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Genome-wide association study for agronomic and physiological traits in spring wheat evaluated in a range of heat prone environments

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Abstract

Key message

We identified 27 stable loci associated with agronomic traits in spring wheat using genome-wide association analysis, some of which confirmed previously reported studies. GWAS peaks identified in regions where no QTL for grain yield per se has been mapped to date, provide new opportunities for gene discovery and creation of new cultivars with desirable alleles for improving yield and yield stability in wheat.

Abstract

We undertook large-scale genetic analysis to determine marker-trait associations (MTAs) underlying agronomic and physiological performance in spring wheat using genome-wide association studies (GWAS). Field trials were conducted at seven sites in three countries (Sudan, Egypt, and Syria) over 2–3 years in each country. Twenty-five agronomic and physiological traits were measured on 188 wheat genotypes. After correcting for population structure and relatedness, a total of 245 MTAs distributed over 66 loci were associated with agronomic traits in individual and mean performance across environments respectively; some of which confirmed previously reported loci. Of these, 27 loci were significantly associated with days to heading, thousand kernel weight, grain yield, spike length, and leaf rolling for mean performance across environments. Despite strong QTL by environment interactions, eight of the loci on chromosomes 1A, 1D, 5A, 5D, 6B, 7A, and 7B had pleiotropic effects on days to heading and yield components (TKW, SM−2, and SNS). The winter-type alleles at the homoeologous VRN1 loci significantly increased days to heading and grain yield in optimal environments, but decreased grain yield in heat prone environments. Top 20 high-yielding genotypes, ranked by additive main effects and multiplicative interaction (AMMI), had low kinship relationship and possessed 4–5 favorable alleles for GY MTAs except two genotypes, Shadi-4 and Qafzah-11/Bashiq-1–2. This indicated different yield stability mechanisms due to potentially favorable rare alleles that are uncharacterized. Our results will enable wheat breeders to effectively introgress several desirable alleles into locally adapted germplasm in developing wheat varieties with high yield stability and enhanced heat tolerance.

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Acknowledgements

Funding was provided by Grains Research and Development Corporation and ICARDA (Grant No. ICA00009).

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  1. Awais Rasheed and Emeka C. Okechukwu contributed equally to the manuscript.

Authors and Affiliations

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

    Francis C. Ogbonnaya, Abdulqader Jighly, Tadesse Wuletaw & Adel Hagras

  2. Grain Research and Development Corporation (GRDC), Barton, ACT, 2600, Australia

    Francis C. Ogbonnaya

  3. Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China

    Awais Rasheed

  4. International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China

    Awais Rasheed

  5. Department of Crop Science, University of Nigeria, Nsukka, Nigeria

    Emeka C. Okechukwu, Michael I. Uguru & Christian U. Agbo

  6. School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK

    Emeka C. Okechukwu

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

    Abdulqader Jighly

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

    Abdulqader Jighly

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

    Farid Makdis

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  1. Francis C. Ogbonnaya
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Ogbonnaya, F.C., Rasheed, A., Okechukwu, E.C. et al. Genome-wide association study for agronomic and physiological traits in spring wheat evaluated in a range of heat prone environments. Theor Appl Genet 130, 1819–1835 (2017). https://doi.org/10.1007/s00122-017-2927-z

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