QTL identification for seed weight and size based on a high-density SLAF-seq genetic map in peanut (Arachis hypogaea L.)

Abstract

BackgroundThe cultivated peanut is an important oil and cash crop grown worldwide. To meet the growing demand for peanut production each year, genetic studies and enhanced selection efficiency are essential, including linkage mapping, genome-wide association study, bulked-segregant analysis and marker-assisted selection. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for high density genetic map (HDGM) construction and quantitative trait loci (QTLs) mapping. In this study, a HDGM was constructed using SLAF-seq leading to identification of QTL for seed weight and size in peanut.ResultsA recombinant inbred line (RIL) population was advanced from a cross between a cultivar ‘Huayu36’ and a germplasm line ‘6–13’ with contrasting seed weight, size and shape. Based on the cultivated peanut genome, a HDGM was constructed with 3866 loci consisting of SLAF-seq and simple sequence repeat (SSR) markers distributed on 20 linkage groups (LGs) covering a total map distance of 1266.87 cM. Phenotypic data of four seed related traits were obtained in four environments, which mostly displayed normal distribution with varied levels of correlation. A total of 27 QTLs for 100 seed weight (100SW), seed length (SL), seed width (SW) and length to width ratio (L/W) were identified on 8 chromosomes, with LOD values of 3.16–31.55 and explaining phenotypic variance (PVE) from 0.74 to 83.23%. Two stable QTL regions were identified on chromosomes 2 and 16, and gene content within these regions provided valuable information for further functional analysis of yield component traits.ConclusionsThis study represents a new HDGM based on the cultivated peanut genome using SLAF-seq and SSRs. QTL mapping of four seed related traits revealed two stable QTL regions on chromosomes 2 and 16, which not only facilitate fine mapping and cloning these genes, but also provide opportunity for molecular breeding of new peanut cultivars with improved seed weight and size.

Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut

“…The deployment of the “Axiom_ Arachis ” array with 58,233 SNPs [ 25 ] in groundnut facilitated generation of high-throughput genotyping data for high-resolution trait mapping [ 45 ]. The studies also showed that SLAF-seq can help developing denser genetic map than GBS or SNP array [ 46 , 47 , 48 ].…”

Identification of consistent QTL for time to maturation in Virginia-type Peanut (Arachis hypogaea L.)

“…All effects were defined as random to calculate the heritability rates. Broad sense heritability ( H 2 ) was estimated with the equation H 2 = σ g 2 /(σ g 2 + σ ge 2 + σ e 2 ), by the ANOVA analysis with QTL IciMapping v4.2 ( http://www.isbreeding.net/software/?type=detail&id=29 ) [ 46 ]. The σ g 2 , σ e 2 and σ ge 2 denoted the variances of genotypes (G), environment (E) and interaction of genotypes and environments (G x E).…”

Fine-Mapping of a Wild Genomic Region Involved in Pod and Seed Size Reduction on Chromosome A07 in Peanut (Arachis hypogaea L.)

“…Several studies reported QTLs controlling pod/seed weight and size in peanut [12,[15][16][17][18][19][20][21][22][23][24][25][26]. However, a few of them involved crosses between wild and cultivated species.…”