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Genetic Architecture of Delayed Senescence, Biomass, and Grain Yield under Drought Stress in Cowpea

Wellington Muchero1¤a, Philip A. Roberts1*, Ndeye N. Diop2¤b, Issa Drabo3, Ndiaga Cisse4,
Timothy J. Close2, Satoru Muranaka5, Ousmane Boukar5, Jeffrey D. Ehlers2¤c
1 Department of Nematology, University of California Riverside, Riverside, California, United States of America, 2 Department of Botany & Plant Sciences, University of
California Riverside, Riverside, California, United States of America, 3 Institut de l’environment et des Rechercheres Agricole, Kamboinse, Burkina Faso, 4 Senegalese
Institute of Agricultural Research, Bambey, Senegal, 5 The International Institute of Tropical Agriculture, Ibadan, Nigeria

Abstract
The stay-green phenomenon is a key plant trait with wide usage in managing crop production under limited water
conditions. This trait enhances delayed senescence, biomass, and grain yield under drought stress. In this study we sought
to identify QTLs in cowpea (Vigna unguiculata) consistent across experiments conducted in Burkina Faso, Nigeria, Senegal,
and the United States of America under limited water conditions. A panel of 383 diverse cowpea accessions and a
recombinant inbred line population (RIL) were SNP genotyped using an Illumina 1536 GoldenGate assay. Phenotypic data
from thirteen experiments conducted across the four countries were used to identify SNP-trait associations based on linkage
disequilibrium association mapping, with bi-parental QTL mapping as a complementary strategy. We identified seven loci,
five of which exhibited evidence suggesting pleiotropic effects (stay-green) between delayed senescence, biomass, and
grain yield. Further, we provide evidence suggesting the existence of positive pleiotropy in cowpea based on positively
correlated mean phenotypic values (0.34, r ,0.87) and allele effects (0.07, r ,0.86) for delayed senescence and grain yield
across three African environments. Three of the five putative stay-green QTLs, Dro-1, 3, and 7 were identified in both RILs
and diverse germplasm with resolutions of 3.2 cM or less for each of the three loci, suggesting that these may be valuable
targets for marker-assisted breeding in cowpea. Also, the co-location of early vegetative delayed senescence with biomass
and grain yield QTLs suggests the possibility of using delayed senescence at the seedling stage as a rapid screening tool for
post-flowering drought tolerance in cowpea breeding. BLAST analysis using EST sequences harboring SNPs with the highest
associations provided a genomic context for loci identified in this study in closely related common bean (Phaseolus vulgaris)
and soybean (Glycine max) reference genomes.