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

Shengzhong Zhang,Xiaohui Hu,Fenggao Cui,Yi Shen,Chunming Wang,Weiqiang Yang,Libo Zhao,Ye Chu,Huarong Miao,Tingting Xu,Jiancheng Zhang,Jing Chen

doi:10.1186/s12870-019-2164-5

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.

Highlights

The cultivated peanut is an important oil and cash crop grown worldwide
To further elucidate genomic regions conditioning seed related traits in peanut, we developed a recombinant inbred line (RIL) population for Quantitative trait locus (QTL) mapping
A new high density genetic map with 3866 SLAF and simple sequence repeat (SSR) loci was constructed based on the released cultivated peanut genome

Summary

Introduction

The 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. Various genetic strategies to define QTLs or genes associated with seed traits have been conducted, including linkage mapping [2, 4], genome-wide association studies [5, 6] and bulked-segregant analyses [7]. Combined with the generation sequencing (NGS), a number of SNP-based genotyping technologies, especially SLAF-seq, have been applied to HDGM construction and QTL analysis in several species, such as sesame [17], soybean [18], cucumber [19, 20], cotton [21] and peanut [8, 22, 23]. A HDGM for cultivated peanut has been constructed based on SNP and SSR markers

Methods

Results

Discussion

Conclusion