A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs Export

@article{citeulike:6029603, abstract = {10.1073/pnas.0905886106 Consensus genetic linkage maps provide a genomic framework for quantitative trait loci identification, map-based cloning, assessment of genetic diversity, association mapping, and applied breeding in marker-assisted selection schemes. Among \^{a}€œorphan crops\^{a}€ with limited genomic resources such as cowpea [ (L.) Walp.] (2 = 2 = 22), the use of transcript-derived SNPs in genetic maps provides opportunities for automated genotyping and estimation of genome structure based on synteny analysis. Here, we report the development and validation of a high-throughput EST-derived SNP assay for cowpea, its application in consensus map building, and determination of synteny to reference genomes. SNP mining from 183,118 ESTs sequenced from 17 cDNA libraries yielded \^{a}‰ˆ10,000 high-confidence SNPs from which an Illumina 1,536-SNP GoldenGate genotyping array was developed and applied to 741 recombinant inbred lines from six mapping populations. Approximately 90\% of the SNPs were technically successful, providing 1,375 dependable markers. Of these, 928 were incorporated into a consensus genetic map spanning 680 cM with 11 linkage groups and an average marker distance of 0.73 cM. Comparison of this cowpea genetic map to reference legumes, soybean () and , revealed extensive macrosynteny encompassing 85 and 82\%, respectively, of the cowpea map. Regions of soybean genome duplication were evident relative to the simpler diploid cowpea. Comparison with revealed extensive genomic rearrangement with some conserved microsynteny. These results support evolutionary closeness between cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes.}, author = {Muchero, Wellington and Diop, Ndeye N. and Bhat, Prasanna R. and Fenton, Raymond D. and Wanamaker, Steve and Pottorff, Marti and Hearne, Sarah and Cisse, Ndiaga and Fatokun, Christian and Ehlers, Jeffrey D. and Roberts, Philip A. and Close, Timothy J.}, citeulike-article-id = {6029603}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0905886106}, citeulike-linkout-1 = {http://www.pnas.org/content/106/43/18159.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/106/43/18159.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19826088}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19826088}, day = {27}, doi = {10.1073/pnas.0905886106}, journal = {Proceedings of the National Academy of Sciences}, keywords = {dataset, est, plants, qtl, vigna}, month = {October}, number = {43}, pages = {18159--18164}, posted-at = {2009-10-28 22:44:59}, priority = {2}, title = {A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs}, url = {http://dx.doi.org/10.1073/pnas.0905886106}, volume = {106}, year = {2009} }

TY - JOUR ID - citeulike:6029603 L3 - citeulike-article-id:6029603 N2 - 10.1073/pnas.0905886106 Consensus genetic linkage maps provide a genomic framework for quantitative trait loci identification, map-based cloning, assessment of genetic diversity, association mapping, and applied breeding in marker-assisted selection schemes. Among “orphan crops” with limited genomic resources such as cowpea [ (L.) Walp.] (2 = 2 = 22), the use of transcript-derived SNPs in genetic maps provides opportunities for automated genotyping and estimation of genome structure based on synteny analysis. Here, we report the development and validation of a high-throughput EST-derived SNP assay for cowpea, its application in consensus map building, and determination of synteny to reference genomes. SNP mining from 183,118 ESTs sequenced from 17 cDNA libraries yielded ≈10,000 high-confidence SNPs from which an Illumina 1,536-SNP GoldenGate genotyping array was developed and applied to 741 recombinant inbred lines from six mapping populations. Approximately 90% of the SNPs were technically successful, providing 1,375 dependable markers. Of these, 928 were incorporated into a consensus genetic map spanning 680 cM with 11 linkage groups and an average marker distance of 0.73 cM. Comparison of this cowpea genetic map to reference legumes, soybean () and , revealed extensive macrosynteny encompassing 85 and 82%, respectively, of the cowpea map. Regions of soybean genome duplication were evident relative to the simpler diploid cowpea. Comparison with revealed extensive genomic rearrangement with some conserved microsynteny. These results support evolutionary closeness between cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes. IS - 43 JF - Proceedings of the National Academy of Sciences EP - 18164 TI - A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs VL - 106 SP - 18159 KW - dataset KW - est KW - plants KW - qtl KW - vigna AU - Muchero, Wellington AU - Diop, Ndeye AU - Bhat, Prasanna AU - Fenton, Raymond AU - Wanamaker, Steve AU - Pottorff, Marti AU - Hearne, Sarah AU - Cisse, Ndiaga AU - Fatokun, Christian AU - Ehlers, Jeffrey AU - Roberts, Philip AU - Close, Timothy PY - 2009/10/27/ UR - http://dx.doi.org/10.1073/pnas.0905886106 ER -