ii) Rice Straw Mulched (MC), (iii) Compost Fertilizer (CF), (iv) In-Organic Fertilizer (AF), (v) Legume Cover crop (CC). Soil physical and maize growth properties namely soil moisture, soil texture, soil bulk density, plant height, biomass, and yield were investigated. The results showed that composting land increased soil water availability and provided nutrient to crops and thus increase soil physical properties, maize growth and yield. Although inorganic fertilizer also increased plant growth and yield, but it did not improve soil physical properties.

From many, one: genetic control of prolificacy during maize domestication.

Directory of Open Access Journals (Sweden)

David M Wills

2013-06-01

Full Text Available A reduction in number and an increase in size of inflorescences is a common aspect of plant domestication. When maize was domesticated from teosinte, the number and arrangement of ears changed dramatically. Teosinte has long lateral branches that bear multiple small ears at their nodes and tassels at their tips. Maize has much shorter lateral branches that are tipped by a single large ear with no additional ears at the branch nodes. To investigate the genetic basis of this difference in prolificacy (the number of ears on a plant, we performed a genome-wide QTL scan. A large effect QTL for prolificacy (prol1.1 was detected on the short arm of chromosome 1 in a location that has previously been shown to influence multiple domestication traits. We fine-mapped prol1.1 to a 2.7 kb "causative region" upstream of the grassy tillers1 (gt1 gene, which encodes a homeodomain leucine zipper transcription factor. Tissue in situ hybridizations reveal that the maize allele of prol1.1 is associated with up-regulation of gt1 expression in the nodal plexus. Given that maize does not initiate secondary ear buds, the expression of gt1 in the nodal plexus in maize may suppress their initiation. Population genetic analyses indicate positive selection on the maize allele of prol1.1, causing a partial sweep that fixed the maize allele throughout most of domesticated maize. This work shows how a subtle cis-regulatory change in tissue specific gene expression altered plant architecture in a way that improved the harvestability of maize.

Repetition and the Concept of Repetition

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Arne Grøn

2013-11-01

Full Text Available This paper offers a description of the meaning of the category of repetition. Firstly, it is pointed out that Constantin uses repetition as a concept that means the creation of epochs; the passing from Greece to Modernity is accomplished distinguishing between recollection, a concept that looks back to the past, and repetition, a concept that looks forward to future. Secondly, it is showed that the category of repetition, as a religious category, relates with what Climacus calls “ethic despair” and with what Vigilius calls “second ethics”; it is through repetition that it can be understood that sin finds its place in ethics and these shows the tension between it and dogmatics. And thirdly, it is showed that the descovery of the new category of repetition is a rediscovery of what Kierkegaard calls category of spirit; repetition has for its object the individuality, and coming to be oneself is what Kierkegaard undertands as liberty. At the end of the paper it is questioned if the category of repetition is inconsistent with the book Repetition.

Aflatoxins and fumonisin contamination of marketed maize, maize ...

African Journals Online (AJOL)

Aflatoxins and fumonisin contamination of marketed maize, maize bran and maize used as animal feed in northern ... PROMOTING ACCESS TO AFRICAN RESEARCH ... African Journal of Food, Agriculture, Nutrition and Development.

A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize

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Wenbin Mei

2017-05-01

Full Text Available Identifying and characterizing alternative splicing (AS enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined. Additionally, differences in AS between the two genotypes B73 and Mo17 are greatest within genes expressed in seed. We demonstrate that changes in the level of alternatively spliced transcripts (intron retention and exon skipping do not solely reflect differences in total transcript abundance, and we present evidence that intron retention may act to fine-tune gene expression across seed development stages. Furthermore, we have identified temperature sensitive AS in maize and demonstrate that drought-induced changes in AS involve distinct sets of genes in reproductive and vegetative tissues. Examining our identified AS isoforms within B73 × Mo17 recombinant inbred lines (RILs identified splicing QTL (sQTL. The 43.3% of cis-sQTL regulated junctions are actually identified as alternatively spliced junctions in our analysis, while 10 Mb windows on each side of 48.2% of trans-sQTLs overlap with splicing related genes. Using sorghum as an out-group enabled direct examination of loss or conservation of AS between homeologous genes representing the two subgenomes of maize. We identify several instances where AS isoforms that are conserved between one maize homeolog and its sorghum ortholog are absent from the second maize homeolog, suggesting that these AS isoforms may have been lost after the maize whole genome duplication event. This comprehensive analysis provides new insights into the complexity of AS in maize.

Overexpression of a modiifed AM79 aroA gene in transgenic maize confers high tolerance to glyphosate

Institute of Scientific and Technical Information of China (English)

REN Zhen-jing; CAO Gao-yi; ZHANG Yu-wen; LIU Yan; LIU Yun-jun

2015-01-01

It has previously been shown that a bacterial 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) encoding gene AM79 aroA can be a candidate gene to develop glyphosate-tolerant transgenic crops (Cao et al. 2012). In this study, AM79 aroA was redesigned using the plant biased codons and eliminating the motifs which would lead to the instability of mRNA, to create a synthetic gene that would be expressed highly in plant cel s. The redesigned and artiifcial y synthesized gene, named as mAM79, was cloned into plant expression vector pM3301UbiSpAM79, where mAM79 is fused with signal peptide sequence of pea rib-1,5-bisphospate carboxylase (rbcS) smal subunit and control ed by ubiquitin promoter. The plasmid was transformed into maize (Zea mays) immature embryos using Agrobacterium-mediated transformation method. Total 74 regenerated plants were obtained and PCR analysis showed that these transgenic plants had the integration of mAM79. Southern blot analysis was performed on the genomic DNA from four transgenic lines, and the result showed that one or two copies of mAM79 were integrated into maize genome. RT-PCR analysis result indicated that mAM79 was highly transcribed in transgenic maize plants. When sprayed with glyphosate, transgenic maize line AM85 and AM72 could tolerate 4-fold of commercial usage of glyphosate;however, al the non-transgenic maize plants were kil ed by glyphosate. The results in this study conifrmed that mAM79 could be used to develop glyphosate-tolerant maize, and the obtained transgenic maize lines could be used for the breeding of glyphosate-tolerant maize.

Chemical and nutritional values of maize and maize products ...

African Journals Online (AJOL)

Maize and maize products in selected grain markets within Kaduna, Nigeria, were obtained and investigated for proximate and mineral composition analysis using Atomic Absorption Spectrophotometer (AAS) and flame photometer. Proximate composition of maize and maize products were in the range of 11.6- 20 .0% ...

Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize.

Science.gov (United States)

Wei, Kai-Fa; Chen, Juan; Chen, Yan-Feng; Wu, Ling-Juan; Xie, Dao-Xin

2012-04-01

The WRKY transcription factors function in plant growth and development, and response to the biotic and abiotic stresses. Although many studies have focused on the functional identification of the WRKY transcription factors, much less is known about molecular phylogenetic and global expression analysis of the complete WRKY family in maize. In this study, we identified 136 WRKY proteins coded by 119 genes in the B73 inbred line from the complete genome and named them in an orderly manner. Then, a comprehensive phylogenetic analysis of five species was performed to explore the origin and evolutionary patterns of these WRKY genes, and the result showed that gene duplication is the major driving force for the origin of new groups and subgroups and functional divergence during evolution. Chromosomal location analysis of maize WRKY genes indicated that 20 gene clusters are distributed unevenly in the genome. Microarray-based expression analysis has revealed that 131 WRKY transcripts encoded by 116 genes may participate in the regulation of maize growth and development. Among them, 102 transcripts are stably expressed with a coefficient of variation (CV) value of WRKY genes with the CV value of >15% are further analysed to discover new organ- or tissue-specific genes. In addition, microarray analyses of transcriptional responses to drought stress and fungal infection showed that maize WRKY proteins are involved in stress responses. All these results contribute to a deep probing into the roles of WRKY transcription factors in maize growth and development and stress tolerance.

A Foxtail mosaic virus Vector for Virus-Induced Gene Silencing in Maize1[OPEN

Science.gov (United States)

Mei, Yu; Kernodle, Bliss M.; Hill, John H.

2016-01-01

Plant viruses have been widely used as vectors for foreign gene expression and virus-induced gene silencing (VIGS). A limited number of viruses have been developed into viral vectors for the purposes of gene expression or VIGS in monocotyledonous plants, and among these, the tripartite viruses Brome mosaic virus and Cucumber mosaic virus have been shown to induce VIGS in maize (Zea mays). We describe here a new DNA-based VIGS system derived from Foxtail mosaic virus (FoMV), a monopartite virus that is able to establish systemic infection and silencing of endogenous maize genes homologous to gene fragments inserted into the FoMV genome. To demonstrate VIGS applications of this FoMV vector system, four genes, phytoene desaturase (functions in carotenoid biosynthesis), lesion mimic22 (encodes a key enzyme of the porphyrin pathway), iojap (functions in plastid development), and brown midrib3 (caffeic acid O-methyltransferase), were silenced and characterized in the sweet corn line Golden × Bantam. Furthermore, we demonstrate that the FoMV infectious clone establishes systemic infection in maize inbred lines, sorghum (Sorghum bicolor), and green foxtail (Setaria viridis), indicating the potential wide applications of this viral vector system for functional genomics studies in maize and other monocots. PMID:27208311

Identification and expression profiling analysis of TCP family genes involved in growth and development in maize.

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Chai, Wenbo; Jiang, Pengfei; Huang, Guoyu; Jiang, Haiyang; Li, Xiaoyu

2017-10-01

The TCP family is a group of plant-specific transcription factors. TCP genes encode proteins harboring bHLH structure, which is implicated in DNA binding and protein-protein interactions and known as the TCP domain. TCP genes play important roles in plant development and have been evolutionarily and functionally elaborated in various plants, however, no overall phylogenetic analysis or expression profiling of TCP genes in Zea mays has been reported. In the present study, a systematic analysis of molecular evolution and functional prediction of TCP family genes in maize ( Z . mays L.) has been conducted. We performed a genome-wide survey of TCP genes in maize, revealing the gene structure, chromosomal location and phylogenetic relationship of family members. Microsynteny between grass species and tissue-specific expression profiles were also investigated. In total, 29 TCP genes were identified in the maize genome, unevenly distributed on the 10 maize chromosomes. Additionally, ZmTCP genes were categorized into nine classes based on phylogeny and purifying selection may largely be responsible for maintaining the functions of maize TCP genes. What's more, microsynteny analysis suggested that TCP genes have been conserved during evolution. Finally, expression analysis revealed that most TCP genes are expressed in the stem and ear, which suggests that ZmTCP genes influence stem and ear growth. This result is consistent with the previous finding that maize TCP genes represses the growth of axillary organs and enables the formation of female inflorescences. Altogether, this study presents a thorough overview of TCP family in maize and provides a new perspective on the evolution of this gene family. The results also indicate that TCP family genes may be involved in development stage in plant growing conditions. Additionally, our results will be useful for further functional analysis of the TCP gene family in maize.

Maize transformation technology development for commercial event generation

Science.gov (United States)

Que, Qiudeng; Elumalai, Sivamani; Li, Xianggan; Zhong, Heng; Nalapalli, Samson; Schweiner, Michael; Fei, Xiaoyin; Nuccio, Michael; Kelliher, Timothy; Gu, Weining; Chen, Zhongying; Chilton, Mary-Dell M.

2014-01-01

Maize is an important food and feed crop in many countries. It is also one of the most important target crops for the application of biotechnology. Currently, there are more biotech traits available on the market in maize than in any other crop. Generation of transgenic events is a crucial step in the development of biotech traits. For commercial applications, a high throughput transformation system producing a large number of high quality events in an elite genetic background is highly desirable. There has been tremendous progress in Agrobacterium-mediated maize transformation since the publication of the Ishida et al. (1996) paper and the technology has been widely adopted for transgenic event production by many labs around the world. We will review general efforts in establishing efficient maize transformation technologies useful for transgenic event production in trait research and development. The review will also discuss transformation systems used for generating commercial maize trait events currently on the market. As the number of traits is increasing steadily and two or more modes of action are used to control key pests, new tools are needed to efficiently transform vectors containing multiple trait genes. We will review general guidelines for assembling binary vectors for commercial transformation. Approaches to increase transformation efficiency and gene expression of large gene stack vectors will be discussed. Finally, recent studies of targeted genome modification and transgene insertion using different site-directed nuclease technologies will be reviewed. PMID:25140170

Maize transformation technology development for commercial event generation.

Science.gov (United States)

Que, Qiudeng; Elumalai, Sivamani; Li, Xianggan; Zhong, Heng; Nalapalli, Samson; Schweiner, Michael; Fei, Xiaoyin; Nuccio, Michael; Kelliher, Timothy; Gu, Weining; Chen, Zhongying; Chilton, Mary-Dell M

2014-01-01

Maize is an important food and feed crop in many countries. It is also one of the most important target crops for the application of biotechnology. Currently, there are more biotech traits available on the market in maize than in any other crop. Generation of transgenic events is a crucial step in the development of biotech traits. For commercial applications, a high throughput transformation system producing a large number of high quality events in an elite genetic background is highly desirable. There has been tremendous progress in Agrobacterium-mediated maize transformation since the publication of the Ishida et al. (1996) paper and the technology has been widely adopted for transgenic event production by many labs around the world. We will review general efforts in establishing efficient maize transformation technologies useful for transgenic event production in trait research and development. The review will also discuss transformation systems used for generating commercial maize trait events currently on the market. As the number of traits is increasing steadily and two or more modes of action are used to control key pests, new tools are needed to efficiently transform vectors containing multiple trait genes. We will review general guidelines for assembling binary vectors for commercial transformation. Approaches to increase transformation efficiency and gene expression of large gene stack vectors will be discussed. Finally, recent studies of targeted genome modification and transgene insertion using different site-directed nuclease technologies will be reviewed.

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

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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

[Short interspersed repetitive sequences (SINEs) and their use as a phylogenetic tool].

Science.gov (United States)

Kramerov, D A; Vasetskiĭ, N S

2009-01-01

The data on one of the most common repetitive elements of eukaryotic genomes, short interspersed elements (SINEs), are reviewed. Their structure, origin, and functioning in the genome are discussed. The variation and abundance of these neutral genomic markers makes them a convenient and reliable tool for phylogenetic analysis. The main methods of such analysis are presented, and the potential and limitations of this approach are discussed using specific examples.

Direct extraction of genomic DNA from maize with aqueous ionic liquid buffer systems for applications in genetically modified organisms analysis.

Science.gov (United States)

Gonzalez García, Eric; Ressmann, Anna K; Gaertner, Peter; Zirbs, Ronald; Mach, Robert L; Krska, Rudolf; Bica, Katharina; Brunner, Kurt

2014-12-01

To date, the extraction of genomic DNA is considered a bottleneck in the process of genetically modified organisms (GMOs) detection. Conventional DNA isolation methods are associated with long extraction times and multiple pipetting and centrifugation steps, which makes the entire procedure not only tedious and complicated but also prone to sample cross-contamination. In recent times, ionic liquids have emerged as innovative solvents for biomass processing, due to their outstanding properties for dissolution of biomass and biopolymers. In this study, a novel, easily applicable, and time-efficient method for the direct extraction of genomic DNA from biomass based on aqueous-ionic liquid solutions was developed. The straightforward protocol relies on extraction of maize in a 10 % solution of ionic liquids in aqueous phosphate buffer for 5 min at room temperature, followed by a denaturation step at 95 °C for 10 min and a simple filtration to remove residual biopolymers. A set of 22 ionic liquids was tested in a buffer system and 1-ethyl-3-methylimidazolium dimethylphosphate, as well as the environmentally benign choline formate, were identified as ideal candidates. With this strategy, the quality of the genomic DNA extracted was significantly improved and the extraction protocol was notably simplified compared with a well-established method.

Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.

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Carol Soderlund

2009-11-01

Full Text Available Full-length cDNA (FLcDNA sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5' and 3' UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs, only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org.

New tool to assemble repetitive regions using next-generation sequencing data

Science.gov (United States)

Kuśmirek, Wiktor; Nowak, Robert M.; Neumann, Łukasz

2017-08-01

The next generation sequencing techniques produce a large amount of sequencing data. Some part of the genome are composed of repetitive DNA sequences, which are very problematic for the existing genome assemblers. We propose a modification of the algorithm for a DNA assembly, which uses the relative frequency of reads to properly reconstruct repetitive sequences. The new approach was implemented and tested, as a demonstration of the capability of our software we present some results for model organisms. The new implementation, using a three-layer software architecture was selected, where the presentation layer, data processing layer, and data storage layer were kept separate. Source code as well as demo application with web interface and the additional data are available at project web-page: http://dnaasm.sourceforge.net.

TCUP: A novel hAT transposon active in maize tissue culture

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Alan eSmith

2012-01-01

Full Text Available Transposable elements are capable of inducing heritable de novo genetic variation. The sequences capable of reactivation, and environmental factors that induce mobilization, remain poorly defined even in well-studied genomes such as maize. We treated maize tissue culture with the demethylating agent 5-aza-2-deoxcytidine and examined long-term tissue culture lines to discover silenced transposable elements that have the potential to induce heritable genetic variation. Through these screens we have identified a novel low copy number hAT transposon, Tissue Culture Up-Regulated (TCUP, which is transcribed at high levels in long-term maize Black Mexican Sweet (BMS tissue culture and up-regulated in response to treatment with 5-aza-2-deoxycytidine. Analysis of the TIGR Maize Gene Index revealed that this element is the most frequently represented EST from the BMS cell culture library and is not represented in other tissue libraries, which is the basis for its name. A full-length sequence was assembled in inbred B73 that contains the putative functional motifs required for autonomous movement of a hAT transposon. Transposon display detected movement of TCUP in two long-term tissue cultured cell lines of the genotype Hi-II AxB and BMS. This research implicates TCUP as a transposon that is capable of reactivation and which may also be particularly sensitive to the stress of the tissue culture environment. Our findings are consistent with the hypothesis that epigenetic alterations potentiate genomic responses to stress during clonal propagation of plants.

Transcriptome analysis of cadmium-treated roots in maize (Zea mays L.

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Runqing Yue

2016-08-01

Full Text Available Cadmium (Cd is a heavy metal and is highly toxic to all plant species. However, the underlying molecular mechanism controlling the effects of auxin on the Cd stress response in maize is largely unknown. In this study, the transcriptome produced by maize ‘Zheng 58’ root responses to Cd stress was sequenced using Illumina sequencing technology. In our study, six RNA-seq libraries yielded a total of 244 million clean short reads and 30.37 Gb of sequence data. A total of 6342 differentially expressed genes (DEGs were grouped into 908 Gene Ontology (GO categories and 198 Kyoto Encyclopedia of Genes and Genomes terms. GO term enrichment analysis indicated that various auxin signaling pathway-related GO terms were significantly enriched in DEGs. Comparison of the transcript abundances for auxin biosynthesis, transport, and downstream response genes revealed a universal expression response under Cd treatment. Furthermore, our data showed that free indole-3-acetic acid (IAA levels were significantly reduced; but IAA oxidase activity was up-regulated after Cd treatment in maize roots. The analysis of Cd activity in maize roots under different Cd and auxin conditions confirmed that auxin affected Cd accumulation in maize seedlings. These results will improve our understanding of the complex molecular mechanisms underlying the response to Cd stress in maize roots.

Resistance of maize varieties to the maize weevil Sitophilus zeamais

African Journals Online (AJOL)

This study aimed at evaluating commonly used maize varieties, collected from Melkasa and Bako Agricultural Research Centers and Haramaya University, Ethiopia, against the maize weevil Sitophilus zeamais Motsch., one of the most important cosmopolitan stored product pests in maize. A total of 13 improved maize ...

Intercropping Maize With Legumes for Sustainable Highland Maize Production

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Adirek Punyalue

2018-02-01

Full Text Available Residue burning to prepare soil for maize growing deprives the soil of both protective cover and organic matter, and it exacerbates environmental issues such as Southeast Asia's haze problem. This paper reports on a study that evaluated the effectiveness of maize/legume intercropping as an alternative to maize cultivation with residue burning. Cowpea (Vigna unguiculata, mung bean (V. radiata, rice bean (V. umbellata, and lablab (Lablab purpureus were sown into a standing maize crop 30 days before harvest, and the results were compared with a maize crop grown using residue burning as the method for land preparation at Pang Da Agricultural Station in Chiang Mai, Thailand, in a replicated trial conducted over 3 growing seasons from 2012 to 2014. Intercropping increased maize grain yield by 31–53% and left 70–170% more residue containing 113–230% more nitrogen than the maize sown after residue burning, depending on the legume, and decreased weed dry weight by two-thirds after 2 seasons. Soil biodiversity was enriched by the intercrops, with a doubling in the spore density of arbuscular mycorrhizal fungi in the root-zone soil and increased abundance, diversity (Shannon index, and richness of the soil macrofauna. The abundance of soil animals increased with crop residue dry weight (r = 0.90, P < 0.05 and nitrogen content (r = 0.98, P < 0.01. The effect of intercropping on maize grain yield and accumulation of residue and nitrogen were then confirmed in a participatory experiment involving farmers in 2 highland villages in the Phrao and Chiang Dao districts of Chiang Mai Province with maize and rice bean in 2015. The effects of maize/legume intercropping—increased nitrogen accumulation and crop residue, enhanced soil biodiversity, suppression of weeds, and protection of the soil surface, which enabled the maize to be sown without land clearing with fire—should all contribute to sustainable highland maize production.

Molecular Evolution and Genetic Variation of G2-Like Transcription Factor Genes in Maize.

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Fang Liu

Full Text Available The productivity of maize (Zea mays L. depends on the development of chloroplasts, and G2-like transcription factors play a central role in regulating chloroplast development. In this study, we identified 59 G2-like genes in the B73 maize genome and systematically analyzed these genes at the molecular and evolutionary levels. Based on gene structure character, motif compositions and phylogenetic analysis, maize G2-like genes (ZmG1- ZmG59 were divided into seven groups (I-VII. By synteny analysis, 18 collinear gene pairs and strongly conserved microsyntny among regions hosting G2-like genes across maize and sorghum were found. Here, we showed that the vast majority of ZmG gene duplications resulted from whole genome duplication events rather than tandem duplications. After gene duplication events, some ZmG genes were silenced. The functions of G2-like genes were multifarious and most genes that are expressed in green tissues may relate to maize photosynthesis. The qRT-PCR showed that the expression of these genes was sensitive to low temperature and drought. Furthermore, we analyzed differences of ZmGs specific to cultivars in temperate and tropical regions at the population level. Interestingly, the single nucleotide polymorphism (SNP analysis revealed that nucleotide polymorphism associated with different temperature zones. Above all, G2-like genes were highly conserved during evolution, but polymorphism could be caused due to a different geographical location. Moreover, G2-like genes might be related to cold and drought stresses.

Comparative molecular cytogenetics of major repetitive sequence families of three Dendrobium species (Orchidaceae) from Bangladesh

Science.gov (United States)

Begum, Rabeya; Alam, Sheikh Shamimul; Menzel, Gerhard; Schmidt, Thomas

2009-01-01

Background and Aims Dendrobium species show tremendous morphological diversity and have broad geographical distribution. As repetitive sequence analysis is a useful tool to investigate the evolution of chromosomes and genomes, the aim of the present study was the characterization of repetitive sequences from Dendrobium moschatum for comparative molecular and cytogenetic studies in the related species Dendrobium aphyllum, Dendrobium aggregatum and representatives from other orchid genera. Methods In order to isolate highly repetitive sequences, a c0t-1 DNA plasmid library was established. Repeats were sequenced and used as probes for Southern hybridization. Sequence divergence was analysed using bioinformatic tools. Repetitive sequences were localized along orchid chromosomes by fluorescence in situ hybridization (FISH). Key Results Characterization of the c0t-1 library resulted in the detection of repetitive sequences including the (GA)n dinucleotide DmoO11, numerous Arabidopsis-like telomeric repeats and the highly amplified dispersed repeat DmoF14. The DmoF14 repeat is conserved in six Dendrobium species but diversified in representative species of three other orchid genera. FISH analyses showed the genome-wide distribution of DmoF14 in D. moschatum, D. aphyllum and D. aggregatum. Hybridization with the telomeric repeats demonstrated Arabidopsis-like telomeres at the chromosome ends of Dendrobium species. However, FISH using the telomeric probe revealed two pairs of chromosomes with strong intercalary signals in D. aphyllum. FISH showed the terminal position of 5S and 18S–5·8S–25S rRNA genes and a characteristic number of rDNA sites in the three Dendrobium species. Conclusions The repeated sequences isolated from D. moschatum c0t-1 DNA constitute major DNA families of the D. moschatum, D. aphyllum and D. aggregatum genomes with DmoF14 representing an ancient component of orchid genomes. Large intercalary telomere-like arrays suggest chromosomal

Directed PCR-free engineering of highly repetitive DNA sequences

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Preissler Steffen

2011-09-01

Full Text Available Abstract Background Highly repetitive nucleotide sequences are commonly found in nature e.g. in telomeres, microsatellite DNA, polyadenine (poly(A tails of eukaryotic messenger RNA as well as in several inherited human disorders linked to trinucleotide repeat expansions in the genome. Therefore, studying repetitive sequences is of biological, biotechnological and medical relevance. However, cloning of such repetitive DNA sequences is challenging because specific PCR-based amplification is hampered by the lack of unique primer binding sites resulting in unspecific products. Results For the PCR-free generation of repetitive DNA sequences we used antiparallel oligonucleotides flanked by restriction sites of Type IIS endonucleases. The arrangement of recognition sites allowed for stepwise and seamless elongation of repetitive sequences. This facilitated the assembly of repetitive DNA segments and open reading frames encoding polypeptides with periodic amino acid sequences of any desired length. By this strategy we cloned a series of polyglutamine encoding sequences as well as highly repetitive polyadenine tracts. Such repetitive sequences can be used for diverse biotechnological applications. As an example, the polyglutamine sequences were expressed as His6-SUMO fusion proteins in Escherichia coli cells to study their aggregation behavior in vitro. The His6-SUMO moiety enabled affinity purification of the polyglutamine proteins, increased their solubility, and allowed controlled induction of the aggregation process. We successfully purified the fusions proteins and provide an example for their applicability in filter retardation assays. Conclusion Our seamless cloning strategy is PCR-free and allows the directed and efficient generation of highly repetitive DNA sequences of defined lengths by simple standard cloning procedures.

Variation in DNA Methylation Patterns is More Common among Maize Inbreds than among Tissues

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Steven R. Eichten

2013-07-01

Full Text Available Chromatin modifications, such as DNA methylation, can provide heritable, epigenetic regulation of gene expression in the absence of genetic changes. A role for DNA methylation in meiotically stable marking of repetitive elements and other sequences has been demonstrated in plants. Methylation of DNA is also proposed to play a role in development through providing a mitotic memory of gene expression states established during cellular differentiation. We sought to clarify the relative levels of DNA methylation variation among different genotypes and tissues in maize ( L.. We have assessed genomewide DNA methylation patterns in leaf, immature tassel, embryo, and endosperm tissues of two inbred maize lines: B73 and Mo17. There are hundreds of regions of differential methylation present between the two genotypes. In general, the same regions exhibit differential methylation between B73 and Mo17 in each of the tissues that were surveyed. In contrast, there are few examples of tissue-specific DNA methylation variation. Only a subset of regions with tissue-specific variation in DNA methylation show similar patterns in both genotypes of maize and even fewer are associated with altered gene expression levels among the tissues. Our data indicates a limited impact of DNA methylation on developmental gene regulation within maize.

Coordination of the maize transcriptome by a conserved circadian clock

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Harmon Frank G

2010-06-01

Full Text Available Abstract Background The plant circadian clock orchestrates 24-hour rhythms in internal physiological processes to coordinate these activities with daily and seasonal changes in the environment. The circadian clock has a profound impact on many aspects of plant growth and development, including biomass accumulation and flowering time. Despite recent advances in understanding the circadian system of the model plant Arabidopsis thaliana, the contribution of the circadian oscillator to important agronomic traits in Zea mays and other cereals remains poorly defined. To address this deficit, this study investigated the transcriptional landscape of the maize circadian system. Results Since transcriptional regulation is a fundamental aspect of circadian systems, genes exhibiting circadian expression were identified in the sequenced maize inbred B73. Of the over 13,000 transcripts examined, approximately 10 percent displayed circadian expression patterns. The majority of cycling genes had peak expression at subjective dawn and dusk, similar to other plant circadian systems. The maize circadian clock organized co-regulation of genes participating in fundamental physiological processes, including photosynthesis, carbohydrate metabolism, cell wall biogenesis, and phytohormone biosynthesis pathways. Conclusions Circadian regulation of the maize genome was widespread and key genes in several major metabolic pathways had circadian expression waveforms. The maize circadian clock coordinated transcription to be coincident with oncoming day or night, which was consistent with the circadian oscillator acting to prepare the plant for these major recurring environmental changes. These findings highlighted the multiple processes in maize plants under circadian regulation and, as a result, provided insight into the important contribution this regulatory system makes to agronomic traits in maize and potentially other C4 plant species.

Identification of a maize chlorotic dwarf virus silencing suppressor protein

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Maize chlorotic dwarf virus (MCDV), a member of the genus Waikavirus, family Secoviridae, has a 11784 nt (+)ssRNA genome that encodes a 389 kDa proteolytically processed polyprotein. We show that an N-terminal 78kDa polyprotein (R78) has silencing suppressor activity, that it is cleaved by the viral...

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

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Chung, Dongjun; Kuan, Pei Fen; Li, Bo; Sanalkumar, Rajendran; Liang, Kun; Bresnick, Emery H; Dewey, Colin; Keleş, Sündüz

2011-07-01

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

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Dongjun Chung

2011-07-01

Full Text Available Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads. This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads. Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.

Expanding probe repertoire and improving reproducibility in human genomic hybridization

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Dorman, Stephanie N.; Shirley, Ben C.; Knoll, Joan H. M.; Rogan, Peter K.

2013-01-01

Diagnostic DNA hybridization relies on probes composed of single copy (sc) genomic sequences. Sc sequences in probe design ensure high specificity and avoid cross-hybridization to other regions of the genome, which could lead to ambiguous results that are difficult to interpret. We examine how the distribution and composition of repetitive sequences in the genome affects sc probe performance. A divide and conquer algorithm was implemented to design sc probes. With this approach, sc probes can include divergent repetitive elements, which hybridize to unique genomic targets under higher stringency experimental conditions. Genome-wide custom probe sets were created for fluorescent in situ hybridization (FISH) and microarray genomic hybridization. The scFISH probes were developed for detection of copy number changes within small tumour suppressor genes and oncogenes. The microarrays demonstrated increased reproducibility by eliminating cross-hybridization to repetitive sequences adjacent to probe targets. The genome-wide microarrays exhibited lower median coefficients of variation (17.8%) for two HapMap family trios. The coefficients of variations of commercial probes within 300 nt of a repetitive element were 48.3% higher than the nearest custom probe. Furthermore, the custom microarray called a chromosome 15q11.2q13 deletion more consistently. This method for sc probe design increases probe coverage for FISH and lowers variability in genomic microarrays. PMID:23376933

Gibberellins Promote Brassinosteroids Action and Both Increase Heterosis for Plant Height in Maize (Zea mays L.

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Songlin Hu

2017-06-01

Full Text Available Brassinosteroids (BRs and Gibberellins (GAs are two classes of plant hormones affecting plant height (PHT. Thus, manipulation of BR and GA levels or signaling enables optimization of crop grain and biomass yields. We established backcross (BC families, selected for increased PHT, in two elite maize inbred backgrounds. Various exotic accessions used in the germplasm enhancement in maize project served as donors. BC1-derived doubled haploid lines in the same two elite maize inbred backgrounds established without selection for plant height were included for comparison. We conducted genome-wide association studies to explore the genetic control of PHT by BR and GA. In addition, we used BR and GA inhibitors to compare the relationship between PHT, BR, and GA in inbred lines and heterozygotes from a physiological and biological perspective. A total of 73 genomic loci were discovered to be associated with PHT, with seven co-localized with GA, and two co-localized with BR candidate genes. PHT determined in field trials was significantly correlated with seedling stage BR and GA inhibitor responses. However, this observation was only true for maize heterozygotes, not for inbred lines. Path analysis results suggest that heterozygosity increases GA levels, which in turn promote BR levels. Thus, at least part of heterosis for PHT in maize can be explained by increased GA and BR levels, and seedling stage hormone inhibitor response is promising to predict heterosis for PHT.

Breeding of maize types with specific traits at the Maize Research Institute, Zemun Polje

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Pajić Zorica

2007-01-01

Full Text Available Maize is primarily grown as an energy crop, but the use of different specific versions, such as high-oil maize, high-lysine maize, waxy maize, white-seeded maize, popping maize and sweet maize, is quite extensive. Speciality maize, due to its traits and genetic control of these traits, requires a particular attention in handling breeding material during the processes of breeding. It is especially related to prevention of uncontrolled pollination. In order to provide successful selection for a certain trait, the following specific procedures in evaluation of the trait are necessary: the estimation of a popping volume and flake quality in popping maize; the determination of sugars and harvest maturity in sweet maize; the determination of oil in selected samples of high-oil maize types, and so forth. Breeding programmes for speciality maize, except high-amylose maize, have been implemented at the Maize Research Institute, Zemun Polje, Belgrade, for the last 45 years. A great number of high-yielding sweet maize hybrids, popping maize, high-oil and high-lysine, flint and white-seeded maize hybrids were developed during this 45-year period. Auspicious selection and breeding for these traits is facilitated by the abundant genetic variability and technical and technological possibilities necessary for successful selection.

