Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 May 12:12:661742.
doi: 10.3389/fgene.2021.661742. eCollection 2021.

Genome-Wide Association Analysis and Genomic Prediction for Adult-Plant Resistance to Septoria Tritici Blotch and Powdery Mildew in Winter Wheat

Admas Alemu  1 , Gintaras Brazauskas  2 , David S Gaikpa  1 , Tina Henriksson  3 , Bulat Islamov  4 , Lise Nistrup Jørgensen  5 , Mati Koppel  6 , Reine Koppel  4 , Žilvinas Liatukas  2 , Jan T Svensson  7 , Aakash Chawade  1
Affiliations

Genome-Wide Association Analysis and Genomic Prediction for Adult-Plant Resistance to Septoria Tritici Blotch and Powdery Mildew in Winter Wheat

Admas Alemu et al. Front Genet. .

Abstract

Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici and powdery mildew (PM) caused by Blumeria graminis f.sp tritici (Bgt) are among the forefront foliar diseases of wheat that lead to a significant loss of grain yield and quality. Resistance breeding aimed at developing varieties with inherent resistance to STB and PM diseases has been the most sustainable and environment-friendly approach. In this study, 175 winter wheat landraces and historical cultivars originated from the Nordic region were evaluated for adult-plant resistance (APR) to STB and PM in Denmark, Estonia, Lithuania, and Sweden. Genome-wide association study (GWAS) and genomic prediction (GP) were performed based on the adult-plant response to STB and PM in field conditions using 7,401 single-nucleotide polymorphism (SNP) markers generated by 20K SNP chip. Genotype-by-environment interaction was significant for both disease scores. GWAS detected stable and environment-specific quantitative trait locis (QTLs) on chromosomes 1A, 1B, 1D, 2B, 3B, 4A, 5A, 6A, and 6B for STB and 2A, 2D, 3A, 4B, 5A, 6B, 7A, and 7B for PM adult-plant disease resistance. GP accuracy was improved when assisted with QTL from GWAS as a fixed effect. The GWAS-assisted GP accuracy ranged within 0.53-0.75 and 0.36-0.83 for STB and PM, respectively, across the tested environments. This study highlights that landraces and historical cultivars are a valuable source of APR to STB and PM. Such germplasm could be used to identify and introgress novel resistance genes to modern breeding lines.

Keywords: GWAS; Septoria tritici blotch; genebank; genomic prediction; powdery mildew; wheat.

PubMed Disclaimer

Conflict of interest statement

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.

Figures

FIGURE 1
FIGURE 1
Frequency distribution (left) and box plot (right) of the BLUEs of (A) STB and (B) PM diseases scores combined from five environments using 175 winter wheat genotypes.
FIGURE 2
FIGURE 2
A scatter plot for r2 values of pairwise SNPs showing genome-wide linkage disequilibrium (LD) decay. The blue curve line is the smoothing spline regression model fitted to LD decay. The horizontal red line is the standard critical r2 value of the genome (r2 = 0.3), and the vertical yellow line is the genetic distance (1.6 cM) at the intersect between the standard critical and the LD decay curve. The vertical green line is the genetic distance (2.0 cM) at which the LD half-decay (r2 = 0.23, the vertical orange line) intersect with the LD decay curve.
FIGURE 3
FIGURE 3
(A) Manhattan (left) and Q–Q (right) plots for GWAS result of adult-plant resistance response to STB and (B) box plots for STB resistance values grouped by alleles of the SNP markers RAC875_rep_c116515_181, wsnp_Ex_c33012_41567026, and wsnp_Ku_c38451_47086066.
FIGURE 4
FIGURE 4
(A) Manhattan (left) and Q–Q (right) plots for GWAS result of adult-plant resistance response to PM and (B) box plots for STB resistance values grouped by alleles of the SNP markers RFL_Contig2834_890, Ku_c43151_811, and wsnp_Ex_c790_1554988.
FIGURE 5
FIGURE 5
Box plot for the genomic prediction accuracy of the ridge regression BLUP (RR-BLUP) and weighted RR BLUP (wRR-BLUP) models for adult-plant resistance to (A) STB and (B) PM. Comb, combined; EE, Estonia; LT, Lithuania; SE, Sweden; DK, Denmark; Years: 1, 2018-2019; 2, 2019-2020.
See this image and copyright information in PMC

References

    1. Alam M. A., Xue F., Wang C., Ji W. (2011). Powdery mildew resistance genes in wheat: identification and genetic analysis. J. Mol. Biol. Res. 1 20–39. 10.5539/jmbr.v1n1p20 - DOI
    1. Alemu A., Feyissa T., Maccaferri M., Sciara G., Tuberosa R., Ammar K., et al. (2021). Genome-wide association analysis unveils novel QTLs for seminal root system architecture traits in Ethiopian durum wheat. BMC Genomics 22:20. 10.1186/s12864-020-07320-4 - DOI - PMC - PubMed
    1. Alvarado G., Rodríguez F. M., Pacheco A., Burgueño J., Crossa J., Vargas M., et al. (2020). META-R: A software to analyze data from multi-environment plant breeding trials. Crop J. 8 745–756. 10.1016/j.cj.2020.03.010 - DOI
    1. Arraiano L. S., Brown J. K. M. (2006). Identification of isolate-specific and partial resistance to septoria tritici blotch in 238 European wheat cultivars and breeding lines. Plant Pathol. 55 726–738. 10.1111/j.1365-3059.2006.01444.x - DOI
    1. Arraiano L. S., Chartrain L., Bossolini E., Slatter H. N., Keller B., Brown J. K. M. (2007). A gene in European wheat cultivars for resistance to an African isolate of Mycosphaerella graminicola. Plant Pathol. 56 73–78. 10.1111/j.1365-3059.2006.01499.x - DOI

LinkOut - more resources