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Rapid identification of an adult plant stripe rust resistance gene in hexaploid wheat by high-throughput SNP array genotyping of pooled extremes

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Abstract

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High-throughput SNP array analysis of pooled extreme phenotypes in a segregating population by KASP marker genotyping permitted rapid, cost-effective location of a stripe rust resistance QTL in wheat.

Abstract

German wheat cultivar “Friedrichswerther” has exhibited high levels of adult plant resistance (APR) to stripe rust in field environments for many years. F2:3 lines and F6 recombinant inbred line (RILs) populations derived from a cross between Friedrichswerther and susceptible landrace Mingxian 169 were evaluated in the field in 2013, 2016 and 2017. Illumina 90K iSelect SNP arrays were used to genotype bulked extreme pools and parents; 286 of 1135 polymorphic SNPs were identified on chromosome 6B. Kompetitive Allele-Specific PCR (KASP) markers were used to verify the chromosome region associated with the resistance locus. A linkage map was constructed with 18 KASP-SNP markers, and a major effect QTL was identified within a 1.4 cM interval flanked by KASP markers IWB71602 and IWB55937 in the region 6BL3-0-0.36. The QTL, named QYr.nwafu-6BL, was stable across environments, and explained average 54.4 and 47.8% of the total phenotypic variation in F2:3 lines and F6 RILs, respectively. On the basis of marker genotypes, pedigree analysis and relative genetic distance QYr.nwafu-6BL is likely to be a new APR QTL. Combined high-throughput SNP array genotyping of pooled extremes and validation by KASP assays lowers sequencing costs compared to genome-wide association studies with SNP arrays, and more importantly, permits rapid isolation of major effect QTL in hexaploid wheat as well as improving accuracy of mapping in the QTL region. QYr.nwafu-6BL with flanking KASP markers developed and verified in a subset of 236 diverse lines can be used in marker-assisted selection to improve stripe rust resistance in breeding programs.

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Acknowledgements

The authors are grateful to Prof. R. A. McIntosh, Plant Breeding Institute, University of Sydney, for critical review of this manuscript. This study was financially supported by the National Basic Research Program of China (No. 2013CB127700), the National Key Research and Development Program of China (Grant No. 2016YFE0108600), the earmarked fund for Modern Agro-industry Technology Research System (No. CARS-3-1-11) and National Natural Science Foundation of China (31371924).

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  1. State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

    Jianhui Wu, Qilin Wang, Qingdong Zeng & Zhensheng Kang

  2. State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

    Shengjie Liu, Jingmei Mu, Shuo Huang, Shizhou Yu & Dejun Han

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122_2017_2984_MOESM1_ESM.pptx

Fig. S1 Seedling reactions and adult plant responses produced by FRIED when infected with 7 Pst races in greenhouse. CYR29, CYR31, CYR32, CYR33, Su11-7 and V26/CH42 were tested in our previous study (Han et al. 2012). CYR34 was tested in this study (PPTX 4332 kb)

122_2017_2984_MOESM2_ESM.pptx

Fig. S2 Genotypic plots from selected KASP assays. The X- and Y-axes indicate FAM- and HEX-fluorescence units, respectively. The central cluster (green) is comprised of heterozygous individuals, whereas clusters near the axes are homozygous for either MX169 (HEX; red) or FRIED (FAM; blue) alleles. Black dots in the lower left indicate a water control (non-template control, NTC) and pink dots represent missing or failed data. (A, B) Marker IWB11702 and IWB5932 results for the F2 population, each showing three clusters. (C, D, E) IWA3289 and IWB55937 results for the F6 population showing two major clusters. (F, G, H, I) Results of genotyping with IWA1839, IWB71602, IWA4501 and IWB60085 in 236 diverse cultivars and landraces, each showing two main clusters (PPTX 1031 kb)

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Wu, J., Liu, S., Wang, Q. et al. Rapid identification of an adult plant stripe rust resistance gene in hexaploid wheat by high-throughput SNP array genotyping of pooled extremes. Theor Appl Genet 131, 43–58 (2018). https://doi.org/10.1007/s00122-017-2984-3

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