Comparative QTL mapping of resistance to sugarcane mosaic virus in maize based on bioinformatics

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Xiangling L(U); Xinhai LI; Chuanxiao XIE; Zhuanfang HAO; Hailian JI; Liyu SHI; Shihuang ZHANG

2008-01-01

The development of genomics and bioinfor-matics offers new tools for comparative gene mapping. In this paper, an integrated QTL map for sugarcane mosaic virus (SCMV) resistance in maize was constructed by compiling a total of 81 QTL loci available, using the Genetic Map IBM2 2005 Neighbors as reference. These 81 QTL loci were scattered on 7 chromosomes of maize, and most of them were clustered on chromosomes 3 and 6. By using the method of meta-analysis, we identified one "consensus QTL" on chromosome 3 covering a genetic distance of 6.44 cM, and two on chromosome 6 covering genetic distances of 16 cM and 27.48 cM, respectively. Four positional candidate resistant genes were identified within the "consensus QTL" on chromosome 3 via the strategy of comparative genomics. These results suggest that application of a combination of meta-analysis within a species with sequence homology comparison in a related model plant is an efficient approach to identify the major QTL and its candidate gene(s) for the target traits. The results of this study provide useful information for iden-tifying and cloning the major gene(s) conferring resistance to SCMV in maize.

Chromosomal organization of repetitive DNAs in Hordeum bogdanii and H. brevisubulatum (Poaceae

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Quanwen Dou

2016-10-01

Full Text Available Molecular karyotypes of H. bogdanii Wilensky, 1918 (2n = 14, and H. brevisubulatum Link, 1844 ssp. brevisubulatum (2n = 28, were characterized by physical mapping of several repetitive sequences. A total of 18 repeats, including all possible di- or trinucleotide SSR (simple sequence repeat motifs and satellite DNAs, such as pAs1, 5S rDNA, 45S rDNA, and pSc119.2, were used as probes for fluorescence in situ hybridization on root-tip metaphase chromosomes. Except for the SSR motifs AG, AT and GC, all the repeats we examined produced detectable hybridization signals on chromosomes of both species. A detailed molecular karyotype of the I genome of H. bogdanii is described for the first time, and each repetitive sequence is physically mapped. A high degree of chromosome variation, including aneuploidy and structural changes, was observed in H. brevisubulatum. Although the distribution of repeats in the chromosomes of H. brevisubulatum is different from that of H. bogdanii, similar patterns between the two species imply that the autopolyploid origin of H. brevisubulatum is from a Hordeum species with an I genome. A comparison of the I genome and the other Hordeum genomes, H, Xa and Xu, shows that colocalization of motifs AAC, ACT and CAT and colocalization of motifs AAG and AGG are characteristic of the I genome. In addition, we discuss the evolutionary significance of repeats in the genome during genome differentiation.

[A method for genetic transformation of maize for resistance to viral diseases].

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Valdez, Marta; Madriz, Kenneth; Ramírez, Pilar

2004-09-01

A system for the genetic transformation of maize was developed for two Costa Rican varieties: CR-7 and Diamantes 8843, that can allow the subsequent transfer of viral-derived genes in order to confer resistance to the disease caused by maize rayado fino virus (MRFV). The method is based on particle bombardment of organogenic calli derived from shoot tips. On the other hand, the molecular construction pRFcp-bar, containing the coat protein gene of MRFV and the marker gene bar, was elaborated. For the visual selection of the transformed material was used also the plasmid pDM803 that contains the reporter gene uidA (GUS). The results indicate that devices evaluated: the PIG ("Particle Inflow Gun") and the Bio-Rad are both enough efficient to transfer foreign genes to the genome of the maize.

Breeding of maize types with specific traits at the Maize Research Institute, Zemun Polje

OpenAIRE

Pajić Zorica

2007-01-01

Maize is primarily grown as an energy crop, but the use of different specific versions, such as high-oil maize, high-lysine maize, waxy maize, white-seeded maize, popping maize and sweet maize, is quite extensive. Speciality maize, due to its traits and genetic control of these traits, requires a particular attention in handling breeding material during the processes of breeding. It is especially related to prevention of uncontrolled pollination. In order to provide successful selection for a...

Genetic, Genomic, and Breeding Approaches to Further Explore Kernel Composition Traits and Grain Yield in Maize

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Da Silva, Helena Sofia Pereira

2009-01-01

Maize ("Zea mays L.") is a model species well suited for the dissection of complex traits which are often of commercial value. The purpose of this research was to gain a deeper understanding of the genetic control of maize kernel composition traits starch, protein, and oil concentration, and also kernel weight and grain yield. Germplasm with…

Whole-genome in-silico subtractive hybridization (WISH - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of Schistosoma mansoni

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Parrinello Hugues

2010-06-01

Full Text Available Abstract Background Emerging methods of massive sequencing that allow for rapid re-sequencing of entire genomes at comparably low cost are changing the way biological questions are addressed in many domains. Here we propose a novel method to compare two genomes (genome-to-genome comparison. We used this method to identify sex-specific sequences of the human blood fluke Schistosoma mansoni. Results Genomic DNA was extracted from male and female (heterogametic S. mansoni adults and sequenced with a Genome Analyzer (Illumina. Sequences are available at the NCBI sequence read archive http://www.ncbi.nlm.nih.gov/Traces/sra/ under study accession number SRA012151.6. Sequencing reads were aligned to the genome, and a pseudogenome composed of known repeats. Straightforward comparative bioinformatics analysis was performed to compare male and female schistosome genomes and identify female-specific sequences. We found that the S. mansoni female W chromosome contains only few specific unique sequences (950 Kb i.e. about 0.2% of the genome. The majority of W-specific sequences are repeats (10.5 Mb i.e. about 2.5% of the genome. Arbitrarily selected W-specific sequences were confirmed by PCR. Primers designed for unique and repetitive sequences allowed to reliably identify the sex of both larval and adult stages of the parasite. Conclusion Our genome-to-genome comparison method that we call "whole-genome in-silico subtractive hybridization" (WISH allows for rapid identification of sequences that are specific for a certain genotype (e.g. the heterogametic sex. It can in principle be used for the detection of any sequence differences between isolates (e.g. strains, pathovars or even closely related species.

Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus.

OpenAIRE

Sanford, J; Forrester, L; Chapman, V; Chandley, A; Hastie, N

1984-01-01

The major and the minor satellite sequences of Mus musculus were undermethylated in both sperm and oocyte DNAs relative to the amount of undermethylation observed in adult somatic tissue DNA. This hypomethylation was specific for satellite sequences in sperm DNA. Dispersed repetitive and low copy sequences show a high degree of methylation in sperm DNA; however, a dispersed repetitive sequence was undermethylated in oocyte DNA. This finding suggests a difference in the amount of total genomic...

Genomic Dissection of Leaf Angle in Maize (Zea mays L. Using a Four-Way Cross Mapping Population.

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Junqiang Ding

Full Text Available Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL on leaf angle detected by inclusive composite interval mapping (ICIM. ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs. Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize.

Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize.

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Pophaly, Saurabh D; Tellier, Aurélien

2015-12-01

The maize ancestor experienced a recent whole-genome duplication (WGD) followed by gene erosion which generated two subgenomes, the dominant subgenome (maize1) experiencing fewer deletions than maize2. We take advantage of available extensive polymorphism and gene expression data in maize to study purifying selection and gene expression divergence between WGD retained paralog pairs. We first report a strong correlation in nucleotide diversity between duplicate pairs, except for upstream regions. We then show that maize1 genes are under stronger purifying selection than maize2. WGD retained genes have higher gene dosage and biased Gene Ontologies consistent with previous studies. The relative gene expression of paralogs across tissues demonstrates that 98% of duplicate pairs have either subfunctionalized in a tissuewise manner or have diverged consistently in their expression thereby preventing functional complementation. Tissuewise subfunctionalization seems to be a hallmark of transcription factors, whereas consistent repression occurs for macromolecular complexes. We show that dominant gene expression is a strong determinant of the strength of purifying selection, explaining the inferred stronger negative selection on maize1 genes. We propose a novel expression-based classification of duplicates which is more robust to explain observed polymorphism patterns than the subgenome location. Finally, upstream regions of repressed genes exhibit an enrichment in transposable elements which indicates a possible mechanism for expression divergence. © The Author 2015. 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.

LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes

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Feuillet Catherine

2010-11-01

Full Text Available Abstract Background Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with molecular markers. High Information Content Fingerprinting has become the method of choice for large and repetitive genomes such as those of maize, barley, and wheat. However, the high level of repeated DNA present in these genomes requires the application of very stringent criteria to ensure a reliable assembly with the FingerPrinted Contig (FPC software, which often results in short contig lengths (of 3-5 clones before merging as well as an unreliable assembly in some difficult regions. Difficulties can originate from a non-linear topological structure of clone overlaps, low power of clone ordering algorithms, and the absence of tools to identify sources of gaps in Minimal Tiling Paths (MTPs. Results To address these problems, we propose a novel approach that: (i reduces the rate of false connections and Q-clones by using a new cutoff calculation method; (ii obtains reliable clusters robust to the exclusion of single clone or clone overlap; (iii explores the topological contig structure by considering contigs as networks of clones connected by significant overlaps; (iv performs iterative clone clustering combined with ordering and order verification using re-sampling methods; and (v uses global optimization methods for clone ordering and Band Map construction. The elements of this new analytical framework called Linear Topological Contig (LTC were applied on datasets used previously for the construction of the physical map of wheat chromosome 3B with FPC. The performance of LTC vs. FPC was compared also on the simulated BAC libraries based on the known genome sequences for chromosome 1 of rice and chromosome 1 of maize. Conclusions The results show that compared to other methods, LTC enables the construction of highly

Sheep manure vermicompost supplemented with a native diazotrophic bacteria and mycorrhizas for maize cultivation.

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Gutiérrez-Miceli, F A; Moguel-Zamudio, B; Abud-Archila, M; Gutiérrez-Oliva, V F; Dendooven, L

2008-10-01

An orthogonal experimental design L9 (3(4)) with 10 repetitions was used to investigate the effect of Glomus claroideum (0, 1 or 2g(-1) plant), G. fasciculatum (0, 1 or 2g plant(-1)), native diazotrophic bacteria (0, 10(3) and 10(5) UFC ml(-1)) and sheep manure vermicompost (0%, 5% and 10% v/v) on maize plant growth, N and P in leaves and mycorrhization percent. Vermicompost explained most of the variation found for leaf number, wet weight, stem height, and diameter. Both mycorrhizas increased the plant wet weight but G. fasciculatum the most. Mycorrhization increased the P content, but not the N content. Mycorrhizal colonization increased when diazotrophic bacteria and vermicompost were added. It was found that weight of maize plants cultivated in peat moss amended with vermicompost increased when supplemented with G. fasciculatum and diazotrophic bacteria.

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

International Nuclear Information System (INIS)

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)

Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes

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Rebecca M. Davidson

2011-11-01

Full Text Available Transcriptome sequencing is a powerful method for studying global expression patterns in large, complex genomes. Evaluation of sequence-based expression profiles during reproductive development would provide functional annotation to genes underlying agronomic traits. We generated transcriptome profiles for 12 diverse maize ( L. reproductive tissues representing male, female, developing seed, and leaf tissues using high throughput transcriptome sequencing. Overall, ∼80% of annotated genes were expressed. Comparative analysis between sequence and hybridization-based methods demonstrated the utility of ribonucleic acid sequencing (RNA-seq for expression determination and differentiation of paralagous genes (∼85% of maize genes. Analysis of 4975 gene families across reproductive tissues revealed expression divergence is proportional to family size. In all pairwise comparisons between tissues, 7 (pre- vs. postemergence cobs to 48% (pollen vs. ovule of genes were differentially expressed. Genes with expression restricted to a single tissue within this study were identified with the highest numbers observed in leaves, endosperm, and pollen. Coexpression network analysis identified 17 gene modules with complex and shared expression patterns containing many previously described maize genes. The data and analyses in this study provide valuable tools through improved gene annotation, gene family characterization, and a core set of candidate genes to further characterize maize reproductive development and improve grain yield potential.

Transcriptomic Analysis of Long Non-Coding RNAs and Coding Genes Uncovers a Complex Regulatory Network That Is Involved in Maize Seed Development

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Ming Zhu

2017-10-01

Full Text Available Long non-coding RNAs (lncRNAs have been reported to be involved in the development of maize plant. However, few focused on seed development of maize. Here, we identified 753 lncRNA candidates in maize genome from six seed samples. Similar to the mRNAs, lncRNAs showed tissue developmental stage specific and differential expression, indicating their putative role in seed development. Increasing evidence shows that crosstalk among RNAs mediated by shared microRNAs (miRNAs represents a novel layer of gene regulation, which plays important roles in plant development. Functional roles and regulatory mechanisms of lncRNAs as competing endogenous RNAs (ceRNA in plants, particularly in maize seed development, are unclear. We combined analyses of consistently altered 17 lncRNAs, 840 mRNAs and known miRNA to genome-wide investigate potential lncRNA-mediated ceRNA based on “ceRNA hypothesis”. The results uncovered seven novel lncRNAs as potential functional ceRNAs. Functional analyses based on their competitive coding-gene partners by Gene Ontology (GO and KEGG biological pathway demonstrated that combined effects of multiple ceRNAs can have major impacts on general developmental and metabolic processes in maize seed. These findings provided a useful platform for uncovering novel mechanisms of maize seed development and may provide opportunities for the functional characterization of individual lncRNA in future studies.

Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process

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James A. Shapiro

2016-06-01

Full Text Available The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.

Decomposition and fertilizing effects of maize stover and chromolaena odorata on maize yield

International Nuclear Information System (INIS)

Tetteh, F.M.; Safo, E.Y.; Quansah, C.

2008-01-01

The quality, rates of decomposition and the fertilizing effect of chromolaena odorata, and maize stover were determined in field experiments as surface application or buried in litter bags. Studies on the effect of plant materials of contrasting qualities (maize stover and C. odorata) applied sole (10 Mg ha -1 ) and mixed, on maize grain and biomass yield were also conducted on the Asuansi (Ferric Acrisol) soil series. Total nitrogen content of the residues ranged from 0.85% in maize stover to 3.50% in C. odorata. Organic carbon ranged from 34.90% in C. odorata to 48.50% in maize stover. Phosphorus ranged from 0.10% in maize stover to 0.76% in C. odorata. In the wet season, the decomposition rate constants (k) were 0.0319 day -1 for C. odorata, and 0.0081 for maize stover. In the dry season, the k values were 0.0083 for C. odorata, and 0.0072 day -1 for maize stover. Burying of the plant materials reduced the half-life (t 50 ) periods from 18 to 10 days for C. odorata, and 45 to 20 days for maize stover. Maize grain yield of 2556 kg ha -1 was obtained in sole C. odorata (10 Mg ha -1 ) compared with 2167 kg ha -1 for maize stover. Mixing of maize stover and C. odorata residues improved the nutrient content as well as nutrient release by the mixtures resulting in greater maize grain yields in the mixtures than the sole maize stover treatment. It is recommended that C. odorata be used as green manure, mulching or composting material to improve fertility. (au)

Presence of a polyA tail at the 3’-end of Maize rayado fino virus RNA

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Maize rayado fino virus (MRFV) is the type member of the genus Marafivirus in the family Tymoviridae, yet is distinct from other members of the genus in that its genome reportedly lacks a poly(A) tail at the 3’-terminus. Using naïve and targeted PCR-based approaches, we now show that the MRFV genom...

An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize.

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Char, Si Nian; Neelakandan, Anjanasree K; Nahampun, Hartinio; Frame, Bronwyn; Main, Marcy; Spalding, Martin H; Becraft, Philip W; Meyers, Blake C; Walbot, Virginia; Wang, Kan; Yang, Bing

2017-02-01

CRISPR/Cas9 is a powerful genome editing tool in many organisms, including a number of monocots and dicots. Although the design and application of CRISPR/Cas9 is simpler compared to other nuclease-based genome editing tools, optimization requires the consideration of the DNA delivery and tissue regeneration methods for a particular species to achieve accuracy and efficiency. Here, we describe a public sector system, ISU Maize CRISPR, utilizing Agrobacterium-delivered CRISPR/Cas9 for high-frequency targeted mutagenesis in maize. This system consists of an Escherichia coli cloning vector and an Agrobacterium binary vector. It can be used to clone up to four guide RNAs for single or multiplex gene targeting. We evaluated this system for its mutagenesis frequency and heritability using four maize genes in two duplicated pairs: Argonaute 18 (ZmAgo18a and ZmAgo18b) and dihydroflavonol 4-reductase or anthocyaninless genes (a1 and a4). T 0 transgenic events carrying mono- or diallelic mutations of one locus and various combinations of allelic mutations of two loci occurred at rates over 70% mutants per transgenic events in both Hi-II and B104 genotypes. Through genetic segregation, null segregants carrying only the desired mutant alleles without the CRISPR transgene could be generated in T 1 progeny. Inheritance of an active CRISPR/Cas9 transgene leads to additional target-specific mutations in subsequent generations. Duplex infection of immature embryos by mixing two individual Agrobacterium strains harbouring different Cas9/gRNA modules can be performed for improved cost efficiency. Together, the findings demonstrate that the ISU Maize CRISPR platform is an effective and robust tool to targeted mutagenesis in maize. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize

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Jia, Shangang; Li, Aixia; Morton, Kyla; Avoles-Kianian, Penny; Kianian, Shahryar F.; Zhang, Chi; Holding, David

2016-01-01

To better understand maize endosperm filling and maturation, we used γ-irradiation of the B73 maize reference line to generate mutants with opaque endosperm and reduced kernel fill phenotypes, and created a population of 1788 lines including 39 Mo17 × F2s showing stable, segregating, and viable kernel phenotypes. For molecular characterization of the mutants, we developed a novel functional genomics platform that combined bulked segregant RNA and exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. To exemplify the utility of the mutants and provide proof-of-concept for the bioinformatics platform, we present detailed characterization of line 937, an opaque mutant harboring a 6203 bp in-frame deletion covering six exons within the Opaque-1 gene. In addition, we describe mutant line 146 which contains a 4.8 kb intragene deletion within the Sugary-1 gene and line 916 in which an 8.6 kb deletion knocks out a Cyclin A2 gene. The publically available algorithm developed in this work improves the identification of causative deletions and its corresponding gaps within mapping peaks. This study demonstrates the utility of γ-irradiation for forward genetics in large nondense genomes such as maize since deletions often affect single genes. Furthermore, we show how this classical mutagenesis method becomes applicable for functional genomics when combined with state-of-the-art genomics tools. PMID:27261000

Production of antihypertensive peptides by enzymatic zein hydrolysate from maize-zea mays ssp. mexicana introgression line

International Nuclear Information System (INIS)

Wang, L.; Zhang, X.; Qiao, Y.; Qu, M.

2014-01-01

Teosintes are essential gene reservoir for maize breeding improvement, among which Zea mays ssp. mexicana has many valuable traits deserved to be transferred into maize genetic background. In this study, one maize-teosinte introgression line SD00100 was selected from the population of Zea mays ssp. mexicana as wild parent. This introgression line manifested the outstanding agricultural traits similar to maize parent Ye 515 and alien genetic material was identified by genomic in situ hybridization (GISH). To produce bioactive peptides with potent angiotensin converting enzyme (ACE) inhibitory activity, zein extracted from endosperm meal was then undergone enzymatic hydrolysis with thermolysin and the hydrolysate was then filtered through a 3 kDa cut-off membrane. ACE inhibitory activity of permeate from Ye 515 and SD00100 was evaluated by RP-HPLC. The IC50 values of the peptides obtained from maize parent and the introgression line were 96.9 micro g/ml and 22.9 micro g/ml, respectively, with significant difference between them. Our results showed that an outstanding inbred maize line was obtained for production of antihypertensive peptides as well as for further development of functional food. (author)

Repetitive elements dynamics in cell identity programming, maintenance and disease

KAUST Repository

Bodega, Beatrice

2014-12-01

The days of \\'junk DNA\\' seem to be over. The rapid progress of genomics technologies has been unveiling unexpected mechanisms by which repetitive DNA and in particular transposable elements (TEs) have evolved, becoming key issues in understanding genome structure and function. Indeed, rather than \\'parasites\\', recent findings strongly suggest that TEs may have a positive function by contributing to tissue specific transcriptional programs, in particular as enhancer-like elements and/or modules for regulation of higher order chromatin structure. Further, it appears that during development and aging genomes experience several waves of TEs activation, and this contributes to individual genome shaping during lifetime. Interestingly, TEs activity is major target of epigenomic regulation. These findings are shedding new light on the genome-phenotype relationship and set the premises to help to explain complex disease manifestation, as consequence of TEs activity deregulation.

Defining the maize transcriptome de novo using deep RNA-Seq

Energy Technology Data Exchange (ETDEWEB)

Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin; Wang, Zhong

2011-06-01

De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.

Defining the maize transcriptome de novo using deep RNA-Seq

Energy Technology Data Exchange (ETDEWEB)

Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin; Wang, Zhong

2011-06-02

De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.

Sequence-indexed mutations in maize using the UniformMu transposon-tagging population

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Baier John

2007-05-01

Full Text Available Abstract Background Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flanking Sequence Tags (FSTs map each mutant to a specific locus within the genome. In maize, FSTs have been generated using DNA transposons. Transposable elements can generate unstable insertions that are difficult to analyze for simple knockout phenotypes. Transposons can also generate somatic insertions that fail to segregate in subsequent generations. Results Transposon insertion sites from 106 UniformMu FSTs were tested for inheritance by locus-specific PCR. We confirmed 89% of the FSTs to be germinal transposon insertions. We found no evidence for somatic insertions within the 11% of insertion sites that were not confirmed. Instead, this subset of insertion sites had errors in locus-specific primer design due to incomplete or low-quality genomic sequences. The locus-specific PCR assays identified a knockout of a 6-phosphogluconate dehydrogenase gene that co-segregates with a seed mutant phenotype. The mutant phenotype linked to this knockout generates novel hypotheses about the role for the plastid-localized oxidative pentose phosphate pathway during grain-fill. Conclusion We show that FSTs from the UniformMu population identify stable, germinal insertion sites in maize. Moreover, we show that these sequence-indexed mutations can be readily used for reverse genetic analysis. We conclude from these data that the current collection of 1,882 non-redundant insertion sites from UniformMu provide a genome-wide resource for reverse genetics.

GENETIC DIVERSITY OF S3 MAIZE GENOTYPES RESISTANT TO DOWNY MILDEW BASED ON SSR MARKERS

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Amran Muis

2016-02-01

Full Text Available The compulsory requirement for releasing new high yielding maize varieties is resistance to downy mildew. The study aimed to determine the level of homozygosity, genetic diversity, and  genetic distance of 30 S3 genotypes of maize. Number of primers to be used were 30 polymorphic SSR loci which are distributed over the entire maize genomes. The S3 genotypes used were resistant to downy mildew with homozygosity level of >80%, genetic distance between the test and tester strains >0.7, and anthesis silking interval (ASI between inbred lines and tester lines was maximum 3 days. The results showed that 30 SSR primers used were spread evenly across the maize genomes which were manifested in the representation of SSR loci on each chromosome of a total of 10 chromosomes. The levels of polymorphism ranged from 0.13 to 0.78, an average of 0.51, and the number of alleles ranged from 2 to 8 alleles per SSR locus, an average of 4 alleles per SSR locus. The size of nucleotides in each locus also varied from 70 to 553 bp. Cophenetic correlation value (r at 0.67 indicated that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA was less reliable for differentiating genotypes in five groups. Of the total of 30 genotypes analyzed, 17 genotypes had homozygosity level of >80% so it can be included in the hybrid assembly program.

Advances in Maize Transformation Technologies and Development of Transgenic Maize.

Science.gov (United States)

Yadava, Pranjal; Abhishek, Alok; Singh, Reeva; Singh, Ishwar; Kaul, Tanushri; Pattanayak, Arunava; Agrawal, Pawan K

2016-01-01

Maize is the principal grain crop of the world. It is also the crop where genetic engineering has been employed to a great extent to improve its various traits. The ability to transform maize is a crucial step for application of gene technology in maize improvement. There have been constant improvements in the maize transformation technologies over past several years. The choice of genotype and the explant material to initiate transformation and the different types of media to be used in various stages of tissue culture can have significant impact on the outcomes of the transformation efforts. Various methods of gene transfer, like the particle bombardment, protoplast transformation, Agrobacterium -mediated, in planta transformation, etc., have been tried and improved over years. Similarly, various selection systems for retrieval of the transformants have been attempted. The commercial success of maize transformation and transgenic development is unmatched by any other crop so far. Maize transformation with newer gene editing technologies is opening up a fresh dimension in transformation protocols and work-flows. This review captures the various past and recent facets in improvement in maize transformation technologies and attempts to present a comprehensive updated picture of the current state of the art in this area.

Genomic comparison of the endophyte Herbaspirillum seropedicae SmR1 and the phytopathogen Herbaspirillum rubrisubalbicans M1 by suppressive subtractive hybridization and partial genome sequencing.

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Monteiro, Rose A; Balsanelli, Eduardo; Tuleski, Thalita; Faoro, Helison; Cruz, Leonardo M; Wassem, Roseli; de Baura, Valter A; Tadra-Sfeir, Michelle Z; Weiss, Vinícius; DaRocha, Wanderson D; Muller-Santos, Marcelo; Chubatsu, Leda S; Huergo, Luciano F; Pedrosa, Fábio O; de Souza, Emanuel M

2012-05-01

Herbaspirillum rubrisubalbicans M1 causes the mottled stripe disease in sugarcane cv. B-4362. Inoculation of this cultivar with Herbaspirillum seropedicae SmR1 does not produce disease symptoms. A comparison of the genomic sequences of these closely related species may permit a better understanding of contrasting phenotype such as endophytic association and pathogenic life style. To achieve this goal, we constructed suppressive subtractive hybridization (SSH) libraries to identify DNA fragments present in one species and absent in the other. In a parallel approach, partial genomic sequence from H. rubrisubalbicans M1 was directly compared in silico with the H. seropedicae SmR1 genome. The genomic differences between the two organisms revealed by SSH suggested that lipopolysaccharide and adhesins are potential molecular factors involved in the different phenotypic behavior. The cluster wss probably involved in cellulose biosynthesis was found in H. rubrisubalbicans M1. Expression of this gene cluster was increased in H. rubrisubalbicans M1 cells attached to the surface of maize root, and knockout of wssD gene led to decrease in maize root surface attachment and endophytic colonization. The production of cellulose could be responsible for the maize attachment pattern of H. rubrisubalbicans M1 that is capable of outcompeting H. seropedicae SmR1. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Transcriptome Dynamics during Maize Endosperm Development.

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Jianzhou Qu

Full Text Available The endosperm is a major organ of the seed that plays vital roles in determining seed weight and quality. However, genome-wide transcriptome patterns throughout maize endosperm development have not been comprehensively investigated to date. Accordingly, we performed a high-throughput RNA sequencing (RNA-seq analysis of the maize endosperm transcriptome at 5, 10, 15 and 20 days after pollination (DAP. We found that more than 11,000 protein-coding genes underwent alternative splicing (AS events during the four developmental stages studied. These genes were mainly involved in intracellular protein transport, signal transmission, cellular carbohydrate metabolism, cellular lipid metabolism, lipid biosynthesis, protein modification, histone modification, cellular amino acid metabolism, and DNA repair. Additionally, 7,633 genes, including 473 transcription factors (TFs, were differentially expressed among the four developmental stages. The differentially expressed TFs were from 50 families, including the bZIP, WRKY, GeBP and ARF families. Further analysis of the stage-specific TFs showed that binding, nucleus and ligand-dependent nuclear receptor activities might be important at 5 DAP, that immune responses, signalling, binding and lumen development are involved at 10 DAP, that protein metabolic processes and the cytoplasm might be important at 15 DAP, and that the responses to various stimuli are different at 20 DAP compared with the other developmental stages. This RNA-seq analysis provides novel, comprehensive insights into the transcriptome dynamics during early endosperm development in maize.

Association and linkage analysis of aluminum tolerance genes in maize.

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Allison M Krill

Full Text Available BACKGROUND: Aluminum (Al toxicity is a major worldwide constraint to crop productivity on acidic soils. Al becomes soluble at low pH, inhibiting root growth and severely reducing yields. Maize is an important staple food and commodity crop in acidic soil regions, especially in South America and Africa where these soils are very common. Al exclusion and intracellular tolerance have been suggested as two important mechanisms for Al tolerance in maize, but little is known about the underlying genetics. METHODOLOGY: An association panel of 282 diverse maize inbred lines and three F2 linkage populations with approximately 200 individuals each were used to study genetic variation in this complex trait. Al tolerance was measured as net root growth in nutrient solution under Al stress, which exhibited a wide range of variation between lines. Comparative and physiological genomics-based approaches were used to select 21 candidate genes for evaluation by association analysis. CONCLUSIONS: Six candidate genes had significant results from association analysis, but only four were confirmed by linkage analysis as putatively contributing to Al tolerance: Zea mays AltSB like (ZmASL, Zea mays aluminum-activated malate transporter2 (ALMT2, S-adenosyl-L-homocysteinase (SAHH, and Malic Enzyme (ME. These four candidate genes are high priority subjects for follow-up biochemical and physiological studies on the mechanisms of Al tolerance in maize. Immediately, elite haplotype-specific molecular markers can be developed for these four genes and used for efficient marker-assisted selection of superior alleles in Al tolerance maize breeding programs.

Characterization of a Novel Polerovirus Infecting Maize in China.

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Chen, Sha; Jiang, Guangzhuang; Wu, Jianxiang; Liu, Yong; Qian, Yajuan; Zhou, Xueping

2016-04-28

A novel virus, tentatively named Maize Yellow Mosaic Virus (MaYMV), was identified from the field-grown maize plants showing yellow mosaic symptoms on the leaves collected from the Yunnan Province of China by the deep sequencing of small RNAs. The complete 5642 nucleotide (nt)-long genome of the MaYMV shared the highest nucleotide sequence identity (73%) to Maize Yellow Dwarf Virus-RMV. Sequence comparisons and phylogenetic analyses suggested that MaYMV represents a new member of the genus Polerovirus in the family Luteoviridae. Furthermore, the P0 protein encoded by MaYMV was demonstrated to inhibit both local and systemic RNA silencing by co-infiltration assays using transgenic Nicotiana benthamiana line 16c carrying the GFP reporter gene, which further supported the identification of a new polerovirus. The biologically-active cDNA clone of MaYMV was generated by inserting the full-length cDNA of MaYMV into the binary vector pCB301. RT-PCR and Northern blot analyses showed that this clone was systemically infectious upon agro-inoculation into N. benthamiana. Subsequently, 13 different isolates of MaYMV from field-grown maize plants in different geographical locations of Yunnan and Guizhou provinces of China were sequenced. Analyses of their molecular variation indicate that the 3' half of P3-P5 read-through protein coding region was the most variable, whereas the coat protein- (CP-) and movement protein- (MP-)coding regions were the most conserved.

Characterization of a Novel Polerovirus Infecting Maize in China

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Sha Chen

2016-04-01

Full Text Available A novel virus, tentatively named Maize Yellow Mosaic Virus (MaYMV, was identified from the field-grown maize plants showing yellow mosaic symptoms on the leaves collected from the Yunnan Province of China by the deep sequencing of small RNAs. The complete 5642 nucleotide (nt-long genome of the MaYMV shared the highest nucleotide sequence identity (73% to Maize Yellow Dwarf Virus-RMV. Sequence comparisons and phylogenetic analyses suggested that MaYMV represents a new member of the genus Polerovirus in the family Luteoviridae. Furthermore, the P0 protein encoded by MaYMV was demonstrated to inhibit both local and systemic RNA silencing by co-infiltration assays using transgenic Nicotiana benthamiana line 16c carrying the GFP reporter gene, which further supported the identification of a new polerovirus. The biologically-active cDNA clone of MaYMV was generated by inserting the full-length cDNA of MaYMV into the binary vector pCB301. RT-PCR and Northern blot analyses showed that this clone was systemically infectious upon agro-inoculation into N. benthamiana. Subsequently, 13 different isolates of MaYMV from field-grown maize plants in different geographical locations of Yunnan and Guizhou provinces of China were sequenced. Analyses of their molecular variation indicate that the 3′ half of P3–P5 read-through protein coding region was the most variable, whereas the coat protein- (CP- and movement protein- (MP-coding regions were the most conserved.

Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers.

Science.gov (United States)

Zhang, Xiao; Zhang, Hua; Li, Lujiang; Lan, Hai; Ren, Zhiyong; Liu, Dan; Wu, Ling; Liu, Hailan; Jaqueth, Jennifer; Li, Bailin; Pan, Guangtang; Gao, Shibin

2016-08-31

representatively not only illustrates the foundation and evolution trend of maize breeding resource as a theoretical reference for the improvement of heterosis, but also provides plenty of information for genetic researches such as genome-wide association study and marker-assisted selection in the future.

Development, applications and distribution of DNA markers for genetic information for sorghum and maize improvement

International Nuclear Information System (INIS)

Lee, M.

