Understanding the genetics of quality traits in groundnut: GWAS highlights drought-responsive markers and candidate...

The study identified novel, drought-responsive markers and potential candidate genes for kernel quality traits under drought stress which are important genomic resources to breed resilient and nutritious groundnut varieties. Nutritional quality traits are crucial in crop breeding, especially with climate change affecting quality and yield. Increasing dry spells in semiarid regions require understanding drought stress effects on oil, protein, and fatty acid contents of groundnut kernels, and the molecular mechanisms governing these traits. The study showed a reduction in oil content and increase in protein content in a MAGIC population of groundnut under drought stress. MAGIC population exhibited high diversity with 13,937 polymorphic markers and are valuable for the genetic dissection of complex traits as compared to a RIL population with 800 polymorphic markers. Genome-wide association study (GWAS) employing multi-locus models such as BLINK, and MLMM identified 45 significant MTAs for oil, protein, oleic acid, palmitic acid, stearic acid, and linoleic acid under normal and drought stress across all chromosomes except A06, B01, B02, B03, B04, B05, and B06. Fourteen SNPs are identified with > 10% PVE linked to six quality traits, seven pleiotropic SNPs associated with multiple traits, and nine SNPs in both models across at least in two environments. Potential candidate genes for quality traits under drought stress are RING finger proteins and protein kinases for oil content; CASP-like protein and geranylgeranyl diphosphate reductase (GLDR) for protein content, and fatty acid desaturase 2, MYB transcription factor, and AMMECR1 family for oleic and palmitic acid content having role in various biosynthetic and lipid pathways. The MTAs identified in this study hold potential for development into assays for genomic-assisted selection to enhance nutritional quality and drought resilience in groundnut.