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Genome- wide structural and functional variant discovery of rice landraces using genotyping by sequencing

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Abstract

Rice landraces are vital genetic resources for agronomic and quality traits but the undeniable collection of Kerala landraces remains poorly delineated. To effectively conserve, manage, and use these resources, understanding the genomic structure of germplasm is essential. Genotyping by sequencing (GBS) enables identification of an immense number of single nucleotide polymorphism (SNP) and insertion deletion (InDel) from 96 rice germplasm. In the present study, a total of 16.9 × 107 reads were generated, and among that 16.3 × 107 reads were mapped to the indica reference genome. Exploring GBS data unfolded a wide genomic variations including 82,59,639 SNPs and 1,07,140 Indels. Both neighbor-joining tree and principal coordinate analysis with InDel markers revealed the selected germplasm in this study as highly diverse in structure. We assembled unmapped reads which were further employed for gene ontology analysis. These unmapped sequences that are generally expelled from subsequent studies of GBS data analysis may exist as an unexplored resort for several novel significant biological findings. The discovery of SNPs from the haplotyping results of GS3 and GIF1 genes provided insight into marker- assisted selection based on grain size and yield and can be utilized for rice yield improvement. To our knowledge, this is the first report on structural variation analysis using the GBS platform in rice landraces collected from Kerala. Genomic information from this study endows with valuable resources for perceptive rice landrace structure and can also facilitate sequencing-based molecular breeding.

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GBS data can be shared based on mutual agreement and plant material can be shared for scientific purposes.

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Funding

Supported by Department of Science and Technology–Science and Engineering Research Board, Government of India (Grant No. ECR/2016/001934).

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Authors and Affiliations

  1. Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India

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

  2. South Asia hub, ICRISAT Campus, International Rice Research Institute, Secundarabad, Telangana, India

    Krishna T. Sundaram

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  1. Smitha Kunhiraman Vasumathy
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  2. Maya Peringottillam
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  3. Krishna T. Sundaram
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  4. S. Hari Krishna Kumar
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  5. Manickavelu Alagu
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Contributions

Conceptualization: MA, SKV; Methodology: KTS, HKKS, SKV; Formal analysis and investigation: SKV, HKKS; Writing—original draft preparation: SKV; Writing—review and editing: MA; Funding acquisition: MA; Resources: MP; Supervision: MA.

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Correspondence to Manickavelu Alagu.

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Vasumathy, S.K., Peringottillam, M., Sundaram, K.T. et al. Genome- wide structural and functional variant discovery of rice landraces using genotyping by sequencing. Mol Biol Rep 47, 7391–7402 (2020). https://doi.org/10.1007/s11033-020-05794-9

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