Hybridisation-based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley.

Camilla Beate Hill,Matthew Hayden,Dean Diepeveen,Lee‐Anne Mcfawn,Paul Telfer,Cong Tan,Kerrie Forrest,Yanhao Xu,David Moody,Xiao‐Qi Zhang,Sharon Westcott,Tefera Tolera Angessa,Josquin Tibbits,Chengdao Li,Debbie Wong

doi:10.1111/pbi.13029

Abstract

SummaryBarley (Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here, we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target‐capture method was used to detect genome‐wide polymorphisms in a panel of 174 flowering time‐related genes, chosen based on prior knowledge from barley, rice and Arabidopsis thaliana. Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas.

Highlights

Barley (Hordeum vulgare L.) is one of the earliest domesticated crops found at Neolithic farming sites in the Fertile Crescent of the Eastern Mediterranean region (Abbo et al, 2010)
To maximise phenotypic differences in phenology and grain yield, accessions representing six and two row types, spring and winter growth habit, as well as malting and feed-end-use were selected, with an emphasis on spring-type (92%) and two-row varieties (90%) (Figure S1b), these being most relevant to the major barley production areas in Australia, Europe and North America
We applied a target capture approach based on in-solution hybridization which enabled the rapid and cost-effective identification of candidate genes associated with phenology and other important agronomic traits in barley

Summary

Introduction

Barley (Hordeum vulgare L.) is one of the earliest domesticated crops found at Neolithic farming sites in the Fertile Crescent of the Eastern Mediterranean region (Abbo et al, 2010). Barley has been adapted across a range of diverse agricultural environments and is cultivated on 46.9 million hectares of land in more than 100 countries worldwide (FAOSTAT 2016, http://www.fao.org/faostat). Yield is a challenging breeding target as it is controlled by a large number of genes with varying effects, and strongly influenced by genotype by environment interactions (complex trait) (Araus et al, 2008). Phenology genes that determine heading date and photoperiod sensitivity drive adaptation to different geographic environments and cropping systems (Andres and Coupland, 2012; Russell et al, 2016). Little is known about how natural genetic variation within phenology genes impacts grain yield and adaptation in barley

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Discussion

Conclusion