Population structure and marker–trait association analysis of the US peanut (Arachis hypogaea L.) mini-core collection

Abstract

Peanut (Arachis hypogaea L.) is one of the most important oilseed and nutritional crops in the world. To efficiently utilize the germplasm collection, a peanut mini-core containing 112 accessions was established in the United States. To determine the population structure and its impact on marker-trait association, this mini-core collection was assessed by genotyping 94 accessions with 81 SSR markers and two functional SNP markers from fatty acid desaturase 2 (FAD2). Seed quality traits (including oil content, fatty acid composition, flavonoids, and resveratrol) were obtained through nuclear magnetic resonance (NMR), gas chromatography (GC), and high-performance liquid chromatography (HPLC) analysis. Genetic diversity and population structure analysis identified four major subpopulations that are related to four botanical varieties. Model comparison with different levels of population structure and kinship control was conducted for each trait and association analyses with the selected models verified that the functional SNP from the FAD2A gene is significantly associated with oleic acid (C18:1), linoleic acid (C18:2), and oleic-to-linoleic (O/L) ratio across this diverse collection. Even though the allele distribution of FAD2A was structured among the four subpopulations, the effect of FAD2A gene remained significant after controlling population structure and had a likelihood-ratio-based R ( 2 ) (R ( LR ) ( 2 ) ) value of 0.05 (oleic acid), 0.09 (linoleic acid), and 0.07 (O/L ratio) because the FAD2A alleles were not completely fixed within subpopulations. Our genetic analysis demonstrated that this peanut mini-core panel is suitable for association mapping. Phenotypic characterization for seed quality traits and association testing of the functional SNP from FAD2A gene provided information for further breeding and genetic research.

Genomewide Association Studies for 50 Agronomic Traits in Peanut Using the ‘Reference Set’ Comprising 300 Genotypes from 48 Countries of the Semi-Arid Tropics of the World

“…Two DArT markers (gnPt-739706 and gnPt-736685) with five appearances each and two SSR markers (GM1901, GM2480) with three appearances each showed good consistency. MTAs identified for OLE possessed lower PV than the earlier identified MTA conducted on ‘US-mini core collection’ (53.57% PV) while MTAs identified for OLR were little higher than the PV% of earlier study (42.35%) [34].…”

Insights into the Indian Peanut Genotypes for ahFAD2 Gene Polymorphism Regulating Its Oleic and Linoleic Acid Fluxes

“…These tools have been successfully utilized for the screening of peanut germplasm (Chu et al, 2007; Wang et al, 2011a,b, 2013b; Mukri et al, 2012). However, no such efforts have been reported for the Indian peanut cultivars and advanced breeding lines, which are being used in improving the O/L ratio of the Indian genotypes by the breeders.…”

Molecular genetic diversity and association mapping of morphine content and agronomic traits in Turkish opium poppy (Papaver somniferum) germplasm

“…Although AM has been extensively applied in major crop species, relatively little work has been done in nonmodel plants such as poppy. Some exceptions include work in teosinte, oat, peanut, loblolly pine, and sesame that used LD to identify significant associations between molecular markers and agronomic traits (Weber et al 2008;Achleitner et al 2008;Wang et al 2011;Eckert et al 2012;Wei et al 2013). The main problem in AM is the occurrence of false-positive associations due to population structure and the relatedness of individuals.…”