Genetic Variation and Association Mapping of Seed-Related Traits in Cultivated Peanut (Arachis hypogaea L.) Using Single-Locus Simple Sequence Repeat Markers

Abstract

Cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB, 2n = 4x = 40), valued for its edible oil and digestible protein. Seed size and weight are important agronomical traits significantly influence the yield and nutritional composition of peanut. However, the genetic basis of seed-related traits remains ambiguous. Association mapping is a powerful approach for quickly and efficiently exploring the genetic basis of important traits in plants. In this study, a total of 104 peanut accessions were used to identify molecular markers associated with seed-related traits using 554 single-locus simple sequence repeat (SSR) markers. Most of the accessions had no or weak relationship in the peanut panel. The linkage disequilibrium (LD) decayed with the genetic distance of 1cM at the genome level and the LD of B subgenome decayed faster than that of the A subgenome. Large phenotypic variation was observed for four seed-related traits in the association panel. Using mixed linear model with population structure and kinship, a total of 30 significant SSR markers were detected to be associated with four seed-related traits (P < 1.81 × 10-3) in different environments, which explained 11.22–32.30% of the phenotypic variation for each trait. The marker AHGA44686 was simultaneously and repeatedly associated with seed length and hundred-seed weight in multiple environments with large phenotypic variance (26.23 ∼ 32.30%). The favorable alleles of associated markers for each seed-related trait and the optimal combination of favorable alleles of associated markers were identified to significantly enhance trait performance, revealing a potential of utilization of these associated markers in peanut breeding program.

Four QTL clusters containing major and stable QTLs for saturated fatty acid contents in a dense genetic map of cultivated peanut (Arachis hypogaea L.)

“…Fatty acid composition of 99 accessions is presented in Table S7. Genotyping of 554 SSR markers in 99 accessions with Zhonghua 10 and ICG12625 has been reported previously (Zhao et al 2017). SSR m a r k e r s , s u c h a s A H G S 1 5 7 9 , A H G S 0 2 8 8 , AHGA17736, AGGS1039 adjoining to CLB04-1, CLB04-2, CLB04-3, and CLB06, respectively, and marker AGGS0186 within CLB04-3, were found to be polymorphic in 99 accessions (Fig.…”

Dissection of the genetic basis of oil content in Chinese peanut cultivars through association mapping

“…The screening of genome-wide SSR marker in the peanut panel produced high number (3,663) of alleles including 629 unique alleles showing high molecular diversity. For example, this panel of 292 Chinese cultivated accessions showed on par average allele number (2.99 to 8.10 per locus), gene diversity (0.51) and PIC (0.45) as compared to average allele number (6.28 per locus), gene diversity (0.11 to 0.59) and PIC (0.21 to 0.53) in other Chinese germplasm collections or US peanut mini-core collection[26][27][28]. On the other hand, the higher values for average allele number(22.21), gene diversity (0.74) and PIC (0.72) was observed in the peanut 'reference set' of ICRISAT[23] which may due to the diverse genotypes included from 48 countries representing global diversity including wild accessions.…”

Dissection of the genetic basis of oil content in Chinese peanut cultivars by association mapping

“…The trait of oil content was inherited in an additive manner for oil crops [13,[36][37][38], which could facilitate pyramiding associated loci straightforward in the breeding program. In this study, associated markers were widely located on chromosome A03, A04, A08, A09, A10, B01, B06, B07, and B08 based on the information from previous linkage maps and the physical location on genome [39][40][41][42].…”