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

Autor: Takumi Morita, Shuyu Liu, Anne C. Roulin, Chenggen Chu, Simon G. Krattinger, Beat Keller, Hirokazu Handa, Michael Abrouk, Jesse Poland, Naveenkumar Athiyannan, Yveline Pailles, Thomas Müller, Christoph Stritt
Přispěvatelé: University of Zurich, Krattinger, Simon G
Jazyk: angličtina
Rok vydání: 2021
Předmět:
0106 biological sciences
0301 basic medicine
Candidate gene
Plant genetics
DNA Copy Number Variations
genetic structures
QH301-705.5
Gene Dosage
Medicine (miscellaneous)
Color
Locus (genetics)
1100 General Agricultural and Biological Sciences
2700 General Medicine
Biology
580 Plants (Botany)
01 natural sciences
Polymorphism
Single Nucleotide
General Biochemistry
Genetics and Molecular Biology
Chromosomes
Plant
Article
UFSP13-7 Evolution in Action: From Genomes to Ecosystems
03 medical and health sciences
Gene mapping
10126 Department of Plant and Microbial Biology
1300 General Biochemistry
Genetics and Molecular Biology
Gene Expression Regulation
Plant
Genetic variation
MYB
10211 Zurich-Basel Plant Science Center
Biology (General)
Triticum
Plant Proteins
Genetics
Haplotype
Glume
food and beverages
Genetic Variation
High-Throughput Nucleotide Sequencing
2701 Medicine (miscellaneous)
030104 developmental biology
Phenotype
Haplotypes
Metagenomics
General Agricultural and Biological Sciences
Genome
Plant
010606 plant biology & botany
Genome-Wide Association Study
Transcription Factors
Zdroj: Communications Biology, Vol 4, Iss 1, Pp 1-11 (2021)
Communications Biology
ISSN: 2399-3642
Popis: 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.
Krattinger, Abrouk et al. use genome wide association study and haplotype analyses to investigate the genetics of glume colour in ten reference grade wheat genomes. Haplotype comparison identifies a MYB transcription factor as a candidate gene for red glume colour.
Databáze: OpenAIRE
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