2001-01-01

This final report summarizes the progress made towards the enhancement and distribution of genetic resources (e.g. genetic stocks, seed and DNA clones) used for basic and applied aspects of the genetic improvement of maize and sorghum. The genetic maps of maize and sorghum were improved through comparative mapping of RFLP loci detected by 124 maize cDNA clones and through the development of a new mapping population of maize. Comparative mapping between maize and sorghum and maize and rice, using the set of 124 maize cDNA clones (and other clones) in each study, substantiated previous observations of extensive conservation of locus order but it also provided strong evidence of numerous large-scale chromosomal rearrangements. The new mapping population for maize (intermated B73xMo17, 'IBM') was created by random intermating during the first segregating generation. Intermating for four generations prior to the derivation of recombinant inbred lines (RILs) increased the frequency of recombinants at many regions of the maize genome and provided better genetic resolution of locus order. Expansion of the maize genetic map was not uniform along the length of a linkage group and was less than the theoretical expectation. The 350 IBM RILs were genotyped at 512 loci detected by DNA clones, including 76 of the 124 supported by this contract. The production of the sorghum mapping population of RILs from the cross CK60xPI229828 has been delayed by weather conditions that were not conducive to plant growth and seed development. Seed of the IBM RILs have been distributed (approximately 5000 RILs in total) to 16 research organizations in the public and private sector. The DNA clones have been distributed (1,206 in total) to nine research labs. Further distribution of the seed and clones will be managed by curators at stock centers in the public domain. (author)

Maize kernel evolution:From teosinte to maize

Science.gov (United States)

Maize is the most productive and highest value commodity in the US and around the world: over 1 billion tons were produced each year in 2013 and 2014. Together, maize, rice and wheat comprise over 60% of the world’s caloric intake, with wide regional variability in the importance of each crop. The i...

Harnessing maize biodiversity

Science.gov (United States)

Maize is a remarkably diverse species, adapted to a wide range of climatic conditions and farming practices. The latitudinal range of maize is immense, ranging from 54°N in Alberta, Canada, to 45°S in the province of Chubut, Argentina. In terms of altitude, maize is cultivated from sea level to 4000...

Characterization of phenylpropanoid pathway genes within European maize (Zea mays L.) inbreds

DEFF Research Database (Denmark)

Andersen, Jeppe Reitan; Zein, Imad; Wenzel, Gerhard

2008-01-01

genomic fragments of six putative phenylpropanoid pathway genes in a panel of elite European inbred lines of maize (Zea mays L.) contrasting in forage quality traits. Six loci, encoding C4H, 4CL1, 4CL2, C3H, F5H, and CAD, displayed different levels of nucleotide diversity and linkage disequilibrium (LD...

Display of a Maize cDNA library on baculovirus infected insect cells

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Jones Ian M

2008-08-01

Full Text Available Abstract Background Maize is a good model system for cereal crop genetics and development because of its rich genetic heritage and well-characterized morphology. The sequencing of its genome is well advanced, and new technologies for efficient proteomic analysis are needed. Baculovirus expression systems have been used for the last twenty years to express in insect cells a wide variety of eukaryotic proteins that require complex folding or extensive posttranslational modification. More recently, baculovirus display technologies based on the expression of foreign sequences on the surface of Autographa californica (AcMNPV have been developed. We investigated the potential of a display methodology for a cDNA library of maize young seedlings. Results We constructed a full-length cDNA library of young maize etiolated seedlings in the transfer vector pAcTMVSVG. The library contained a total of 2.5 × 105 independent clones. Expression of two known maize proteins, calreticulin and auxin binding protein (ABP1, was shown by western blot analysis of protein extracts from insect cells infected with the cDNA library. Display of the two proteins in infected insect cells was shown by selective biopanning using magnetic cell sorting and demonstrated proof of concept that the baculovirus maize cDNA display library could be used to identify and isolate proteins. Conclusion The maize cDNA library constructed in this study relies on the novel technology of baculovirus display and is unique in currently published cDNA libraries. Produced to demonstrate proof of principle, it opens the way for the development of a eukaryotic in vivo display tool which would be ideally suited for rapid screening of the maize proteome for binding partners, such as proteins involved in hormone regulation or defence.

Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts.

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Trofimova, Irina; Krasikova, Alla

2016-12-01

Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.

Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer

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Nicholas C. Gomez

2016-11-01

Full Text Available Chromatin regulation is critical for differentiation and disease. However, features linking the chromatin environment of stem cells with disease remain largely unknown. We explored chromatin accessibility in embryonic and multipotent stem cells and unexpectedly identified widespread chromatin accessibility at repetitive elements. Integrating genomic and biochemical approaches, we demonstrate that these sites of increased accessibility are associated with well-positioned nucleosomes marked by distinct histone modifications. Differentiation is accompanied by chromatin remodeling at repetitive elements associated with altered expression of genes in relevant developmental pathways. Remarkably, we found that the chromatin environment of Ewing sarcoma, a mesenchymally derived tumor, is shared with primary mesenchymal stem cells (MSCs. Accessibility at repetitive elements in MSCs offers a permissive environment that is exploited by the critical oncogene responsible for this cancer. Our data demonstrate that stem cells harbor a unique chromatin landscape characterized by accessibility at repetitive elements, a feature associated with differentiation and oncogenesis.

Isolation, structural analysis, and expression characteristics of the maize nuclear factor Y gene families

International Nuclear Information System (INIS)

Zhang, Zhongbao; Li, Xianglong; Zhang, Chun; Zou, Huawen; Wu, Zhongyi

2016-01-01

NUCLEAR FACTOR-Y (NF-Y) has been shown to play an important role in growth, development, and response to environmental stress. A NF-Y complex, which consists of three subunits, NF-YA, NF-YB, and, NF-YC, binds to CCAAT sequences in a promoter to control the expression of target genes. Although NF-Y proteins have been reported in Arabidopsis and rice, a comprehensive and systematic analysis of ZmNF-Y genes has not yet been performed. To examine the functions of ZmNF-Y genes in this family, we isolated and characterized 50 ZmNF-Y (14 ZmNF-YA, 18 ZmNF-YB, and 18 ZmNF-YC) genes in an analysis of the maize genome. The 50 ZmNF-Y genes were distributed on all 10 maize chromosomes, and 12 paralogs were identified. Multiple alignments showed that maize ZmNF-Y family proteins had conserved regions and relatively variable N-terminal or C-terminal domains. The comparative syntenic map illustrated 40 paralogous NF-Y gene pairs among the 10 maize chromosomes. Microarray data showed that the ZmNF-Y genes had tissue-specific expression patterns in various maize developmental stages and in response to biotic and abiotic stresses. The results suggested that ZmNF-YB2, 4, 8, 10, 13, and 16 and ZmNF-YC6, 8, and 15 were induced, while ZmNF-YA1, 3, 4, 6, 7, 10, 12, and 13, ZmNF-YB15, and ZmNF-YC3 and 9 were suppressed by drought stress. ZmNF-YA3, ZmNF-YA8 and ZmNF-YA12 were upregulated after infection by the three pathogens, while ZmNF-YA1 and ZmNF-YB2 were suppressed. These results indicate that the ZmNF-Ys may have significant roles in the response to abiotic and biotic stresses. - Highlights: • We indicated a total of 50 members of ZmNF-Y gene family in maize genome. • We analyzed gene structure, protein architecture of ZmNF-Y genes. • Evolution pattern and phylogenic relationships were analyzed among 50 ZmNF-Y genes. • Expression pattern of ZmNF-Ys were detected in various maize tissues. • Transcript levels of ZmNF-Ys were measured under various abiotic and biotic stresses.

V-SINEs: A New Superfamily of Vertebrate SINEs That Are Widespread in Vertebrate Genomes and Retain a Strongly Conserved Segment within Each Repetitive Unit

Science.gov (United States)

Ogiwara, Ikuo; Miya, Masaki; Ohshima, Kazuhiko; Okada, Norihiro

2002-01-01

We have identified a new superfamily of vertebrate short interspersed repetitive elements (SINEs), designated V-SINEs, that are widespread in fishes and frogs. Each V-SINE includes a central conserved domain preceded by a 5′-end tRNA-related region and followed by a potentially recombinogenic (TG)n tract, with a 3′ tail derived from the 3′ untranslated region (UTR) of the corresponding partner long interspersed repetitive element (LINE) that encodes a functional reverse transcriptase. The central domain is strongly conserved and is even found in SINEs in the lamprey genome, suggesting that V-SINEs might be ∼550 Myr old or older in view of the timing of divergence of the lamprey lineage from the bony fish lineage. The central conserved domain might have been subject to some form of positive selection. Although the contemporary 3′ tails of V-SINEs differ from one another, it is possible that the original 3′ tail might have been replaced, via recombination, by the 3′ tails of more active partner LINEs, thereby retaining retropositional activity and the ability to survive for long periods on the evolutionary time scale. It seems plausible that V-SINEs may have some function(s) that have been maintained by the coevolution of SINEs and LINEs during the evolution of vertebrates. [The sequences reported in this paper have been deposited in the DDBJ/GenBank database under accession nos. AB072981–AB073004. Supplemental figures are available online at http://www.genome.org.] PMID:11827951

Repetitive Stress Injuries

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... Safe Videos for Educators Search English Español Repetitive Stress Injuries KidsHealth / For Teens / Repetitive Stress Injuries What's ... t had any problems since. What Are Repetitive Stress Injuries? Repetitive stress injuries (RSIs) are injuries that ...

Isolation and characterization of subgenomic DNAs encapsidated in 'single' T = 1 isometric particles of Maize streak virus

International Nuclear Information System (INIS)

Casado, Carolina G.; Javier Ortiz, G.; Padron, Eric; Bean, Samantha J.; McKenna, Robert; Agbandje-McKenna, Mavis; Boulton, Margaret I.

2004-01-01

'Single' T = 1 isometric particles of Maize streak virus (MSV) have been isolated from infected maize leaves. Biochemical and genetic characterizations show that these particles contain subgenomic (sg) MSV DNA encapsidated by the MSV coat protein. The largest sg DNA is 1.56 kb, slightly larger than half genome size, although sg DNAs as small as 0.2 kb were also cloned. The sg DNAs are not infectious, and they do not appear to play a role in the pathogenicity of MSV. This is the first report of sg DNAs for MSV and, to our knowledge, the first time that encapsidated sg DNAs have been characterized at the sequence level for any geminivirus. These data will assist in our investigations into the role of genomic DNA in the formation of the unique geminate capsid architecture of the Geminiviridae

Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias.

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Li, Lin; Briskine, Roman; Schaefer, Robert; Schnable, Patrick S; Myers, Chad L; Flagel, Lex E; Springer, Nathan M; Muehlbauer, Gary J

2016-11-04

Gene duplication is prevalent in many species and can result in coding and regulatory divergence. Gene duplications can be classified as whole genome duplication (WGD), tandem and inserted (non-syntenic). In maize, WGD resulted in the subgenomes maize1 and maize2, of which maize1 is considered the dominant subgenome. However, the landscape of co-expression network divergence of duplicate genes in maize is still largely uncharacterized. To address the consequence of gene duplication on co-expression network divergence, we developed a gene co-expression network from RNA-seq data derived from 64 different tissues/stages of the maize reference inbred-B73. WGD, tandem and inserted gene duplications exhibited distinct regulatory divergence. Inserted duplicate genes were more likely to be singletons in the co-expression networks, while WGD duplicate genes were likely to be co-expressed with other genes. Tandem duplicate genes were enriched in the co-expression pattern where co-expressed genes were nearly identical for the duplicates in the network. Older gene duplications exhibit more extensive co-expression variation than younger duplications. Overall, non-syntenic genes primarily from inserted duplications show more co-expression divergence. Also, such enlarged co-expression divergence is significantly related to duplication age. Moreover, subgenome dominance was not observed in the co-expression networks - maize1 and maize2 exhibit similar levels of intra subgenome correlations. Intriguingly, the level of inter subgenome co-expression was similar to the level of intra subgenome correlations, and genes from specific subgenomes were not likely to be the enriched in co-expression network modules and the hub genes were not predominantly from any specific subgenomes in maize. Our work provides a comprehensive analysis of maize co-expression network divergence for three different types of gene duplications and identifies potential relationships between duplication types

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

Science.gov (United States)

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).

Science.gov (United States)

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.

Biological and molecular characterization of a putative new sobemovirus infecting Imperata cylindrica and maize in Africa.

Science.gov (United States)

Sérémé, Drissa; Lacombe, Séverine; Konaté, Moumouni; Pinel-Galzi, Agnès; Traoré, Valentin Stanislas Edgar; Hébrard, Eugénie; Traoré, Oumar; Brugidou, Christophe; Fargette, Denis; Konaté, Gnissa

2008-01-01

A new virus was isolated from both the grass Imperata cylindrica and maize plants that had yellow mottle symptoms in Burkina Faso, West Africa. The virus has isometric particles ca. 32 nm in diameter. The experimental host range was restricted to Rottboellia exaltata. Virions were isolated from leaves of systemically infected maize plants. Koch's postulates were completed by mechanically inoculating uninfected Imperata or maize with either purified virus or sap from infected Imperata plants. Virion preparations were used to produce a specific polyclonal antiserum, and an enzyme-linked immunosorbent assay test was set up. The full genome of the virus was sequenced, and it comprised 4,547 nucleotides. Phylogenetic studies indicated that the virus is closely related to rice yellow mottle virus, a sobemovirus that infects monocotyledons in Africa, and is more distantly related to cocksfoot mottle virus, another sobemovirus that infects monocotyledons. Although the virus can infect R. exaltata experimentally, it differs from Rottboellia yellow mottle virus, a member of a tentative species of the genus Sobemovirus that also infects monocotyledons in Africa. Particle morphology, serological properties, genomic organization, and phylogenetic analysis are all consistent with assignment of the new virus to the genus Sobemovirus. The name Imperata yellow mottle virus is proposed.

The Salmon Smai Family of Short Interspersed Repetitive Elements (Sines): Interspecific and Intraspecific Variation of the Insertion of Sines in the Genomes of Chum and Pink Salmon

OpenAIRE

Takasaki, N.; Yamaki, T.; Hamada, M.; Park, L.; Okada, N.

1997-01-01

The genomes of chum salmon and pink salmon contain a family of short interspersed repetitive elements (SINEs), designated the salmon SmaI family. It is restricted to these two species, a distribution that suggests that this SINE family might have been generated in their common ancestor. When insertions of the SmaI SINEs at 10 orthologous loci of these species were analyzed, however, it was found that there were no shared insertion sites between chum and pink salmon. Furthermore, at six loci w...

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii

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Pieter De Maayer

2017-09-01

Full Text Available Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart’s wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii.

Science.gov (United States)

De Maayer, Pieter; Aliyu, Habibu; Vikram, Surendra; Blom, Jochen; Duffy, Brion; Cowan, Don A; Smits, Theo H M; Venter, Stephanus N; Coutinho, Teresa A

2017-01-01

Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart's wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes , has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis . While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.

Cercospora zeina from Maize in South Africa Exhibits High Genetic Diversity and Lack of Regional Population Differentiation.

Science.gov (United States)

Muller, Mischa F; Barnes, Irene; Kunene, Ncobile T; Crampton, Bridget G; Bluhm, Burton H; Phillips, Sonia M; Olivier, Nicholas A; Berger, Dave K

2016-10-01

South Africa is one of the leading maize-producing countries in sub-Saharan Africa. Since the 1980s, Cercospora zeina, a causal agent of gray leaf spot of maize, has become endemic in South Africa, and is responsible for substantial yield reductions. To assess genetic diversity and population structure of C. zeina in South Africa, 369 isolates were collected from commercial maize farms in three provinces (KwaZulu-Natal, Mpumalanga, and North West). These isolates were evaluated with 14 microsatellite markers and species-specific mating type markers that were designed from draft genome sequences of C. zeina isolates from Africa (CMW 25467) and the United States (USPA-4). Sixty alleles were identified across 14 loci, and gene diversity values within each province ranged from 0.18 to 0.35. High levels of gene flow were observed (Nm = 5.51), and in a few cases, identical multilocus haplotypes were found in different provinces. Overall, 242 unique multilocus haplotypes were identified with a low clonal fraction of 34%. No distinct population clusters were identified using STRUCTURE, principal coordinate analysis, or Weir's theta θ statistic. The lack of population differentiation was supported by analysis of molecular variance tests, which indicated that only 2% of the variation was attributed to variability between populations from each province. Mating type ratios of MAT1-1 and MAT1-2 idiomorphs from 335 isolates were not significantly different from a 1:1 ratio in all provinces, which provided evidence for sexual reproduction. The draft genome of C. zeina CMW 25467 exhibited a complete genomic copy of the MAT1-1 idiomorph as well as exonic fragments of MAT genes from both idiomorphs. The high level of gene diversity, shared haplotypes at different geographical locations within South Africa, and presence of both MAT idiomorphs at all sites indicates widespread dispersal of C. zeina between maize fields in the country as well as evidence for sexual recombination. The

Meiotic transmission of an in vitro-assembled autonomous maize minichromosome.

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Shawn R Carlson

2007-10-01

Full Text Available Autonomous chromosomes are generated in yeast (yeast artificial chromosomes and human fibrosarcoma cells (human artificial chromosomes by introducing purified DNA fragments that nucleate a kinetochore, replicate, and segregate to daughter cells. These autonomous minichromosomes are convenient for manipulating and delivering DNA segments containing multiple genes. In contrast, commercial production of transgenic crops relies on methods that integrate one or a few genes into host chromosomes; extensive screening to identify insertions with the desired expression level, copy number, structure, and genomic location; and long breeding programs to produce varieties that carry multiple transgenes. As a step toward improving transgenic crop production, we report the development of autonomous maize minichromosomes (MMCs. We constructed circular MMCs by combining DsRed and nptII marker genes with 7-190 kb of genomic maize DNA fragments containing satellites, retroelements, and/or other repeats commonly found in centromeres and using particle bombardment to deliver these constructs into embryogenic maize tissue. We selected transformed cells, regenerated plants, and propagated their progeny for multiple generations in the absence of selection. Fluorescent in situ hybridization and segregation analysis demonstrated that autonomous MMCs can be mitotically and meiotically maintained. The MMC described here showed meiotic segregation ratios approaching Mendelian inheritance: 93% transmission as a disome (100% expected, 39% transmission as a monosome crossed to wild type (50% expected, and 59% transmission in self crosses (75% expected. The fluorescent DsRed reporter gene on the MMC was expressed through four generations, and Southern blot analysis indicated the encoded genes were intact. This novel approach for plant transformation can facilitate crop biotechnology by (i combining several trait genes on a single DNA fragment, (ii arranging genes in a defined

Effects of biochar application on morphological traits in maize and soybean

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Šeremešić Srđan I.

2015-01-01

Full Text Available This paper analyses the effects of the biochar application morphologi­cal traits in maize and soybean under semi-controlled conditions. During the study, the in­creasing doses of biochar (0%, 0.5%, 1, 3, and 5% were incorporated in three soil types: Alluvium, Humogley and Chernozem to determine plant height and shoot weight. The ex­periment was set up as fully randomized design with three repetitions. The plants were grown in pots of 5 l with controlled watering and N fertilization. The research results have shown that there are differences in terms of biochar effects on soils. The greatest effect on plant height and shoot weight was obtained when the biochar was applied to Humogley soil and lower effects were found on the Alluvium soil. The increase in aboveground mass of maize and soybeans was significantly conditioned by adding different doses of biochar. Based on these results, it can be concluded that adding biochar can significantly affect the growth of plants. This is a consequence of the changes it causes in soil, which requires further tests to complement the current findings. [Projekat Ministarstva nauke Republike Srbije, br. TR031072 i br. TR031073

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.

Assessment of maize stem borer damage on hybrid maize varieties in Chitwan, Nepal

OpenAIRE

Buddhi Bahadur Achhami; Santa Bahadur BK; Ghana Shyam Bhandari

2015-01-01

Maize is the second most important cereal crop in Nepal. However, national figure of grain production still remains below than the world's average grain production per unit area. Thus, this experiment was designed to determine the suitable time of maize planting, and to assess the peak period of one of the major insects, maize stem borer, in Chitwan condition. The results showed that plant damage percentage as per the maize planting month varies significantly, and the average plant damage per...

Risk Adjusted Production Efficiency of Maize Farmers in Ethiopia: Implication for Improved Maize Varieties Adoption

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Sisay Diriba Lemessa

2017-09-01

Full Text Available This study analyzes the technical efficiency and production risk of 862 maize farmers in major maize producing regions of Ethiopia. It employs the stochastic frontier approach (SFA to estimate the level of technical efficiencies of stallholder farmers. The stochastic frontier approach (SFA uses flexible risk properties to account for production risk. Thus, maize production variability is assessed from two perspectives, the production risk and the technical efficiency. The study also attempts to determine the socio-economic and farm characteristics that influence technical efficiency of maize production in the study area. The findings of the study showed the existence of both production risk and technical inefficiency in maize production process. Input variables (amounts per hectare such as fertilizer and labor positively influence maize output. The findings also show that farms in the study area exhibit decreasing returns to scale. Fertilizer and ox plough days reduce output risk while labor and improved seed increase output risk. The mean technical efficiency for maize farms is 48 percent. This study concludes that production risk and technical inefficiency prevents the maize farmers from realizing their frontier output. The best factors that improve the efficiency of the maize farmers in the study area include: frequency of extension contact, access to credit and use of intercropping. It was also realized that altitude and terracing in maize farms had influence on farmer efficiency.

High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth.

Science.gov (United States)

Zhang, Xuehai; Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Xiong, Lizhong; Yang, Wanneng; Yan, Jianbing

2017-03-01

With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize ( Zea mays ) recombinant inbred line population ( n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. © 2017 American Society of Plant Biologists. All Rights Reserved.

Dissecting grain yield pathways and their interactions with grain dry matter content by a two-step correlation approach with maize seedling transcriptome

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Melchinger Albrecht E

2010-04-01

Full Text Available Abstract Background The importance of maize for human and animal nutrition, but also as a source for bio-energy is rapidly increasing. Maize yield is a quantitative trait controlled by many genes with small effects, spread throughout the genome. The precise location of the genes and the identity of the gene networks underlying maize grain yield is unknown. The objective of our study was to contribute to the knowledge of these genes and gene networks by transcription profiling with microarrays. Results We assessed the grain yield and grain dry matter content (an indicator for early maturity of 98 maize hybrids in multi-environment field trials. The gene expression in seedlings of the parental inbred lines, which have four different genetic backgrounds, was assessed with genome-scale oligonucleotide arrays. We identified genes associated with grain yield and grain dry matter content using a newly developed two-step correlation approach and found overlapping gene networks for both traits. The underlying metabolic pathways and biological processes were elucidated. Genes involved in sucrose degradation and glycolysis, as well as genes involved in cell expansion and endocycle were found to be associated with grain yield. Conclusions Our results indicate that the capability of providing energy and substrates, as well as expanding the cell at the seedling stage, highly influences the grain yield of hybrids. Knowledge of these genes underlying grain yield in maize can contribute to the development of new high yielding varieties.

Predicting chromosomal locations of genetically mapped loci in maize using the Morgan2McClintock Translator.

Science.gov (United States)

Lawrence, Carolyn J; Seigfried, Trent E; Bass, Hank W; Anderson, Lorinda K

2006-03-01

The Morgan2McClintock Translator permits prediction of meiotic pachytene chromosome map positions from recombination-based linkage data using recombination nodule frequency distributions. Its outputs permit estimation of DNA content between mapped loci and help to create an integrated overview of the maize nuclear genome structure.

Comparative genomics reveals insights into avian genome evolution and adaptation

Science.gov (United States)

Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

2015-01-01

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

Polymorphisms in O-methyltransferase genes are associated with stover cell wall digestibility in European maize (Zea mays L.)

DEFF Research Database (Denmark)

Brenner, Everton A; Zein, Imad; Chen, Yongsheng

2010-01-01

Background OMT (O-methyltransferase) genes are involved in lignin biosynthesis, which relates to stover cell wall digestibility. Reduced lignin content is an important determinant of both forage quality and ethanol conversion efficiency of maize stover. Results Variation in genomic sequences codi...

The genome of Arabidopsis thaliana.

OpenAIRE

Goodman, H M; Ecker, J R; Dean, C

1995-01-01

Arabidopsis thaliana is a small flowering plant that is a member of the family cruciferae. It has many characteristics--diploid genetics, rapid growth cycle, relatively low repetitive DNA content, and small genome size--that recommend it as the model for a plant genome project. The current status of the genetic and physical maps, as well as efforts to sequence the genome, are presented. Examples are given of genes isolated by using map-based cloning. The importance of the Arabidopsis project ...

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.

Functional genomics strategies with transposons in rice

NARCIS (Netherlands)

Greco, R.

2003-01-01

Rice is a major staple food crop and a recognizedmonocotylenedousmodel plant from which gene function discovery is projected to contribute to improvements in a variety of cereals like wheat and maize. The recent release of rough drafts of the rice genome sequence for public

Screening of promising maize genotypes against maize weevil (Sitophilus zeamais Motschulky) in storage condition

OpenAIRE

Ram B Paneru; Resham B Thapa

2017-01-01

The maize weevil (Sitophilus zeamais Motschulsky) is a serious pest of economic importance in stored grains. It causes major damage to stored maize grain thereby reducing its weight, quality and germination. An experiment was conducted in randomized complete block design (RCBD) with 3 replications to screen 32 maize genotypes against maize weevil in no-choice and free-choice conditions at Entomology Division, Khumaltar, Lalitpur (Room temperature: Maximum 24-32°C and Minimum 18-27°C). The fin...

Exploring karyotype diversity of Argentinian Guaraní maize landraces: Relationship among South American maize.

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María Florencia Realini

Full Text Available In Argentina there are two different centers of maize diversity, the Northeastern (NEA and the Northwestern (NWA regions of the country. In NEA, morphological studies identified 15 landraces cultivated by the Guaraní communities in Misiones Province. In the present study we analyzed the karyotype diversity of 20 populations of Guaraní maize landraces through classical and molecular cytogenetic analyses. Our results demonstrate significant intra and inter-populational variation in the percentage, number, size, chromosome position and frequencies of the heterochromatic blocks, which are called knobs. Knob sequence analysis (180-bp and TR-1 did not show significant differences among Guaraní populations. B chromosomes were not detected, and abnormal 10 (AB10 chromosomes were found with low frequency (0.1≥f ≤0.40 in six populations. Our results allowed karyotypic characterization of each analyzed population, defining for the first time the chromosomal constitution of maize germplasm from NEA. The multivariate analysis (PCoA and UPGMA of karyotype parameters allowed the distinction between two populations groups: the Popcorn and the Floury maize populations. These results are in agreement with previously published microsatellite and morphological/phenological studies. Finally, we compared our karyotype results with those previously reported for NWA and Central Region of South America maize. Our data suggest that there are important differences between maize from NEA and NWA at the karyotype level, supporting the hypothesis that there are two pathways of input of South America maize. Our results also confirm the existence of two centers of diversification of Argentinian native maize, NWA and NEA. This work contributes new knowledge about maize diversity, which is relevant for future plans to improve commercial maize, and for conservation of agrobiodiversity.

Molecular genetics: Step by step implementation in maize breeding

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Konstantinov Kosana

2007-01-01

Full Text Available Efficiency in plant breeding is determined primarily by the ability to screen for genetic polymorphism, productivity and yield stability early in program. Dependent on the knowledge about the biochemical bases of the trait and nature of its genetic control, trait could be modified either through mutagenesis of genes controlling it or through the transfer of already existing mutant genes, controlling desired trait to different plant genotypes by classic crossing. Objective of this report is to present partly results on the investigation of the possibilities to apply ionizing radiations (fast neutrons, γ -rays and chemical mutagens (EI, iPMS, EMS, ENU to get maize and wheat mutants with increased amount and improved protein quality. Besides this approach in mutation breeding, results on the very early investigation of biochemical background of opaque -2 mutation including use of coupled cell - free RNA and protein synthesis containing components from both wild and opaque - 2 maize genotypes (chromatin, RNA polymerase, microsomall fraction, protein bodies will be presented. Partial results on opaque - 2 gene incorporation in different genetic background are reviewed. Part of report is dealing with different classes of molecular markers (proteins, RFLP, AFLP, RAPD, and SSR application in maize genome polymorphism investigation. Besides application of different molecular markers classes in the investigation of heterosis phenomena they are useful in biochemical pathway of important traits control determination as well. .

Mind the gap; seven reasons to close fragmented genome assemblies.

Science.gov (United States)

Thomma, Bart P H J; Seidl, Michael F; Shi-Kunne, Xiaoqian; Cook, David E; Bolton, Melvin D; van Kan, Jan A L; Faino, Luigi

2016-05-01

Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions. Copyright © 2015 Elsevier Inc. All rights reserved.

Occurrence of toxigenic fungi in maize and maize-gluten meal from Pakistan

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Muhammad Kashif SALEEMI

2012-05-01

Full Text Available The present study was designed to isolate and identify toxigenic mycoflora of maize and maize-gluten meal. A total of 82 samples of maize and 8 samples of maize-gluten meal were collected from Faisalabad district of Pakistan over a period of two years. These samples were inoculated on different culture media. Fungal contamination of maize and maize-gluten was 56% and 75% of samples, respectively. Isolation frequencies of different genera isolated from maize were Aspergillus 33%; Penicillium 28%; Fusarium 10%; and Alternaria 1%. Isolation frequency among species was maximum for P. verrucosum, followed by A. niger aggregates, A. ochraceous, A. flavus, P. chrysogenum, A. parasiticus, A. carbonarius, Fusarium spp. and Alternaria spp. Relative density of Aspergillus isolates was maximum for A. niger aggregates and A. ochraceous (30% each followed by A. flavus (26%, A. parasiticus (11% and A. carbonarius (3%. Percentage of toxigenic fungi among Aspergillus isolates was 52%. Aflatoxigenic isolates of A. flavus and A. parasiticus were 43 and 67% and ochratoxigenic isolates of A. carbonarius, A. ochraceous and A. niger aggregates were 100, 63 and 38%, respectively. Aspergillus parasiticus produced higher concentrations of AFB1 (maximum 1374.23 ng g-1 than A. flavus (maximum 635.50 ng g-1. Ochratoxin A production potential of A. ochraceous ranged from 1.81 to 9523.1 ng g-1, while in A. niger aggregates it was 1.30 to 1758.6 ng g-1. Isolation frequencies of fungal genera from maize-gluten meal were Aspergillus (63% and Penicillium (50%. A. flavus was the most frequently isolated species. Percentage of toxigenic fungi among Aspergillus isolates was 40%. Aflatoxigenic isolates of A. flavus were 33% and ochratoxigenic isolates of A. ochraceous were 100%.

Global maize production, utilization, and consumption.

Science.gov (United States)

Ranum, Peter; Peña-Rosas, Juan Pablo; Garcia-Casal, Maria Nieves

2014-04-01

Maize (Zea mays), also called corn, is believed to have originated in central Mexico 7000 years ago from a wild grass, and Native Americans transformed maize into a better source of food. Maize contains approximately 72% starch, 10% protein, and 4% fat, supplying an energy density of 365 Kcal/100 g and is grown throughout the world, with the United States, China, and Brazil being the top three maize-producing countries in the world, producing approximately 563 of the 717 million metric tons/year. Maize can be processed into a variety of food and industrial products, including starch, sweeteners, oil, beverages, glue, industrial alcohol, and fuel ethanol. In the last 10 years, the use of maize for fuel production significantly increased, accounting for approximately 40% of the maize production in the United States. As the ethanol industry absorbs a larger share of the maize crop, higher prices for maize will intensify demand competition and could affect maize prices for animal and human consumption. Low production costs, along with the high consumption of maize flour and cornmeal, especially where micronutrient deficiencies are common public health problems, make this food staple an ideal food vehicle for fortification. © 2014 New York Academy of Sciences. The World Health Organization retains copyright and all other rights in the manuscript of this article as submitted for publication.

Breeding of speciality maize for industrial purposes

OpenAIRE

Pajić Zorica; Radosavljević Milica; Filipović Milomir; Todorović Goran; Srdić Jelena; Pavlov Milovan

2010-01-01

The breeding programme on speciality maize with specific traits was established at the Maize Research Institute, Zemun Polje, several decades ago. The initial material was collected, new methods applying to breeding of speciality maize, i.e. popping maize, sweet maize and white-seeded maize, were introduced. The aim was to enhance and improve variability of the initial material for breeding these three types of maize. Then, inbred lines of good combining abilities were developed and used as c...

Aflatoxin levels in maize and maize products during the 2004 food ...

African Journals Online (AJOL)

Aflatoxin levels in maize and maize products during the 2004 food poisoning ... district were received at the National Public Health Laboratory Services (NPHLS). On analysis, they were found to be highly contaminated with aflatoxin B1.

Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

Energy Technology Data Exchange (ETDEWEB)

Schulman, Al

2009-08-09

Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

A chromosome conformation capture ordered sequence of the barley genome

Czech Academy of Sciences Publication Activity Database

Mascher, M.; Gundlach, H.; Himmelbach, A.; Beier, S.; Twardziok, S. O.; Wicker, T.; Šimková, Hana; Staňková, Helena; Vrána, Jan; Chan, S.; Munoz-Amatrian, M.; Houben, A.; Doležel, Jaroslav; Ayling, S.; Lonardi, S.; Mayer, K.F.X.; Zhang, G.; Braumann, I.; Spannagl, M.; Li, C.; Waugh, R.; Stein, N.

