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Abstract Background Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). Results Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' × 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. Conclusion These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.

Re-examining historical datasets is a proposed use for association mapping (AM) and is particularly valuable when the data describes time-consuming and/or expensive to measure traits. A collection of 91 elite two-row malting barley (Hordeum vulgare L.) lines entered in the western Canadian Cooperative Two-Row Barley Trials over a 13- yr period were analyzed by AM to identify markers associated with seven malting quality traits. A linear mixed-model incorporating population structure and familial relatedness identified 27 diversity array technology (DArT) markers associated with malting quality. These markers will assist selection of parents with complementary allele combinations for future crosses and help identify progeny with the desired alleles. Putative candidate expressed sequence tags (ESTs) responsible for marker-trait associations were identified for 19 of the 27 DArT markers and include genes important for seed storage protein accumulation, gibberellin-mediated gene expression, seed storage mobilization, and dormancy. Efforts to identify novel variability in these genes may present opportunities to improve malting quality. doi: 10.2135/cropsci2009.06.0334

With the advancement of molecular marker technology and computer software, mapping quantitative trait loci (QTL) for complex traits in agricultural crops is frequent; however, exploitation of these QTL in practical breeding programs s limited. Here we report the validation of molecular markers linked to net blotch resistance QTL and their utilization in a barley (Hordeum vulgare L.) breeding program. Barley net blotch, caused by Pyrenophora teres Drechs. [anamorph: Drechslera teres (Sacc.) Shoemaker], is a serious foliar disease in Canada and other parts of the world. Simple sequence repeat (SSR) markers linked to net-form net blotch (NFNB) resistance QTL (QRpt6) and spot-form net blotch (SFNB) resistance QTL (QRpts4) were validated in two barley populations unrelated to the original mapping population. Marker-assisted selection (MAS) was performed with SSR markers to select resistant and susceptible lines in two other populations. The lines homozygous for the resistant-parent alleles at both marker loci had significantly lower infection than lines homozygous for the susceptible-parent alleles at both markers, indicating that MAS for net blotch resistance is practical. Since the major QTL, QRpt6, may provide adequate NFNB field resistance in western Canada, the plan for the Crop Development Centre (CDC) barley breeding program is to routinely utilize MAS for QRpt6 followed by normal field screening in disease nurseries to select the most resistant lines having additional resistance provided by less critical genes associated with other identified QTL. The CDC program has implemented routine MAS for QRpt6 and recommends this approach to other barley breeding programs. doi: 10.2135/cropsci2009.01.0011

Molecular marker technology shows potential to select and combine favorable alleles via genotypic selection and can be used to develop improved crop cultivars with considerable resource savings. In the present investigation, the utility of molecular markers for net blotch resistance identified in Australian breeding material was investigated for Canadian breeding material. Screening 42 Canadian, Australian, and international barley (Hordeum vulgare L.) lines with 10 Canadian Pyrenophora teres Drechs. isolates identified three lines resistant to all isolates evaluated. Net-form net blotch isolates were more virulent than spot-form net blotch isolates. The strong agreement between seedling and adult-plant reactions indicated that seedling screening could be useful for selection for adult-plant resistance. Evaluation of the inheritance of resistance in four Australian populations against Canadian P. teres isolates revealed one to three resistance genes, depending on the isolate used. The majority of Australian barley mapping population parents were susceptible to Canadian P. teres isolates, suggesting markers linked to their resistance may not be useful for Canadian breeding; however, some molecular markers identified by Australian workers could be used for Canadian barley breeding. This study demonstrates that the differences in germplasm and fungal pathogen strains used in different countries result in molecular markers that may not be applicable in all breeding programs for that crop.

Cowpea [Vigna unguiculata (L.) Walp] is an important grain legume crop grown for its protein rich grains. It is an inexpensive source of protein in the diets of people in sub-Saharan Africa. The International Institute of Tropical Agriculture (IITA) has been working on the improvement of cowpea for more than 30 yr. Over 60 countries receive cowpea cultivars improved by IITA for testing and adoption where needed. Many of these cultivars have identical parentage but look very different morphologically when grown in the field. Forty-six microsatellite DNA markers were used to evaluate genetic similarities among 90 cowpea breeding lines developed at IITA. Twenty-seven primer pairs could amplify polymorphic single-locus microsatellites from all of these materials. Two to seven alleles per primer were detected with a polymorphic information content varying from 0.02 to 0.73 By means of only five polymorphic microsatellite primers, 88 of the 90 cowpea lines could be distinguished. A dendrogram based on the microsatellite polymorphisms generally agreed with the pedigree of the cowpea lines., COWPEA is one of the world's important legume food crops. At least 12.5 million hectares of cowpea are cultivated with an annual production of over 3 million metric tons worldwide [...]

