Population structure analysis and association mapping for iron deficiency chlorosis in worldwide cowpea (Vigna unguiculata (L.) Walp) germplasm

Cowpea ( Vigna unguiculata L. Walp) is a legume consumed for its high protein content. It provides nutrient-dense food opportunities for human consumption. Iron deficiency chlorosis (IDC) manifests as yellowing of the leaves and reduced plant growth, resulting in reduced yield potential. Use of IDC tolerant cowpea cultivars is an efficient method to address this problem. The objectives of this study were to conduct a population structure analysis, to carry out an association mapping study, and to identify SNP markers associated with IDC tolerance in cowpea. A total of 353 cowpea accessions were evaluated for tolerance/susceptibly to low soluble iron conditions on higher pH soils. A total of 1006 SNP markers postulated from genotyping-by-sequencing were used after filtering for population structure and association analysis studies. Results revealed that: (1) a substantial variability in degree of tolerance to low soluble iron conditions was found among the cowpea accessions; (2) delta K peak was identified at K equal to 2, indicating two subpopulations within the cowpea accessions tested for adaptation to IDC, a second delta peak corresponding to K equal to 3 was also found; and (3) nine SNP markers, C35081162_3130, Scaffold16136_2033, Scaffold1764_4741, Scaffold18262_4480, Scaffold30165_15499, Scaffold47194_5530, Scaffold73235_6677, Scaffold77932_9959, and Scaffold86559_7193, were significantly associated with IDC tolerance in cowpea. These results can be used as tools to select cowpea genotypes tolerant to IDC under low soluble iron conditions.