Construction of High-Density Genetic Map in Barley through Restriction-Site Associated DNA Sequencing

Gaofeng Zhou; Qisen Zhang; Xiao-Qi Zhang; Cong Tan; Chengdao Li

doi:10.1371/journal.pone.0133161

Construction of High-Density Genetic Map in Barley through Restriction-Site Associated DNA Sequencing

PLoS One. 2015 Jul 16;10(7):e0133161. doi: 10.1371/journal.pone.0133161. eCollection 2015.

Authors

Gaofeng Zhou¹, Qisen Zhang², Xiao-Qi Zhang³, Cong Tan³, Chengdao Li⁴

Affiliations

¹ Department of Agriculture and Food, South Perth, WA, Australia.
² Australian Export Grains Innovation Centre, South Perth, WA, Australia.
³ Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia.
⁴ Department of Agriculture and Food, South Perth, WA, Australia; Australian Export Grains Innovation Centre, South Perth, WA, Australia; Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia.

Abstract

Genetic maps in barley are usually constructed from a limited number of molecular markers such as SSR (simple sequence repeat) and DarT (diversity arrays technology). These markers must be first developed before being used for genotyping. Here, we introduce a new strategy based on sequencing progeny of a doubled haploid population from Baudin × AC Metcalfe to construct a genetic map in barley. About 13,547 polymorphic SNP tags with >93% calling rate were selected to construct the genetic map. A total of 12,998 SNP tags were anchored to seven linkage groups which spanned a cumulative 967.6 cM genetic distance. The high-density genetic map can be used for QTL mapping and the assembly of WGS and BAC contigs. The genetic map was evaluated for its effectiveness and efficiency in QTL mapping and candidate gene identification. A major QTL for plant height was mapped at 105.5 cM on chromosome 3H. This QTL with LOD value of 13.01 explained 44.5% of phenotypic variation. This strategy will enable rapid and efficient establishment of high-density genetic maps in other species.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genome, Plant
Hordeum / anatomy & histology
Hordeum / genetics*
Polymorphism, Single Nucleotide
Quantitative Trait Loci*
Sequence Analysis, DNA

Grants and funding

This work was supported by the fund from Grains Research and Development Corporation (GRDC) of Australia (DAW00233.), Department of Agriculture and Food Western Australia, and Western Australian State Agricultural Biotechnology Centre (SABC).