Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat.
Autor: | Makhoul M; Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany., Chawla HS; Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.; Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada., Wittkop B; Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany., Stahl A; Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany., Voss-Fels KP; Institute for Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany., Zetzsche H; Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany., Snowdon RJ; Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany., Obermeier C; Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany. |
---|---|
Jazyk: | angličtina |
Zdroj: | Frontiers in plant science [Front Plant Sci] 2022 Jul 15; Vol. 13, pp. 942461. Date of Electronic Publication: 2022 Jul 15 (Print Publication: 2022). |
DOI: | 10.3389/fpls.2022.942461 |
Abstrakt: | The gene VERNALIZATION1 ( VRN1 ) is a key controller of vernalization requirement in wheat. The genome of hexaploid wheat ( Triticum aestivum ) harbors three homoeologous VRN1 loci on chromosomes 5A, 5B, and 5D. Structural sequence variants including small and large deletions and insertions and single nucleotide polymorphisms (SNPs) in the three homoeologous VRN1 genes not only play an important role in the control of vernalization requirement, but also have been reported to be associated with other yield related traits of wheat. Here we used single-molecule sequencing of barcoded long-amplicons to assay the full-length sequences (∼13 kbp plus 700 bp from the promoter sequence) of the three homoeologous VRN1 genes in a panel of 192 predominantly European winter wheat cultivars. Long read sequences revealed previously undetected duplications, insertions and single-nucleotide polymorphisms in the three homoeologous VRN1 genes. All the polymorphisms were confirmed by Sanger sequencing. Sequence analysis showed the predominance of the winter alleles vrn-A1 , vrn-B1 , and vrn-D1 across the investigated cultivars. Associations of SNPs and structural variations within the three VRN1 genes with 20 economically relevant traits including yield, nodal root-angle index and quality related traits were evaluated at the levels of alleles, haplotypes, and copy number variants. Cultivars carrying structural variants within VRN1 genes showed lower grain yield, protein yield and biomass compared to those with intact genes. Cultivars carrying a single vrn-A1 copy and a unique haplotype with a high number of SNPs were found to have elevated grain yield, kernels per spike and kernels per m 2 along with lower grain sedimentation values. In addition, we detected a novel SNP polymorphism within the G-quadruplex region of the promoter of vrn-A1 that was associated with deeper roots in winter wheat. Our findings show that multiplex, single-molecule long-amplicon sequencing is a useful tool for detecting variants in target genes within large plant populations, and can be used to simultaneously assay sequence variants among target multiple gene homoeologs in polyploid crops. Numerous novel VRN1 haplotypes and alleles were identified that showed significantly associations to economically important traits. These polymorphisms were converted into PCR or KASP assays for use in marker-assisted breeding. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2022 Makhoul, Chawla, Wittkop, Stahl, Voss-Fels, Zetzsche, Snowdon and Obermeier.) |
Databáze: | MEDLINE |
Externí odkaz: |