Features of transcriptional dynamics of the duplicated <i>Vernalization‐B1</i> gene in wheat (<i>Triticum</i> spp.)

Muterko, Alexandr; Салина, Е. А.

doi:10.1111/pbr.12981

Cited by 3 publications

(2 citation statements)

References 27 publications

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“…This is in agreement with the study of Würschum et al (2015) and Dixon et al (2019) who did not find an effect of VRN-A1 CNV on flowering time. Díaz et al (2012); Dixon et al (2019) , and Muterko and Salina (2021) showed an effect of CNV on vernalization requirement. We found strong correlations with six other agronomic traits.…”

Section: Discussionmentioning

confidence: 95%

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Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat

et al. 2022

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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 m2 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.

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Section: Discussionmentioning

confidence: 95%

“…This gene is considered to be a copy of the Vrn-A1 gene on chromosome 5A. Recently, copy numbers for the dominant alleles of VRN-A1 and recessive allele of VRN-B1 have been detected in different species of wheat by Muterko and Salina, 2018 , 2019 , 2021 and Strejčková et al (2021) .…”

Section: Introductionmentioning

confidence: 99%

Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat

et al. 2022

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Copy Number Variation and Expression Dynamics of the Dominant Vernalization-A1a Allele in Wheat

Muterko

2023

Plant Mol Biol Rep

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Chromosome diversity in Dasypyrum villosum, an important genetic and trait resource for hexaploid wheat engineering

Fang

et al. 2022

Annals of Botany

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Background and Aims Dasypyrum villosum (2n = 2x = 14) harbors potentially beneficial genes for hexaploid and tetraploid wheat improvement. Highly diversified chromosome variation exists among and within accessions due to its open-pollination nature. The wheat-D. villosum T6VS·6AL translocation was widely used in breeding mainly because gene Pm21 in the 6VS segment conferred high and lasting powdery mildew resistance. However, the widespread use of this translocation may narrow genetic base of wheat. A better solution for this issue is to utilize diversified D. villosum accessions as genetic source for wheat breeding. Analysis of cytological and genetic polymorphisms among D. villosum accessions also provides genetic evolution information of the species. Using cytogenetic and molecular tools we analyzed genetic polymorphisms among D. villosum accessions and developed consensus karyotypes to assist the introgression of beneficial genes from D. villosum into wheat. Methods A multiplex probe of repeats for FISH, GISH and molecular markers were used to detect chromosome polymorphisms among D. villosum accessions. The polymorphic signal block types, chromosome heterogeneity and heterozygosity, and chromosome polymorphic information content (CPIC) were used in genetic diversity analysis. Key Results Consensus karyotypes of D. villosum were developed, and the homoeologous status of individual D. villosum chromosomes relative to wheat were determined. The tandem repeat probes of pSc119.2, (GAA)10 and AFA family produced high-resolution signals not only showing different signal patterns in D. villosum chromosomes but also revealed the varied distribution of tandem repeats among chromosomes and accessions. A total of 106 polymorphic chromosomes were identified from 13 D. villosum accessions and high levels of chromosomal heterozygosity and heterogeneity were observed. A subset of 56 polymorphic chromosomes was transferred into durum wheat through wide crosses, and seven polymorphic chromosomes are described in two newly developed durum-D. villosum amphidiploids. Conclusions Consensus karyotypes of D. villosum and oligonucleotide FISH facilitated identification of polymorphic signal blocks and a high level of chromosomal heterozygosity and heterogeneity among D. villosum accessions, seen in newly developed amphiploids. The abundant genetic diversity of D. villosum and range of alleles, exploitable through interploid crosses, backcrosses and recombination – chromosome engineering – allow introduction of biotic and abiotic stress resistances into wheat, translating into increasing yield, end-use quality and crop sustainability.

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Features of transcriptional dynamics of the duplicated Vernalization‐B1 gene in wheat (Triticum spp.)

Cited by 3 publications

References 27 publications

Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat

Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat

Copy Number Variation and Expression Dynamics of the Dominant Vernalization-A1a Allele in Wheat

Chromosome diversity in Dasypyrum villosum, an important genetic and trait resource for hexaploid wheat engineering

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