Dissection of the Genetic Basis of Yield-Related Traits in the Chinese Peanut Mini-Core Collection Through Genome-Wide Association Studies
2021
Peanut is an important legume crop worldwide. To uncover the genetic basis
of yield features and assist breeding in the future, we conducted genome-wide
association studies (GWAS) for six yield-related traits of the Chinese peanut mini core
collection. The seed (pod) size and weight of the population were investigated
under four different environments, and these traits showed highly positive correlations
in pairwise combinations. We sequenced the Chinese peanut mini-core collection
using genotyping-by-sequencing approach and identified 105,814 high-quality single nucleotide
polymorphisms (SNPs). The population structure analysis showed essentially
subspecies patterns in groups and obvious geographical distribution patterns in
subgroups. A total of 79 significantly associated loci (P < 4.73 x 10-7 were
detected for the six yield-related traits through GWAS. Of these, 31 associations
were consistently detected in multiple environments, and 15 loci were commonly
detected to be associated with multiple traits. Two major loci located on chromosomal
pseudomolecules A06 and A02 showed pleiotropic effects on yield-related traits,
explaining 20% phenotypic variations across environments. The two genomic regions
were found 46 putative candidate genes based on gene annotation and expression
profile. The diagnostic marker for the yield-related traits from non-synonymous
SNP (Aradu-A06-107901527) was successfully validated, achieving a high correlation
between nucleotide polymorphism and phenotypic variation. This study provided
insights into the genetic basis of yield-related traits in peanut and verified one diagnostic
marker to facilitate marker-assisted selection for developing high-yield peanut varieties.
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