Field evaluation and genomic regions discovery conferring resistance to Cowpea Scab (Sphaceloma sp.) in Uganda

Abstract

Cowpea (Vigna unguiculata L. Walp) is a vital leguminous crop consumed in most parts of Sub-Saharan Africa. Productivity of the crop in Uganda is limited by multiple constraints, cowpea scab caused by Sphaceloma Sp. being one of them. It is a fungal disease affecting production leading to significant yield losses. The aim was to identify genotypes resistant to cowpea scab and deploy genome-wide association study (GWAS) to map cowpea genomic regions linked to scab resistance. The response of 200 cowpea minicore collection subset obtained from the University of California Riverside (UCR) and 10 local checks to cowpea scab disease were tested across two locations and two seasons in Uganda. The experiment was conducted under natural disease infestation environment. High significant differences (P≤0.001) for reaction to scab disease was observed among genotypes based on the Area under Disease Progress Curve (AUDPC) data. The analysis also revealed significant location-by-season (LxS) and genotype-by-location-by-season (GxLxS) interaction effects. Exotic cowpea genotypes were more resistant to scab compared to the local checks in the 4 environments (2 locations x 2 seasons). A number of genotypes such as Cameroon-12-58, Early Scarlet, Gorda, INIA-40, IT00K-901-6, and IT83D-442 showed consistent moderate resistance to scab infection in all environments with a potential of being good sources of resistance. The exotic genotypes also revealed higher grain yield compared to local checks. Genome Wide Association Study (GWAS), using 42,889 SNP panel identified three genomic regions associated with scab resistance. These regions were marked by the following significant SNPs: SNP ID 2_ 17311 located at a P value of 1.41E-05 on chromosome 8, SNP ID 2_ 22004 located at a P value of 1.09E-05 on chromosome 8 and SNP ID 2_11897 located at a P value of 1.74E-05 on chromosome 9. These SNPs were found to span the regions occupied by the genes: Vigun08g220100, Vigun09g065900 and Vigun08g219500 respectively.