2017-01-01

Roč. 544, č. 7651 (2017), s. 427-433 ISSN 0028-0836 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : bacterial artificial chromosomes * inverted-repeat elements * complex-plant genomes * hi-c * environmental adaptation * ltr retrotransposons * structural variation * maize genome * software * database Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 40.137, year: 2016

Newly discovered young CORE-SINEs in marsupial genomes.

Science.gov (United States)

Munemasa, Maruo; Nikaido, Masato; Nishihara, Hidenori; Donnellan, Stephen; Austin, Christopher C; Okada, Norihiro

2008-01-15

Although recent mammalian genome projects have uncovered a large part of genomic component of various groups, several repetitive sequences still remain to be characterized and classified for particular groups. The short interspersed repetitive elements (SINEs) distributed among marsupial genomes are one example. We have identified and characterized two new SINEs from marsupial genomes that belong to the CORE-SINE family, characterized by a highly conserved "CORE" domain. PCR and genomic dot blot analyses revealed that the distribution of each SINE shows distinct patterns among the marsupial genomes, implying different timing of their retroposition during the evolution of marsupials. The members of Mar3 (Marsupialia 3) SINE are distributed throughout the genomes of all marsupials, whereas the Mac1 (Macropodoidea 1) SINE is distributed specifically in the genomes of kangaroos. Sequence alignment of the Mar3 SINEs revealed that they can be further divided into four subgroups, each of which has diagnostic nucleotides. The insertion patterns of each SINE at particular genomic loci, together with the distribution patterns of each SINE, suggest that the Mar3 SINEs have intensively amplified after the radiation of diprotodontians, whereas the Mac1 SINE has amplified only slightly after the divergence of hypsiprimnodons from other macropods. By compiling the information of CORE-SINEs characterized to date, we propose a comprehensive picture of how SINE evolution occurred in the genomes of marsupials.

Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus

Czech Academy of Sciences Publication Activity Database

Vu, G.T.H.; Schmutzer, T.; Bull, F.; Cao, H.X.; Fuchs, J.; Tran, T.D.; Jovtchev, G.; Pistrick, K.; Stein, N.; Pečinka, A.; Neumann, Pavel; Novák, Petr; Macas, Jiří; Dear, P.H.; Blattner, F.R.; Scholz, U.; Schubert, I.

2015-01-01

Roč. 8, č. 3 (2015) ISSN 1940-3372 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : Genlisea * genome * repetitive sequences Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.509, year: 2015

Comparative Analysis of Repetitive DNA between the Main Vectors of Chagas Disease: Triatoma infestans and Rhodnius prolixus.

Science.gov (United States)

Pita, Sebastián; Mora, Pablo; Vela, Jesús; Palomeque, Teresa; Sánchez, Antonio; Panzera, Francisco; Lorite, Pedro

2018-04-24

Chagas disease or American trypanosomiasis affects six to seven million people worldwide, mostly in Latin America. This disease is transmitted by hematophagous insects known as "kissing bugs" (Hemiptera, Triatominae), with Triatoma infestans and Rhodnius prolixus being the two most important vector species. Despite the fact that both species present the same diploid chromosome number (2 n = 22), they have remarkable differences in their total DNA content, chromosome structure and genome organization. Variations in the DNA genome size are expected to be due to differences in the amount of repetitive DNA sequences. The T. infestans genome-wide analysis revealed the existence of 42 satellite DNA families. BLAST searches of these sequences against the R. prolixus genome assembly revealed that only four of these satellite DNA families are shared between both species, suggesting a great differentiation between the Triatoma and Rhodnius genomes. Fluorescence in situ hybridization (FISH) location of these repetitive DNAs in both species showed that they are dispersed on the euchromatic regions of all autosomes and the X chromosome. Regarding the Y chromosome, these common satellite DNAs are absent in T. infestans but they are present in the R. prolixus Y chromosome. These results support a different origin and/or evolution in the Y chromosome of both species.

Discovering Complete Quasispecies In Bacterial Genomes

OpenAIRE

Bertels, Frederic; Gokhale, Chaitanya; Traulsen, Arne

2017-01-01

Mobile genetic elements can be found in almost all genomes. Possibly the most common nonautonomous mobile genetic elements in bacteria are repetitive extragenic palindromic doublets forming hairpins (REPINs) that can occur hundreds of times within a genome. The sum of all REPINs in a genome can be viewed as an evolving population because REPINs replicate and mutate. In contrast to most other biological populations, we know the exact composition of the REPIN population and the sequence of each...

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

Directory of Open Access Journals (Sweden)

Graner Andreas

2008-10-01

Full Text Available Abstract Background Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR index can be generated to map repetitive regions in genomic sequences. Results We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised. Conclusion An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences regions in uncharacterised genomic sequences. The restriction that a particular

Screening of promising maize genotypes against maize weevil (Sitophilus zeamais Motschulky in storage condition

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Ram B Paneru

2017-12-01

Full Text Available The maize weevil (Sitophilus zeamais Motschulsky is a serious pest of economic importance in stored grains. It causes major damage to stored maize grain thereby reducing its weight, quality and germination. An experiment was conducted in randomized complete block design (RCBD with 3 replications to screen 32 maize genotypes against maize weevil in no-choice and free-choice conditions at Entomology Division, Khumaltar, Lalitpur (Room temperature: Maximum 24-32°C and Minimum 18-27°C. The findings showed that the maize genotypes had different response to maize weevil damage ranging from susceptible to tolerance. The genotypes Manakamana-3, Lumle White POP Corn and Ganesh-2 showed their tolerance to S. zeamais as evidenced by lower number of weevil emerged/attracted, lower amount of grain debris release and lower proportion of bored grains, while the genotype ZM-627 was the most susceptible to weevil damage in both tests. The other remaining genotypes were intermediate types. This information is useful to improve grain protection in storage and varietal improvement/release program.

Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus.

Science.gov (United States)

Sanford, J; Forrester, L; Chapman, V; Chandley, A; Hastie, N

1984-03-26

The major and the minor satellite sequences of Mus musculus were undermethylated in both sperm and oocyte DNAs relative to the amount of undermethylation observed in adult somatic tissue DNA. This hypomethylation was specific for satellite sequences in sperm DNA. Dispersed repetitive and low copy sequences show a high degree of methylation in sperm DNA; however, a dispersed repetitive sequence was undermethylated in oocyte DNA. This finding suggests a difference in the amount of total genomic DNA methylation between sperm and oocyte DNA. The methylation levels of the minor satellite sequences did not change during spermiogenesis, and were not associated with the onset of meiosis or a specific stage in sperm development.

High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth1[OPEN

Science.gov (United States)

Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Yang, Wanneng

2017-01-01

With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. PMID:28153923

Rhipicephalus microplus strain Deutsch, whole genome shotgun sequencing project Version 2

Science.gov (United States)

The cattle tick, Rhipicephalus (Boophilus) microplus, has a genome over 2.4 times the size of the human genome, and with over 70% of repetitive DNA, this genome would prove very costly to sequence at today's prices and difficult to assemble and analyze. Cot filtration/selection techniques were used ...

Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat

Czech Academy of Sciences Publication Activity Database

Liu, M.; Stiller, J.; Holušová, Kateřina; Vrána, Jan; Liu, D.; Doležel, Jaroslav; Liu, C.

2016-01-01

Roč. 6, NOV 8 (2016), č. článku 36398. ISSN 2045-2322 R&D Projects: GA MŠk(CZ) LO1204; GA ČR GBP501/12/G090 Institutional support: RVO:61389030 Keywords : triticum-aestivum l. * fusarium crown rot * pan-genome * hexaploid wheat * bread wheat * draft genome * rna-seq * maize * transcriptome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.259, year: 2016

Experimental hybrid evaluation of maize, for the Colombian Atlantic coast; Evaluacion de hibridos experimentales de maiz para la costa Atlantica colombiana

Energy Technology Data Exchange (ETDEWEB)

Urrea, R; Navas Arboleda, A A; Mejia, S; Ospina, J G

1998-07-01

To determine the yield potential and phenotypic stability four they were evaluated hybrid experimental simple and seven commercial witness of maize in eleven towns (L), during 1995 and 1996. The used experimental design was at random of complete blocks with four repetitions with parcels of four furrows of five m of longitude, distanced 0.90 m between furrows and 0.45 among blows (49 383 plts/ha) it Differ highly significant (smaller p 0.01) they were detected among genotype (G) and for the interaction G x L in the varieties yield. The analysis of stability of Eberhart and Russell (1966) it indicated that the genotypes had similar regression values; however, a clear tendency was observed to differentiate the behavior in yield of certain materials. The hybrid one experimental there are 76 and the commercial HR 661, they showed a good stability for yield.

Consumer preferences for maize products in urban Kenya.

Science.gov (United States)

De Groote, Hugo; Kimenju, Simon Chege

2012-06-01

New maize varieties have been biofortified with provitamin A, mainly a-carotene, which renders the grain yellow or orange. Unfortunately, many African consumers prefer white maize. The maize consumption patterns in Africa are, however, not known. To determine which maize products African consumers prefer to purchase and which maize preparations they prefer to eat. A survey of 600 consumers was conducted in Nairobi, Kenya, at three types of maize outlets: posho mills (small hammer mills), kiosks, and supermarkets. Clients of posho mills had lower incomes and less education than those of kiosks and supermarkets. The preferred maize product of the posho-mill clients was artisanal maize meal; the preferred product of the others was industrial maize meal. Maize is the preferred staple for lunch and dinner, eaten as a stiff porridge (ugali), followed by boiled maize and beans (githeri), regardless of socioeconomic background. For breakfast, only half the consumers prefer maize, mostly as a soft porridge (uji). This proportion is higher in low-income groups. Consumers show a strong preference for white maize over yellow, mostly for its organoleptic characteristics, and show less interest in biofortified maize. Maize is the major food staple in Nairobi, mostly eaten in a few distinct preparations. For biofortified yellow maize to be accepted, a strong public awareness campaign to inform consumers is needed, based on a sensory evaluation and the mass media, in particular on radio in the local language.

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

Czech Academy of Sciences Publication Activity Database

Novák, Petr; Neumann, Pavel; Macas, Jiří

2010-01-01

Roč. 11, č. 1 (2010), s. 378-389 ISSN 1471-2105 R&D Projects: GA MŠk(CZ) OC10037; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50510513 Keywords : repetitive DNA * plant genome * next generation sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.028, year: 2010

Maize variety and method of production

Science.gov (United States)

Pauly, Markus; Hake, Sarah; Kraemer, Florian J

2014-05-27

The disclosure relates to a maize plant, seed, variety, and hybrid. More specifically, the disclosure relates to a maize plant containing a Cal-1 allele, whose expression results in increased cell wall-derived glucan content in the maize plant. The disclosure also relates to crossing inbreds, varieties, and hybrids containing the Cal-1 allele to produce novel types and varieties of maize plants.

Genomic characterization of large heterochromatic gaps in the human genome assembly.

Directory of Open Access Journals (Sweden)

Nicolas Altemose

2014-05-01

Full Text Available The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats, Human Satellites 2 and 3 (HSat2,3. The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithms, and as a result, the sequence composition and potential biological functions of these regions remain largely unexplored. Furthermore, existing genomic tools designed to predict consensus-based descriptions of repeat families cannot be readily applied to complex satellite repeats such as HSat2,3, which lack a consistent repeat unit reference sequence. Here we present an alignment-free method to characterize complex satellites using whole-genome shotgun read datasets. Utilizing this approach, we classify HSat2,3 sequences into fourteen subfamilies and predict their chromosomal distributions, resulting in a comprehensive satellite reference database to further enable genomic studies of heterochromatic regions. We also identify 1.3 Mb of non-repetitive sequence interspersed with HSat2,3 across 17 unmapped assembly scaffolds, including eight annotated gene predictions. Finally, we apply our satellite reference database to high-throughput sequence data from 396 males to estimate array size variation of the predominant HSat3 array on the Y chromosome, confirming that satellite array sizes can vary between individuals over an order of magnitude (7 to 98 Mb and further demonstrating that array sizes are distributed differently within distinct Y haplogroups. In summary, we present a novel framework for generating initial reference databases for unassembled genomic regions enriched with complex satellite DNA, and we further demonstrate the utility of these reference databases for studying patterns of sequence variation within human populations.

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

Science.gov (United States)

Staňková, Helena; Hastie, Alex R; Chan, Saki; Vrána, Jan; Tulpová, Zuzana; Kubaláková, Marie; Visendi, Paul; Hayashi, Satomi; Luo, Mingcheng; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

2016-07-01

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Assessment of maize stem borer damage on hybrid maize varieties in Chitwan, Nepal

Directory of Open Access Journals (Sweden)

Buddhi Bahadur Achhami

2015-12-01

Full Text Available Maize is the second most important cereal crop in Nepal. However, national figure of grain production still remains below than the world's average grain production per unit area. Thus, this experiment was designed to determine the suitable time of maize planting, and to assess the peak period of one of the major insects, maize stem borer, in Chitwan condition. The results showed that plant damage percentage as per the maize planting month varies significantly, and the average plant damage percentage by stem borer was up to 18.11%. Length of the feeding tunnel in maize stem was significantly higher in January than July. In case of exit holes made by borer counted more than four holes per plant that were planted in the month of January. All in all, except the tunnel length measurement per plant, we observed similar pattern in other borer damage parameters such as exit whole counts and plant damage percentage within the tested varieties. Stem borer damage was not significantly affect on grain yield.

The mobile genetic element Alu in the human genome

Energy Technology Data Exchange (ETDEWEB)

Novick, G.E. [Florida International Univ., Miami, FL (United States); Batzer, M.A.; Deininger, P.L. [Louisiana State Univ. Medical Center, New Orleans, LA (United States)] [and others

1996-01-01

Genetic material has been traditionally envisioned as relatively static with the exception of occasional, often deleterious mutations. The sequence DNA-to-RNA-to-protein represented for many years the central dogma relating gene structure and function. Recently, the field of molecular genetics has provided revolutionary information on the dynamic role of repetitive elements in the function of the genetic material and the evolution of humans and other organisms. Alu sequences represent the largest family of short interspersed repetitive elements (SINEs) in humans, being present in an excess of 500,000 copies per haploid genome. Alu elements, as well as the other repetitive elements, were once considered to be useless. Today, the biology of Alu transposable elements is being widely examined in order to determine the molecular basis of a growing number of identified diseases and to provide new directions in genome mapping and biomedical research. 66 refs., 5 figs.

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize.

Directory of Open Access Journals (Sweden)

Jinliang Yang

2017-09-01

Full Text Available Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD analysis and perform genomic prediction analyses in which we weigh blocks on the basis of complementation for segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding.

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize.

Science.gov (United States)

Yang, Jinliang; Mezmouk, Sofiane; Baumgarten, Andy; Buckler, Edward S; Guill, Katherine E; McMullen, Michael D; Mumm, Rita H; Ross-Ibarra, Jeffrey

2017-09-01

Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD) analysis and perform genomic prediction analyses in which we weigh blocks on the basis of complementation for segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding.

Maize cob losses and their effects on the poverty status of maize

African Journals Online (AJOL)

This study analysed fresh maize cob losses and its effect on the poverty status of maize farmers in Edo State,. Nigeria. The specific .... is the poverty gap for ... Total cost. 162,367.48. 100.00. Returns. Total expected yield (N). 327,966.63. _.

MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research

OpenAIRE

Lawrence, Carolyn J.; Harper, Lisa C.; Schaeffer, Mary L.; Sen, Taner Z.; Seigfried, Trent E.; Campbell, Darwin A.

2008-01-01

In 2001 maize became the number one production crop in the world with the Food and Agriculture Organization of the United Nations reporting over 614 million tonnes produced. Its success is due to the high productivity per acre in tandem with a wide variety of commercial uses. Not only is maize an excellent source of food, feed, and fuel, but also its by-products are used in the production of various commercial products. Maize's unparalleled success in agriculture stems from basic research, th...

Genetic resources in maize breeding

Directory of Open Access Journals (Sweden)

Anđelković Violeta

2017-01-01

Full Text Available Maize, wheat and rice are the most important cereals grown in the world. It is predicted that by 2025 maize is likely to become the crop with the greatest production globally. Conservation of maize germplasm provides the main resources for increased food and feed production. Conservation in gene banks (ex-situ is dominant strategy for maize conservation. More than 130 000 maize accessions, e.g. about 40% of total number, are stored in ten largest gene banks worldwide and Maize Research Institute Zemun Polje (MRIZP gene bank, with about 6000 accessions, is among them. Organized collecting missions started in 1961. in the former Yugoslavian territory, and up today, more than 2000 local maize landraces were stored. Pre-breeding activities that refer to identification of desirable traits from unadapted germplasm within genebank, result in materials expected to be included in breeding programs. Successful examples are LAMP, GEM and GENRES projects. At the end of XX century, at MRIZP genebank two pre-breeding activities were undertaken: eco-core and elite-core collections were created and landraces fulfilled particular criteria were chosen. In the last decade, MRIZP genebank collection was used for identification of sources for drought tolerance and improved grain quality. According to agronomic traits and general combining ability, two mini-core collections were created and included in commercial breeding programs.

Large scale analysis of small repeats via mining of the human genome

NARCIS (Netherlands)

van den Berg, I.; Bosnacki, D.; Hilbers, P.A.J.

2009-01-01

Small repetitive sequences, called tandem repeats, are abundant throughout the human genome, both in coding and in non-coding regions. Their role is still mostly unknown, but at least 20 of those repetitive sequences have been related to neurodegenerative disorders. The mutational process that is

Detection of genetically modified maize in processed foods sold commercially in iran by qualitative PCR.

Science.gov (United States)

Rabiei, Maryam; Mehdizadeh, Mehrangiz; Rastegar, Hossein; Vahidi, Hossein; Alebouyeh, Mahmoud

2013-01-01

Detection of genetically modified organisms (GMOs) in food is an important issue for all the subjects involved in food control and customer's right. Due to the increasing number of GMOs imported to Iran during the past few years, it has become necessary to screen the products in order to determine the identity of the consumed daily foodstuffs. In this study, following the extraction of genomic DNA from processed foods sold commercially in Iran, qualitative PCR was performed to detect genetically modified maize. The recombinant DNA target sequences were detected with primers highly specific for each investigated transgene such as CaMV35s gene, Bt-11, MON810 and Bt-176 separately. Based on the gel electrophoresis results, Bt- 11 and MON810 events were detected in some maize samples, while, in none of them Bt- 176 modified gene was detected. For the first time, the results demonstrate the presence of genetically modified maize in Iranian food products, reinforcing the need for the development of labeling system and valid quantitative methods in routine analyses.

Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey

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Varala Kranthi

2007-05-01

Full Text Available Abstract Background Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA. Results We sequenced 78 million base-pairs of randomly sheared soybean DNA which passed our quality criteria. Computational analysis of the survey sequences provided global information on the abundant repetitive sequences in soybean. The sequence was used to determine the copy number across regions of large genomic clones or contigs and discover higher-order structures within satellite repeats. We have created an annotated, online database of sequences present in multiple copies in the soybean genome. The low bias of pyrosequencing against repeat sequences is demonstrated by the overall composition of the survey data, which matches well with past estimates of repetitive DNA content obtained by DNA re-association kinetics (Cot analysis. Conclusion This approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. In addition, we show that partial sequencing can provide access to partial protein-coding sequences.

Maize lethal necrosis (MLN), an emerging threat to maize-based food security in sub-Saharan Africa

Science.gov (United States)

In sub-Saharan Africa, maize is a staple food and key determinant of food security for smallholder farming communities. Pest and disease outbreaks are key constraints to maize productivity. In September 2011, a serious disease outbreak, later diagnosed as maize lethal necrosis (MLN), was reported on...

Functional mechanisms of drought tolerance in subtropical maize (Zea mays L.) identified using genome-wide association mapping.

Science.gov (United States)

Thirunavukkarasu, Nepolean; Hossain, Firoz; Arora, Kanika; Sharma, Rinku; Shiriga, Kaliyugam; Mittal, Swati; Mohan, Sweta; Namratha, Pottekatt Mohanlal; Dogga, Sreelatha; Rani, Tikka Shobha; Katragadda, Sumalini; Rathore, Abhishek; Shah, Trushar; Mohapatra, Trilochan; Gupta, Hari Shankar

2014-12-24

Earlier studies were focused on the genetics of temperate and tropical maize under drought. We identified genetic loci and their association with functional mechanisms in 240 accessions of subtropical maize using a high-density marker set under water stress. Out of 61 significant SNPs (11 were false-discovery-rate-corrected associations), identified across agronomic traits, models, and locations by subjecting the accessions to water stress at flowering stage, 48% were associated with drought-tolerant genes. Maize gene models revealed that SNPs mapped for agronomic traits were in fact associated with number of functional traits as follows: stomatal closure, 28; flowering, 15; root development, 5; detoxification, 4; and reduced water potential, 2. Interactions of these SNPS through the functional traits could lead to drought tolerance. The SNPs associated with ABA-dependent signalling pathways played a major role in the plant's response to stress by regulating a series of functions including flowering, root development, auxin metabolism, guard cell functions, and scavenging reactive oxygen species (ROS). ABA signalling genes regulate flowering through epigenetic changes in stress-responsive genes. ROS generated by ABA signalling are reduced by the interplay between ethylene, ABA, and detoxification signalling transductions. Integration of ABA-signalling genes with auxin-inducible genes regulates root development which in turn, maintains the water balance by regulating electrochemical gradient in plant. Several genes are directly or indirectly involved in the functioning of agronomic traits related to water stress. Genes involved in these crucial biological functions interacted significantly in order to maintain the primary as well as exclusive functions related to coping with water stress. SNPs associated with drought-tolerant genes involved in strategic biological functions will be useful to understand the mechanisms of drought tolerance in subtropical maize.

RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize

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Ren, Wen; Yang, Fengling; He, Hang; Zhao, Jiuran

2015-01-01

The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signal transduction pathway that is involved in plant development and stress responses. As the first component of this phosphorelay cascade, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascade to promote the appropriate cellular responses; however, the functions of MAPKKKs in maize are unclear. Here, we identified 71 MAPKKK genes, of which 14 were novel, based on a computational analysis of the maize (Zea mays L.) genome. Using an RNA-seq analysis in the leaf, stem and root of maize under well-watered and drought-stress conditions, we identified 5,866 differentially expressed genes (DEGs), including 8 MAPKKK genes responsive to drought stress. Many of the DEGs were enriched in processes such as drought stress, abiotic stimulus, oxidation-reduction, and metabolic processes. The other way round, DEGs involved in processes such as oxidation, photosynthesis, and starch, proline, ethylene, and salicylic acid metabolism were clearly co-expressed with the MAPKKK genes. Furthermore, a quantitative real-time PCR (qRT-PCR) analysis was performed to assess the relative expression levels of MAPKKKs. Correlation analysis revealed that there was a significant correlation between expression levels of two MAPKKKs and relative biomass responsive to drought in 8 inbred lines. Our results indicate that MAPKKKs may have important regulatory functions in drought tolerance in maize. PMID:26599013

Analysis of stability and adaptability of QPM hybrids of maize growing in different Colombian agroecological zones

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Ever Andrés vargas Escobar

2016-01-01

Full Text Available Energy is maize´s biggest contribution for humans and animals. Scientist have been trying to increase its protein level since 1896, it wasn´t until the 60´s when the opaque gene O2 was discovered. In its recessive state, the gene causes the quality of the maize protein to increase, due to the growth of the Globulin protein and the reduction of Zein protein. Known as Quality Protein Maize (QPM, they can double the essential amino acids Lysine and Tryptophan´s percentages when compared with normal maize endosperm. In a commercial scenario, there is a need for high yielding genotypes adapted to different environments; it is also desirable to have a better protein quality. In the present study, 9 yellow endosperm QPM hybrids, developed by FENALCE from CIMMYT´s germoplasm and a normal commercial endosperm check were tested in 6 agro ecological zones: Wet Caribbean, Dry Caribbean, Orinoco, Valley of the Cauca River, Valley of the Magdalena River and the Coffee Growing Zone. A randomized complete block design was used in 17 environments and four repetitions. Variables concerning the plant and yield components were measured, but for this study the grain yield was the only taken. Additionally samples were taken to assess the content of Tryptophan. The stability and adaptability analysis was made using the Eberhart and Russell, Lin and Binns and AMMI models. The QPM hybrid that stood out for all the environments was QPM 303 and QPM 305 for unfavorable environments. Both retain their biochemical characteristics of protein quality and are stable in the evaluated environments according to the statistical models that were used.

Genomic Characterization for Parasitic Weeds of the Genus Striga by Sample Sequence Analysis

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Matt C. Estep

2012-03-01

Full Text Available Generation of ∼2200 Sanger sequence reads or ∼10,000 454 reads for seven Lour. DNA samples (five species allowed identification of the highly repetitive DNA content in these genomes. The 14 most abundant repeats in these species were identified and partially assembled. Annotation indicated that they represent nine long terminal repeat (LTR retrotransposon families, three tandem satellite repeats, one long interspersed element (LINE retroelement, and one DNA transposon. All of these repeats are most closely related to repetitive elements in other closely related plants and are not products of horizontal transfer from their host species. These repeats were differentially abundant in each species, with the LTR retrotransposons and satellite repeats most responsible for variation in genome size. Each species had some repetitive elements that were more abundant and some less abundant than the other species examined, indicating that no single element or any unilateral growth or decrease trend in genome behavior was responsible for variation in genome size and composition. Genome sizes were determined by flow sorting, and the values of 615 Mb [ (L. Kuntze], 1330 Mb [ (Willd. Vatke], 1425 Mb [ (Delile Benth.] and 2460 Mb ( Benth. suggest a ploidy series, a prediction supported by repetitive DNA sequence analysis. Phylogenetic analysis using six chloroplast loci indicated the ancestral relationships of the five most agriculturally important species, with the unexpected result that the one parasite of dicotyledonous plants ( was found to be more closely related to some of the grass parasites than many of the grass parasites are to each other.

Repetition and Translation Shifts

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Simon Zupan

2006-06-01

Full Text Available Repetition manifests itself in different ways and at different levels of the text. The first basic type of repetition involves complete recurrences; in which a particular textual feature repeats in its entirety. The second type involves partial recurrences; in which the second repetition of the same textual feature includes certain modifications to the first occurrence. In the article; repetitive patterns in Edgar Allan Poe’s short story “The Fall of the House of Usher” and its Slovene translation; “Konec Usherjeve hiše”; are compared. The author examines different kinds of repetitive patterns. Repetitions are compared at both the micro- and macrostructural levels. As detailed analyses have shown; considerable microstructural translation shifts occur in certain types of repetitive patterns. Since these are not only occasional; sporadic phenomena; but are of a relatively high frequency; they reduce the translated text’s potential for achieving some of the gothic effects. The macrostructural textual property particularly affected by these shifts is the narrator’s experience as described by the narrative; which suffers a reduction in intensity.

Inventory and general analysis of the ATP-binding cassette (ABC) gene superfamily in maize (Zea mays L.).

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Pang, Kaiyuan; Li, Yanjiao; Liu, Menghan; Meng, Zhaodong; Yu, Yanli

2013-09-10

The metabolic functions of ATP-binding cassette (or ABC) proteins, one of the largest families of proteins presented in all organisms, have been investigated in many protozoan, animal and plant species. To facilitate more systematic and complicated studies on maize ABC proteins in the future, we present the first complete inventory of these proteins, including 130 open reading frames (ORFs), and provide general descriptions of their classifications, basic structures, typical functions, evolution track analysis and expression profiles. The 130 ORFs were assigned to eight subfamilies based on their structures and homological features. Five of these subfamilies consist of 109 proteins, containing transmembrane domains (TM) performing as transporters. The rest three subfamilies contain 21 soluble proteins involved in various functions other than molecular transport. A comparison of ABC proteins among nine selected species revealed either convergence or divergence in each of the ABC subfamilies. Generally, plant genomes contain far more ABC genes than animal genomes. The expression profiles and evolution track of each maize ABC gene were further investigated, the results of which could provide clues for analyzing their functions. Quantitative real-time polymerase chain reaction experiments (PCR) were conducted to detect induced expression in select ABC genes under several common stresses. This investigation provides valuable information for future research on stress tolerance in plants and potential strategies for enhancing maize production under stressful conditions. Copyright © 2013 Elsevier B.V. All rights reserved.

Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes.

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Stella A G D Salvo

Full Text Available Embryogenic tissue culture systems are utilized in propagation and genetic engineering of crop plants, but applications are limited by genotype-dependent culture response. To date, few genes necessary for embryogenic callus formation have been identified or characterized. The goal of this research was to enhance our understanding of gene expression during maize embryogenic tissue culture initiation. In this study, we highlight the expression of candidate genes that have been previously regarded in the literature as having important roles in somatic embryogenesis. We utilized RNA based sequencing (RNA-seq to characterize the transcriptome of immature embryo explants of the highly embryogenic and regenerable maize genotype A188 at 0, 24, 36, 48, and 72 hours after placement of explants on tissue culture initiation medium. Genes annotated as functioning in stress response, such as glutathione-S-transferases and germin-like proteins, and genes involved with hormone transport, such as PINFORMED, increased in expression over 8-fold in the study. Maize genes with high sequence similarity to genes previously described in the initiation of embryogenic cultures, such as transcription factors BABY BOOM, LEAFY COTYLEDON, and AGAMOUS, and important receptor-like kinases such as SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASES and CLAVATA, were also expressed in this time course study. By combining results from whole genome transcriptome analysis with an in depth review of key genes that play a role in the onset of embryogenesis, we propose a model of coordinated expression of somatic embryogenesis-related genes, providing an improved understanding of genomic factors involved in the early steps of embryogenic culture initiation in maize and other plant species.

Identification of resistance to Maize rayado fino virus in maize inbred lines

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Maize rayado fino virus (MRFV) is one of the most important virus diseases of maize in America. Severe yield losses, ranging from 10 to 50% in landraces to nearly 100% in contemporary cultivars, have been reported. Resistance has been reported in populations, but few inbred lines have been identifie...

Genomic insight into the common carp (Cyprinus carpio genome by sequencing analysis of BAC-end sequences

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Wang Jintu

2011-04-01

Full Text Available Abstract Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio, a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3

Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences

Science.gov (United States)

2011-01-01

Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES) are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio), a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3,100 microsyntenies, covering over 50% of

Snake Genome Sequencing: Results and Future Prospects.

Science.gov (United States)

Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

2016-12-01

Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

Snake Genome Sequencing: Results and Future Prospects

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Harald M. I. Kerkkamp

2016-12-01

Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

Insights into Conifer Giga-Genomes1

Science.gov (United States)

De La Torre, Amanda R.; Birol, Inanc; Bousquet, Jean; Ingvarsson, Pär K.; Jansson, Stefan; Jones, Steven J.M.; Keeling, Christopher I.; MacKay, John; Nilsson, Ove; Ritland, Kermit; Street, Nathaniel; Yanchuk, Alvin; Zerbe, Philipp; Bohlmann, Jörg

2014-01-01

Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world’s forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20–30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes. PMID:25349325

Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping.

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Zhang, Yunxia; Cheng, Chunyan; Li, Ji; Yang, Shuqiong; Wang, Yunzhu; Li, Ziang; Chen, Jinfeng; Lou, Qunfeng

2015-09-25

Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in

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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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.

Comparative diversity of arthropods on Bt maize and non-Bt maize in two different cropping systems in South Africa.

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Truter, J; Van Hamburg, H; Van Den Berg, J

2014-02-01

The biodiversity of an agroecosystem is not only important for its intrinsic value but also because it influences ecological functions that are vital for crop production in sustainable agricultural systems and the surrounding environment. A concern about genetically modified (GM) crops is the potential negative impact that such crops could have on diversity and abundance of nontarget organisms, and subsequently on ecosystem functions. Therefore, it is essential to assess the potential environmental risk of the release of a GM crop and to study its effect on species assemblages within that ecosystem. Assessment of the impact of Bt maize on the environment is hampered by the lack of basic checklists of species present in maize agroecosystems. The aims of the study were to compile a checklist of arthropods that occur on maize in South Africa and to compare the diversity and abundance of arthropods and functional groups on Bt maize and non-Bt maize. Collections of arthropods were carried out during two growing seasons on Bt maize and non-Bt maize plants at two localities. Three maize fields were sampled per locality during each season. Twenty plants, each of Bt maize and non-Bt maize, were randomly selected from the fields at each site. The arthropods collected during this study were classified to morphospecies level and grouped into the following functional groups: detritivores, herbivores, predators, and parasitoids. Based on feeding strategy, herbivores and predators were further divided into sucking herbivores or predators (piercing-sucking mouthparts) and chewing herbivores or predators (chewing mouthparts). A total of 8,771 arthropod individuals, comprising 288 morphospecies and presenting 20 orders, were collected. Results from this short-term study indicated that abundance and diversity of arthropods in maize and the different functional guilds were not significantly affected by Bt maize, either in terms of diversity or abundance.

Effects of maize maturity at harvest and dietary proportion of maize silage on intake and performance of growing/finishing bulls

DEFF Research Database (Denmark)

Zaralis, K.; Nørgaard, P.; Helander, C.

