Multi-locus genome-wide association studies (ML-GWAS) reveal novel genomic regions associated with seedling and adult plant stage leaf rust resistance in bread wheat (Triticum aestivum L.)

    Vikas, V K and Pradhan, A K and Budhlakoti, N and Mishra, D C and Chandra, T and Bhardwaj, S C and Kumar, S and Sivasamy, M and Jayaprakash, P and Nisha, R and Shajitha, P and Peter, J and Geetha, M and Mir, R R and Singh, K and Kumar, S (2022) Multi-locus genome-wide association studies (ML-GWAS) reveal novel genomic regions associated with seedling and adult plant stage leaf rust resistance in bread wheat (Triticum aestivum L.). Heredity, 128. pp. 434-449. ISSN 1365-2540

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    Abstract

    Leaf rust is one of the important diseases limiting global wheat production and productivity. To identify quantitative trait nucleotides (QTNs) or genomic regions associated with seedling and adult plant leaf rust resistance, multilocus genome-wide association studies (ML-GWAS) were performed on a panel of 400 diverse wheat genotypes using 35 K single-nucleotide polymorphism (SNP) genotyping assays and trait data of leaf rust resistance. Association analyses using six multi-locus GWAS models revealed a set of 201 significantly associated QTNs for seedling and 65 QTNs for adult plant resistance (APR), explaining 1.98–31.72% of the phenotypic variation for leaf rust. Among these QTNs, 51 reliable QTNs for seedling and 15 QTNs for APR were consistently detected in at least two GWAS models and were considered reliable QTNs. Three genomic regions were pleiotropic, each controlling two to three pathotype-specific seedling resistances to leaf rust. We also identified candidate genes, such as leucine-rich repeat receptor-like (LRR) protein kinases, P-loop containing nucleoside triphosphate hydrolase and serine-threonine/tyrosine-protein kinases (STPK), which have a role in pathogen recognition and disease resistance linked to the significantly associated genomic regions. The QTNs identified in this study can prove useful in wheat molecular breeding programs aimed at enhancing resistance to leaf rust and developing next-generation leaf rust-resistant varieties.

    Item Type: Article
    Divisions: Genebank
    CRP: UNSPECIFIED
    Uncontrolled Keywords: Genetics, Genome-wide association studies
    Subjects: Others > Wheat
    Depositing User: Mr Nagaraju T
    Date Deposited: 13 Mar 2024 10:25
    Last Modified: 13 Mar 2024 10:25
    URI: http://oar.icrisat.org/id/eprint/12571
    Official URL: https://www.nature.com/articles/s41437-022-00525-1
    Projects: UNSPECIFIED
    Funders: UNSPECIFIED
    Acknowledgement: The authors are highly thankful to the Indian Council of Agricultural Research for the financial support provided for this work. The authors are also thankful to the National Bureau of Plant Genetic Resources, New Delhi for providing germplasm lines for evaluation; the Indian Agricultural Statistics Research Institute, New Delhi for providing computational support; and the Indian Agricultural Research Institute, Regional Station, Wellington and Indian Institute of Wheat and Barley Research, Karnal for providing all support for screening wheat genotypes for leaf rust. The Authors duly acknowledge efforts of Dr. Philomin Juliana, Associate scientist, CIMMYT for English language editing.
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