Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.)

Abstract

Peanut (Arachis hypogaea L.) is one of the important oil crops of the world. In this study, we aimed to evaluate the genetic diversity of 384 peanut germplasms including 100 Korean germplasms and 284 core collections from the United States Department of Agriculture (USDA) using an Axiom_Arachis array with 58K single-nucleotide polymorphisms (SNPs). We evaluated the evolutionary relationships among 384 peanut germplasms using a genome-wide association study (GWAS) of seed aspect ratio data processed by ImageJ software. In total, 14,030 filtered polymorphic SNPs were identified from the peanut 58K SNP array. We identified five SNPs with significant associations to seed aspect ratio on chromosomes Aradu.A09, Aradu.A10, Araip.B08, and Araip.B09. AX-177640219 on chromosome Araip.B08 was the most significantly associated marker in GAPIT and Regularization method. Phosphoenolpyruvate carboxylase (PEPC) was found among the eleven genes within a linkage disequilibrium (LD) of the significant SNPs on Araip.B08 and could have a strong causal effect in determining seed aspect ratio. The results of the present study provide information and methods that are useful for further genetic and genomic studies as well as molecular breeding programs in peanuts.

Genome-Wide Association Study of Leaf Chlorophyll Content Using High-Density SNP Array in Peanuts (Arachis hypogaea L.)

“…The quality and quantity of the extracted DNA were determined using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and 1% agarose gel electrophoresis. The high-density SNP array Axiom_Arachis (Thermo Fisher Scientific, Waltham, MA, USA) with 58K SNPs was used to obtain the genotyping data [37].…”

“…Candidate genes within a 200 kb region upstream or downstream of the peak SNPs according to the previous linkage disequilibrium (LD) decay results were selected using the PeanutBase website tool (https://www.peanutbase.org) (21 November 2021) [37].…”

“…Out of the 58K SNPs, a total of 47,837 SNPs presented polymorphisms (Supplementary Table S3 and Figure 1a). After eliminating SNPs with high levels of missing data (>20%), heterozygosity (>20%), or low minor allele frequency (MAF) (<0.01), a total of 20,623 SNPs were selected for future association analysis [37]. Of the 20,623 SNPs, 9370 and 11,253 SNPs were derived from subgenomes A and B, respectively.…”

“…High-density SNP arrays have been used for high-resolution genetic mapping of target traits, genome selection, and genome-wide association studies (GWAS) [37][38][39][40]. In the case of peanuts, it was necessary to develop SNP chips with high-throughput genotyping because of the large genome size and low genetic diversity [38].…”

Peanut Germplasm Evaluation for Agronomic Traits and Disease Resistance under a Two-Season Cropping System in Taiwan

“…Pandey et al (2017) [24] genotyped 300 peanut accessions from ICRISAT, using the Axiom Arachis SNP array. Similarly, a mixed population (100 samples from South Korea and 284 samples from USDA) was genotyped by SNP array to understand the genetic diversity of the mixed population [25].…”