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Genomic insights into the genetic signatures of selection and seed trait loci in cultivated peanut
Journal article   Open access   Peer reviewed

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

Yiyang Liu, Libin Shao, Jing Zhou, Rongchong Li, Manish K. Pandey, Yan Han, Feng Cui, Jialei Zhang, Feng Guo, Jing Chen, …
Journal of advanced research, Vol.42, pp.237-248
2022
DOI: https://doi.org/10.1016/j.jare.2022.01.016
PMID: 36513415
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Published3.24 MBDownloadView
CC BY-NC-ND V4.0,  Open Access

Abstract

Evolution Genomic diversity GWAS Peanut Seed traits
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 genomic-selection 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.

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Collaboration types
Domestic collaboration
International collaboration
Citation topics
3 Agriculture, Environment & Ecology
3.4 Crop Science
3.4.96 QTL
Web Of Science research areas
Genetics & Heredity
ESI research areas
Molecular Biology & Genetics
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