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

Authors: ABROUK, MICHAEL - King Abdullah University Of Science And Technology; ATHIYANNAN, NAVEENKUMAR - King Abdullah University Of Science And Technology; MULLER, THOMAS - University Of Zurich; PAILLES, YVELINE - King Abdullah University Of Science And Technology; CHRISTOPH, STRITT - University Of Zurich; ROULIN, ANNE - University Of Zurich; Chu, Chenggen; LIU, SHUYU - Texas A&M Agrilife; ADHIKARI, LAXMAN - Kansas State University; WU, SHUANGYE - Kansas State University; RAUPP, JOHN - Kansas State University; HANDA, HIROKAZU - Kyoto University; MORITA, TAKUMI - Kyoto University; POLAND, JESSE - Kansas State University; KELLER, BEAT - University Of Zurich; KRATTINGER, SIMON - King Abdullah University Of Science And Technology

Submitted to: Communications Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/25/2021
Publication Date: 3/19/2021
Citation: Abrouk, M., Athiyannan, N., Muller, T., Pailles, Y., Christoph, S., Roulin, A.C., Chu, C.N., Liu, S., Adhikari, L., Wu, S., Raupp, J., Handa, H., Morita, T., Poland, J., Keller, B., Krattinger, S.G. 2021. Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color. Communications Biology. 4. Article e375. https://doi.org/10.1038/s42003-021-01908-6.
DOI: https://doi.org/10.1038/s42003-021-01908-6

Interpretive Summary: Glumes are leaf-like structures of grass species including wheat. Glume color is an important trait to characterize wheat varieties. Red glumes were frequent in Central European in Europe before the 20th century. This study analyzed different wheat varieties with red glume in Europe and determined that a gene called Rg-B1 was associated with glume color. This study demonstrated that using multiple reference genomes can be used to rapidly identify genes controlling important wheat traits.

Technical 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.