Genomic insights into the genetic signatures of selection and seed trait loci in cultivated peanut

Introduction: Cultivated peanut (Arachis hypogaea L.) is an important oil crop for human nutrition and is cultivated in >100 countries. However, the present knowledge of its genomic diversity, evolution, and loci related to the seed traits is limited. Objectives: Our study intended to (1) uncover the population structure and the demographic history of peanuts, (2) identify signatures of selection that occurred during peanut improvement breeding, and (3) detect and verify the functions of candidate genes associated with seed traits. Methods: We explored the population relationship and the evolution of peanuts using a largescale single nucleotide polymorphism dataset generated from the genome-wide resequencing of 203 cultivated peanuts. Genetic diversity and genomic scan analyses were applied to identify selective loci for genomicselection breeding. Genome-wide association studies, transgenic experiments, and RNA-seq were employed to identify the candidate genes associated with seed traits. Results: Our study revealed that the 203 resequenced accessions were divided into four genetic groups, consistent with their botanical classification. Moreover, the var. peruviana and var. fastigiata subpopulations have diverged to a greater extent than the others, and var. peruviana may be the earliest variant in the evolution from tetraploid ancestors. A recent dramatic expansion in the effective population size of the cultivated peanuts ca. 300-500 years ago was also noted. Selective sweeps underlying quantitative trait loci and genes of seed size, plant architecture, and disease resistance coincide with the major goals of improved peanut breeding compared with the landrace and cultivar populations. Genome-wide association testing with functional analysis led to the identification of two genes involved in seed weight and seed length regulation. Conclusion: Our study provides valuable information for understanding the genomic diversity and the evolution of peanuts and serves as a genomic basis for improving peanut cultivars. (c) 2022 The Authors. Published by Elsevier B.V. on behalf of Cairo University. This is an open access article

Automated summary

By analyzing the resequencing data of 203 cultivated peanuts, we revealed the genetic diversity and evolutionary history of peanuts. We found that the population structure of cultivated peanuts is consistent with their botanical classification, and the var. peruviana may be the earliest variant. Cultivated peanuts experienced a sudden expansion in population size compared to landraces and cultivars. Two genes associated with seed traits were identified through functional analysis.