Phenotyping of genomic selection panel for resistance to foliar fungal diseases and nutritional quality traits in groundnut

The present investigation was aimed to evaluate Genomic Selection Panel (GSP) comprising 340 diverse improved germplasm for two major foliar fungal diseases i.e. rust and late leaf spot (LLS), yield and nutritional quality traits in multi-location evaluation trials. The study was also aimed to conduct a preliminary evaluation of GSP for the level of genetic and molecular diversity, and allelic richness for the targeted traits which is a pre-requisite for Genomic Selection. Marker-trait association for different traits such as disease resistance, yield and nutritional quality was also done to validate markers on a diverse set of genotypes and to find significant markers linked to the traits of interest that can potentially be deployed in marker-assisted breeding. The results revealed significant genotypic, environment and genotype × environment interaction variances for all the traits studied. Breeding lines with high levels of resistance to LLS and rust and that are stable across the environments were identified that will be used as parents in breeding resistant varieties. The negative association of both the diseases with yield and nutritional quality traits indicates an adverse effect of LLS and rust on these traits. Sufficient level of phenotypic and molecular diversity and allelic richness (33 alleles per locus) was observed in GSP for both the diseases with a higher number of unique and rare alleles per locus. Low level of genetic variability in GSP reported for nutritional quality traits across the environments indicated that improvement of these characters was not attempted in the breeding program in the absence of robust, non-destructive and cost-effective phenotyping tools. So, there is a need of robust phenotyping and advance genomic tools to improve the quality traits in groundnut. The stable genotypes identified for the traits under study will be useful to develop new cultivars that are least influenced by environment. Grouping of genotypes based on marker data corresponded well with their botanical classification, place of breeding and expression of different traits across the environment. Deployment of identified potential marker-trait association explaining high phenotypic variation for LLS (GM 1009, GM 2301 and TC6H03) and rust (GM 2301 and IPAHM 103) in marker-assisted breeding would enhance intensity and accuracy of selection. There was high frequency (25.9%) of mutant allele of ahFAD2A reported in GSP whereas, mutant allele of ahFAD2B gene was not detected, except for SunOleic 95R a high oleic genotype released by the USA. More efforts need to be diverted to develop high oleic lines through incorporating both the mutant alleles into desirable genetic backgrounds. There was no significant difference in the mean oleic acid observed for individuals carrying mutant allele on A genome (ahFAD2A) with individual carrying wild-type allele. Therefore, it is concluded that presence of both the mutant alleles is required for desired levels of high oleic content