Development of a High-Density Genetic Map Based on Specific Length Amplified Fragment Sequencing and Its Application in Quantitative Trait Loci Analysis for Yield-Related Traits in Cultivated Peanut.

Zhihui Wang,Huifang Jiang,Dongxin Huai,Boshou Liao,Liying Yan,Zhaohua Zhang,Yanping Kang,Yong Lei,Liyun Wan,Ke Cheng

doi:10.3389/fpls.2018.00827

Abstract

High-density genetic maps (HDGMs) are very useful for genomic studies and quantitative trait loci (QTL) mapping. However, the low frequency of DNA polymorphisms in peanut has limited the quantity of available markers and hindered the construction of a HDGM. This study generated a peanut genetic map with the highest number of high-quality SNPs based on specific locus amplified fragment sequencing (SLAF-seq) technology and a newly constructed RIL population (“ZH16” × “sd-H1”). The constructed HDGM included 3,630 SNP markers belonging to 2,636 bins on 20 linkage groups (LGs), and it covers 2,098.14 cM in length, with an average marker distance of 0.58 cM. This HDGM was applied for the following collinear comparison, scaffold anchoring and analysis of genomic characterization including recombination rates and segregation distortion in peanut. For QTL mapping of investigated 14 yield-related traits, a total of 62 QTLs were detected on 12 chromosomes across 3 environments, and the co-localization of QTLs was observed for these traits which were significantly correlated on phenotype. Two stable co-located QTLs for seed- and pod-related traits were significantly identified in the chromosomal end of B06 and B07, respectively. The construction of HDGM and QTL analysis for yield-related traits in this study provide useful information for fine mapping and functional analysis of genes as well as molecular marker-assisted breeding.

Highlights

Peanut (Arachis hypogaea L., 2n = 20) is an economically important oilseed crop that is cultivated worldwide and it is one of the major grain legumes in tropical and subtropical regions
Considering the low rate of DNA polymorphisms in peanut, we sequenced a high amount of data of the parents and the recombinant inbred line (RIL) population to obtain a sufficient number of markers
Investigations on the genetic diversity of peanut germplasm resources have indicated that cultivated peanut possesses an extremely narrow genetic base (Jiang et al, 2010; Ren et al, 2010; Belamkar et al, 2011; Wang et al, 2011; Mukri et al, 2012; Upadhyaya et al, 2012), which is likely due to its monophyletic origin from a single hybridization event between two ancient diploid species (Burow et al, 2009)

Summary

Introduction

Initial genetic maps were mainly developed based on the first generation molecular markers including random amplified polymorphic DNA (RAPD) (Hilu and Stalker, 1995), restriction fragment length polymorphism (RFLP) (Halward et al, 1993, 2011) and amplified fragment length polymorphism (AFLP) (He and Prakash, 1997; Tallury et al, 2005). These genetic maps commonly have low marker density with total marker numbers

Methods

Results

Conclusion