Genome-wide association analysis in peanut accessions uncovers the genetic basis regulating oil and fatty acid variation.

Background: The cultivated peanut, Arachis hypogaea L., is a critical oil and food crop worldwide. Improving seed oil quality in peanut has long been an aim of breeders. However, our knowledge of the genetic basis of selecting for seed nutritional traits is limited. Based on AhFAD2A and AhFAD2B, scientists have now developed higher oleic acid (80-84%) in peanut. Decoding the genetic makeup behind natural variation in kernel oil and fatty acid concentrations is crucial for molecular breeding-based nutrient quantity and quality manipulation.

Results: Herein, we recognized 87 quantitative trait loci (QTLs) in 45 genomic regions for the concentrations of oil, oleic acid, and linoleic acid, as well as the oleic acid to linoleic acid (O/L) ratio via a genome-wide association study (GWAS) involving 499 peanut accessions. Eight QTLs explained more than 15% of the phenotypic variation in peanut accessions. Among the 45 potential genes significantly related to the four traits, only three genes displayed annotation to the fatty acid pathway. Furthermore, on the basis of pleiotropism or linkage data belonging to the identified singular QTLs, we generated a trait-locus axis to better elucidate the genetic background behind the observed oil and fatty acid concentration association. Expression analysis indicated that arahy.AV6GAN and arahy.NNA8KD have higher expressions in the seeds.

Conclusion: This natural population consisting of 499 peanut accessions combined with high-density SNPs will provide a better choice for identifying peanut QTLs/genes in the future. Together, our results provide strong evidence for the genetic mechanism behind oil biosynthesis in peanut, facilitating future advances in multiple fatty acid component generation via pyramiding of desirable QTLs.