Development of a high-density genetic linkage map and identification of flowering time QTLs in adzuki bean (Vigna angularis).

Changyou Liu,Yan Wang,Jing Tian,Zhimin Cao,Baojie Fan,Qiuzhu Su,Zhixiao Zhang

doi:10.1038/srep39523

Changyou Liu, Yan Wang + Show 5 more

Open Access

https://doi.org/10.1038/srep39523

Copy DOI

Abstract

A high-density linkage map is crucial for the identification of quantitative trait loci (QTLs), positional cloning, and physical map assembly. Here, we report the development of a high-density linkage map based on specific length amplified fragment sequencing (SLAF-seq) for adzuki bean and the identification of flowering time-related QTLs. Through SLAF library construction and Illumina sequencing of a recombinant inbred line (RIL) population, a total of 4425 SLAF markers were developed and assigned to 11 linkage groups (LGs). After binning the SLAF markers that represented the same genotype, the final linkage map of 1628.15 cM contained 2032 markers, with an average marker density of 0.80 cM. Comparative analysis showed high collinearity with two adzuki bean physical maps and a high degree of synteny with the reference genome of common bean (Phaseolus vulgaris). Using this map, one major QTL on LG03 and two minor QTLs on LG05 associated with first flowering time (FLD) were consistently identified in tests over a two-year period. These results provide a foundation that will be useful for future genomic research, such as identifying QTLs for other important traits, positional cloning, and comparative mapping in legumes.

Highlights

A high-density linkage map is crucial for the identification of quantitative trait loci (QTLs), positional cloning, and physical map assembly
The genetic map developed in this study contains 4425 SLAF markers, a majority of which are anchored to the adzuki bean draft genome scaffolds
Compared to the genetic map constructed by Han et al.[8], the number of mapped loci (486 vs 4425), marker density (1.85 converted into map distances (cM) vs 0.8 cM), and total map length (832.1 cM vs 1628.15 cM) are significantly improved in this dense genetic linkage map

Summary

Introduction

A high-density linkage map is crucial for the identification of quantitative trait loci (QTLs), positional cloning, and physical map assembly. Comparative analysis showed high collinearity with two adzuki bean physical maps and a high degree of synteny with the reference genome of common bean (Phaseolus vulgaris) Using this map, one major QTL on LG03 and two minor QTLs on LG05 associated with first flowering time (FLD) were consistently identified in tests over a two-year period. Based on the development of next-generation sequencing technology, several high-throughput methods for SNP and insertion/deletion polymorphism (InDel) marker identification and genotyping have been developed These methods include restriction site-associated (RAD) sequencing (RADseq)[15], genotyping-by-sequencing(GBS)[16], and specific length amplified fragment sequencing (SLAF-seq)[17]. The specific objectives were (a) to construct a high-density genetic map of adzuki bean based on the SLAF-seq high-throughput method and (b) to identify QTLs associated with FLD over two years

Objectives

Methods

Results

Conclusion