Rapid gene isolation in barley and wheat by mutant chromosome sequencing.

Javier Sánchez-Martín,Brande B H Wulff,Sreya Ghosh,Jaroslav Doležel,Marie Kubaláková,Beat Keller,Severine Hurni,Burkhard Steuernagel,Thomas Wicker,Simon G Krattinger,Nikolai Adamski,Gerhard Herren,Jan Vrána

doi:10.1186/s13059-016-1082-1

Abstract

Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to parental chromosomes. We apply MutChromSeq to six mutants each of the barley Eceriferum-q gene and the wheat Pm2 genes. This approach unambiguously identified single candidate genes that were verified by Sanger sequencing of additional mutants. MutChromSeq enables reference-free forward genetics in barley and wheat, thus opening up their pan-genomes to functional genomics.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1082-1) contains supplementary material, which is available to authorized users.

Highlights

The extraordinary success of wheat and barley as major worldwide crops is underpinned by their adaptability to diverse environments, high yield and nutritional content
We propose MutChromSeq, a gene cloning method which does not rely on recombination or fine-mapping
Genome complexity reduction by chromosome flow sorting and high-throughput sequencing

Summary

Introduction

The extraordinary success of wheat and barley as major worldwide crops is underpinned by their adaptability to diverse environments, high yield and nutritional content. Identification and manipulation of the genes controlling these traits will help to sustainably increase yields and ensure global food security. The large genomes of barley (5.5 Gb) and wheat (17 Gb) coupled with extensive regions of suppressed recombination [1, 2] make traditional map-based gene isolation in these crops both time-consuming and costly. In plants with small genomes, such as Arabidopsis and rice, whole genome sequencing on mapping populations has proven a powerful approach to aid gene isolation [3, 4]. Whole genome sequencing and comparison of multiple independently derived mutants belonging to the same complementation group permits direct gene identification with little or no requirement for recombination [5, 6]. Because of the genome size of barley and wheat, sequencing whole genomes in multiple

Objectives

Methods

Results

Discussion

Conclusion