A Genome-Wide Scan Divulges Key Loci Involved in Resistance to Aphids (Aphis craccivora) in Cowpea (Vigna unguiculata)

Abstract

Cowpea aphids (Aphis craccivora Koch) double as a direct damaging pest and a virus vector to cowpea, threatening the economic yield of the crop. Given the multiple ecotypes, different alleles have been implicated in aphid resistance, necessitating the identification of key genes involved. The present study implemented a genome-wide scan using 365 cowpea mini-core accessions to decipher loci involved in resistance to aphid ecotype from Kano, Nigeria. Accessions were artificially inoculated with A. craccivora in insect-proof cages and damage severity assessed at 21 days after infestation. Significant phenotypic differences based on aphid damage severity were registered among the accessions. Skewed phenotypic distributions were depicted in the population, suggesting the involvement of major genes in the control of resistance. A genome-wide scan identified three major regions on chromosomes Vu10, Vu08 and Vu02, and two minor ones on chromosomes Vu01 and Vu06, that were significantly associated with aphid resistance. These regions harbored several genes, out of which, five viz Vigun01g233100.1, Vigun02g088900.1, Vigun06g224900.1, Vigun08g030200.1 and Vigun10g031100.1 were the most proximal to the peak single nucleotide polymorphisms (SNPs) positions. These genes are expressed under stress signaling, mechanical wounding and insect feeding. The uncovered loci contribute towards establishing a marker-assisted breeding platform and building durable resistance against aphids in cowpea.

Genetic progress in cowpea [Vigna unguiculata (L.) Walp.] stemming from breeding modernization efforts at the International Institute of Tropical Agriculture

“…More genomic resources and tools utilized by the cowpea breeding program have been extensively reviewed (Abdoul et al, 2023;Boukar et al, 2016Boukar et al, , 2018. These resources are being exploited for quantitative trait loci (QTL) mapping of key traits such as aphid resistance (Huynh et al, 2015;Kusi et al, 2018;Ongom et al, 2022), bacterial blight resistance (Agbicodo et al, 2010), heat tolerance (Lucas et al, 2013), drought tolerance , and striga resistance among others (Abdoul et al, 2023;Boukar et al, 2016). Among these QTL, aphid and bacterial blight resistance markers have been deployed in our program for forward breeding while striga, heat, drought, flower thrips, and seed size markers are being validated for utilization in marker-assisted selection.…”

“…B. Singh et al., 2006; B. B. Singh & Emechebe, 1990), insect resistance (Boukar et al., 2020; Myers et al., 1996; Omoigui, Ekeuro, et al., 2017; Ongom et al., 2022; S. R. Singh, 1977; Togola et al., 2020), high protein and mineral contents (Boukar et al., 2011), high yield potential, and early to medium maturity (Boukar et al., 2019; Kamara et al., 2012; Ongom, Fatokun, Togola, Oyebode, et al., 2021; B. B. Singh, 2007; B.…”

“…Molecular markers have also been deployed to understand genetic diversity and structure in germplasm being utilized in the breeding program (C. Fatokun et al., 2018; Gbedevi et al., 2021; Muñoz‐Amatriaín et al., 2021). Genome mapping of key traits has been conducted (Agbicodo et al., 2010; Huynh et al., 2015; Kusi et al., 2018; Ongom et al., 2022), and markers associated with some of these traits, especially aphids and bacterial blight resistances, were deployed in forward breeding. In addition to developing genomic tools, the program adjusted the breeding scheme, moving from traditional pedigree to single seed descent (SSD) for rapid generation advancement, enabling at least three generations per year coupled with molecular screening for seed purity and quality.…”