Genome-Wide Association-Based Identification of Alleles, Genes and Haplotypes Influencing Yield in Rice (Oryza sativa L.) Under Low-Phosphorus Acidic Lowland Soils

    James, M and Tyagi, W and Magudeeswari, P and Neeraja, C N and Rai, M (2024) Genome-Wide Association-Based Identification of Alleles, Genes and Haplotypes Influencing Yield in Rice (Oryza sativa L.) Under Low-Phosphorus Acidic Lowland Soils. International Journal of Molecular Sciences (TSI), 25 (21). pp. 1-20. ISSN 1661-6596

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    Abstract

    Rice provides poor yields in acidic soils due to several nutrient deficiencies and metal toxicities. The low availability of phosphorus (P) in acidic soils offers a natural condition for screening genotypes for grain yield and phosphorus utilization efficiency (PUE). The objective of this study was to phenotype a subset of indica rice accessions from 3000 Rice Genome Project (3K-RGP) under acidic soils and find associated genes and alleles. A panel of 234 genotypes, along with checks, were grown under low-input acidic soils for two consecutive seasons, followed by a low-P-based hydroponic screening experiment. The heritability of the agro-morphological traits was high across seasons, and Ward’s clustering method identified 46 genotypes that can be used as low-P-tolerant donors in acidic soil conditions. Genotypes ARC10145, RPA5929, and K1559-4, with a higher grain yield than checks, were identified. Over 29 million SNPs were retrieved from the Rice SNP-Seek database, and after quality control, they were utilized for a genome-wide association study (GWAS) with seventeen traits. Ten quantitative trait nucleotides (QTNs) for three yield traits and five QTNs for PUE were identified. A set of 34 candidate genes for yield-related traits was also identified. An association study using this indica panel for an already reported 1.84 Mbp region on chromosome 2 identified genes Os02g09840 and Os02g08420 for yield and PUE, respectively. A haplotype analysis for the candidate genes identified favorable allelic combinations. Donors carrying the superior haplotypic combinations for the identified genes could be exploited in future breeding programs.

    Item Type: Article
    Divisions: Global Research Program - Accelerated Crop Improvement
    CRP: UNSPECIFIED
    Uncontrolled Keywords: peak SNP, acidic soils, rice, GWAS, haplotype
    Subjects: Others > Genetic Engineering
    Others > Rice
    Others > Soil
    Depositing User: Mr Nagaraju T
    Date Deposited: 24 Apr 2025 03:31
    Last Modified: 24 Apr 2025 03:31
    URI: http://oar.icrisat.org/id/eprint/13047
    Official URL: https://www.mdpi.com/1422-0067/25/21/11673
    Projects: UNSPECIFIED
    Funders: UNSPECIFIED
    Acknowledgement: We acknowledge the help of all the people who collaborated in scoring the agronomic traits. Funding: Department of Biotechnology funding to W.T. (Grant No. BT/566/NE/U-excel/2016/72) and National Agriculture Science Foundation (NASF) of Indian Council of Agricultural Research, Govt of India (Grant No. NASF/BGAM-9020/2022-23) to M.R. and C.N.N. M.J. was supported by the DST Inspire Fellowship (No. DST/INSPIRE Fellowship/2019/IF190255) for his doctoral degree.
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