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Genetic diversity and population structure of rice (Oryza sativa L.) landraces from Kerala, India analyzed through genotyping-by-sequencing

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Abstract

Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for developing dominant strategies for the sustainable management of genetically diverse crops. We attempt to fill the existing research lacuna in the molecular characterization of potent rice landraces in Kerala. Genotyping-by-sequencing (GBS) was performed on 96 Kerala rice accessions to identify single-nucleotide polymorphisms (SNPs), to examine the genetic diversity, population structure, and to delineate linkage disequilibrium (LD) pattern. GBS identified 5856 high-quality SNPs. The structure analysis indicated three subpopulations with the highest probability for population clustering with significant genetic differentiation, confirmed by principal component analysis. The genome-wide LD decay distance was 772 kb, at which the r2 dropped to half its maximum value. The analysis of genetic properties of the identified SNP panel with an average polymorphism information content (PIC) value of 0.22 and a minor allele frequency (MAF) > 0.1 unveiled their efficacy in genome-wide association studies (GWAS). High FST (0.266) and low Nm (0.692) portray a strong genetic differentiation among the rice landraces, complementing the genetic structuring observed in the studied population. Slow LD decay in the rice landraces reflects their self-pollinating behavior and the indirect selection of desired traits by domestication. Moreover, the high LD entails only a minimum number of SNP markers for detecting marker–trait association. The diverse germplasm utilized in this study can be further utilized to disclose genetic variants associated with phenotypic traits and define signatures of selection via GWAS and selective sweep, respectively.

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Acknowledgements

The authors acknowledge the Central University of Kerala for providing the research facilities. MP extends thanks to the University Grant Commission (UGC) for awarding financial aid.

Funding

This research was supported by grants from the Department of Science and Technology-Science and Engineering Research Board (DST-SERB), Government of India (Grant No. ECR/2016/001934) to AM.

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  1. Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye (PO), Kasaragod, Kerala, 671316, India

    Maya Peringottillam, Smitha Kunhiraman Vasumathy, Hari Krishna Kumar Selvakumar & Manickavelu Alagu

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  1. Maya Peringottillam
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  2. Smitha Kunhiraman Vasumathy
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  3. Hari Krishna Kumar Selvakumar
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  4. Manickavelu Alagu
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AM conceived and supervised the research work, and acquired research grant for the research; MP, SKV prepared genetic materials; HKKS, MP performed data analyses; MP wrote the manuscript; all authors read and approved the final manuscript.

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Correspondence to Manickavelu Alagu.

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Peringottillam, M., Kunhiraman Vasumathy, S., Selvakumar, H.K. et al. Genetic diversity and population structure of rice (Oryza sativa L.) landraces from Kerala, India analyzed through genotyping-by-sequencing. Mol Genet Genomics 297, 169–182 (2022). https://doi.org/10.1007/s00438-021-01844-4

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