AUTHOR=Lucas Mitchell R., Huynh Bao-Lam , Vinholes Patricia d., Cisse Ndiaga , Drabo Issa , Ehlers Jeffrey D., Roberts Philip A., Close Timothy J. TITLE=Association Studies and Legume Synteny Reveal Haplotypes Determining Seed Size in Vigna unguiculata JOURNAL=Frontiers in Plant Science VOLUME=4 YEAR=2013 URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2013.00095 DOI=10.3389/fpls.2013.00095 ISSN=1664-462X ABSTRACT=

Highly specific seed market classes for cowpea and other grain legumes exist because grain is most commonly cooked and consumed whole. Size, shape, color, and texture are critical features of these market classes and breeders target development of cultivars for market acceptance. Resistance to biotic and abiotic stresses that are absent from elite breeding material are often introgressed through crosses to landraces or wild relatives. When crosses are made between parents with different grain quality characteristics, recovery of progeny with acceptable or enhanced grain quality is problematic. Thus genetic markers for grain quality traits can help in pyramiding genes needed for specific market classes. Allelic variation dictating the inheritance of seed size can be tagged and used to assist the selection of large seeded lines. In this work we applied 1,536-plex SNP genotyping and knowledge of legume synteny to characterize regions of the cowpea genome associated with seed size. These marker-trait associations will enable breeders to use marker-based selection approaches to increase the frequency of progeny with large seed. For 804 individuals derived from eight bi-parental populations, QTL analysis was used to identify markers linked to 10 trait determinants. In addition, the population structure of 171 samples from the USDA core collection was identified and incorporated into a genome-wide association study which supported more than half of the trait-associated regions important in the bi-parental populations. Seven of the total 10 QTLs were supported based on synteny to seed size associated regions identified in the related legume soybean. In addition to delivering markers linked to major trait determinants in the context of modern breeding, we provide an analysis of the diversity of the USDA core collection of cowpea to identify genepools, migrants, admixture, and duplicates.