Integration of snRNA-seq and GWAS reveals AhWRI1-03a regulating seed oil content in Peanuts (Arachis hypogaea L.)

Peanut is a major global economic crop with its seeds rich in oil and unsaturated fatty acids. However, the genes expression network of seeds development on single-cell resolution is unclear, here we conducted single-nucleus RNA-seq (snRNA-seq) on peanut seeds, classifying 35,082 single-cells into 13 clusters and identifying three major cell-types (coat, cotyledon, embryonic axis). Combining pseudo-time analysis and bulk transcriptome identified the coat serving as the starting point of seed cell differentiation and elucidated the cotyledon and embryonic axis development heterogeneity with different transcription factors interaction network induced pathways. Further snRNA-seq integrated with GWAS oil trait SNP data, a novel nuclear-localized WRINKLED gene AhWRI1-03a was identified to highly expressed in the early seed coat, overexpression of AhWRI1-03a enhanced the oil accumulation in Arabidopsis seed, and the molecular marker was designed based on the AhWRI1-03a haplotypes SNP locus mutation for breeding application. Our study established the single-nucleus transcriptome landscape of peanut seeds, and integrated the snRNA-seq and GWAS to characterize the AhWRI1-03a is a target gene in the next application of high oil content peanut variety breeding.