Multi-locus Genome-Wide Association Study Uncovers Candidate Genes for Early Leaf Spot and Rust Resistance in Groundnut

Early leaf spot (ELS) and rust, caused by Cercospora arachidicola and Puccinia arachidis respectively, are major fungal diseases limiting global groundnut (Arachis hypogaea L.) production. Mini-core set was evaluated for ELS at 3 locations Senegal, Malawi and Mali and for rust at Dharwad for three seasons using the modified 9-point scale. High-density genotyping was performed using whole genome resequencing data to identify genomic regions associated with early leaf spot and rust resistance. After quality filtering, 561,009 high-confidence SNPs were obtained. To dissect the genetic architecture of resistance to these diseases, genome-wide association study (GWAS) was conducted on 184 diverse groundnut mini-core lines which revealed four marker trait associations (MTAs) significantly associated with ELS resistance and twelve MTAs associated with rust resistance, collectively explaining 10–59% of the phenotypic variance. The most significant SNPs were Ah01_48511619 and Ah17_133493906 for rust resistance, which were clearly differentiating the resistant and susceptible minicore lines and also validated in other diverse populations. These SNPs encode sterol c4-methyl oxidase 1-2 and MYB transcription factor. Sterol c4-methyl oxidase 1-2 is involved in brassinosteroids biosynthesis which inturn has a role in salicylic acid pathway and MYB transcription factor involved in activation of WRKY disease resistance genes to combat against fungal pathogens. For ELS resistance, the most significant SNP (Ah14_140021024) is associated with MYB transcription factor explaining phenotypic variance of 59%. The validated markers and the predicted candidate genes can be useful in integrating favorable alleles into elite cultivars through marker-assisted selection (MAS) for the development of cultivars with improved disease resistance. The ELS markers can be utilized in the breeding programs upon further validation.