2014-01-01

Whole-crop maize silage as forage in diets of finishing cattle can promote high intakes and thus, enhances animal performance. In the present study we evaluated the effect of whole-crop maize maturity at harvest and the proportion of maize-silage in diets of finishing bulls, on feed intake...... of treatments, involving two maturity stages of maize at harvest (i.e. dough stage or dent stage) and two maize silage proportions (i.e. 100% maize silage or 50% maize and 50% grass silage). The diets were offered ad libitum as total mixed rations (TMRs) with inclusion of concentrates (i.e. rolled barley; dried...... distillers’ grain plus soluble; cold-pressed rapeseed cake) in a 40% proportion on DM basis. All animals were slaughtered at a target body weight of 630 kg. Bulls fed on diets containing maize silage as sole forage achieved higher live-weight gain (P

Identification of two new repetitive elements and chromosomal mapping of repetitive DNA sequences in the fish Gymnothorax unicolor (Anguilliformes: Muraenidae

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E. Coluccia

2011-05-01

Full Text Available Muraenidae is a species-rich family, with relationships among genera and species and taxonomy that have not been completely clarified. Few cytogenetic studies have been conducted on this family, and all of them showed the same diploid chromosome number (2n=42 but with conspicuous karyotypic variation among species. The Mediterranean moray eel Gymnothorax unicolor was previously cytogenetically studied using classical techniques that allowed the characterization of its karyotype structure and the constitutive heterochromatin and argyrophilic nucleolar organizer regions (Ag-NORs distribution pattern. In the present study, we describe two new repetitive elements (called GuMboI and GuDdeI obtained from restricted genomic DNA of G. unicolor that were characterized by Southern blot and physically localized by in situ hybridization on metaphase chromosomes. As they are highly repetitive DNA sequences, they map in heterochromatic regions. However, while GuDdeI was localized in the centromeric regions, the GuMboI fraction was distributed on some centromeres and was co-localized with the nucleolus organizer region (NOR. Comparative analysis with other Mediterranean species such as Muraena helena pointed out that these DNA fractions are species-specific and could potentially be used for species discrimination. As a new contribution to the karyotype of this species, we found that the major ribosomal genes are localized on acrocentric chromosome 9 and that the telomeres of each chromosome are composed of a tandem repeat derived from a poly-TTAGGG DNA sequence, as it occurs in most vertebrate species. The results obtained add new information useful in comparative genomics at the chromosomal level and contribute to the cytogenetic knowledge regarding this fish family, which has not been extensively studied.

Bacterial endophytes from wild maize suppress Fusarium graminearum in modern maize and inhibit mycotoxin accumulation

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Walaa Kamel Mousa

2015-10-01

Full Text Available Wild maize (teosinte has been reported to be less susceptible to pests than their modern maize (corn relatives. Endophytes, defined as microbes that inhabit plants without causing disease, are known for their ability to antagonize plant pests and pathogens. We hypothesized that the wild relatives of modern maize may host endophytes that combat pathogens. Fusarium graminearum is the fungus that causes Gibberella Ear Rot (GER in modern maize and produces the mycotoxin, deoxynivalenol (DON. In this study, 215 bacterial endophytes, previously isolated from diverse maize genotypes including wild teosintes, traditional landraces and modern varieties, were tested for their ability to antagonize F. graminearum in vitro. Candidate endophytes were then tested for their ability to suppress GER in modern maize in independent greenhouse trials. The results revealed that three candidate endophytes derived from wild teosintes were most potent in suppressing F. graminearum in vitro and GER in a modern maize hybrid. These wild teosinte endophytes could suppress a broad spectrum of fungal pathogens of modern crops in vitro. The teosinte endophytes also suppressed DON mycotoxin during storage to below acceptable safety threshold levels. A fourth, less robust anti-fungal strain was isolated from a modern maize hybrid. Three of the anti-fungal endophytes were predicted to be Paenibacillus polymyxa, along with one strain of Citrobacter. Microscopy studies suggested a fungicidal mode of action by all four strains. Molecular and biochemical studies showed that the P. polymyxa strains produced the previously characterized anti-Fusarium compound, fusaricidin. Our results suggest that the wild relatives of modern crops may serve as a valuable reservoir for endophytes in the ongoing fight against serious threats to modern agriculture. We discuss the possible impact of crop evolution and domestication on endophytes in the context of plant defense.

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing.

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Alexander William Eastman

2015-01-01

Full Text Available Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing

"Achieving Mexico’s Maize Potential"

OpenAIRE

Antonio Turrent Fernández; Timothy A. Wise; Elise Garvey

2012-01-01

Rising agricultural prices, combined with growing import dependence, have driven Mexico’s food import bill over $20 billion per year and increased its agricultural trade deficit. Mexico imports one-third of its maize, overwhelmingly from the United States, but three million producers grow most of the country’s white maize, which is used primarily for tortillas and many other pluricultural products for human consumption. Yield gaps are large among the country’s small to medium-scale maize farm...

Exploring maize-legume intercropping systems in Southwest Mexico

NARCIS (Netherlands)

Flores-Sanchez, D.; Pastor, A.V.; Lantinga, E.A.; Rossing, W.A.H.; Kropff, M.J.

2013-01-01

Maize yields in continuous maize production systems of smallholders in the Costa Chica, a region in Southwest Mexico, are low despite consistent inputs of fertilizers and herbicides. This study was aimed at investigating the prospects of intercropping maize (Zea mays L.) and maize-roselle (Hibiscus

Climatic and non-climatic drivers of spatiotemporal maize-area dynamics across the northern limit for maize production

DEFF Research Database (Denmark)

Odgaard, Mette Vestergaard; Bøcher, Peder Klith; Dalgaard, Tommy

2011-01-01

It is expected that the ongoing anthropogenic climate change will drive changes in agricultural production and its geographic distribution. Here, we assess the extent to which climate change is already driving spatiotemporal dynamics in maize production in Denmark. We use advanced spatial...... regression modeling with multi-model averaging to assess the extent to which the recent spatiotemporal dynamics of the maize area in Denmark are driven by climate (temperature as represented by maize heating units [MHU] and growing-season precipitation), climate change and non-climatic factors (cattle...... cultivation and cattle farming, probably reflecting a change to a more favorable climate for maize cultivation: in the beginning of the study period, northern areas were mostly too cold for maize cultivation, irrespective of cattle density, but this limitation has been diminishing as climate has warmed...

A Nonword Repetition Task for Speakers with Misarticulations: The Syllable Repetition Task (SRT)

Science.gov (United States)

Shriberg, Lawrence D.; Lohmeier, Heather L.; Campbell, Thomas F.; Dollaghan, Christine A.; Green, Jordan R.; Moore, Christopher A.

2009-01-01

Purpose: Conceptual and methodological confounds occur when non(sense) word repetition tasks are administered to speakers who do not have the target speech sounds in their phonetic inventories or who habitually misarticulate targeted speech sounds. In this article, the authors (a) describe a nonword repetition task, the Syllable Repetition Task…

Survey of Candidate Genes for Maize Resistance to Infection by Aspergillus flavus and/or Aflatoxin Contamination

Science.gov (United States)

Hawkins, Leigh K.; Tang, Juliet D.; Tomashek, John; Alves Oliveira, Dafne; Ogunola, Oluwaseun F.; Smith, J. Spencer; Williams, W. Paul

2018-01-01

Many projects have identified candidate genes for resistance to aflatoxin accumulation or Aspergillus flavus infection and growth in maize using genetic mapping, genomics, transcriptomics and/or proteomics studies. However, only a small percentage of these candidates have been validated in field conditions, and their relative contribution to resistance, if any, is unknown. This study presents a consolidated list of candidate genes identified in past studies or in-house studies, with descriptive data including genetic location, gene annotation, known protein identifiers, and associated pathway information, if known. A candidate gene pipeline to test the phenotypic effect of any maize DNA sequence on aflatoxin accumulation resistance was used in this study to determine any measurable effect on polymorphisms within or linked to the candidate gene sequences, and the results are published here. PMID:29385107

Survey of Candidate Genes for Maize Resistance to Infection by Aspergillus flavus and/or Aflatoxin Contamination

Directory of Open Access Journals (Sweden)

Leigh K. Hawkins

2018-01-01

Full Text Available Many projects have identified candidate genes for resistance to aflatoxin accumulation or Aspergillus flavus infection and growth in maize using genetic mapping, genomics, transcriptomics and/or proteomics studies. However, only a small percentage of these candidates have been validated in field conditions, and their relative contribution to resistance, if any, is unknown. This study presents a consolidated list of candidate genes identified in past studies or in-house studies, with descriptive data including genetic location, gene annotation, known protein identifiers, and associated pathway information, if known. A candidate gene pipeline to test the phenotypic effect of any maize DNA sequence on aflatoxin accumulation resistance was used in this study to determine any measurable effect on polymorphisms within or linked to the candidate gene sequences, and the results are published here.

Genome-wide expression of transcriptomes and their co-expression pattern in subtropical maize (Zea mays L. under waterlogging stress.

Directory of Open Access Journals (Sweden)

Nepolean Thirunavukkarasu

Full Text Available Waterlogging causes extensive damage to maize crops in tropical and subtropical regions. The identification of tolerance genes and their interactions at the molecular level will be helpful to engineer tolerant genotypes. A whole-genome transcriptome assay revealed the specific role of genes in response to waterlogging stress in susceptible and tolerant genotypes. Genes involved in the synthesis of ethylene and auxin, cell wall metabolism, activation of G-proteins and formation of aerenchyma and adventitious roots, were upregulated in the tolerant genotype. Many transcription factors, particularly ERFs, MYB, HSPs, MAPK, and LOB-domain protein were involved in regulation of these traits. Genes responsible for scavenging of ROS generated under stress were expressed along with those involved in carbohydrate metabolism. The physical locations of 21 genes expressed in the tolerant genotype were found to correspond with the marker intervals of known QTLs responsible for development of adaptive traits. Among the candidate genes, most showed synteny with genes of sorghum and foxtail millet. Co-expression analysis of 528 microarray samples including 16 samples from the present study generated seven functional modules each in the two genotypes, with differing characteristics. In the tolerant genotype, stress genes were co-expressed along with peroxidase and fermentation pathway genes.

Phenomics allows identification of genomic regions affecting maize stomatal conductance with conditional effects of water deficit and evaporative demand.

Science.gov (United States)

Prado, Santiago Alvarez; Cabrera-Bosquet, Llorenç; Grau, Antonin; Coupel-Ledru, Aude; Millet, Emilie J; Welcker, Claude; Tardieu, François

2018-02-01

Stomatal conductance is central for the trades-off between hydraulics and photosynthesis. We aimed at deciphering its genetic control and that of its responses to evaporative demand and water deficit, a nearly impossible task with gas exchanges measurements. Whole-plant stomatal conductance was estimated via inversion of the Penman-Monteith equation from data of transpiration and plant architecture collected in a phenotyping platform. We have analysed jointly 4 experiments with contrasting environmental conditions imposed to a panel of 254 maize hybrids. Estimated whole-plant stomatal conductance closely correlated with gas-exchange measurements and biomass accumulation rate. Sixteen robust quantitative trait loci (QTLs) were identified by genome wide association studies and co-located with QTLs of transpiration and biomass. Light, vapour pressure deficit, or soil water potential largely accounted for the differences in allelic effects between experiments, thereby providing strong hypotheses for mechanisms of stomatal control and a way to select relevant candidate genes among the 1-19 genes harboured by QTLs. The combination of allelic effects, as affected by environmental conditions, accounted for the variability of stomatal conductance across a range of hybrids and environmental conditions. This approach may therefore contribute to genetic analysis and prediction of stomatal control in diverse environments. © 2017 John Wiley & Sons Ltd.

Experimental hybrid evaluation of maize, for the Colombian Atlantic coast

International Nuclear Information System (INIS)

Urrea, R.; Navas Arboleda, A.A.; Mejia, S.; Ospina, J.G.

1998-01-01

To determine the yield potential and phenotypic stability four they were evaluated hybrid experimental simple and seven commercial witness of maize in eleven towns (L), during 1995 and 1996. The used experimental design was at random of complete blocks with four repetitions with parcels of four furrows of five m of longitude, distanced 0.90 m between furrows and 0.45 among blows (49 383 plts/ha) it Differ highly significant (smaller p 0.01) they were detected among genotype (G) and for the interaction G x L in the varieties yield. The analysis of stability of Eberhart and Russell (1966) it indicated that the genotypes had similar regression values; however, a clear tendency was observed to differentiate the behavior in yield of certain materials. The hybrid one experimental there are 76 and the commercial HR 661, they showed a good stability for yield

Recombination in diverse maize is stable, predictable, and associated with genetic load.

Science.gov (United States)

Rodgers-Melnick, Eli; Bradbury, Peter J; Elshire, Robert J; Glaubitz, Jeffrey C; Acharya, Charlotte B; Mitchell, Sharon E; Li, Chunhui; Li, Yongxiang; Buckler, Edward S

2015-03-24

Among the fundamental evolutionary forces, recombination arguably has the largest impact on the practical work of plant breeders. Varying over 1,000-fold across the maize genome, the local meiotic recombination rate limits the resolving power of quantitative trait mapping and the precision of favorable allele introgression. The consequences of low recombination also theoretically extend to the species-wide scale by decreasing the power of selection relative to genetic drift, and thereby hindering the purging of deleterious mutations. In this study, we used genotyping-by-sequencing (GBS) to identify 136,000 recombination breakpoints at high resolution within US and Chinese maize nested association mapping populations. We find that the pattern of cross-overs is highly predictable on the broad scale, following the distribution of gene density and CpG methylation. Several large inversions also suppress recombination in distinct regions of several families. We also identify recombination hotspots ranging in size from 1 kb to 30 kb. We find these hotspots to be historically stable and, compared with similar regions with low recombination, to have strongly differentiated patterns of DNA methylation and GC content. We also provide evidence for the historical action of GC-biased gene conversion in recombination hotspots. Finally, using genomic evolutionary rate profiling (GERP) to identify putative deleterious polymorphisms, we find evidence for reduced genetic load in hotspot regions, a phenomenon that may have considerable practical importance for breeding programs worldwide.

Molecular typing of Lactobacillus brevis isolates from Korean food using repetitive element-polymerase chain reaction.

Science.gov (United States)

Kaur, Jasmine; Sharma, Anshul; Lee, Sulhee; Park, Young-Seo

2018-06-01

Lactobacillus brevis is a part of a large family of lactic acid bacteria that are present in cheese, sauerkraut, sourdough, silage, cow manure, feces, and the intestinal tract of humans and rats. It finds its use in food fermentation, and so is considered a "generally regarded as safe" organism. L. brevis strains are extensively used as probiotics and hence, there is a need for identifying and characterizing these strains. For identification and discrimination of the bacterial species at the subspecific level, repetitive element-polymerase chain reaction method is a reliable genomic fingerprinting tool. The objective of the present study was to characterize 13 strains of L. brevis isolated from various fermented foods using repetitive element-polymerase chain reaction. Repetitive element-polymerase chain reaction was performed using three primer sets, REP, Enterobacterial Repetitive Intergenic Consensus (ERIC), and (GTG) 5 , which produced different fingerprinting patterns that enable us to distinguish between the closely related strains. Fingerprinting patterns generated band range in between 150 and 5000 bp with REP, 200-7500 bp with ERIC, and 250-2000 bp with (GTG) 5 primers, respectively. The Jaccard's dissimilarity matrices were used to obtain dendrograms by the unweighted neighbor-joining method using genetic dissimilarities based on repetitive element-polymerase chain reaction fingerprinting data. Repetitive element-polymerase chain reaction proved to be a rapid and easy method that can produce reliable results in L. brevis species.

Pollen-Mediated Gene Flow in Maize: Implications for Isolation Requirements and Coexistence in Mexico, the Center of Origin of Maize.

Science.gov (United States)

Baltazar, Baltazar M; Castro Espinoza, Luciano; Espinoza Banda, Armando; de la Fuente Martínez, Juan Manuel; Garzón Tiznado, José Antonio; González García, Juvencio; Gutiérrez, Marco Antonio; Guzmán Rodríguez, José Luis; Heredia Díaz, Oscar; Horak, Michael J; Madueño Martínez, Jesús Ignacio; Schapaugh, Adam W; Stojšin, Duška; Uribe Montes, Hugo Raúl; Zavala García, Francisco

2015-01-01

Mexico, the center of origin of maize (Zea mays L.), has taken actions to preserve the identity and diversity of maize landraces and wild relatives. Historically, spatial isolation has been used in seed production to maintain seed purity. Spatial isolation can also be a key component for a strategy to minimize pollen-mediated gene flow in Mexico between transgenic maize and sexually compatible plants of maize conventional hybrids, landraces, and wild relatives. The objective of this research was to generate field maize-to-maize outcrossing data to help guide coexistence discussions in Mexico. In this study, outcrossing rates were determined and modeled from eight locations in six northern states, which represent the most economically important areas for the cultivation of hybrid maize in Mexico. At each site, pollen source plots were planted with a yellow-kernel maize hybrid and surrounded by plots with a white-kernel conventional maize hybrid (pollen recipient) of the same maturity. Outcrossing rates were then quantified by assessing the number of yellow kernels harvested from white-kernel hybrid plots. The highest outcrossing values were observed near the pollen source (12.9% at 1 m distance). The outcrossing levels declined sharply to 4.6, 2.7, 1.4, 1.0, 0.9, 0.5, and 0.5% as the distance from the pollen source increased to 2, 4, 8, 12, 16, 20, and 25 m, respectively. At distances beyond 20 m outcrossing values at all locations were below 1%. These trends are consistent with studies conducted in other world regions. The results suggest that coexistence measures that have been implemented in other geographies, such as spatial isolation, would be successful in Mexico to minimize transgenic maize pollen flow to conventional maize hybrids, landraces and wild relatives.

Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome.

Science.gov (United States)

Cavallini, Andrea; Natali, Lucia; Zuccolo, Andrea; Giordani, Tommaso; Jurman, Irena; Ferrillo, Veronica; Vitacolonna, Nicola; Sarri, Vania; Cattonaro, Federica; Ceccarelli, Marilena; Cionini, Pier Giorgio; Morgante, Michele

2010-02-01

A sample-sequencing strategy combined with slot-blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome, it appears that no transposon family has been amplified to very high levels in sunflower. All other known classes of transposable elements were also found. One family of unknown nature (contig 61) was the most repeated in the sunflower genome. The evolution of the repetitive component in the Helianthus genus and in other Asteraceae was studied by comparative analysis of the hybridization of total genomic DNAs from these species to the sunflower small-insert library and compared to gene-based phylogeny. Very little similarity is observed between Helianthus species and two related Asteraceae species outside of the genus. Most repetitive elements are similar in annual and perennial Helianthus species indicating that sequence amplification largely predates such divergence. Gypsy-like elements are more represented in the annuals than in the perennials, while copia-like elements are similarly represented, attesting a different amplification history of the two superfamilies of LTR-retrotransposons in the Helianthus genus.

Genomic repeat abundances contain phylogenetic signal

Czech Academy of Sciences Publication Activity Database

Dodsworth, S.; Chase, M.W.; Kelly, L.J.; Leitch, I.J.; Macas, Jiří; Novák, Petr; Piednoël, M.; Weiß-Schneeweiss, H.; Leitch, A.R.

2015-01-01

Roč. 64, č. 1 (2015), s. 112-126 ISSN 1063-5157 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : Repetitive DNA * continuous characters * genomics * next-generation sequencing * phylogenetics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.225, year: 2015

Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth.

Science.gov (United States)

Bluhm, Burton H; Dhillon, Braham; Lindquist, Erika A; Kema, Gert Hj; Goodwin, Stephen B; Dunkle, Larry D

2008-11-04

The ascomycete fungus Cercospora zeae-maydis is an aggressive foliar pathogen of maize that causes substantial losses annually throughout the Western Hemisphere. Despite its impact on maize production, little is known about the regulation of pathogenesis in C. zeae-maydis at the molecular level. The objectives of this study were to generate a collection of expressed sequence tags (ESTs) from C. zeae-maydis and evaluate their expression during vegetative, infectious, and reproductive growth. A total of 27,551 ESTs was obtained from five cDNA libraries constructed from vegetative and sporulating cultures of C. zeae-maydis. The ESTs, grouped into 4088 clusters and 531 singlets, represented 4619 putative unique genes. Of these, 36% encoded proteins similar (E value zeae-maydis, providing specific targets for characterization by molecular genetics and functional genomics. The EST data establish a foundation for future studies in evolutionary and comparative genomics among species of Cercospora and other groups of plant pathogenic fungi.

Maize, tropical (Zea mays L.).

Science.gov (United States)

Assem, Shireen K

2015-01-01

Maize (Zea mays L.) is the third most important food crop globally after wheat and rice. In sub-Saharan Africa, tropical maize has traditionally been the main staple of the diet; 95 % of the maize grown is consumed directly as human food and as an important source of income for the resource-poor rural population. The biotechnological approach to engineer biotic and abiotic traits implies the availability of an efficient plant transformation method. The production of genetically transformed plants depends both on the ability to integrate foreign genes into target cells and the efficiency with which plants are regenerated. Maize transformation and regeneration through immature embryo culture is the most efficient system to regenerate normal transgenic plants. However, this system is highly genotype dependent. Genotypes adapted to tropic areas are difficult to regenerate. Therefore, transformation methods used with model genotypes adapted to temperate areas are not necessarily efficient with tropical lines. Agrobacterium-mediated transformation is the method of choice since it has been first achieved in 1996. In this report, we describe a transformation method used successfully with several tropical maize lines. All the steps of transformation and regeneration are described in details. This protocol can be used with a wide variety of tropical lines. However, some modifications may be needed with recalcitrant lines.

Effect of Bambara nut and cowpea intercropped with maize at different times on nutritive quality of maize for ruminant feeding

Directory of Open Access Journals (Sweden)

Olanite, J. A.

2017-06-01

Full Text Available Effects of Bambara nut and cowpea planted with maize at different times on nutritive quality of maize forage were investigated. The study was laid out in a Completely Randomized Design and the treatments were combination of crop types (Bambara nut-maize (MB and Cowpea-maize (MC and planting times of legumes (2 wks before planting maize, 2WBPM and 2 wks after planting maize, 2WAPM, and sole maize (as control. An experimental field measuring 19 m � 11 m was divided into 3 replicates; each replicate was sub-divided into 5 plots of dimension 3 m2 each, with 1 m and 2 m inter-plots and inter-blocks spacing respectively. Maize forage samples were harvested on each plot at 10 wks after planting, oven-dried, milled and analyzed to evaluate the chemical composition, mineral composition, in vitro gas production and post-incubation characteristics. Results revealed significant differences (P<0.05 among treatments with the highest (95.00% and least DM (92.12% values were recorded for MB 2WBPM and MC 2WAPM, respectively. CP values ranged from 10.36% in MB 2WBPM to 15.67% in MC 2WBPM but not significantly different from 14.19 % recorded for sole maize. Ash ranged from 7.00% in MB 2WAPM to 10.00% in sole maize. MC 2WBPM and sole maize had the highest (50.63% and least (38.40% in ADF content (P<0.05. ADL value (7.25% observed in MB 2WBPM was the highest, compared to the least (5.00% in sole maize. Sole maize recorded the least (40.40% and highest (25.91% cellulose and hemicellulose contents, respectively while MC 2WAPM had the highest (50.88% and lowest (15.80% values for cellulose and hemicellulose, respectively. Ca content (4.55g/kg of MB 2WAPM was lower than the other treatments. P content ranged from 3.54 g/kg in MB 2WAPM to 12.02 g/kg in MC 2WAPM. Gas production rates only varied (P<0.05 at the 3rd, 6th, 24th and 48th hours of incubation. MB 2WBPM yielded highest values of short chain fatty acids (0.09 �mol and metabolizable energy (3.08 MJ/kg while MB

The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens.

Science.gov (United States)

Sánchez-Vallet, Andrea; Fouché, Simone; Fudal, Isabelle; Hartmann, Fanny E; Soyer, Jessica L; Tellier, Aurélien; Croll, Daniel

2018-05-16

Filamentous pathogens, including fungi and oomycetes, pose major threats to global food security. Crop pathogens cause damage by secreting effectors that manipulate the host to the pathogen's advantage. Genes encoding such effectors are among the most rapidly evolving genes in pathogen genomes. Here, we review how the major characteristics of the emergence, function, and regulation of effector genes are tightly linked to the genomic compartments where these genes are located in pathogen genomes. The presence of repetitive elements in these compartments is associated with elevated rates of point mutations and sequence rearrangements with a major impact on effector diversification. The expression of many effectors converges on an epigenetic control mediated by the presence of repetitive elements. Population genomics analyses showed that rapidly evolving pathogens show high rates of turnover at effector loci and display a mosaic in effector presence-absence polymorphism among strains. We conclude that effective pathogen containment strategies require a thorough understanding of the effector genome biology and the pathogen's potential for rapid adaptation. Expected final online publication date for the Annual Review of Phytopathology Volume 56 is August 25, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Characterization of Indian and exotic quality protein maize (QPM ...

African Journals Online (AJOL)

Polymorphism analysis and genetic diversity of normal maize and quality protein maize (QPM) inbreds among locally well adapted germplasm is a prerequisite for hybrid maize breeding program. The diversity analyses of 48 maize accessions including Indian and exotic germplasm using 75 simple sequence repeat (SSR) ...

Screening of different insecticides against maize shoot fly atherigona soccata (Rond.) and maize borer. chilo partellus (swinh.)

International Nuclear Information System (INIS)

Shahid, M.A.; Rana, Z.A.; Haq, I.; Tariq, H.

2010-01-01

Field studies were carried out in the research area of the Ayub Agricultural Research Institute, Faisalabad to determine the most effective maize seed treatment against maize shoot fly Atherigona soccata (Rond.) and insecticide against maize borer Chilo partellus (Swinh.) Trials were conducted following RCBD and replicated three times during 2005-2006. Two seed treatments Confider (imidacloprid) 70 WS and pensidor 72% WP (5 and 7 mg/kg seed) along with Confider (imidaclorid) 200 SC at the rate 40 ml/acre in the trial against maize shoot fly whereas, flubendiamide 48%, emamection 1.9 EC, spinosad 240 EC. carbofuran 3 G, indoxacarb 150 SC, alphacypermethrine 20 EC, monomehypo 5 G, bifenthrin 10 EC, cartap 4G, cyhalothrine 2.5 EC, cypermethrin 10 EC at the rate 20 ml, 150 ml, 40 ml, 8 kg, 150 ml, 200 ml, 5 kg, 150 ml, 6 kg. 250 ml and 300 ml per acre against maize borer were treated keeping one plo ast untreated check. Treatments were repeated as borer infestation reached above 5% level. All the seed treatments showed significant control of maize shoot fly in spite of dose 5 or 7 mg/kg seed along with foliar spray of confider 200 SC. The insecticides viz. flubendiamide 48% SC. emamectin 1.9 EC, spinosad 240 EC and carbofuran 3 G. indoxacarb 150 SC. alpha cypermethrin 20 EC, not only responded highest yield 5765, 5294, 5289, 5215, 5168 and 5025 kg/ha respectively but also manage the maize borer below ETL. (author)

A(maize)ing attraction: gravid Anopheles arabiensis are attracted and oviposit in response to maize pollen odours.

Science.gov (United States)

Wondwosen, Betelehem; Hill, Sharon R; Birgersson, Göran; Seyoum, Emiru; Tekie, Habte; Ignell, Rickard

2017-01-23

Maize cultivation contributes to the prevalence of malaria mosquitoes and exacerbates malaria transmission in sub-Saharan Africa. The pollen from maize serves as an important larval food source for Anopheles mosquitoes, and females that are able to detect breeding sites where maize pollen is abundant may provide their offspring with selective advantages. Anopheles mosquitoes are hypothesized to locate, discriminate among, and select such sites using olfactory cues, and that synthetic volatile blends can mimic these olfactory-guided behaviours. Two-port olfactometer and two-choice oviposition assays were used to assess the attraction and oviposition preference of gravid Anopheles arabiensis to the headspace of the pollen from two maize cultivars (BH-660 and ZM-521). Bioactive compounds were identified using combined gas chromatography and electroantennographic detection from the headspace of the cultivar found to be most attractive (BH-660). Synthetic blends of the volatile compounds were then assessed for attraction and oviposition preference of gravid An. arabiensis, as above. Here the collected headspace volatiles from the pollen of two maize cultivars was shown to differentially attract and stimulate oviposition in gravid An. arabiensis. Furthermore, a five-component synthetic maize pollen odour blend was identified, which elicited the full oviposition behavioural repertoire of the gravid mosquitoes. The cues identified from maize pollen provide important substrates for the development of novel control measures that modulate gravid female behaviour. Such measures are irrespective of indoor or outdoor feeding and resting patterns, thus providing a much-needed addition to the arsenal of tools that currently target indoor biting mosquitoes.

The evolutionary value of recombination is constrained by genome modularity.

Directory of Open Access Journals (Sweden)

Darren P Martin

2005-10-01

Full Text Available Genetic recombination is a fundamental evolutionary mechanism promoting biological adaptation. Using engineered recombinants of the small single-stranded DNA plant virus, Maize streak virus (MSV, we experimentally demonstrate that fragments of genetic material only function optimally if they reside within genomes similar to those in which they evolved. The degree of similarity necessary for optimal functionality is correlated with the complexity of intragenomic interaction networks within which genome fragments must function. There is a striking correlation between our experimental results and the types of MSV recombinants that are detectable in nature, indicating that obligatory maintenance of intragenome interaction networks strongly constrains the evolutionary value of recombination for this virus and probably for genomes in general.

Enzymatically Generated CRISPR Libraries for Genome Labeling and Screening.

Science.gov (United States)

Lane, Andrew B; Strzelecka, Magdalena; Ettinger, Andreas; Grenfell, Andrew W; Wittmann, Torsten; Heald, Rebecca

2015-08-10

CRISPR-based technologies have emerged as powerful tools to alter genomes and mark chromosomal loci, but an inexpensive method for generating large numbers of RNA guides for whole genome screening and labeling is lacking. Using a method that permits library construction from any source of DNA, we generated guide libraries that label repetitive loci or a single chromosomal locus in Xenopus egg extracts and show that a complex library can target the E. coli genome at high frequency. Copyright © 2015 Elsevier Inc. All rights reserved.

Applying CSM-CERES-Maize to define a sowing window for irrigated maize crop - The Riacho´s Farm case study

Directory of Open Access Journals (Sweden)

Denise Freitas Silva

2011-08-01

Full Text Available Irrigation use constitutes an alternative to improve maize production in Central Minas Gerais State, Brazil. However, even under adequate water supply conditions, other environmental factors may influence maize crop growth and development and may, ultimately, affect grain yield. This study aimed to establish a sowing window for irrigated maize crop, based on simulation results obtained with the decision support model CSM-CERES-Maize. Simulations were made for crop management conditions of Riacho´s Farm, located in Matozinhos, Minas Gerais State, Brazil. It was employed the model´s seasonal tool, along with a data set containing 46 years of weather data records, to simulate maize yield for weekly sowing scenarios, starting on August 1st and ending on July 24th of each year. One defined an irrigated maize sowing window, taking into account the yield break risk that a farmer would be willing to take. The model proved to be an interesting tool to assist in decision making, regarding crop and irrigation management, for an irrigated maize production system. Assuming a 10% yield break in the expected average maximum maize yield, it was defined as sowing window, the period from January 23rd to March 6th, with February 20th as the best sowing date. Other sowing windows may be established according to the risk that the farmer would be willing to take.

Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines.

Science.gov (United States)

Zhou, Zhiqiang; Zhang, Chaoshu; Zhou, Yu; Hao, Zhuanfang; Wang, Zhenhua; Zeng, Xing; Di, Hong; Li, Mingshun; Zhang, Degui; Yong, Hongjun; Zhang, Shihuang; Weng, Jianfeng; Li, Xinhai

2016-03-03

Plant architecture attributes, such as plant height, ear height, and internode number, have played an important role in the historical increases in grain yield, lodging resistance, and biomass in maize (Zea mays L.). Analyzing the genetic basis of variation in plant architecture using high density QTL mapping will be of benefit for the breeding of maize for many traits. However, the low density of molecular markers in existing genetic maps has limited the efficiency and accuracy of QTL mapping. Genotyping by sequencing (GBS) is an improved strategy for addressing a complex genome via next-generation sequencing technology. GBS has been a powerful tool for SNP discovery and high-density genetic map construction. The creation of ultra-high density genetic maps using large populations of advanced recombinant inbred lines (RILs) is an efficient way to identify QTL for complex agronomic traits. A set of 314 RILs derived from inbreds Ye478 and Qi319 were generated and subjected to GBS. A total of 137,699,000 reads with an average of 357,376 reads per individual RIL were generated, which is equivalent to approximately 0.07-fold coverage of the maize B73 RefGen_V3 genome for each individual RIL. A high-density genetic map was constructed using 4183 bin markers (100-Kb intervals with no recombination events). The total genetic distance covered by the linkage map was 1545.65 cM and the average distance between adjacent markers was 0.37 cM with a physical distance of about 0.51 Mb. Our results demonstrated a relatively high degree of collinearity between the genetic map and the B73 reference genome. The quality and accuracy of the bin map for QTL detection was verified by the mapping of a known gene, pericarp color 1 (P1), which controls the color of the cob, with a high LOD value of 80.78 on chromosome 1. Using this high-density bin map, 35 QTL affecting plant architecture, including 14 for plant height, 14 for ear height, and seven for internode number were detected

Status and prospects of maize research in Nepal

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Govind KC

2015-12-01

Full Text Available Food and nutritional securities are the major threats coupled with declining factor productivity and climate change effects in Nepal. Maize being the principal food crops of the majority of the hill people and source of animal feed for ever growing livestock industries in Terai of Nepal. Despite the many efforts made to increase the maize productivity in the country, the results are not much encouraging. Many of the maize based technologies developed and recommended for the farmers to date are not fully adopted. Therefore, problem is either on technology development or on dissemination or on both. Considering the above facts, some of the innovative and modern approaches of plant breeding and crop management technologies to increase the maize yield need to be developed and disseminated. There is a need for location-specific maize production technologies, especially for lowland winter maize, marginal upland maize production system, and resource poor farmers. Research efforts can be targeted to address both yield potential and on-farm yields by reducing the impacts of abiotic and biotic constraints. Therefore, in order to streamline the future direction of maize research in Nepal, an attempt has been made in this article to highlight the present status and future prospects with few key pathways.

