Identification of genetic loci for early maturity in spring bread wheat using the association analysis and gene dissection

Abstract

Background: Early maturity in spring bread wheat is highly desirable in the regions where it enables the plants to evade high temperatures and plant pathogens at the end of the growing season.

Methods: To reveal the genetic loci responsible for the maturity time association analysis was carried out based on phenotyping for an 11-year period and high-throughput SNP genotyping of a panel of the varieties contrasting for this trait. The expression of candidate genes was verified using qPCR. The association between the SNP markers and the trait was validated using the biparental F_2:3 population.

Results: Our data showed that under long-day conditions, the period from seedling to maturity is mostly influenced by the time from heading to maturity, rather than the heading time. The QTLs associated with the trait were located on 2A, 3B, 4A, 5B, 7A and 7B chromosomes with the 7BL locus being the most significant and promising for its SNPs accelerated the maturity time by about 9 days. Gene dissection in this locus detected a number of candidates, the best being TraesCS7B02G391800 (bZIP9) and TraesCS7B02G412200 (photosystem II reaction center). The two genes are predominantly expressed in the flag leaf while flowering. The effect of the SNPs was verified in F_2:3 population and confirmed the association of the 4A, 5B and 7BL loci with the maturity time.

Keywords: Association mapping; Candidate genes; Common wheat; Maturity time.

Figure 1. Correlation matrix plot indicating the significance levels between the estimated developmental periods.

The lower triangular matrix is composed by the bivariate scatter plots. The upper triangular matrix shows the Spearman correlation plus significance level (as stars). Each significance level is associated to a symbol: p-values 0.001 (***).

Figure 2. Summary of genome-wide association studies (GWAS) for maturity time.

(A) Manhattan plots based on the linear mixed model using kinship and Q matrices. The bar under every chromosome corresponds to marker density. (B) Quantile–quantile plots representing the expected vs the observed log₁₀ p-values. (C) Linkage disequilibrium plot representing the association of significant SNP markers. The designations inside the blocks represent the chromosomes corresponding to SNP markers. The color key (bottom right) indicates LD strength from 0 to 1 depending on the color density.

Figure 3. Barplots of candidate-gene relative expressions in early- and late-maturing wheat varieties.

Error bars indicate standard deviation (SD). The asterisks indicate significant differences (**p < 0.01).

Figure 4. Boxplots of maturity time variation in groups of genotypes with diûerent SNPs.

YWRR and YKRRNYR are designation of heterozygous genotypes. “n” denotes the number of samples in each group.

Figure 5. Summary information about candidate gene TraesCS7B02G391800.

(A) Expression patterns of TraesCS7B02G391800 in different tissues and developmental stages visualized using the Wheat efpBrowser (https://bar.utoronto.ca/efp_wheat/), which utilizes expression data published in Ramírez-González et al. (2018) and Winter et al. (2007). EfpBrowser, which is a part of BAR (The Bio-Analytic Resource for Plant Biology), is under the U.S. Public Domain. (B) Localization of significant SNPs in the TraesCS7B02G391800 sequence using the GrainGenes genome browser (Yao et al., 2022). GrainGenes provide information for free public use. (C) Candidate gene network designed using the KnetMiner (https://knetminer.com/, Hassani-Pak et al., 2021). KnetMiner is under the MIT license.