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Population genetic analysis and scans for adaptation and contemporary selection footprints provide genomic insight into aus, indica and japonica rice cultivars diversification

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Abstract

Following domestication, rice cultivars have been spread worldwide to different climates and have experienced selection pressures to improve desirable traits. This has resulted in diverse cultivars that display variations in phenotypic traits, such as stress tolerance, grain size, and yield. To better understand the genomic composition arising from cultivar’s development and local adaptation, high-density genotypes (containing 286,183 single-nucleotide polymorphisms after the quality control) of 1284 rice cultivars of aus, indica, and temperate and tropical japonica were scanned for diversifying signatures by applying a pairwise comparison of fixation index (Fst) test. Each cultivar’s population was investigated for contemporary selection using the integrated haplotype score test. Signatures of diversifying selection among the pairwise comparisons were found in genomic regions mainly involved in response to stress (pathogens, drought, heat, cold) and development and morphology of various structures, such as root, pollen, spikelet, and grain. The most significant diversification signal between indica and japonica cultivars was detected at the location of ROX2 gene. Aus with indica comparison detected the most divergent signal at important candidate genes of OsEXPA8 and OsEXPA9, whereas temperate with tropical japonica comparison resulted in two well-known candidate genes OsHCT4 and OsGpx4. Recent selection analysis detected different patterns of contemporary selection in genomic regions related to rice breeding standard criteria such as stress tolerance, seed germination, starch content, and flowering time. Our findings highlight the underlying molecular basis of adaptive divergence and propose that modern rice breeding may provide additional diversification among rice cultivars.

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Acknowledgements

The authors are grateful to all the researchers involved in Rice Diversity Project for sharing the data publicly for research purposes.

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Authors and Affiliations

  1. Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N 4H5, Canada

    Seyed Milad Vahedi

  2. Department of Chemistry, Faculty of Basic Sciences, University of Hormozgan, Bandar Abbas, 79161-93145, Iran

    Moslem Momen

  3. Department of Animal Science, Faculty of Agriculture Engineering, University of Kurdistan, Sanandaj, 66177-15175, Iran

    Seyedeh Fatemeh Mousavi

  4. Department of Biotechnology, Animal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, 31466-18361, Iran

    Mohammad Hossein Banabazi

  5. Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden

    Mohammad Hossein Banabazi

  6. Sugar Beet Research Department, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful 333, Iran

    Mohammad Saeed Hasanvandi

  7. Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53705, USA

    Madhav Bhatta

  8. Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful 333, Iran

    Mahmoud Amiri Roudbar

  9. Department of Animal Science, University of Zanjan, Zanjan, Iran

    Siavash Salek Ardestani

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  1. Seyed Milad Vahedi
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Contributions

SV, MA, SS conceived the study. SV, MM, SM carried out the analyses. SV, MA, and SS interpreted the results. SV drafted the manuscript. MB, MH, and MB edited and reviewed the manuscript. All authors read and approved the final manuscript.

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Correspondence to Mahmoud Amiri Roudbar.

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Corresponding editor: Durgadas P. Kasbekar

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Vahedi, S.M., Momen, M., Mousavi, S.F. et al. Population genetic analysis and scans for adaptation and contemporary selection footprints provide genomic insight into aus, indica and japonica rice cultivars diversification. J Genet 102, 43 (2023). https://doi.org/10.1007/s12041-023-01440-y

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  • DOI: https://doi.org/10.1007/s12041-023-01440-y

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