Identification of small secreted peptides (SSPs) in maize and expression analysis of partial SSP genes in reproductive tissues.

Science.gov (United States)

Li, Ye Long; Dai, Xin Ren; Yue, Xun; Gao, Xin-Qi; Zhang, Xian Sheng

2014-10-01

Maize 1,491 small secreted peptides were identified, which were classified according to the character of peptide sequences. Partial SSP gene expressions in reproductive tissues were determined by qRT-PCR. Small secreted peptides (SSPs) are important cell-cell communication messengers in plants. Most information on plant SSPs come from Arabidopsis thaliana and Oryza sativa, while little is known about the SSPs of other grass species such as maize (Zea mays). In this study, we identified 1,491 SSP genes from maize genomic sequences. These putative SSP genes were distributed throughout the ten maize chromosomes. Among them, 611 SSPs were classified into 198 superfamilies according to their conserved domains, and 725 SSPs with four or more cysteines at their C-termini shared similar cysteine arrangements with their counterparts in other plant species. Moreover, the SSPs requiring post-translational modification, as well as defensin-like (DEFL) proteins, were identified. Further, the expression levels of 110 SSP genes were analyzed in reproductive tissues, including male flower, pollen, silk, and ovary. Most of the genes encoding basal-layer antifungal peptide-like, small coat proteins-like, thioredoxin-like proteins, γ-thionins-like, and DEFL proteins showed high expression levels in the ovary and male flower compared with their levels in silk and mature pollen. The rapid alkalinization factor-like genes were highly expressed only in the mature ovary and mature pollen, and pollen Ole e 1-like genes showed low expression in silk. The results of this study provide basic information for further analysis of SSP functions in the reproductive process of maize.

Potato Genome Sequencing: A Short Glimpse of the Non-Repetitive.

Science.gov (United States)

Potato is the world’s number one vegetable crop. The potato is a member of the Solanaceae family that contains other crops such tomato pepper and eggplant as well as model species tobacco and petunia. Tomato is both an important crop as well as a model species for genetic and physical genomic info...

The mechanisms of root exudates of maize in improvement of iron nutrition of peanut in peanut/maize intercropping system by 14C tracer technique

International Nuclear Information System (INIS)

Zuo Yuanmei; Chen Qing; Zhang Fusuo

2004-01-01

The related mechanisms of root exudates of maize in improvement iron nutrition of peanut intercropped with maize was investigated by 14 C tracer technique. Neighboring roots between maize and peanut were separated by a 30 μm nylon net, the iron nutrition of peanut was also improved just like normal intercropping of maize and peanut. The results proved that root exudates of maize played an important role in improvement iron nutrition of peanut. The photosynthesis carbohydrate of maize could exuded into the rhizosphere of peanut and transfer into shoot and root of peanut in intercropping system. Root exudates of maize could increased efficiency of iron in soil and improved iron utilization of peanut

Selection for drought tolerance in two tropical maize populations ...

African Journals Online (AJOL)

Drought is a major factor limiting maize (Zea mays L.) yield in much of the world. The need to breed maize cultivars with improved drought tolerance is apparent. This study compared two maize populations, ZM601 and ZM607 for drought tolerance during flowering, the most drought-vulnerable period for the maize plant.

Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination

Energy Technology Data Exchange (ETDEWEB)

Hoang, Margaret L.; Tan, Frederick J.; Lai, David C.; Celniker, Sue E.; Hoskins, Roger A.; Dunham, Maitreya J.; Zheng, Yixian; Koshland, Douglas

2010-08-27

Genome rearrangements often result from non-allelic homologous recombination (NAHR) between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs) induce NAHR-dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR) occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR-dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer.

Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination.

Directory of Open Access Journals (Sweden)

Margaret L Hoang

2010-12-01

Full Text Available Genome rearrangements often result from non-allelic homologous recombination (NAHR between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs induce NAHR-dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR-dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer.

Effects of maize planting patterns on the performance of cassava ...

African Journals Online (AJOL)

sola

The design was a split-plot arrangement, laid out in a randomized ... significant differences (P<0.05) between the treatments in the growth and yield parameters of maize. The mean effects of companion crops on maize leaf area were 0.61, 0.60, 0.60 and 0.52 m2/plant for sole maize, maize / melon, maize / cassava and.

Developing Inset Resistant Maize Varieties for Food Security in Kenya

International Nuclear Information System (INIS)

Mugo, S.

2002-01-01

The Insect Resistant Maize for Africa (IRMA) project aims at increasing maize production and food security through development and deployment of stem borer resistant maize germplasm developed using conventional and through biotechnology methods such as Bt maize. Bt maize offers farmers an effective and practical option for controlling stem borers. It was recognized that the development and routine use of Bt maize will require addressing relevant bio-safety, environmental, and community concerns and research and information gathering activities are in place to address these concerns and research and information gathering activities are in place to address these concerns. Suitable Bt gene have been acquired or synthesized and back-crossed into elite maize germplasm at CIMMYT-Mexico, and the effective Cry-proteins against the major maize stem borers in Kenya were identified to better target pests. Stem borer resistant maize germplasm is being developed through conventional breeding, using locally adapted and exotic germplasm. for safe and effective deployment of Bt maize,studies on its impacts on target and non-target arthropods as well as studies on the effects of Bt maize on key non-target arthropods as well as studies on gene flow are underway. Insect resistance management strategies are being developed through quantifying the effectiveness, ???. Socioeconomic impact studies are revealing factors in the society that may influence the adoption of Bt maize in Kenya. Also, baseline data, essential for the monitoring and evaluation of the Bt maize technology in Kenya, has been established. Technology transfer and capacity building, creating awareness and communications have received attention in the project. This paper describes the major research activities as they relate to development of the stem bore resistant maize germplasm

High quality maize centromere 10 sequence reveals evidence of frequent recombination events

Directory of Open Access Journals (Sweden)

Thomas Kai Wolfgruber

2016-03-01

Full Text Available The ancestral centromeres of maize contain long stretches of the tandemly arranged CentC repeat. The abundance of tandem DNA repeats and centromeric retrotransposons (CR have presented a significant challenge to completely assembling centromeres using traditional sequencing methods. Here we report a nearly complete assembly of the 1.85 Mb maize centromere 10 from inbred B73 using PacBio technology and BACs from the reference genome project. The error rates estimated from overlapping BAC sequences are 7 x 10-6 and 5 x 10-5 for mismatches and indels, respectively. The number of gaps in the region covered by the reassembly was reduced from 140 in the reference genome to three. Three expressed genes are located between 92 and 477 kb of the inferred ancestral CentC cluster, which lies within the region of highest centromeric repeat density. The improved assembly increased the count of full-length centromeric retrotransposons from 5 to 55 and revealed a 22.7 kb segmental duplication that occurred approximately 121,000 years ago. Our analysis provides evidence of frequent recombination events in the form of partial retrotransposons, deletions within retrotransposons, chimeric retrotransposons, segmental duplications including higher order CentC repeats, a deleted CentC monomer, centromere-proximal inversions, and insertion of mitochondrial sequences. Double-strand DNA break (DSB repair is the most plausible mechanism for these events and may be the major driver of centromere repeat evolution and diversity. This repair appears to be mediated by microhomology, suggesting that tandem repeats may have evolved to facilitate the repair of frequent DSBs in centromeres.

Genetic Factors Involved in Fumonisin Accumulation in Maize Kernels and Their Implications in Maize Agronomic Management and Breeding.

Science.gov (United States)

Santiago, Rogelio; Cao, Ana; Butrón, Ana

2015-08-20

Contamination of maize with fumonisins depends on the environmental conditions; the maize resistance to contamination and the interaction between both factors. Although the effect of environmental factors is a determinant for establishing the risk of kernel contamination in a region, there is sufficient genetic variability among maize to develop resistance to fumonisin contamination and to breed varieties with contamination at safe levels. In addition, ascertaining which environmental factors are the most important in a region will allow the implementation of risk monitoring programs and suitable cultural practices to reduce the impact of such environmental variables. The current paper reviews all works done to address the influence of environmental variables on fumonisin accumulation, the genetics of maize resistance to fumonisin accumulation, and the search for the biochemical and/or structural mechanisms of the maize plant that could be involved in resistance to fumonisin contamination. We also explore the outcomes of breeding programs and risk monitoring of undertaken projects.

RESPONSIVENESS OF SPATIAL PRICE VOLATILITY TO INCREASED GOVERNMENT PARTICIPATION IN MAIZE GRAIN AND MAIZE MEAL MARKETING IN ZAMBIA

OpenAIRE

Syampaku, E.M; Mafimisebi, Taiwo Ejiola

2014-01-01

The study analyzed the responsiveness of maize grain and maize meal spatial price volatilities to increased government participation in maize grain marketing in Zambia using descriptive statistics and vector auto-regression (VAR). This was achieved by comparing spatial price volatility means and spatial price means for the period under increased government participation with respective means for periods under limited government participation. Also, spatial price volatilities were regressed ag...

The genome of the pear (Pyrus bretschneideri Rehd.).

Science.gov (United States)

Wu, Jun; Wang, Zhiwen; Shi, Zebin; Zhang, Shu; Ming, Ray; Zhu, Shilin; Khan, M Awais; Tao, Shutian; Korban, Schuyler S; Wang, Hao; Chen, Nancy J; Nishio, Takeshi; Xu, Xun; Cong, Lin; Qi, Kaijie; Huang, Xiaosan; Wang, Yingtao; Zhao, Xiang; Wu, Juyou; Deng, Cao; Gou, Caiyun; Zhou, Weili; Yin, Hao; Qin, Gaihua; Sha, Yuhui; Tao, Ye; Chen, Hui; Yang, Yanan; Song, Yue; Zhan, Dongliang; Wang, Juan; Li, Leiting; Dai, Meisong; Gu, Chao; Wang, Yuezhi; Shi, Daihu; Wang, Xiaowei; Zhang, Huping; Zeng, Liang; Zheng, Danman; Wang, Chunlei; Chen, Maoshan; Wang, Guangbiao; Xie, Lin; Sovero, Valpuri; Sha, Shoufeng; Huang, Wenjiang; Zhang, Shujun; Zhang, Mingyue; Sun, Jiangmei; Xu, Linlin; Li, Yuan; Liu, Xing; Li, Qingsong; Shen, Jiahui; Wang, Junyi; Paull, Robert E; Bennetzen, Jeffrey L; Wang, Jun; Zhang, Shaoling

2013-02-01

The draft genome of the pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 194× coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these, ~28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other ~5.4-21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30-45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C3'H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.

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)

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...

Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize.

Science.gov (United States)

Thiebaut, Flávia; Rojas, Cristian A; Grativol, Clícia; Motta, Mariana Romeiro; Vieira, Tauan; Regulski, Michael; Martienssen, Robert A; Farinelli, Laurent; Hemerly, Adriana S; Ferreira, Paulo C G

2014-09-06

Small RNA (sRNA) has been described as a regulator of gene expression. In order to understand the role of maize sRNA (Zea mays-hybrid UENF 506-8) during association with endophytic nitrogen-fixing bacteria, we analyzed the sRNA regulated by its association with two diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense. Deep sequencing analysis was done with RNA extracted from plants inoculated with H. seropedicae, allowing the identification of miRNA and siRNA. A total of 25 conserved miRNA families and 15 novel miRNAs were identified. A dynamic regulation in response to inoculation was also observed. A hypothetical model involving copper-miRNA is proposed, emphasizing the fact that the up-regulation of miR397, miR398, miR408 and miR528, which is followed by inhibition of their targets, can facilitate association with diazotrophic bacteria. Similar expression patterns were observed in samples inoculated with A. brasilense. Moreover, novel miRNA and siRNA were classified in the Transposable Elements (TE) database, and an enrichment of siRNA aligned with TE was observed in the inoculated samples. In addition, an increase in 24-nt siRNA mapping to genes was observed, which was correlated with an increase in methylation of the coding regions and a subsequent reduction in transcription. Our results show that maize has RNA-based silencing mechanisms that can trigger specific responses when plants interact with beneficial endophytic diazotrophic bacteria. Our findings suggest important roles for sRNA regulation in maize, and probably in other plants, during association with diazotrophic bacteria, emphasizing the up-regulation of Cu-miRNA.

The SULTR gene family in maize (Zea mays L.): Gene cloning and expression analyses under sulfate starvation and abiotic stress.

Science.gov (United States)

Huang, Qin; Wang, Meiping; Xia, Zongliang

2018-01-01

Sulfur is an essential macronutrient required for plant growth, development and stress responses. The family of sulfate transporters (SULTRs) mediates the uptake and translocation of sulfate in higher plants. However, basic knowledge of the SULTR gene family in maize (Zea mays L.) is scarce. In this study, a genome-wide bioinformatic analysis of SULTR genes in maize was conducted, and the developmental expression patterns of the genes and their responses to sulfate starvation and abiotic stress were further investigated. The ZmSULTR family includes eight putative members in the maize genome and is clustered into four groups in the phylogenetic tree. These genes displayed differential expression patterns in various organs of maize. For example, expression of ZmSULTR1;1 and ZmSULTR4;1 was high in roots, and transcript levels of ZmSULTR3;1 and ZmSULTR3;3 were high in shoots. Expression of ZmSULTR1;2, ZmSULTR2;1, ZmSULTR3;3, and ZmSULTR4;1 was high in flowers. Also, these eight genes showed differential responses to sulfate deprivation in roots and shoots of maize seedlings. Transcript levels of ZmSULTR1;1, ZmSULTR1;2, and ZmSULTR3;4 were significantly increased in roots during 12-day-sulfate starvation stress, while ZmSULTR3;3 and ZmSULTR3;5 only showed an early response pattern in shoots. In addition, dynamic transcriptional changes determined via qPCR revealed differential expression profiles of these eight ZmSULTR genes in response to environmental stresses such as salt, drought, and heat stresses. Notably, all the genes, except for ZmSULTR3;3, were induced by drought and heat stresses. However, a few genes were induced by salt stress. Physiological determination showed that two important thiol-containing compounds, cysteine and glutathione, increased significantly under these abiotic stresses. The results suggest that members of the SULTR family might function in adaptations to sulfur deficiency stress and adverse growing environments. This study will lay a

Maize (Zea mays L.).

Science.gov (United States)

Frame, Bronwyn; Warnberg, Katey; Main, Marcy; Wang, Kan

2015-01-01

Agrobacterium tumefaciens-mediated transformation is an effective method for introducing genes into maize. In this chapter, we describe a detailed protocol for genetic transformation of the maize genotype Hi II. Our starting plant material is immature embryos cocultivated with an Agrobacterium strain carrying a standard binary vector. In addition to step-by-step laboratory transformation procedures, we include extensive details in growing donor plants and caring for transgenic plants in the greenhouse.

IMAZAPYR-RESISTANT MAIZE TECHNOLOGY ADOPTION FOR ...

African Journals Online (AJOL)

Prof. Adipala Ekwamu

decisions by protecting maize (Zea mays L.) crop in western Kenya from Striga. Key Words: Adopters, Zea ... Africa, efficient and profitable production of maize is severely constrained by ..... gap by understanding its source. African. Journal of ...

Repetition and lag effects in movement recognition.

Science.gov (United States)

Hall, C R; Buckolz, E

1982-03-01

Whether repetition and lag improve the recognition of movement patterns was investigated. Recognition memory was tested for one repetition, two-repetitions massed, and two-repetitions distributed with movement patterns at lags of 3, 5, 7, and 13. Recognition performance was examined both immediately afterwards and following a 48 hour delay. Both repetition and lag effects failed to be demonstrated, providing some support for the claim that memory is unaffected by repetition at a constant level of processing (Craik & Lockhart, 1972). There was, as expected, a significant decrease in recognition memory following the retention interval, but this appeared unrelated to repetition or lag.

Growth performance and carcass characteristics of Tanzania Shorthorn Zebu cattle finished on molasses or maize grain with rice or maize by-products

DEFF Research Database (Denmark)

Asimwe, I.; Kimambo, A. E.; Laswai, G. H.

2015-01-01

Forty five steers (2.5–3.0 years of age and 200±5 (SEM) kg body weight) were allotted randomly into five diets to assess the effects of finishing Tanzania Shorthorn Zebu (TSZ) cattle in feedlot using diets based on either molasses or maize grain combined with maize or rice by-products. The diets...... were hay and concentrate mixtures of hominy feed with molasses (HFMO), rice polishing with molasses (RPMO), hominy feed with maize meal (HFMM), rice polishing with maize meal (RPMM) and a control of maize meal with molasses (MMMO). All concentrate mixtures contained cotton seed cake, mineral mixture.......35 for HFMO) than in maize grain based diets (6.94, 6.73 and 6.19 for RPMM, MMMO and HFMM, respectively). Energy intake was highest (P

Prediction of the Maximum Number of Repetitions and Repetitions in Reserve From Barbell Velocity.

Science.gov (United States)

García-Ramos, Amador; Torrejón, Alejandro; Feriche, Belén; Morales-Artacho, Antonio J; Pérez-Castilla, Alejandro; Padial, Paulino; Haff, Guy Gregory

2018-03-01

To provide 2 general equations to estimate the maximum possible number of repetitions (XRM) from the mean velocity (MV) of the barbell and the MV associated with a given number of repetitions in reserve, as well as to determine the between-sessions reliability of the MV associated with each XRM. After determination of the bench-press 1-repetition maximum (1RM; 1.15 ± 0.21 kg/kg body mass), 21 men (age 23.0 ± 2.7 y, body mass 72.7 ± 8.3 kg, body height 1.77 ± 0.07 m) completed 4 sets of as many repetitions as possible against relative loads of 60%1RM, 70%1RM, 80%1RM, and 90%1RM over 2 separate sessions. The different loads were tested in a randomized order with 10 min of rest between them. All repetitions were performed at the maximum intended velocity. Both the general equation to predict the XRM from the fastest MV of the set (CV = 15.8-18.5%) and the general equation to predict MV associated with a given number of repetitions in reserve (CV = 14.6-28.8%) failed to provide data with acceptable between-subjects variability. However, a strong relationship (median r 2  = .984) and acceptable reliability (CV  .85) were observed between the fastest MV of the set and the XRM when considering individual data. These results indicate that generalized group equations are not acceptable methods for estimating the XRM-MV relationship or the number of repetitions in reserve. When attempting to estimate the XRM-MV relationship, one must use individualized relationships to objectively estimate the exact number of repetitions that can be performed in a training set.

Purification of high molecular weight genomic DNA from powdery mildew for long-read sequencing

Science.gov (United States)

The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which ...

Repetitive stress leads to impaired cognitive function that is associated with DNA hypomethylation, reduced BDNF and a dysregulated HPA axis.

Science.gov (United States)

Makhathini, Khayelihle B; Abboussi, Oualid; Stein, Dan J; Mabandla, Musa V; Daniels, William M U

2017-08-01

Exposure to repetitive stress has a negative influence on cognitive-affective functioning, with growing evidence that these effects may be mediated by a dysregulated hypothalamic-pituitary-adrenal (HPA) axis, abnormal neurotrophic factor levels and its subsequent impact on hippocampal function. However, there are few data about the effect of repetitive stressors on epigenetic changes in the hippocampus. In the present study, we examine how repetitive restrain stress (RRS) affects cognitive-affective functioning, HPA axis regulation, brain-derived neurotrophic factor (BDNF) levels, and global hippocampal DNA methylation. RRS was induced in rats by restraining the animals for 6h per day for 28 days. The novel object recognition test (NORT) was used to assess cognitive functioning and the open field test (OFT) was performed to assess anxiety-like behavior during the last week of stress. Hippocampal BDNF levels, glucocorticoid (GR) and mineralocorticoid (MR) receptor mRNA were assessed using real-time PCR and confirmed with Western blot, while ELISAs were used to determine plasma corticosterone levels and the global methylation status of the hippocampus. Animals exposed to repetitive stress demonstrated significant alterations in the NORT and OFT, had significantly increased plasma corticosterone and significantly decreased hippocampal BDNF concentrations. The expression levels of GR and MR mRNA and protein levels of these genes were significantly decreased in the stressed group compared to control animals. The global DNA methylation of the hippocampal genome of stressed animals was also significantly decreased compared to controls. The data here are consistent with previous work emphasizing the role of the HPA axis and neurotrophic factors in mediating cognitive-affective changes after exposure to repetitive stressors. Our findings, however, extend the literature by indicating that epigenetic alterations in the hippocampal genome may also play an important role in the

If you negate, you may forget: negated repetitions impair memory compared with affirmative repetitions.

Science.gov (United States)

Mayo, Ruth; Schul, Yaacov; Rosenthal, Meytal

2014-08-01

One of the most robust laws of memory is that repeated activation improves memory. Our study shows that the nature of repetition matters. Specifically, although both negated repetition and affirmative repetition improve memory compared with no repetition, negated repetition hinders memory compared with affirmative repetition. After showing participants different entities, we asked them about features of these entities, leading to either "yes" or "no" responses. Our findings show that correctly negating an incorrect feature of an entity elicits an active forgetting effect compared with correctly affirming its true features. For example, after seeing someone drink a glass of white wine, answering "no" to "was it red wine?" may lead one to greater memory loss of the individual drinking wine at all compared with answering "yes" to "was it white wine?" We find this negation-induced forgetting effect in 4 experiments that differ in (a) the meaning given for the negation, (b) the type of stimuli (visual or verbal), and (c) the memory measure (recognition or free recall). We discuss possible underlying mechanisms and offer theoretical and applied implications of the negation-induced forgetting effect in relation to other known inhibition effects. PsycINFO Database Record (c) 2014 APA, all rights reserved.

CERES-Maize model-based simulation of climate change impacts on maize yields and potential adaptive measures in Heilongjiang Province, China.

Science.gov (United States)

Lin, Yumei; Wu, Wenxiang; Ge, Quansheng

2015-11-01

Climate change would cause negative impacts on future agricultural production and food security. Adaptive measures should be taken to mitigate the adverse effects. The objectives of this study were to simulate the potential effects of climate change on maize yields in Heilongjiang Province and to evaluate two selected typical household-level autonomous adaptive measures (cultivar changes and planting time adjustments) for mitigating the risks of climate change based on the CERES-Maize model. The results showed that flowering duration and maturity duration of maize would be shortened in the future climate and thus maize yield would reduce by 11-46% during 2011-2099 relative to 1981-2010. Increased CO2 concentration would not benefit maize production significantly. However, substituting local cultivars with later-maturing ones and delaying the planting date could increase yields as the climate changes. The results provide insight regarding the likely impacts of climate change on maize yields and the efficacy of selected adaptive measures by presenting evidence-based implications and mitigation strategies for the potential negative impacts of future climate change. © 2014 Society of Chemical Industry.

Organizational heterogeneity of vertebrate genomes.

Science.gov (United States)

Frenkel, Svetlana; Kirzhner, Valery; Korol, Abraham

2012-01-01

Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

Organizational heterogeneity of vertebrate genomes.

Directory of Open Access Journals (Sweden)

Svetlana Frenkel

Full Text Available Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

Agrobacterium- and Biolistic-Mediated Transformation of Maize B104 Inbred.

Science.gov (United States)

Raji, Jennifer A; Frame, Bronwyn; Little, Daniel; Santoso, Tri Joko; Wang, Kan

2018-01-01

Genetic transformation of maize inbred genotypes remains non-routine for many laboratories due to variations in cell competency to induce embryogenic callus, as well as the cell's ability to receive and incorporate transgenes into the genome. This chapter describes two transformation protocols using Agrobacterium- and biolistic-mediated methods for gene delivery. Immature zygotic embryos of maize inbred B104, excised from ears harvested 10-14 days post pollination, are used as starting explant material. Disarmed Agrobacterium strains harboring standard binary vectors and the biolistic gun system Bio-Rad PDS-1000/He are used as gene delivery systems. The herbicide resistant bar gene and selection agent bialaphos are used for identifying putative transgenic type I callus events. Using the step-by-step protocols described here, average transformation frequencies (number of bialaphos resistant T 0 callus events per 100 explants infected or bombarded) of 4% and 8% can be achieved using the Agrobacterium- and biolistic-mediated methods, respectively. An estimated duration of 16-21 weeks is needed using either protocol from the start of transformation experiments to obtaining putative transgenic plantlets with established roots. In addition to laboratory in vitro procedures, detailed greenhouse protocols for producing immature ears as transformation starting material and caring for transgenic plants for seed production are also described.

The complexity of Rhipicephalus (Boophilus microplus genome characterised through detailed analysis of two BAC clones

Directory of Open Access Journals (Sweden)

Valle Manuel

2011-07-01

Full Text Available Abstract Background Rhipicephalus (Boophilus microplus (Rmi a major cattle ectoparasite and tick borne disease vector, impacts on animal welfare and industry productivity. In arthropod research there is an absence of a complete Chelicerate genome, which includes ticks, mites, spiders, scorpions and crustaceans. Model arthropod genomes such as Drosophila and Anopheles are too taxonomically distant for a reference in tick genomic sequence analysis. This study focuses on the de-novo assembly of two R. microplus BAC sequences from the understudied R microplus genome. Based on available R. microplus sequenced resources and comparative analysis, tick genomic structure and functional predictions identify complex gene structures and genomic targets expressed during tick-cattle interaction. Results In our BAC analyses we have assembled, using the correct positioning of BAC end sequences and transcript sequences, two challenging genomic regions. Cot DNA fractions compared to the BAC sequences confirmed a highly repetitive BAC sequence BM-012-E08 and a low repetitive BAC sequence BM-005-G14 which was gene rich and contained short interspersed elements (SINEs. Based directly on the BAC and Cot data comparisons, the genome wide frequency of the SINE Ruka element was estimated. Using a conservative approach to the assembly of the highly repetitive BM-012-E08, the sequence was de-convoluted into three repeat units, each unit containing an 18S, 5.8S and 28S ribosomal RNA (rRNA encoding gene sequence (rDNA, related internal transcribed spacer and complex intergenic region. In the low repetitive BM-005-G14, a novel gene complex was found between to 2 genes on the same strand. Nested in the second intron of a large 9 Kb papilin gene was a helicase gene. This helicase overlapped in two exonic regions with the papilin. Both these genes were shown expressed in different tick life stage important in ectoparasite interaction with the host. Tick specific sequence

The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA

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Lee Robert W

2009-03-01

Full Text Available Abstract Background The magnitude of noncoding DNA in organelle genomes can vary significantly; it is argued that much of this variation is attributable to the dissemination of selfish DNA. The results of a previous study indicate that the mitochondrial DNA (mtDNA of the green alga Volvox carteri abounds with palindromic repeats, which appear to be selfish elements. We became interested in the evolution and distribution of these repeats when, during a cursory exploration of the V. carteri nuclear DNA (nucDNA and plastid DNA (ptDNA sequences, we found palindromic repeats with similar structural features to those of the mtDNA. Upon this discovery, we decided to investigate the diversity and evolutionary implications of these palindromic elements by sequencing and characterizing large portions of mtDNA and ptDNA and then comparing these data to the V. carteri draft nuclear genome sequence. Results We sequenced 30 and 420 kilobases (kb of the mitochondrial and plastid genomes of V. carteri, respectively – resulting in partial assemblies of these genomes. The mitochondrial genome is the most bloated green-algal mtDNA observed to date: ~61% of the sequence is noncoding, most of which is comprised of short palindromic repeats spread throughout the intergenic and intronic regions. The plastid genome is the largest (>420 kb and most expanded (>80% noncoding ptDNA sequence yet discovered, with a myriad of palindromic repeats in the noncoding regions, which have a similar size and secondary structure to those of the mtDNA. We found that 15 kb (~0.01% of the nuclear genome are homologous to the palindromic elements of the mtDNA, and 50 kb (~0.05% are homologous to those of the ptDNA. Conclusion Selfish elements in the form of short palindromic repeats have propagated in the V. carteri mtDNA and ptDNA, resulting in the distension of these genomes. Copies of these same repeats are also found in a small fraction of the nucDNA, but appear to be inert in this

quixotic coupling between irrigation system and maize-cowpea

African Journals Online (AJOL)

ACSS

number row-1 and maize grain yield, respectively. The ridge ... Key Words: Furrow irrigation, water use efficiency, Zea mays. RÉSUMÉ ... important in arid and semi-arid regions, with ... as maize) canopy is not able to intercept all the solar radiation during the growth period. ... Intercropping maize and legumes considerably ...

Nutrient content in maize fertilized with tannery sludge vermicompost and irrigated with domestic wastewater

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Guilherme Malafaia

2016-11-01

Full Text Available This study analyzed the macro and micronutrient content of maize leaves (Zea mays L. grown in soil containing tannery sludge vermicomposting and irrigated with wastewater. The arrangement of the treatments consisted of a factorial 2x6 (two types of irrigation and six kinds of fertilizer in a completely randomized design, with five repetitions, totaling sixty experimental units. The following experimental units, irrigated with supply water (A and household wastewater (R, were established: (T1 Control Soil, with no chemical fertilization and no vermicomposting; (T2 Soil + NPK; (T3 Soil + primary sludge vermicompost; (T4 Soil + P + primary sludge vermicompost; (T5 Soil + P + liming sludge vermicompost; and (T6 Soil + liming sludge vermicompost. For the leaf-tissue analysis, the opposite whole leaf below the first (upper ear was collected from each plant, excluding the midrib at the onset of the female inflorescence. The results showed that both wastewater and the tannery sludge vermicomposts can be a good source of nutrients for maize plants, since the macro and micronutrients in the leaves of plants were satisfactory and no signs or symptoms of toxicity were observed. While leaf analysis alone is insufficient to assess the nutritional status of plants, this study innovatively suggests the potential beneficial use of a combination of wastewater and tannery sludge vermicompost in the cultivation of corn, motivating new research.

Propanol in maize silage at Danish dairy farms

DEFF Research Database (Denmark)

Raun, Birgitte Marie Løvendahl; Kristensen, Niels Bastian

2010-01-01

The objective of the present study was to investigate the prevalence maize silage containing propanol, the seasonal variation in propanol content of maize silage, and correlations between propanol and other fermentation products in maize silage collected from 20 randomly selected Danish dairy farms...... farms, the maize silage had ≥5 g propanol/kg DM. The present study indicates that dairy cows in Denmark are commonly exposed to propanol and that approximately 20% of the dairy cows will have an intake in the range of 75-100 g propanol/d under common feeding conditions....

Water transfer in an alfalfa/maize association

International Nuclear Information System (INIS)

Corak, S.J.; Blevins, D.G.; Pallardy, S.G.

1987-01-01

The authors investigated the possibility of interspecific water transfer in an alfalfa (Medicago sativa L.) and maize (Zea mays L.) association. An alfalfa plant was grown through two vertically stacked plastic tubes. A 5 centimeter air gap between tubes was bridged by alfalfa roots. Five-week old maize plants with roots confined to the top tube were not watered, while associated alfalfa roots had free access to water in the bottom tube (the -/+ treatment). Additional treatments included: top and bottom tubes watered (+/+), top and bottom tubes droughted (-/-), and top tube droughted after removal of alfalfa root bridges and routine removal of alfalfa tillers (-*). Predawn leaf water potential of maize in the -/+ treatment fell to -1.5 megapascals 13 days after the start of drought; thereafter, predawn and midday potentials were maintained near -1.9 megapascals. Leaf water potentials of maize in the -/- and -* treatments declined steadily; all plants in these treatments were completely desiccated before day 50. High levels of tritium activity were detected in water extracted from both alfalfa and maize leaves after 3 H 2 O was injected into the bottom -/+ tube at day 70 or later. Maize in the -/+ treatment was able to survive an otherwise lethal period of drought by utilizing water lost by alfalfa roots

S1 satellite DNA repetitive units display identical structure and overall variability in all Anatolian brown frog taxa.

