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A major quantitative trait locus for cold-responsive gene expression is linked to frost-resistance gene Fr-A2 in common wheat.

ABSTRACT: Low temperature induces expression of Cor (cold-responsive)/Lea (late embryogenesis-abundant) gene family members through C-repeat binding factor (CBF) transcription factors in common wheat. However, the relationship between the genetic loci controlling cold-responsive gene expression and freezing tolerance is unclear. In expression quantitative trait locus (eQTL) analysis, accumulated transcripts of Cor/Lea and CBF genes were quantified in recombinant inbred lines derived from a cross between two common wheat cultivars with different levels of freezing tolerance. Four eQTLs controlling five cold-responsive genes were found, and the major eQTL with the greatest effect was located on the long arm of chromosome 5A. At least the 1D and 5A eQTLs played important roles in development of freezing tolerance in common wheat. The chromosomal location of the 5A eQTL, controlling four cold-responsive genes, coincided with a region homoeologous to a frost-tolerance locus (Fr-A (m) 2) reported as a CBF cluster region in einkorn wheat. The 5A eQTL plays a significant role through Cor/Lea gene expression in cold acclimation of wheat. In addition, our results suggest that one or more CBF copies at the Fr-2 region positively regulate other copies, which might amplify the positive effects of the CBF cluster on downstream Cor/Lea gene activation.

SUBMITTER: Motomura Y

PROVIDER: S-EPMC3621446 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature

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A major quantitative trait locus for cold-responsive gene expression is linked to frost-resistance gene Fr-A2 in common wheat.

Motomura Yoichi Y Kobayashi Fuminori F Iehisa Julio C M JC Takumi Shigeo S

Breeding science 20130301 1

Low temperature induces expression of Cor (cold-responsive)/Lea (late embryogenesis-abundant) gene family members through C-repeat binding factor (CBF) transcription factors in common wheat. However, the relationship between the genetic loci controlling cold-responsive gene expression and freezing tolerance is unclear. In expression quantitative trait locus (eQTL) analysis, accumulated transcripts of Cor/Lea and CBF genes were quantified in recombinant inbred lines derived from a cross between t ...[more]

PMID: 23641182

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Project description:BackgroundIn order to identify genes that might confer and maintain freeze resistance of winter wheat, a comparative transcriptome analysis was performed between control and 4 wk cold-acclimated crown tissue of two winter wheat lines that differ in field freeze survival. The lines, generated by azide mutagenesis of the winter wheat cultivar 'Winoka' were designated FR (75% survival) and FS (30% survival). Using two winter lines for this comparative analysis removed the influence of differential expression of the vernalization genes and allowed our study to focus on Cbf genes located within the Fr-A2 allele independent of the effect of the closely mapped Vrn allele.ResultsVernalization genes, (Vrn-A1, B1 and D1), and the transcription factor gene, TaVrt-2, were up-regulated to the same extent in FR and FS lines with cold acclimation thus confirming that azide mutagenesis had not modified the winter habitat of the lines. One category of Cbf genes, (Cbf-2, -A22 and B-22) reflected an increase in level of expression with cold acclimation in both FR and FS lines. Another category of Cbf genes (Cbf-3, -5, -6, -12, -14 and -19) were differentially expressed between cold-acclimated FR and FS lines relative to the non-acclimated controls. Comparison of expression patterns of the two categories of Cbf genes with the expression patterns of a set of ABA-dependent and -independent Cor/Lea genes revealed similar patterns of expression for this sample of Cor/Lea genes with that for Cbf-2 and -22. This pattern of expression was also exhibited by the Vrn genes.ConclusionSome Cor/Lea genes may be co-regulated by the Vrn genes during cold acclimation and the Vrn genes may also control the expression of Cbf-2, -A22 and -B22. The increased freeze survival by the FR line and the increase in expression levels of wheat Cbf genes, Cbf-3, -5, -6, -12, -14 and -19 with cold acclimation in the FR line suggests a possible gain of function mutation resulting in higher levels of expression of these Cbf genes and increased freeze survival.

Project description:A genome-wide association study (GWAS) for 10 yield and yield component traits was conducted using an association panel comprising 225 diverse spring wheat genotypes. The panel was genotyped using 10,904 SNPs and evaluated for three years (2016-2019), which constituted three environments (E1, E2 and E3). Heritability for different traits ranged from 29.21 to 97.69%. Marker-trait associations (MTAs) were identified for each trait using data from each environment separately and also using BLUP values. Four different models were used, which included three single trait models (CMLM, FarmCPU, SUPER) and one multi-trait model (mvLMM). Hundreds of MTAs were obtained using each model, but after Bonferroni correction, only 6 MTAs for 3 traits were available using CMLM, and 21 MTAs for 4 traits were available using FarmCPU; none of the 525 MTAs obtained using SUPER could qualify after Bonferroni correction. Using BLUP, 20 MTAs were available, five of which also figured among MTAs identified for individual environments. Using mvLMM model, after Bonferroni correction, 38 multi-trait MTAs, for 15 different trait combinations were available. Epistatic interactions involving 28 pairs of MTAs were also available for seven of the 10 traits; no epistatic interactions were available for GNPS, PH, and BYPP. As many as 164 putative candidate genes (CGs) were identified using all the 50 MTAs (CMLM, 3; FarmCPU, 9; mvLMM, 6, epistasis, 21 and BLUP, 11 MTAs), which ranged from 20 (CMLM) to 66 (epistasis) CGs. In-silico expression analysis of CGs was also conducted in different tissues at different developmental stages. The information generated through the present study proved useful for developing a better understanding of the genetics of each of the 10 traits; the study also provided novel markers for marker-assisted selection (MAS) to be utilized for the development of wheat cultivars with improved agronomic traits.Supplementary informationThe online version contains supplementary material available at 10.1007/s11032-021-01240-1.

Dataset Information

A major quantitative trait locus for cold-responsive gene expression is linked to frost-resistance gene Fr-A2 in common wheat.

Publications

A major quantitative trait locus for cold-responsive gene expression is linked to frost-resistance gene Fr-A2 in common wheat.

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