Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

Michael Abrouk,Shuyu Liu,Chenggen Chu,Anne C Roulin,Hirokazu Handa,Simon G Krattinger,Yveline Pailles,Takumi Morita,Beat Keller,Jesse Poland,Naveenkumar Athiyannan,Thomas Müller,Christoph Stritt

doi:10.1038/s42003-021-01908-6

Abstract

The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20th century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.

Highlights

The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars
The markers specific for groups 3 and 4 amplified in all red glume spelt accessions, but not in the white glume accessions (Fig. 3d, Supplementary Data 2). These results show that most Central European spelt accessions carry multiple Rg-B1 alleles, but that only group 3 and 4 alleles were associated with red glumes
The separation of hexaploid wheat into aestivum and spelta has mostly been based on morphological spike characteristics

Summary

Introduction

The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Chromosome-scale reference assemblies of the 10.5 Gb durum cultivar Svevo[7] and the 16 Gb bread wheat cultivar Chinese Spring[6] only became available during the past 2 years These reference genomes provided a first detailed insight into the structure and organization of the complex wheat genomes, but they did not allow to assess species-wide genomic variations. During its migration to Europe, a free-threshing hexaploid wheat might have hybridized with a hulled tetraploid emmer wheat, which gave rise to European spelt[15,16,17]. We used genotyping-by-sequencing (GBS)[25,26] to genotype 267 spelt accessions collected from the entire range of spelt cultivation This comprehensive analysis of the spelt gene pool allowed us to unravel population structure and agricultural history with genome-wide marker coverage. We further demonstrate the usefulness of high-throughput genotyping, association genetics, and haplotype analyses in the ten high-quality wheat genomes by isolating the Rg-B1 gene

Methods

Results

Conclusion