Science.gov (United States)

Picariello, Orfeo; Feliciello, Isidoro; Chinali, Gianni

2016-02-01

S1 satellite DNA from Palearctic brown frogs has a species-specific structure in all European species. We characterized S1 satellite DNA from the Anatolian brown frogs Rana macrocnemis, R. camerani, and R. holtzi in order to define their taxonomic rank and the structure of this satellite in this frog lineage. Southern blots of genomic DNA digested with KpnI, EcoRV, NdeI, NheI, or StuI produced the same pattern of satellite DNA bands. Moreover, quantitative dot blots showed that this satellite DNA accounts for 0.1 % of the genome in all taxa. Analysis of the overall genomic variability of the S1a repeat sequence in specimens from various populations demonstrated that this repetitive unit also has the same size (476 bp), the same most common sequence (MCS) and the same overall variability in all three taxa, and also in R. macrocnemis tavasensis. The S1a repetitive unit presents three deletions of 9, 8 and 1 bp compared to the 494-bp S1a repeat from European frogs. The S1a MCS has three variable positions (sequence WWTK in positions 183-186), due to the presence of two repeat subpopulations with motifs AATG and WWTT in all taxa. Unlike previously analyzed mitochondrial and nuclear sequences that show considerable variations among these taxa, no difference could be detected in the structure and variability of the S1 satellite repetitive units. This suggests that these taxa should belong to a single species. Our results indicate that this satellite DNA variety probably formed when the Anatolian lineage radiated from common ancestor about 4 mya, and since then has maintained its structure in all four taxa examined.

Sub-Saharan African maize-based foods

NARCIS (Netherlands)

Ekpa, Onu; Palacios-Rojas, Natalia; Kruseman, Gideon; Fogliano, Vincenzo; Linnemann, Anita R.

2018-01-01

The demand for maize in Sub-Saharan Africa will triple by 2050 due to rapid population growth, while challenges from climate change will threaten agricultural productivity. Most maize breeding programmes have focused on improving agronomic properties and have paid relatively little attention to

The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly

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J. W. Clouse

2016-03-01

Full Text Available Amaranth ( L. is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32, and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which -like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (, , and and their putative progenitor ( were resequenced. A single nucleotide polymorphism (SNP phylogeny supported the classification of as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for using the BioNano Genomics’ Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet ( L. and estimated, using analysis, the age of the most recent polyploidization event in amaranth.

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives.

Science.gov (United States)

Crossa, José; Pérez-Rodríguez, Paulino; Cuevas, Jaime; Montesinos-López, Osval; Jarquín, Diego; de Los Campos, Gustavo; Burgueño, Juan; González-Camacho, Juan M; Pérez-Elizalde, Sergio; Beyene, Yoseph; Dreisigacker, Susanne; Singh, Ravi; Zhang, Xuecai; Gowda, Manje; Roorkiwal, Manish; Rutkoski, Jessica; Varshney, Rajeev K

2017-11-01

Genomic selection (GS) facilitates the rapid selection of superior genotypes and accelerates the breeding cycle. In this review, we discuss the history, principles, and basis of GS and genomic-enabled prediction (GP) as well as the genetics and statistical complexities of GP models, including genomic genotype×environment (G×E) interactions. We also examine the accuracy of GP models and methods for two cereal crops and two legume crops based on random cross-validation. GS applied to maize breeding has shown tangible genetic gains. Based on GP results, we speculate how GS in germplasm enhancement (i.e., prebreeding) programs could accelerate the flow of genes from gene bank accessions to elite lines. Recent advances in hyperspectral image technology could be combined with GS and pedigree-assisted breeding. Copyright © 2017 Elsevier Ltd. All rights reserved.

DNABIT Compress - Genome compression algorithm.

Science.gov (United States)

Rajarajeswari, Pothuraju; Apparao, Allam

2011-01-22

Data compression is concerned with how information is organized in data. Efficient storage means removal of redundancy from the data being stored in the DNA molecule. Data compression algorithms remove redundancy and are used to understand biologically important molecules. We present a compression algorithm, "DNABIT Compress" for DNA sequences based on a novel algorithm of assigning binary bits for smaller segments of DNA bases to compress both repetitive and non repetitive DNA sequence. Our proposed algorithm achieves the best compression ratio for DNA sequences for larger genome. Significantly better compression results show that "DNABIT Compress" algorithm is the best among the remaining compression algorithms. While achieving the best compression ratios for DNA sequences (Genomes),our new DNABIT Compress algorithm significantly improves the running time of all previous DNA compression programs. Assigning binary bits (Unique BIT CODE) for (Exact Repeats, Reverse Repeats) fragments of DNA sequence is also a unique concept introduced in this algorithm for the first time in DNA compression. This proposed new algorithm could achieve the best compression ratio as much as 1.58 bits/bases where the existing best methods could not achieve a ratio less than 1.72 bits/bases.

Lack of detectable allergenicity in genetically modified maize containing "Cry" proteins as compared to native maize based on in silico & in vitro analysis.

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Chandni Mathur

Full Text Available Genetically modified, (GM crops with potential allergens must be evaluated for safety and endogenous IgE binding pattern compared to native variety, prior to market release.To compare endogenous IgE binding proteins of three GM maize seeds containing Cry 1Ab,1Ac,1C transgenic proteins with non GM maize.An integrated approach of in silico & in vitro methods was employed. Cry proteins were tested for presence of allergen sequence by FASTA in allergen databases. Biochemical assays for maize extracts were performed. Specific IgE (sIgE and Immunoblot using food sensitized patients sera (n = 39 to non GM and GM maize antigens was performed.In silico approaches, confirmed for non sequence similarity of stated transgenic proteins in allergen databases. An insignificant (p> 0.05 variation in protein content between GM and non GM maize was observed. Simulated Gastric Fluid (SGF revealed reduced number of stable protein fractions in GM then non GM maize which might be due to shift of constituent protein expression. Specific IgE values from patients showed insignificant difference in non GM and GM maize extracts. Five maize sensitized cases, recognized same 7 protein fractions of 88-28 kD as IgE bindng in both GM and non-GM maize, signifying absence of variation. Four of the reported IgE binding proteins were also found to be stable by SGF.Cry proteins did not indicate any significant similarity of >35% in allergen databases. Immunoassays also did not identify appreciable differences in endogenous IgE binding in GM and non GM maize.

Maize-Pathogen Interactions: An Ongoing Combat from a Proteomics Perspective

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Olga Pechanova

2015-11-01

Full Text Available Maize (Zea mays L. is a host to numerous pathogenic species that impose serious diseases to its ear and foliage, negatively affecting the yield and the quality of the maize crop. A considerable amount of research has been carried out to elucidate mechanisms of maize-pathogen interactions with a major goal to identify defense-associated proteins. In this review, we summarize interactions of maize with its agriculturally important pathogens that were assessed at the proteome level. Employing differential analyses, such as the comparison of pathogen-resistant and susceptible maize varieties, as well as changes in maize proteomes after pathogen challenge, numerous proteins were identified as possible candidates in maize resistance. We describe findings of various research groups that used mainly mass spectrometry-based, high through-put proteomic tools to investigate maize interactions with fungal pathogens Aspergillus flavus, Fusarium spp., and Curvularia lunata, and viral agents Rice Black-streaked Dwarf Virus and Sugarcane Mosaic Virus.

Maize-Pathogen Interactions: An Ongoing Combat from a Proteomics Perspective.

Science.gov (United States)

Pechanova, Olga; Pechan, Tibor

2015-11-30

Maize (Zea mays L.) is a host to numerous pathogenic species that impose serious diseases to its ear and foliage, negatively affecting the yield and the quality of the maize crop. A considerable amount of research has been carried out to elucidate mechanisms of maize-pathogen interactions with a major goal to identify defense-associated proteins. In this review, we summarize interactions of maize with its agriculturally important pathogens that were assessed at the proteome level. Employing differential analyses, such as the comparison of pathogen-resistant and susceptible maize varieties, as well as changes in maize proteomes after pathogen challenge, numerous proteins were identified as possible candidates in maize resistance. We describe findings of various research groups that used mainly mass spectrometry-based, high through-put proteomic tools to investigate maize interactions with fungal pathogens Aspergillus flavus, Fusarium spp., and Curvularia lunata, and viral agents Rice Black-streaked Dwarf Virus and Sugarcane Mosaic Virus.

Genomic diversity in two related plant species with and without sex chromosomes--Silene latifolia and S. vulgaris.

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Radim Cegan

Full Text Available Genome size evolution is a complex process influenced by polyploidization, satellite DNA accumulation, and expansion of retroelements. How this process could be affected by different reproductive strategies is still poorly understood.We analyzed differences in the number and distribution of major repetitive DNA elements in two closely related species, Silene latifolia and S. vulgaris. Both species are diploid and possess the same chromosome number (2n = 24, but differ in their genome size and mode of reproduction. The dioecious S. latifolia (1C = 2.70 pg DNA possesses sex chromosomes and its genome is 2.5× larger than that of the gynodioecious S. vulgaris (1C = 1.13 pg DNA, which does not possess sex chromosomes. We discovered that the genome of S. latifolia is larger mainly due to the expansion of Ogre retrotransposons. Surprisingly, the centromeric STAR-C and TR1 tandem repeats were found to be more abundant in S. vulgaris, the species with the smaller genome. We further examined the distribution of major repetitive sequences in related species in the Caryophyllaceae family. The results of FISH (fluorescence in situ hybridization on mitotic chromosomes with the Retand element indicate that large rearrangements occurred during the evolution of the Caryophyllaceae family.Our data demonstrate that the evolution of genome size in the genus Silene is accompanied by the expansion of different repetitive elements with specific patterns in the dioecious species possessing the sex chromosomes.

Differential resistance reaction of maize genotypes to maize stem borer (Chilo partellus Swinhoe at Chitwan, Nepal

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Ghanashyam Bhandari

2016-12-01

Full Text Available Maize stem borer (MSB, Chilo partellus Swinhoe, Lepidoptera: Pyralidae is one of the most important insect pest of maize in Nepal. Host plant resistance is the cost-effective, ecologically sound and stable approach to reduce damage by stem borers. Forty four maize genotypes were screened for resistance to maize stem borer at the research field of National Maize Research Program, Rampur during spring seasons (March to June of two consecutive years 2013 and 2014. The maize genotypes were evaluated in randomized complete block design with three replications and data were collected on foliar damage rating, tunnel length and number of exit holes made by the borer. The foliar damage and tunnel length damage were significant for genotypes for both the years. The exit holes were not significant in 2013 but significant in 2014 ranging from 2-6 scale. The foliar rating ranged from 2 to 5.5 in 2013 and 1.1 to 4.5 in 2014 on a 1-9 rating scale. The highly resistant genotypes (10 cm scale. The least susceptible genotypes (<5 cm were RampurSO3F8, RampurSO3FQ02 and RampurS10F18. The genotypes having least exit holes (2.0 in 2014 were RampurSO3F8, RampurSO3FQ02, RampurS10F18. Thus less damage parameters were observed in R-POP-2, RML-5/RML-8, RampurSO3F8, RampurSO3FQ02 and RampurS10F18 and therefore they can be used as parents or as sources of resistance in breeding program.

Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.).

Science.gov (United States)

Mascagni, Flavia; Giordani, Tommaso; Ceccarelli, Marilena; Cavallini, Andrea; Natali, Lucia

2017-08-18

Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels. After determining the relative genome size of each species, genomic DNA was isolated and subjected to Illumina sequencing. Then, different assembling and clustering approaches allowed exploring the repetitive component of all genomes. On average, repetitive DNA in Helianthus species represented more than 75% of the genome, being composed mostly by long terminal repeat retrotransposons. Also, the prevalence of Gypsy over Copia superfamily was observed and, among lineages, Chromovirus was by far the most represented. Although nearly all the same sublineages are present in all species, we found considerable variability in the abundance of diverse retrotransposon lineages and sublineages, especially between annual and perennial species. This large variability should indicate that different events of amplification or loss related to these elements occurred following species separation and should have been involved in species differentiation. Our data allowed us inferring on the extent of interspecific repetitive DNA variation related to LTR-RE abundance, investigating the relationship between changes of LTR-RE abundance and the evolution of the genus, and determining the degree of coevolution of different LTR-RE lineages or sublineages between and within species. Moreover, the data suggested that LTR-RE abundance in a species was affected by the annual or perennial

St2-80: a new FISH marker for St genome and genome analysis in Triticeae.

Science.gov (United States)

Wang, Long; Shi, Qinghua; Su, Handong; Wang, Yi; Sha, Lina; Fan, Xing; Kang, Houyang; Zhang, Haiqin; Zhou, Yonghong

2017-07-01

The St genome is one of the most fundamental genomes in Triticeae. Repetitive sequences are widely used to distinguish different genomes or species. The primary objectives of this study were to (i) screen a new sequence that could easily distinguish the chromosome of the St genome from those of other genomes by fluorescence in situ hybridization (FISH) and (ii) investigate the genome constitution of some species that remain uncertain and controversial. We used degenerated oligonucleotide primer PCR (Dop-PCR), Dot-blot, and FISH to screen for a new marker of the St genome and to test the efficiency of this marker in the detection of the St chromosome at different ploidy levels. Signals produced by a new FISH marker (denoted St 2 -80) were present on the entire arm of chromosomes of the St genome, except in the centromeric region. On the contrary, St 2 -80 signals were present in the terminal region of chromosomes of the E, H, P, and Y genomes. No signal was detected in the A and B genomes, and only weak signals were detected in the terminal region of chromosomes of the D genome. St 2 -80 signals were obvious and stable in chromosomes of different genomes, whether diploid or polyploid. Therefore, St 2 -80 is a potential and useful FISH marker that can be used to distinguish the St genome from those of other genomes in Triticeae.

Fungal Diversity of Maize (Zea Mays L. Grains

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Gulbis Kaspars

2016-06-01

Full Text Available Maize is becoming more and more important crop for dairy farming as forage and as substrate for biogas production. The mycotoxin producing fungi can spoil feed, reduce cattle productivity and cause health problems. The aim of this research was to study the mycoflora of maize grains in order to clarify the fungal composition and verify the presence of potential mycotoxin producing fungi. The grain samples were collected from different maize hybrid performance trial in Research and Study farm “Vecauce” of Latvia University of Agriculture in 2014. The fungi from 14 genera were isolated from surface sterilized grains. The most abundant were Alternaria, Fusarium and Penicillium spp. Mycotoxin producing fungi are present in maize grain mycoflora, and there is a risk that maize production can contain mycotoxins.

Maize Bioactive Peptides against Cancer

Science.gov (United States)

Díaz-Gómez, Jorge L.; Castorena-Torres, Fabiola; Preciado-Ortiz, Ricardo E.; García-Lara, Silverio

2017-06-01

Cancer is one of the main chronic degenerative diseases worldwide. In recent years, consumption of whole-grain cereals and their derived food products has been associated with reduction risks of various types of cancer. Cereals main biomolecules includes proteins, peptides, and amino acids present in different quantities within the grain. The nutraceutical properties associated with peptides exerts biological functions that promote health and prevent this disease. In this review, we report the current status and advances on maize peptides regarding bioactive properties that have been reported such as antioxidant, antihypertensive, hepatoprotective, and anti-tumour activities. We also highlighted its biological potential through which maize bioactive peptides exert anti-cancer activity. Finally, we analyse and emphasize the possible areas of application for maize peptides.

Repetitive Questioning Exasperates Caregivers

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R. C. Hamdy MD

2018-01-01

Full Text Available Repetitive questioning is due to an impaired episodic memory and is a frequent, often presenting, problem in patients with Alzheimer’s disease (amnestic type. It is due to the patients’ difficulties learning new information, retaining it, and recalling it, and is often aggravated by a poor attention span and easy distractibility. A number of factors may trigger and maintain repetitive questioning. Caregivers should try to identify and address these triggers. In the case discussion presented, it is due to the patient’s concerns about her and her family’s safety triggered by watching a particularly violent movie aired on TV. What went wrong in the patient/caregiver interaction and how it could have been avoided or averted are explored. Also reviewed are the impact of repetitive questioning, the challenges it raises for caregivers, and some effective intervention strategies that may be useful to diffuse the angst that caregivers experience with repetitive questioning.

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

Science.gov (United States)

Paschold, Anja; Jia, Yi; Marcon, Caroline; Lund, Steve; Larson, Nick B.; Yeh, Cheng-Ting; Ossowski, Stephan; Lanz, Christa; Nettleton, Dan; Schnable, Patrick S.; Hochholdinger, Frank

2012-01-01

Typically, F1-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots, early in the developmental manifestation of heterotic root traits. The application of statistical methods and a suitable experimental design established that 34,233 (i.e., 86%) of all high-confidence maize genes were expressed in at least one genotype. Nearly 70% of all expressed genes were differentially expressed between the two parents and 42%–55% of expressed genes were differentially expressed between one of the parents and one of the hybrids. In both hybrids, ∼10% of expressed genes exhibited nonadditive gene expression. Consistent with the dominance model (i.e., complementation) for heterosis, 1124 genes that were expressed in the hybrids were expressed in only one of the two parents. For 65 genes, it could be shown that this was a consequence of complementation of genomic presence/absence variation. For dozens of other genes, alleles from the inactive inbred were activated in the hybrid, presumably via interactions with regulatory factors from the active inbred. As a consequence of these types of complementation, both hybrids expressed more genes than did either parental inbred. Finally, in hybrids, ∼14% of expressed genes exhibited allele-specific expression (ASE) levels that differed significantly from the parental-inbred expression ratios, providing further evidence for interactions of regulatory factors from one parental genome with target genes from the other parental genome. PMID:23086286

Strategic Marketing Problems in the Uganda Maize Seed Industry

OpenAIRE

Larson, Donald W.; Mbowa, Swaibu

2004-01-01

Strategic marketing issues and challenges face maize seed marketing firms as farmers increasingly adopt hybrid varieties in a modernizing third world country such as Uganda. The maize seed industry of Uganda has changed dramatically from a government owned, controlled, and operated industry to a competitive market oriented industry with substantial private firm investment and participation. The new maize seed industry is young, dynamic, growing and very competitive. The small maize seed marke...

Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes.

Science.gov (United States)

Jeong, Young-Min; Kim, Namshin; Ahn, Byung Ohg; Oh, Mijin; Chung, Won-Hyong; Chung, Hee; Jeong, Seongmun; Lim, Ki-Byung; Hwang, Yoon-Jung; Kim, Goon-Bo; Baek, Seunghoon; Choi, Sang-Bong; Hyung, Dae-Jin; Lee, Seung-Won; Sohn, Seong-Han; Kwon, Soo-Jin; Jin, Mina; Seol, Young-Joo; Chae, Won Byoung; Choi, Keun Jin; Park, Beom-Seok; Yu, Hee-Ju; Mun, Jeong-Hwan

2016-07-01

This study presents a chromosome-scale draft genome sequence of radish that is assembled into nine chromosomal pseudomolecules. A comprehensive comparative genome analysis with the Brassica genomes provides genomic evidences on the evolution of the mesohexaploid radish genome. Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the chromosome sequences of R. sativus cv. WK10039. The radish genome was sequenced and assembled into 426.2 Mb spanning >98 % of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36 % of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of nine chromosomes in radish was rearranged from the chromosomes of hexaploid progenitor. Overall, this study provides a chromosome-scale draft genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing.

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Margaret Staton

Full Text Available Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence.

Computer-Related Repetitive Stress Injuries

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... Staying Safe Videos for Educators Search English Español Computer-Related Repetitive Stress Injuries KidsHealth / For Parents / Computer-Related Repetitive Stress Injuries What's in this article? ...

Maize production in mid hills of Nepal: from food to feed security

OpenAIRE

Krishna Prasad Timsina; Yuga Nath Ghimire; Jeevan Lamichhane

2016-01-01

This study was undertaken in 2016 to analyze the production and utilization of maize in Nepal. Sixty maize growers from Kavre and Lamjung districts were selected using purposive, cluster and simple random sampling techniques. Similarly, six feed industries and five maize experts from Chitwan district were also interviewed. Study shows 56% of the total areas were used for maize production and 50% of the maize areas were covered by hybrid maize. There was no practice of contract maize productio...

Finding the joker among the maize endogenous reference genes for genetically modified organism (GMO) detection.

Science.gov (United States)

Paternò, Annalisa; Marchesi, Ugo; Gatto, Francesco; Verginelli, Daniela; Quarchioni, Cinzia; Fusco, Cristiana; Zepparoni, Alessia; Amaddeo, Demetrio; Ciabatti, Ilaria

2009-12-09

The comparison of five real-time polymerase chain reaction (PCR) methods targeted at maize ( Zea mays ) endogenous sequences is reported. PCR targets were the alcohol dehydrogenase (adh) gene for three methods and high-mobility group (hmg) gene for the other two. The five real-time PCR methods have been checked under repeatability conditions at several dilution levels on both pooled DNA template from several genetically modified (GM) maize certified reference materials (CRMs) and single CRM DNA extracts. Slopes and R(2) coefficients of all of the curves obtained from the adopted regression model were compared within the same method and among all of the five methods, and the limit of detection and limit of quantitation were analyzed for each PCR system. Furthermore, method equivalency was evaluated on the basis of the ability to estimate the target haploid genome copy number at each concentration level. Results indicated that, among the five methods tested, one of the hmg-targeted PCR systems can be considered equivalent to the others but shows the best regression parameters and a higher repeteability along the dilution range. Thereby, it is proposed as a valid module to be coupled to different event-specific real-time PCR for maize genetically modified organism (GMO) quantitation. The resulting practicability improvement on the analytical control of GMOs is discussed.

The role of short-term memory impairment in nonword repetition, real word repetition, and nonword decoding: A case study.

Science.gov (United States)

Peter, Beate

2018-01-01

In a companion study, adults with dyslexia and adults with a probable history of childhood apraxia of speech showed evidence of difficulty with processing sequential information during nonword repetition, multisyllabic real word repetition and nonword decoding. Results suggested that some errors arose in visual encoding during nonword reading, all levels of processing but especially short-term memory storage/retrieval during nonword repetition, and motor planning and programming during complex real word repetition. To further investigate the role of short-term memory, a participant with short-term memory impairment (MI) was recruited. MI was confirmed with poor performance during a sentence repetition and three nonword repetition tasks, all of which have a high short-term memory load, whereas typical performance was observed during tests of reading, spelling, and static verbal knowledge, all with low short-term memory loads. Experimental results show error-free performance during multisyllabic real word repetition but high counts of sequence errors, especially migrations and assimilations, during nonword repetition, supporting short-term memory as a locus of sequential processing deficit during nonword repetition. Results are also consistent with the hypothesis that during complex real word repetition, short-term memory is bypassed as the word is recognized and retrieved from long-term memory prior to producing the word.

Vulnerability of Maize Yields to Droughts in Uganda

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Terence Epule Epule

2017-03-01

Full Text Available Climate projections in Sub-Saharan Africa (SSA forecast an increase in the intensity and frequency of droughts with implications for maize production. While studies have examined how maize might be affected at the continental level, there have been few national or sub-national studies of vulnerability. We develop a vulnerability index that combines sensitivity, exposure and adaptive capacity and that integrates agroecological, climatic and socio-economic variables to evaluate the national and spatial pattern of maize yield vulnerability to droughts in Uganda. The results show that maize yields in the north of Uganda are more vulnerable to droughts than in the south and nationally. Adaptive capacity is higher in the south of the country than in the north. Maize yields also record higher levels of sensitivity and exposure in the north of Uganda than in the south. Latitudinally, it is observed that maize yields in Uganda tend to record higher levels of vulnerability, exposure and sensitivity towards higher latitudes, while in contrast, the adaptive capacity of maize yields is higher towards the lower latitudes. In addition to lower precipitation levels in the north of the country, these observations can also be explained by poor soil quality in most of the north and socio-economic proxies, such as, higher poverty and lower literacy rates in the north of Uganda.

Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction.

Science.gov (United States)

Wu, Chen; Twort, Victoria G; Crowhurst, Ross N; Newcomb, Richard D; Buckley, Thomas R

2017-11-16

Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects. The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria, the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

OpenAIRE

Elsik, Christine G.; Tellam, Ross L.; Worley, Kim C.; Gibbs, Richard A.; Abatepaulo, Antonio R. R.; Abbey, Colette A.; Adelson, David L.; Aerts, Jan; Ahola, Virpi; Alexander, Lee; Alioto, Tyler; Almeida, Iassudara G.; Amadio, Ariel F.; Anatriello, Elen; Antonarakis, Stylianos E.

2009-01-01

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specifi...

Oven-drying reduces ruminal starch degradation in maize kernels

NARCIS (Netherlands)

Ali, M.; Cone, J.W.; Hendriks, W.H.; Struik, P.C.

2014-01-01

The degradation of starch largely determines the feeding value of maize (Zea mays L.) for dairy cows. Normally, maize kernels are dried and ground before chemical analysis and determining degradation characteristics, whereas cows eat and digest fresh material. Drying the moist maize kernels

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize.

Science.gov (United States)

Kelley, Rowena Y; Gresham, Cathy; Harper, Jonathan; Bridges, Susan M; Warburton, Marilyn L; Hawkins, Leigh K; Pechanova, Olga; Peethambaran, Bela; Pechan, Tibor; Luthe, Dawn S; Mylroie, J E; Ankala, Arunkanth; Ozkan, Seval; Henry, W B; Williams, W P

2010-10-07

Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database

Effect of organic fertilizers on maize production in Eastern Georgia

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Jolokhava, Tamar; Kenchiashvili, Naira; Tarkhnishvili, Maia; Ghambashidze, Giorgi

2016-04-01

Maize remains to be the most important cereal crop in Georgia. Total area of arable land under cereal crops production equals to 184 thousands hectares (FAO statistical yearbook, 2014), from which maize takes the biggest share. Leading position of maize among other cereal crops is caused by its dual purpose as food and feed product. In Spite of a relatively high production of maize to other cereals there is still a high demand on it, especially as feed for animal husbandry. The same tendency is seen in organic production, where producers of livestock and poultry products require organically grown maize, the average yield of which is much less than those produced conventionally. Therefore, it is important to increase productivity of maize in organic farms. Current study aimed to improve maize yield using locally produced organic fertilizers and to compare them to the effect of mineral fertilizers. The study was carried out in Eastern Georgia under dry subtropical climate conditions on local hybrid of maize. This is the first attempt to use hybrid maize (developed with organic plant breeding method) in organic field trials in Georgia. The results shown, that grain yield from two different types of organic fertilizers reached 70% of the yields achieved with industrial mineral fertilizers. As on farm level differences between organic and conventional maize production are much severe, the results from the field trials seems to be promising for future improvement of organic cereal crop production.

Discovery of the first maize-infecting mastrevirus in the Americas using a vector-enabled metagenomics approach.

Science.gov (United States)

Fontenele, Rafaela S; Alves-Freitas, Dione M T; Silva, Pedro I T; Foresti, Josemar; Silva, Paulo R; Godinho, Márcio T; Varsani, Arvind; Ribeiro, Simone G

2018-01-01

The genus Mastrevirus (family Geminiviridae) is composed of single-stranded DNA viruses that infect mono- and dicotyledonous plants and are transmitted by leafhoppers. In South America, there have been only two previous reports of mastreviruses, both identified in sweet potatoes (from Peru and Uruguay). As part of a general viral surveillance program, we used a vector-enabled metagenomics (VEM) approach and sampled leafhoppers (Dalbulus maidis) in Itumbiara (State of Goiás), Brazil. High-throughput sequencing of viral DNA purified from the leafhopper sample revealed mastrevirus-like contigs. Using a set of abutting primers, a 2746-nt circular genome was recovered. The circular genome has a typical mastrevirus genome organization and shares 99% pairwise identity with the one from the leafhopper. This is the first report of a maize-infecting mastrevirus in the Americas, the first identified in a non-vegetatively propagated mastrevirus host in South America, and the first mastrevirus to be identified in Brazil.

A Fungal Effector With Host Nuclear Localization and DNA-Binding Properties Is Required for Maize Anthracnose Development.

Science.gov (United States)

Vargas, Walter A; Sanz-Martín, José M; Rech, Gabriel E; Armijos-Jaramillo, Vinicio D; Rivera, Lina P; Echeverria, María Mercedes; Díaz-Mínguez, José M; Thon, Michael R; Sukno, Serenella A

2016-02-01

Plant pathogens have the capacity to manipulate the host immune system through the secretion of effectors. We identified 27 putative effector proteins encoded in the genome of the maize anthracnose pathogen Colletotrichum graminicola that are likely to target the host's nucleus, as they simultaneously contain sequence signatures for secretion and nuclear localization. We functionally characterized one protein, identified as CgEP1. This protein is synthesized during the early stages of disease development and is necessary for anthracnose development in maize leaves, stems, and roots. Genetic, molecular, and biochemical studies confirmed that this effector targets the host's nucleus and defines a novel class of double-stranded DNA-binding protein. We show that CgEP1 arose from a gene duplication in an ancestor of a lineage of monocot-infecting Colletotrichum spp. and has undergone an intense evolution process, with evidence for episodes of positive selection. We detected CgEP1 homologs in several species of a grass-infecting lineage of Colletotrichum spp., suggesting that its function may be conserved across a large number of anthracnose pathogens. Our results demonstrate that effectors targeted to the host nucleus may be key elements for disease development and aid in the understanding of the genetic basis of anthracnose development in maize plants.

Intercropping maize with cassava or cowpea in Ghana | Ennin ...

African Journals Online (AJOL)

Maize/cassava and maize/cowpea intercrops were evaluated in southern Ghana, over a 5-year period to determine the optimum combination of component crop varieties and component plant population densities to optimize productivity of maize-based intercropping systems. Results indicated that some cowpea varieties ...

Romanian maize

DEFF Research Database (Denmark)

Sauer, Johannes; Balint, Borbala

This research aims at shedding empirical light on the relative efficiency of small-scale maize producers in Romania. Farmers in transition countries still face heavily distorted price systems resulting from imperfect market conditions and socioeconomic and institutional constraints. To capture...

The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats.

Directory of Open Access Journals (Sweden)

Andrew J Alverson

2011-01-01

Full Text Available The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean, and show that despite its unexceptional size (401,262 nt, the genome is unusually depauperate in repetitive DNA and "promiscuous" sequences from the chloroplast and nuclear genomes. Although Vigna lacks the large, recombinationally active repeats typical of most other seed plants, a PCR survey of its modest repertoire of short (38-297 nt repeats nevertheless revealed evidence for recombination across all of them. A set of novel control assays showed, however, that these results could instead reflect, in part or entirely, artifacts of PCR-mediated recombination. Consequently, we recommend that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence content of plant mitochondrial genomes.

Identification and phylogenetic analysis of a novel starch synthase in maize

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Hanmei eLiu

2015-11-01

Full Text Available Starch is an important reserve of carbon and energy in plants, providing the majority of calories in the human diet and animal feed. Its synthesis is orchestrated by several key enzymes, and the amount and structure of starch, affecting crop yield and quality, are determined mainly by starch synthase (SS activity. To date, five SS isoforms, including SSI-IV and Granule Bound Starch Synthase (GBSS have been identified and their physiological functions have been well characterized. Here, we report the identification of a new SS isoform in maize, designated SSV. By searching sequenced genomes, SSV has been found in all green plants with conserved sequences and gene structures. Our phylogenetic analysis based on 780 base pairs has suggested that SSIV and SSV resulted from a gene duplication event, which may have occurred before the algae formation. An expression profile analysis of SSV in maize has indicated that ZmSSV is mainly transcribed in the kernel and ear leaf during the grain filling stage, which is partly similar to other SS isoforms. Therefore, it is likely that SSV may play an important role in starch biosynthesis. Subsequent analysis of SSV function may facilitate understanding the mechanism of starch granules formation, number and structure.

Maize production in mid hills of Nepal: from food to feed security

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Krishna Prasad Timsina

2016-12-01

Full Text Available This study was undertaken in 2016 to analyze the production and utilization of maize in Nepal. Sixty maize growers from Kavre and Lamjung districts were selected using purposive, cluster and simple random sampling techniques. Similarly, six feed industries and five maize experts from Chitwan district were also interviewed. Study shows 56% of the total areas were used for maize production and 50% of the maize areas were covered by hybrid maize. There was no practice of contract maize production. The results revealed that 60%, 25% and 3% of the grain were used for animal feed, food and seed respectively in hill districts. Whereas the remaining amount of the maize (12% was sold to the different buyers. The proportion of maize feed supply to different animals in the study area was varying. Result shows that at least 1.5 million tons of maize is required only to the feed industries affiliated with national feed industry association in Nepal. Similarly, out of total maize used in feed production, 87% of the maize was imported from India each year by feed industries. Analysis shows negative correlation between scale of feed production and use of domestic maize due to unavailability of required quantity of maize in time. The major pre-condition of feed industries for maize buying was moisture content which must be equal or less than 14%. Very little or no inert materials and physical injury, free from fungal attack and bigger size were also the criteria for maize buying. However, some of the feed industries were also thinking about protein and amino acid contents. Result shows 13% and 8.5% increasing demand of poultry feed and animal feed, respectively over the last five year in Nepal. Most likely, maize is known as a means of food security in Nepal, however, in the context of changing utilization patterns at the farm level and also tremendous increasing demand of maize at the industry level suggest to give more focus on development and dissemination of

Synergy Repetition Training versus Task Repetition Training in Acquiring New Skill.

