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Genome-wide DArT and SNP scan for QTL associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in elite ICARDA wheat (Triticum aestivum L.) germplasm

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Abstract

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Identified DArT and SNP markers including a first reported QTL on 3AS, validated large effect APR on 3BS. The different genes can be used to incorporate stripe resistance in cultivated varieties.

Abstract

Stripe rust [yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst)] is a serious disease in wheat (Triticum aestivum). This study employed genome-wide association mapping (GWAM) to identify markers linked to stripe rust resistance genes using Diversity Arrays Technology (DArT®) and single-nucleotide polymorphism (SNP) Infinium 9K assays in 200 ICARDA wheat genotypes, phenotyped for seedling and adult plant resistance in two sites over two growing seasons in Syria. Only 25.8 % of the genotypes showed resistance at seedling stage while about 33 and 44 % showed moderate resistance and resistance response, respectively. Mixed-linear model adjusted for false discovery rate at p < 0.05 identified 12 DArT and 29 SNP markers on chromosome arms 3AS, 3AL, 1AL, 2AL, 2BS, 2BL, 3BS, 3BL, 5BL, 6AL, and 7DS significantly linked to Pst resistance genes. Of these, the locus on 3AS has not been previously reported to confer resistance to stripe rust in wheat. The QTL on 3AS, 3AL, 1AL, 2AL, and 2BS were effective at seedling and adult plant growth stages while those on 3BS, 3BL, 5BL, 6AL and 7DS were effective at adult plant stage. The 3BS QTL was validated in Cham-6 × Cham-8 recombinant inbred line population; composite interval analysis identified a stripe resistance QTL flanked by the DArT marker, wPt-798970, contributed by Cham-6 parent which accounted for 31.2 % of the phenotypic variation. The DArT marker “wPt-798970” lies 1.6 cM away from the 3BS QTL detected within GWAM. Epistatic interactions were also investigated; only the QTL on 1AL, 3AS and 6AL exhibited interactions with other loci. These results suggest that GWAM can be an effective approach for identifying and improving resistance to stripe rust in wheat.

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Abbreviations

APR:

Adult plant resistance

CIMMYT:

International Maize and Wheat Improvement Center

cM:

Centimorgan

DArT:

Diversity array technology

GWAM:

Genome-wide association mapping

ICARDA:

International Center for Agricultural Research in the Dry Areas

LD:

Linkage disequilibrium

MAF:

Minor allele frequency

MLM:

Mixed linear model

QTL:

Quantitative trait loci

SSR:

Simple sequence repeat

SNP:

Single nucleotide polymorphism

Yr:

Stripe rust

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Acknowledgments

The authors gratefully acknowledge the Grains Research and Development Corporation—ACT, Australia, the Generation Challenge Program, Mexico and the International Centre for Agricultural Research in the Dry Areas (ICARDA) for funding this work. The authors are also grateful to the two anonymous referees for their critical reading and constructive suggestions to the manuscript.

Conflict of interest

The authors declare that they have no conflict of interest.

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    Authors and Affiliations

    1. International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5466, Aleppo, Syria

      Abdulqader Jighly, Farid Makdis, Kumarse Nazari, Wuletaw Tadesse, Osman Abdalla & Francis C. Ogbonnaya

    2. Department of Environment and Primary Industries, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia

      Abdulqader Jighly

    3. School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia

      Abdulqader Jighly

    4. INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany

      Benedict C. Oyiga

    5. Center for Development Research (ZEF), Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany

      Benedict C. Oyiga

    6. Field Crops Department, Faculty of Agriculture, University of Aleppo, Aleppo, Syria

      Farid Makdis

    7. General Commission for Scientific Agricultural Research (GCSAR), Agricultural Research Centre of Al-Qamishly, Al-Qamishly, Syria

      Omran Youssef

    8. Grains Research and Development Corporation, P.O. Box 5367, Kingston, ACT, 2604, Australia

      Francis C. Ogbonnaya

    Authors
    1. Abdulqader Jighly
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    2. Benedict C. Oyiga
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    3. Farid Makdis
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    Corresponding author

    Correspondence to Francis C. Ogbonnaya.

    Additional information

    Communicated by M. E. Sorrells.

    A. Jighly and B. C. Oyiga contributed equally to the manuscript.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    122_2015_2504_MOESM1_ESM.ppt

    Supplementary material 1 Figure S1 Pairwise intra-chromosomal LD of chromosomal arm 1BS showing a large LD block (PPT 284 kb)

    122_2015_2504_MOESM2_ESM.ppt

    Supplementary material 2 Figure S2 a The PCA results of the 197 elite lines using polymorphic DArT markers; b the PCA results of the 188 GWAS genotype panel using SNP markers. Genotypes were coloured according to the population structure results (PPT 125 kb)

    122_2015_2504_MOESM3_ESM.ppt

    Supplementary material 3 Figure S3 Decline of linkage disequilibrium (LD) estimated by R 2 against genetic distance in ICARDA elite wheat germplasm showing a scatter plot of estimates of R 2 for a pairs of DArT markers, b pairs of SNP markers, c pairs of both marker systems in significant LD across the wheat genome (PPT 335 kb)

    122_2015_2504_MOESM4_ESM.pptx

    Supplementary material 4 Figure S4 QQ plots for the p values from association analysis for stripe rust resistance using DArT in a Malkiyeh 2009, b Malkiyeh 2010, c Tel-Hadya 2010, d Tel-Hadya 2011; and SNP markers in e Malkiyeh 2009, f Malkiyeh 2010, g Tel-Hadya 2010, h Tel-Hadya 2011 (PPTX 336 kb)

    122_2015_2504_MOESM5_ESM.docx

    Supplementary material 5 Table S1 Genotypes pedigrees, phenotype and their correspondence sub-population using DArT and SNP marker systems (DOCX 23 kb)

    122_2015_2504_MOESM6_ESM.xlsx

    Supplementary material 6 Table S2. The haplotypes of the associated marker for the genotypes with common parents in their pedigrees (XLSX 217 kb)

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    Jighly, A., Oyiga, B.C., Makdis, F. et al. Genome-wide DArT and SNP scan for QTL associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in elite ICARDA wheat (Triticum aestivum L.) germplasm. Theor Appl Genet 128, 1277–1295 (2015). https://doi.org/10.1007/s00122-015-2504-2

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