Genome-wide association study reveals single nucleotide polymorphisms and candidate genes for resistance of cowpea to aphids

Abstract

Cowpea (Vigna unguiculata L. Walp.) is a major crop grown mainly in the arid and semi-arid regions for food and nutritional security. Its production, however, is generally hampered by its susceptibility to sap-sacking aphids (Aphis craccivora Koch). Resistance breeding for cowpea improvement against aphids, has been limited by inadequate understanding of genes responsible for resistance to this cosmopolitan pest. The objective of this study was to identify single nucleotide polymorphisms (SNPs) and candidate genes, associated with resistance of cowpea to aphids. The study evaluated 209 genotypes of the multi-parent advanced generation intercross (MAGIC) population, together with 5 MAGIC parents, cross three different locations for two seasons in Uganda. Significant genetic variation (P<0.001) for aphid resistance was detected in this germplasm. Results revealed three stable and significant SNPs, including 2_30668, 2_43528 and 2_43747; being associated with resistance to aphids. Eleven candidate genes were detected within the significant loci; including 7 genes on chromosome I (Vu01), 3 on chromosome VII (Vu07) and 1 on chromosome IX (Vu09). These putative genes have functions related to host plant resistance and plant defence responses, possibly against cowpea aphids. The significant SNP markers and genes reported may be deployed in marker-assisted breeding strategy, for faster development of aphid resistant cowpea varieties in Uganda.