The genus Avena contains 30 different species from diploid through tetraploid to hexaploid with different genome compositions. Research regarding the origin of the different genomes in the polyploid species has been inconclusive. The objectives of this research were to investigate the phylogenetic relationships of the Avena species by means of polymorphisms in satellite, minisatellite, and microsatellite DNA. A satellite DNA sequence, ASS49, was isolated from a microsatellite-enriched library of the hexaploid oat Avena sativa L. Southern hybridization showed that ASS49 was a species-specific rather than a genome-specific satellite. ASS49 was able to distinguish species that may be the diploid and tetraploid progenitors of hexaploid oat. The phylogenetic relationship of Avena species was further investigated using 40 microsatellite and four minisatellite primers. These results appeared to support the findings with ASS49. It appears that the Ac-genome diploid species (A. canariensis Baum Raj. et Samp.) is the progenitor and A-genome donor of the hexaploid oat rather than the generally believed As-genome species (A. strigosa Schreber). Instead, A. strigosa appears to be a member of a separate lineage of diploid and tetraploid species including the tetraploid species A. abyssinica Hochst., THE GENUS Avena belongs to the Gramineae family. It contains 30 different species which form a distinct polyploid series ranging from diploid through tetraploid to hexaploid with a basic chromosome [...]

Applied Plant Biotechnology. Edited by V.L. CHOPRA, V.S. MALIK, and S.R. BHAT. Science Publishers Inc., P.O. Box 699, Enfield, NH 03748.1999. Hardback, 384 pp., $89.00. ISBN 1-57808-033-9. This book is [...]

Turnip mosaic virus (TuMV) is the major virus infecting crops of the genus Brassica worldwide. A dominant resistance gene, TuRB01b, that confers immunity to the virus isolate UK 1 (a representative pathotype 1 isolate of TuMV) on Brassica rapa was identified in the Chinese cabbage cultivar Tropical Delight. The TuRB01b locus was mapped to a 2.9-cM interval on B. rapa chromosome 6 (A6) that was flanked by RFLP markers pN101e1 and pW137e1. This mapping used a first backcross (B1) population segregating for the resistance gene at TuRB01b and sets of RFLP markers employed in previous mapping experiments in Brassica. Virus-plant interaction phenotypes were assayed in inbred progeny derived from B1 individuals to allow different virus isolates to be tested. Comparative mapping confirmed that A6 of B. rapa was equivalent to chromosome 6 of Brassica napus (A6) and that the map position of TuRB01b in B. rapa could be identical to that of TuRB01 in B. napus. Detailed evaluation of plant-virus interactions showed that TuRB01 and TuRB01b had indistinguishable specificities to a range of TuMV isolates. The possibility that TuRB01 and TuRB01b represent similar or identical alleles at the same A genome resistance locus suggests that B. napus acquired TuRB01 from the B. rapa gene pool. [ABSTRACT FROM AUTHOR]

Genetic control of avirulence in the net blotch pathogen, Pyrenophora teres, was investigated. To establish an appropriate study system, a collection of 10 net form (P. teres f. teres) and spot form (P. teres f. maculata) isolates were evaluated on a set of eight barley lines to identify two isolates with differential virulence on an individual host line. Two net form isolates, WRS 1906, exhibiting avirulence on the cv. Heartland, and WRS 1607, exhibiting high virulence, were mated and 67 progeny were isolated and phenotyped for reaction on Heartland. The population segregated in a 1:1 ratio, 34 avirulent to 33 virulent (χ² = 0.0, P = 1.0), indicating single gene control of WRS 1906 avirulence on Heartland. Bulked segregant analysis was used to identify six amplified fragment length polymorphism markers closely linked to the avirulence gene (AvrHeartland). This work provides evidence that the P. teres-barley pathosystem conforms to the gene-for-gene model and represents an initial step toward map-based cloning of this gene. [ABSTRACT FROM AUTHOR]

Presents information on a study that investigated the molecular map of cultivated oats. Review of related literature; Materials and methods used; Results and discussion.

Molecular mapping of cultivated oats was conducted to update the previous reference map constructed using a recombinant inbred (RI) population derived from Avena byzantina C. Koch cv. Kanota x Avena sativa L. cv. Ogle. In the current work, 607 new markers were scored, many on a larger set of RI lines (133 vs. 71) than previously reported. A robust, updated framework map was developed to resolve linkage associations among 286 markers. The remaining 880 markers were placed individually within the most likely framework interval using chi2 tests. This molecular framework incorporates and builds on previous studies, including physical mapping and linkage mapping in additional oat populations. The resulting map provides a common tool for use by oat researchers concerned with structural genomics, functional genomics, and molecular breeding.