Science.gov (United States)

Patel, Vrajeshri; Craig, Jamie; Schumacher, Michelle; Burns, Martin K; Florescu, Ionut; Vinjamuri, Ramana

2017-01-01

Traditionally, repetitive practice of a task is used to learn a new skill, exhibiting as immediately improved performance. Research suggests, however, that a more experience-based rather than exposure-based training protocol may allow for better transference of the skill to related tasks. In synergy-based motor control theory, fundamental motor skills, such as hand grasping, are represented with a synergy subspace that captures essential motor patterns. In this study, we propose that motor-skill learning through synergy-based mechanisms may provide advantages over traditional task repetition learning. A new task was designed to highlight the range of motion and dexterity of the human hand. Two separate training strategies were tested in healthy subjects: task repetition training and synergy training versus a control. All three groups showed improvements when retested on the same task. When tested on a similar, but different set of tasks, only the synergy group showed improvements in accuracy (9.27% increase) compared to the repetition (3.24% decline) and control (3.22% decline) groups. A kinematic analysis revealed that although joint angular peak velocities decreased, timing benefits stemmed from the initial feed-forward portion of the task (reaction time). Accuracy improvements may have derived from general improved coordination among the four involved fingers. These preliminary results warrant further investigation of synergy-based motor training in healthy individuals, as well as in individuals undergoing hand-based rehabilitative therapy.

An overview of the Phalaenopsis orchid genome through BAC end sequence analysis

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Hsiao Yu-Yun

2011-01-01

Full Text Available Abstract Background Phalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC end sequences (BESs can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding. Results We used two BAC libraries (constructed using the BamHI and HindIII restriction enzymes of Phalaenopsis equestris to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the BamHI and HindIII libraries, respectively, at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the Phalaenopsis genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6% were predicted to represent protein-encoding regions, whereas 1,272 (23.0% contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively, whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6% of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or Arabidopsis, and even fewer mapped to the rice genome. This work will facilitate analysis of the Phalaenopsis genome, and will help clarify similarities and differences in genome composition between orchids and other plant species. Conclusion Using BES analysis, we obtained an overview of the Phalaenopsis genome in terms of gene abundance, the presence of repetitive

Maize flour fortification in Africa: markets, feasibility, coverage, and costs.

Science.gov (United States)

Fiedler, John L; Afidra, Ronald; Mugambi, Gladys; Tehinse, John; Kabaghe, Gladys; Zulu, Rodah; Lividini, Keith; Smitz, Marc-Francois; Jallier, Vincent; Guyondet, Christophe; Bermudez, Odilia

2014-04-01

The economic feasibility of maize flour and maize meal fortification in Kenya, Uganda, and Zambia is assessed using information about the maize milling industry, households' purchases and consumption levels of maize flour, and the incremental cost and estimated price impacts of fortification. Premix costs comprise the overwhelming share of incremental fortification costs and vary by 50% in Kenya and by more than 100% across the three countries. The estimated incremental cost of maize flour fortification per metric ton varies from $3.19 in Zambia to $4.41 in Uganda. Assuming all incremental costs are passed onto the consumer, fortification in Zambia would result in at most a 0.9% increase in the price of maize flour, and would increase annual outlays of the average maize flour-consuming household by 0.2%. The increases for Kenyans and Ugandans would be even less. Although the coverage of maize flour fortification is not likely to be as high as some advocates have predicted, fortification is economically feasible, and would reduce deficiencies of multiple micronutrients, which are significant public health problems in each of these countries. © 2013 New York Academy of Sciences.

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies.

Science.gov (United States)

Utturkar, Sagar M; Klingeman, Dawn M; Hurt, Richard A; Brown, Steven D

2017-01-01

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.

Lack of Detectable Allergenicity in Genetically Modified Maize Containing “Cry” Proteins as Compared to Native Maize Based on In Silico & In Vitro Analysis

Science.gov (United States)

Mathur, Chandni; Kathuria, Pooran C.; Dahiya, Pushpa; Singh, Anand B.

2015-01-01

Background Genetically modified, (GM) crops with potential allergens must be evaluated for safety and endogenous IgE binding pattern compared to native variety, prior to market release. Objective To compare endogenous IgE binding proteins of three GM maize seeds containing Cry 1Ab,1Ac,1C transgenic proteins with non GM maize. Methods An integrated approach of in silico & in vitro methods was employed. Cry proteins were tested for presence of allergen sequence by FASTA in allergen databases. Biochemical assays for maize extracts were performed. Specific IgE (sIgE) and Immunoblot using food sensitized patients sera (n = 39) to non GM and GM maize antigens was performed. Results In silico approaches, confirmed for non sequence similarity of stated transgenic proteins in allergen databases. An insignificant (p> 0.05) variation in protein content between GM and non GM maize was observed. Simulated Gastric Fluid (SGF) revealed reduced number of stable protein fractions in GM then non GM maize which might be due to shift of constituent protein expression. Specific IgE values from patients showed insignificant difference in non GM and GM maize extracts. Five maize sensitized cases, recognized same 7 protein fractions of 88-28 kD as IgE bindng in both GM and non-GM maize, signifying absence of variation. Four of the reported IgE binding proteins were also found to be stable by SGF. Conclusion Cry proteins did not indicate any significant similarity of >35% in allergen databases. Immunoassays also did not identify appreciable differences in endogenous IgE binding in GM and non GM maize. PMID:25706412

The Past, Present, and Future of Human Centromere Genomics

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Megan E. Aldrup-MacDonald

2014-01-01

Full Text Available The centromere is the chromosomal locus essential for chromosome inheritance and genome stability. Human centromeres are located at repetitive alpha satellite DNA arrays that compose approximately 5% of the genome. Contiguous alpha satellite DNA sequence is absent from the assembled reference genome, limiting current understanding of centromere organization and function. Here, we review the progress in centromere genomics spanning the discovery of the sequence to its molecular characterization and the work done during the Human Genome Project era to elucidate alpha satellite structure and sequence variation. We discuss exciting recent advances in alpha satellite sequence assembly that have provided important insight into the abundance and complex organization of this sequence on human chromosomes. In light of these new findings, we offer perspectives for future studies of human centromere assembly and function.

Selection of Suitable DNA Extraction Methods for Genetically Modified Maize 3272, and Development and Evaluation of an Event-Specific Quantitative PCR Method for 3272.

Science.gov (United States)

Takabatake, Reona; Masubuchi, Tomoko; Futo, Satoshi; Minegishi, Yasutaka; Noguchi, Akio; Kondo, Kazunari; Teshima, Reiko; Kurashima, Takeyo; Mano, Junichi; Kitta, Kazumi

2016-01-01

A novel real-time PCR-based analytical method was developed for the event-specific quantification of a genetically modified (GM) maize, 3272. We first attempted to obtain genome DNA from this maize using a DNeasy Plant Maxi kit and a DNeasy Plant Mini kit, which have been widely utilized in our previous studies, but DNA extraction yields from 3272 were markedly lower than those from non-GM maize seeds. However, lowering of DNA extraction yields was not observed with GM quicker or Genomic-tip 20/G. We chose GM quicker for evaluation of the quantitative method. We prepared a standard plasmid for 3272 quantification. The conversion factor (Cf), which is required to calculate the amount of a genetically modified organism (GMO), was experimentally determined for two real-time PCR instruments, the Applied Biosystems 7900HT (the ABI 7900) and the Applied Biosystems 7500 (the ABI7500). The determined Cf values were 0.60 and 0.59 for the ABI 7900 and the ABI 7500, respectively. To evaluate the developed method, a blind test was conducted as part of an interlaboratory study. The trueness and precision were evaluated as the bias and reproducibility of the relative standard deviation (RSDr). The determined values were similar to those in our previous validation studies. The limit of quantitation for the method was estimated to be 0.5% or less, and we concluded that the developed method would be suitable and practical for detection and quantification of 3272.

The response of maize production in Kenya to economic incentives

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Onono, P.A.,

2013-06-01

Full Text Available Agricultural development policy in Kenya has emphasised the use of incentives towards increased production and therefore self-sufficiency in maize which is a basic staple for most households. The channels used to provide incentives to maize farmers over the years include setting higher producer prices; subsidisation of inputs; provision of agricultural credit, research and extension services; construction and maintenance of roads, development of irrigation and water systems; legislative, institutional and macroeconomic reforms. Despite these efforts outputof maize has remained below domestic requirements in most years and the country continues to rely on imports to meet the deficits. Studies have assessed the responsiveness of maize to output price and reported inelastic responses and have recommended policies targeting non-price incentives to complement prices for the required increased production of maize. The studies, however, did not analyse the influence of the non-price incentives on the production of the crop. The findings of those studies are therefore deficient in explaining the relative importance of different non-price incentives and how they complement prices in influencing maize production in Kenya. This study investigated the response of maize production to both price and non-price incentives. The aim of this study was to ascertain the relative importance of non-price factors in influencing production of the crops as well as complementarity between price and non-price incentives. The findings show that maize production responds positively to its output price, development expenditures in agriculture, maize sales to marketing boards, growth in per capita GDP, liberalisation and governance reforms. However, maize production responds negatively to fertiliser price and unfavourable weather conditions. The response of maize output to its price is lower with rising inflation and grain market liberalisation.

"Omics" of maize stress response for sustainable food production: opportunities and challenges.

Science.gov (United States)

Gong, Fangping; Yang, Le; Tai, Fuju; Hu, Xiuli; Wang, Wei

2014-12-01

Maize originated in the highlands of Mexico approximately 8700 years ago and is one of the most commonly grown cereal crops worldwide, followed by wheat and rice. Abiotic stresses (primarily drought, salinity, and high and low temperatures), together with biotic stresses (primarily fungi, viruses, and pests), negatively affect maize growth, development, and eventually production. To understand the response of maize to abiotic and biotic stresses and its mechanism of stress tolerance, high-throughput omics approaches have been used in maize stress studies. Integrated omics approaches are crucial for dissecting the temporal and spatial system-level changes that occur in maize under various stresses. In this comprehensive analysis, we review the primary types of stresses that threaten sustainable maize production; underscore the recent advances in maize stress omics, especially proteomics; and discuss the opportunities, challenges, and future directions of maize stress omics, with a view to sustainable food production. The knowledge gained from studying maize stress omics is instrumental for improving maize to cope with various stresses and to meet the food demands of the exponentially growing global population. Omics systems science offers actionable potential solutions for sustainable food production, and we present maize as a notable case study.

Mixed cropping of groundnuts and maize in East Java

NARCIS (Netherlands)

Hoof, van W.C.H.

1987-01-01

Mixed cropping of groundnuts and maize in East Java was studied by means of a survey of farming practice and by field experiments. The influence of different sowing times and plant density of maize on the development and yield of groundnuts and maize were the main topics in this thesis. Plant

Maize and the Malnutrition Conundrum in South Africa | BOOYENS ...

African Journals Online (AJOL)

In this paper, the author gives an overview of the factors leading to maize becoming a staple food among black people in South Africa. The purported relationship between maize consumption and malnutrition, proposals as well as experimental and practical efforts to correct the dietary deficiencies of maize are briefly ...

The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species.

Science.gov (United States)

Gilchrist, Anthony Stuart; Shearman, Deborah C A; Frommer, Marianne; Raphael, Kathryn A; Deshpande, Nandan P; Wilkins, Marc R; Sherwin, William B; Sved, John A

2014-12-20

The tephritid fruit flies include a number of economically important pests of horticulture, with a large accumulated body of research on their biology and control. Amongst the Tephritidae, the genus Bactrocera, containing over 400 species, presents various species groups of potential utility for genetic studies of speciation, behaviour or pest control. In Australia, there exists a triad of closely-related, sympatric Bactrocera species which do not mate in the wild but which, despite distinct morphologies and behaviours, can be force-mated in the laboratory to produce fertile hybrid offspring. To exploit the opportunities offered by genomics, such as the efficient identification of genetic loci central to pest behaviour and to the earliest stages of speciation, investigators require genomic resources for future investigations. We produced a draft de novo genome assembly of Australia's major tephritid pest species, Bactrocera tryoni. The male genome (650-700 Mbp) includes approximately 150 Mb of interspersed repetitive DNA sequences and 60 Mb of satellite DNA. Assessment using conserved core eukaryotic sequences indicated 98% completeness. Over 16,000 MAKER-derived gene models showed a large degree of overlap with other Dipteran reference genomes. The sequence of the ribosomal RNA transcribed unit was also determined. Unscaffolded assemblies of B. neohumeralis and B. jarvisi were then produced; comparison with B. tryoni showed that the species are more closely related than any Drosophila species pair. The similarity of the genomes was exploited to identify 4924 potentially diagnostic indels between the species, all of which occur in non-coding regions. This first draft B. tryoni genome resembles other dipteran genomes in terms of size and putative coding sequences. For all three species included in this study, we have identified a comprehensive set of non-redundant repetitive sequences, including the ribosomal RNA unit, and have quantified the major satellite DNA

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

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Puigbò, Pere; Lobkovsky, Alexander E; Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

2014-08-21

Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species. We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes. Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.

DNABIT Compress – Genome compression algorithm

Science.gov (United States)

Rajarajeswari, Pothuraju; Apparao, Allam

2011-01-01

Data compression is concerned with how information is organized in data. Efficient storage means removal of redundancy from the data being stored in the DNA molecule. Data compression algorithms remove redundancy and are used to understand biologically important molecules. We present a compression algorithm, “DNABIT Compress” for DNA sequences based on a novel algorithm of assigning binary bits for smaller segments of DNA bases to compress both repetitive and non repetitive DNA sequence. Our proposed algorithm achieves the best compression ratio for DNA sequences for larger genome. Significantly better compression results show that “DNABIT Compress” algorithm is the best among the remaining compression algorithms. While achieving the best compression ratios for DNA sequences (Genomes),our new DNABIT Compress algorithm significantly improves the running time of all previous DNA compression programs. Assigning binary bits (Unique BIT CODE) for (Exact Repeats, Reverse Repeats) fragments of DNA sequence is also a unique concept introduced in this algorithm for the first time in DNA compression. This proposed new algorithm could achieve the best compression ratio as much as 1.58 bits/bases where the existing best methods could not achieve a ratio less than 1.72 bits/bases. PMID:21383923

Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites.

Science.gov (United States)

Mejía-Guerra, María Katherine; Li, Wei; Galeano, Narmer F; Vidal, Mabel; Gray, John; Doseff, Andrea I; Grotewold, Erich

2015-12-01

Core promoters are crucial for gene regulation, providing blueprints for the assembly of transcriptional machinery at transcription start sites (TSSs). Empirically, TSSs define the coordinates of core promoters and other regulatory sequences. Thus, experimental TSS identification provides an essential step in the characterization of promoters and their features. Here, we describe the application of CAGE (cap analysis of gene expression) to identify genome-wide TSSs used in root and shoot tissues of two maize (Zea mays) inbred lines (B73 and Mo17). Our studies indicate that most TSS clusters are sharp in maize, similar to mice, but distinct from Arabidopsis thaliana, Drosophila melanogaster, or zebra fish, in which a majority of genes have broad-shaped TSS clusters. We established that ∼38% of maize promoters are characterized by a broader TATA-motif consensus, and this motif is significantly enriched in genes with sharp TSSs. A noteworthy plasticity in TSS usage between tissues and inbreds was uncovered, with ∼1500 genes showing significantly different dominant TSSs, sometimes affecting protein sequence by providing alternate translation initiation codons. We experimentally characterized instances in which this differential TSS utilization results in protein isoforms with additional domains or targeted to distinct subcellular compartments. These results provide important insights into TSS selection and gene expression in an agronomically important crop. © 2015 American Society of Plant Biologists. All rights reserved.

Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing

DEFF Research Database (Denmark)

Wernersson, Rasmus; Schierup, M.H.; Jorgensen, F.G.

2005-01-01

sequences (0.66X coverage) from the pig genome. The data are hereby released (NCBI Trace repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project") together with an initial evolutionary analysis. The non-repetitive fraction of the sequences was aligned to the UCSC human...

Review: Maize research and production in Nigeria | Iken | African ...

African Journals Online (AJOL)

Maize (Zea mays) is a major important cereal being cultivated in the rainforest and the derived Savannah zones of Nigeria. Land races, improved high yielding and pest and diseases resistant varieties of maize have been developed. Key words: Maize, Zea mays, Nigeria. African Journal of Biotechnology Vol.3(6) 2004: 302- ...

The Combining Ability of Maize Inbred Lines for Grain Yield and ...

African Journals Online (AJOL)

The Combining Ability of Maize Inbred Lines for Grain Yield and Reaction to Grey ... East African Journal of Sciences ... (GLS) to maize production, the national maize research program of Ethiopia ... The information from this study will be useful for the development of high-yielding and GLS disease-resistant maize varieties.

A New Approach to Dissect Nuclear Organization: TALE-Mediated Genome Visualization (TGV).

Science.gov (United States)

Miyanari, Yusuke

2016-01-01

Spatiotemporal organization of chromatin within the nucleus has so far remained elusive. Live visualization of nuclear remodeling could be a promising approach to understand its functional relevance in genome functions and mechanisms regulating genome architecture. Recent technological advances in live imaging of chromosomes begun to explore the biological roles of the movement of the chromatin within the nucleus. Here I describe a new technique, called TALE-mediated genome visualization (TGV), which allows us to visualize endogenous repetitive sequence including centromeric, pericentromeric, and telomeric repeats in living cells.

Extraction and characterization of natural cellulose fibers from maize tassel

CSIR Research Space (South Africa)

Maepa, CE

2015-04-01

Full Text Available This article reports on the extraction and characterization of novel natural cellulose fibers obtained from the maize (tassel) plant. Cellulose was extracted from the agricultural residue (waste biomaterial) of maize tassel. The maize tassel fibers...

Usage of γ-ray treatment for productivity increasing of maize

International Nuclear Information System (INIS)

Ilieva, V.; Dimov, K.

2003-01-01

The aim of this study is to determine the influence of γ irradiation on phosphorus nutrition and maize productivity increasing. The vegetation experiment with irradiated and non-irradiated maize seeds in controlled conditions (moisture and temperature) for determination of phosphorus and phosphorus-gypsum absorption was carried out. The influence of γ irradiation on maize growth, export of mineral elements in maize, phosphorus fertilizing and dry biomass of maize plants are presented. The effect of the moisture of γ irradiated maize seeds (sort 'Knezha' - 3L - 621) on dry substance and yield of green mass is also discussed. Based on the presented experimental data the following conclusion have been made: the maize seeds (sort 'Knezha, hybrid H-708) simulation is useful; in all variants of phosphorus-gypsum absorption the increasing of plant mass yield (absolutely dry) is observed; the absorbed phosphates reserve is enhanced twice; the efficiency of 32 P use in stimulated seeds is higher than in non-stimulated seeds; the phosphorus content in maize (sort 'Knezha' - 2L - 611) is increasing mainly in leaves after X-ray irradiation (750 - 1500 R); γ irradiation (7.5 Gy) stimulate the root system (18%) and side roots development and drying up overcome

Genome Defense Mechanisms in Neurospora and Associated Specialized Proteins

Directory of Open Access Journals (Sweden)

Ranjan Tamuli

2010-06-01

Full Text Available Neurospora crassa, the filamentous fungus possesses widest array of genome defense mechanisms known to any eukaryotic organism, including a process called repeat-induced point mutation (RIP. RIP is a genome defense mechanism that hypermutates repetitive DNA sequences; analogous to genomic imprinting in mammals. As an impact of RIP, Neurospora possesses many fewer genes in multigene families than expected. A DNA methyltransferase homologue, RID was shown to be essential for RIP. Recently, a variant catalytic subunit of translesion DNA polymerase zeta (Pol zeta has been found to be essential for dominant RIP suppressor phenotype. Meiotic silencing and quelling are two other genome defense mechanisms in Neurospora, and proteins required for these two processes have been identified through genetic screens.

Karyotypic evolution and organization of the highly repetitive DNA sequences in the Japanese shrew-moles, Dymecodon pilirostris and Urotrichus talpoides.

Science.gov (United States)

Nakata, A; Yoshimura, A; Kuro-o, M; Obara, Y

2005-01-01

The karyological relationship and organization of highly repetitive DNA sequences in Japanese shrew-moles were studied by zoo-blot hybridization and fluorescence in situ hybridization (FISH). When the genomic DNA of the eastern race of Urotrichus talpoides was digested with PstI, three fragments of highly repetitive DNA sequences, approximately 0.7, 0.9, and 1.4 kb in length, were observed as distinct bands. The results of FISH in the eastern race of U. talpoides using these three fragments separately as probes showed that the 0.7-kb PstI fragment was distributed in the centromeric regions of most chromosomes, and that the 0.9- and 1.4-kb fragments were predominantly located in the C-heterochromatin region of chromosome 13p. Although the western race of U. talpoides also had three PstI fragments, 0.9- and 1.4-kb PstI fragments were more ambiguous than those of the eastern race. The PstI- digested genomic DNA in Dymecodonpilirostris produced only a faint 0.9-kb band, and its signal patterns obtained by zoo-blot hybridization were clearly different from those of U. talpoides. The 0.7-kb fragment of U. talpoides hybridized strongly with the 0.9-kb fragment of D. pilirostris. In a FISH analysis, the 0.9-kb fragment of D. pilirostris hybridized with highly repetitive DNA in the centromeric regions of most chromosomes from both D. pilirostris and U. talpoides. Zoo-blot hybridization and FISH analyses suggest that the 0.9- and 1.4-kb PstI fragments were generated specifically in the genome of U. talpoides after the common ancestor differentiated into two extant shrew-mole species. A difference in the length of the centromeric elements between U. talpoides and D. pilirostris might be observed due to certain modifications of the repeating unit.

Biofuel, land and water: maize, switchgrass or Miscanthus?

International Nuclear Information System (INIS)

Zhuang Qianlai; Qin Zhangcai; Chen Min

2013-01-01

The productive cellulosic crops switchgrass and Miscanthus are considered as viable biofuel sources. To meet the 2022 national biofuel target mandate, actions must be taken, e.g., maize cultivation must be intensified and expanded, and other biofuel crops (switchgrass and Miscanthus) must be cultivated. This raises questions on the use efficiencies of land and water; to date, the demand on these resources to meet the national biofuel target has rarely been analyzed. Here, we present a data-model assimilation analysis, assuming that maize, switchgrass and Miscanthus will be grown on currently available croplands in the US. Model simulations suggest that maize can produce 3.0–5.4 kiloliters (kl) of ethanol for every hectare of land, depending on the feedstock to ethanol conversion efficiency; Miscanthus has more than twice the biofuel production capacity relative to maize, and switchgrass is the least productive of the three potential sources of ethanol. To meet the biofuel target, about 26.5 million hectares of land and over 90 km 3 of water (of evapotranspiration) are needed if maize grain alone is used. If Miscanthus was substituted for maize, the process would save half of the land and one third of the water. With more advanced biofuel conversion technology for Miscanthus, only nine million hectares of land and 45 km 3 of water would probably meet the national target. Miscanthus could be a good alternative biofuel crop to maize due to its significantly lower demand for land and water on a per unit of ethanol basis. (letter)

Production of high-amylose maize lines using RNA interference in ...

African Journals Online (AJOL)

amylose maize lines with a low T-DNA copy number, demonstrating that RNAi is an efficient method for the production of high-amylose maize lines. Key words: Maize, high-amylose, RNA interference, starch branching enzyme gene sbe2a.

Molecular structure and chromosome distribution of three repetitive DNA families in Anemone hortensis L. (Ranunculaceae).

Science.gov (United States)

Mlinarec, Jelena; Chester, Mike; Siljak-Yakovlev, Sonja; Papes, Drazena; Leitch, Andrew R; Besendorfer, Visnja

2009-01-01

The structure, abundance and location of repetitive DNA sequences on chromosomes can characterize the nature of higher plant genomes. Here we report on three new repeat DNA families isolated from Anemone hortensis L.; (i) AhTR1, a family of satellite DNA (stDNA) composed of a 554-561 bp long EcoRV monomer; (ii) AhTR2, a stDNA family composed of a 743 bp long HindIII monomer and; (iii) AhDR, a repeat family composed of a 945 bp long HindIII fragment that exhibits some sequence similarity to Ty3/gypsy-like retroelements. Fluorescence in-situ hybridization (FISH) to metaphase chromosomes of A. hortensis (2n = 16) revealed that both AhTR1 and AhTR2 sequences co-localized with DAPI-positive AT-rich heterochromatic regions. AhTR1 sequences occur at intercalary DAPI bands while AhTR2 sequences occur at 8-10 terminally located heterochromatic blocks. In contrast AhDR sequences are dispersed over all chromosomes as expected of a Ty3/gypsy-like element. AhTR2 and AhTR1 repeat families include polyA- and polyT-tracks, AT/TA-motifs and a pentanucleotide sequence (CAAAA) that may have consequences for chromatin packing and sequence homogeneity. AhTR2 repeats also contain TTTAGGG motifs and degenerate variants. We suggest that they arose by interspersion of telomeric repeats with subtelomeric repeats, before hybrid unit(s) amplified through the heterochromatic domain. The three repetitive DNA families together occupy approximately 10% of the A. hortensis genome. Comparative analyses of eight Anemone species revealed that the divergence of the A. hortensis genome was accompanied by considerable modification and/or amplification of repeats.

Iron and manganese oxides modified maize straw to remove tylosin from aqueous solutions.

Science.gov (United States)

Yin, Yongyuan; Guo, Xuetao; Peng, Dan

2018-08-01

Maize straw modified by iron and manganese oxides was synthesized via a simple and environmentally friendly method. Three maize straw materials, the original maize straw, maize straw modified by manganese oxides and maize straw modified by iron and manganese oxides, were detected by SEM, BET, XPS, XRD and FTIR. The results showed that maize straw was successfully modified and maize straw modified by iron and manganese oxides has a larger surface area than MS. According to the experimental data, the sorption trend could conform to the pseudo-second-order kinetic model well, and the sorption ability of tylosin on sorbents followed the order of original maize straw oxides iron and manganese oxides. The study indicated that manganese oxides and iron-manganese oxides could significantly enhance the sorption capacity of original maize straw. The sorption isotherm data of tylosin on original maize straw fit a linear model well, while Freundlich models were more suitable for maize straw modified by manganese oxides and maize straw modified by iron and manganese oxides. The pH, ionic strength and temperature can affect the sorption process. The sorption mechanisms of tylosin on iron and manganese oxides modified maize straw were attribute to the surface complexes, electrostatic interactions, H bonding and hydrophobic interactions. Copyright © 2018 Elsevier Ltd. All rights reserved.

(SSR) markers for drought tolerance in maize

African Journals Online (AJOL)

Maize is moderately sensitive to drought. Drought affects virtually all aspects of maize growth in varying degrees at all stages, from germination to maturity. Tolerance to drought is genetically and physiologically complicated and inherited quantitatively. Application of molecular-marker aided selection technique for ...

Comparison of species composition and fumonisin production in Aspergillus section Nigri populations in maize kernels from USA and Italy.

Science.gov (United States)

Susca, Antonia; Moretti, Antonio; Stea, Gaetano; Villani, Alessandra; Haidukowski, Miriam; Logrieco, Antonio; Munkvold, Gary

2014-10-01

non-producing strains distributed among the clades: A. welwitschiae, A. niger group 1 and A. niger group 2, confirming the potential of Aspergillus sect. Nigri species to contribute to total fumonisin contamination of maize. A higher percentage of A. niger isolates (72.0%) produced FB2 compared to A. welwitschiae (36.6%). The percentage of FB2-producing A. niger strains was similar in the USA and Italian populations; however, the predominance of A. niger in the USA population suggests a higher potential for fumonisin production. Some strains with fum8 present in the genome did not produce FB2in vitro, confirming the ineffectiveness of fum8 presence as a predictor of FB2 production. Copyright © 2014 Elsevier B.V. All rights reserved.

A comparative study on infestation of three varieties of maize ( Zea ...

African Journals Online (AJOL)

A study was carried out to study the infestation of three maize varieties (Maize suwan I–Y, Maize T2 USR – White single cross and Maize suwan 123) by Sitophilus zeamais Motsch. Infestation was assessed by counting the numbers of alive and dead adults and the number of infested and uninfested seeds. It was found out ...

Effects of temperature changes on maize production in Mozambique

Science.gov (United States)

Harrison, L.; Michaelsen, J.; Funk, Chris; Husak, G.

2011-01-01

We examined intraseasonal changes in maize phenology and heat stress exposure over the 1979-2008 period, using Mozambique meteorological station data and maize growth requirements in a growing degree-day model. Identifying historical effects of warming on maize growth is particularly important in Mozambique because national food security is highly dependent on domestic food production, most of which is grown in already warm to hot environments. Warming temperatures speed plant development, shortening the length of growth periods necessary for optimum plant and grain size. This faster phenological development also alters the timing of maximum plant water demand. In hot growing environments, temperature increases during maize pollination threaten to make midseason crop failure the norm. In addition to creating a harsher thermal environment, we find that early season temperature increases have caused the maize reproductive period to start earlier, increasing the risk of heat and water stress. Declines in time to maize maturation suggest that, independent of effects to water availability, yield potential is becoming increasingly limited by warming itself. Regional variations in effects are a function of the timing and magnitude of temperature increases and growing season characteristics. Continuation of current climatic trends could induce substantial yield losses in some locations. Farmers could avoid some losses through simple changes to planting dates and maize varietal types.

Repetitive Questioning II

Directory of Open Access Journals (Sweden)

R. C. Hamdy MD

2018-02-01

Full Text Available Repetitive questioning is a major problem for caregivers, particularly taxing if they are unable to recognize and understand the reasons why their loved one keeps asking the same question over and over again. Caregivers may be tempted to believe that the patient does not even try to remember the answer given or is just getting obnoxious. This is incorrect. Repetitive questioning is due to the underlying disease: The patient’s short term memory is impaired and he is unable to register, encode, retain and retrieve the answer. If he is concerned about a particular topic, he will keep asking the same question over and over again. To the patient each time she asks the question, it is as if she asked it for the first time. Just answering repetitive questioning by providing repeatedly the same answer is not sufficient. Caregivers should try to identify the underlying cause for this repetitive questioning. In an earlier case study, the patient was concerned about her and her family’s safety and kept asking whether the doors are locked. In this present case study, the patient does not know how to handle the awkward situation he finds himself in. He just does not know what to do. He is not able to adjust to the new unexpected situation. So he repeatedly wants to reassure himself that he is not intruding by asking the same question over and over again. We discuss how the patient’s son-in-law could have avoided this situation and averted the catastrophic ending.

Seed treatments enhance photosynthesis in maize seedlings by reducing infection with Fusarium spp. and consequent disease development in maize

Science.gov (United States)

The effects of a seed treatment on early season growth, seedling disease development, incidence Fusarium spp. infection, and photosynthetic performance of maize were evaluated at two locations in Iowa in 2007. Maize seed was either treated with Cruiser 2Extreme 250 ® (fludioxonil + azoxystrobin + me...

PERFORMANCE OF MAIZE (ZEA MAYS) CULTIVARS AS ...

African Journals Online (AJOL)

IBUKUN

reported to have low remobilisation efficiency and reduced plasticity of seed weight to assimilate availability ... have indicated that the use of organo-mineral fertiliser in maize and melon gave high relative .... The soil physical and chemical characteristics of ..... yield in maize by examining genetic improvement and heterosis.

Deregulation of Lesotho's maize market

OpenAIRE

van Schalkwyk, Herman D.; van Zyl, Johan; Botha, P.W.; Bayley, B.

1997-01-01

During the past year, there have been major policy reforms in Lesotho and South Africa with respect to maize pricing and marketing. In Lesotho the impact of deregulation on producers, consumers and government revenues was substantially lower than it should have been, and as a result Lesotho was not able to reap the full benefits of these changes. This is partly because information on the changes to the maize marketing system did not reach the potential beneficiaries of the new system. Free an...

Growing sensitivity of maize to water scarcity under climate change.

Science.gov (United States)

Meng, Qingfeng; Chen, Xinping; Lobell, David B; Cui, Zhenling; Zhang, Yi; Yang, Haishun; Zhang, Fusuo

2016-01-25

Climate change can reduce crop yields and thereby threaten food security. The current measures used to adapt to climate change involve avoiding crops yield decrease, however, the limitations of such measures due to water and other resources scarcity have not been well understood. Here, we quantify how the sensitivity of maize to water availability has increased because of the shift toward longer-maturing varieties during last three decades in the Chinese Maize Belt (CMB). We report that modern, longer-maturing varieties have extended the growing period by an average of 8 days and have significantly offset the negative impacts of climate change on yield. However, the sensitivity of maize production to water has increased: maize yield across the CMB was 5% lower with rainfed than with irrigated maize in the 1980s and was 10% lower (and even >20% lower in some areas) in the 2000s because of both warming and the increased requirement for water by the longer-maturing varieties. Of the maize area in China, 40% now fails to receive the precipitation required to attain the full yield potential. Opportunities for water saving in maize systems exist, but water scarcity in China remains a serious problem.

Effect and fate of lindane in maize plant

International Nuclear Information System (INIS)

Bennaceur, M.; Ghezal, F.; Klaa, K.

1992-10-01

The fate and effect of lindane in maize plant, soil and predators were studied following insecticide application under field conditions. Respectively 84,2% and 93,3% of lindane residues were lost after 2 and 4 months in soil after treatment. About 90% of the insecticide was lost after one month in maize plant. Lindane residues were present in maize grains (0,205ppm). Lindane decreases the density of many predators in soils such as species of collembola, coccinellidae, formicidae, coleoptera

Combining Maize Base Germplasm for Cold Tolerance Breeding