SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley.

Jibin Wang,Chengdao Li,Hong Luo,Xifeng Ren,Lipan Liu,Dongfa Sun,Genlou Sun

doi:10.1038/srep31741

Abstract

A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley.

Highlights

A high-density linkage map is a valuable tool for functional genomics and breeding
Low quality single nucleotide polymorphisms (SNP) markers excluded as a result of filtering processes comprised of 5,375 markers with inconsistent parental scores, monomorphic and more than 15% missing data
The remaining 4992 polymorphic SNP markers and 153 of the obtained before polymorphic SSR marker met the requirements for use in the construction of a genetic map

Summary

Introduction

A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. The SNP-based high-density genetic map developed and the dwarfing gene btwd[1] mapped in this study provide critical information for position cloning of the btwd[1] gene and molecular breeding of barley. Plant breeders and geneticists have benefited from the availability of tools for the rapid and cost-effective development of molecular marker-based linkage maps[2].

Objectives

Methods

Results

Conclusion