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Resolving population structure and genetic differentiation associated with RAD-SNP loci under selection in tossa jute (Corchorus olitorius L.)

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Abstract

The genetic basis of selection for geographic adaptation and how it has contributed to population structure are unknown in tossa jute (Corchorus olitorius), an important bast fibre crop. We performed restriction site-associated DNA (RAD) sequencing-based (1115 RAD-SNPs) population genomic analyses to investigate genetic differentiation and population structure within a collection of 221 fibre-type lines from across nine geographic regions of the world. Indian populations, with relatively higher overall diversity, were significantly differentiated (based on FST and PCA) from the African and the other Asian populations. There is strong evidence that African C. olitorius was first introduced in peninsular India that could perhaps be its secondary centre of origin. However, multiple later introductions have occurred in central, eastern and northern India. Based on four assignment tests with different statistical bases, we infer that two ancestral subpopulations (African and Indian) structure the C. olitorius populations, but not in accordance with their geographic origins and patterns of diversity. Our results advocate recent migration of C. olitorius through introduction and germplasm exchange across geographical boundaries. We argue that high intraspecific genetic admixture could be associated with increased genetic variance within Indian populations. Employing both subpopulation (FST/GST-outlier) and individual-based (PCAdapt) tests, we detected putative RAD-SNP loci under selection and demonstrated that bast fibre production was an artificial, while abiotic and biotic stresses were natural selection pressures in C. olitorius adaptation. By reinferring the population structure without outlier loci, we propose ad interim that C. olitorius was possibly domesticated as a fibre crop in the Indian subcontinent.

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Acknowledgements

This work was funded by National Agricultural Science Fund (NASF), Indian Council of Agricultural Research (ICAR), New Delhi (Grant ID: GB-2018) and ICAR-Network Project on Transgenics in Crops (Grant ID: ICAR-NPTC-3070). We thank NxGenBio Life Sciences, New Delhi for assistance in RADseq library preparation, Illumina HiSeq™ 2000 sequencing and raw data processing. We also thank Dr. Subhojit Datta for helpful feedback on tossa jute aquaporins. The manuscript was reviewed and approved by the institute. Comments and suggestions on the manuscript from the Editor and two anonymous reviewers are gratefully acknowledged.

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  1. Biotechnology Unit, Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres (CRIJAF), Nilganj, Barrackpore, Kolkata, West Bengal, 700 120, India

    Debabrata Sarkar, Avijit Kundu, Debajeet Das, Avrajit Chakraborty, Nur Alam Mandal, Pratik Satya, Pran Gobinda Karmakar, Chandan Sourav Kar & Jiban Mitra

  2. Department of Genetics and Plant Breeding, North Bengal Agricultural University, Pundibari, Cooch Behar, West Bengal, 736 165, India

    Avijit Kundu

  3. Rice Genome Lab, ICAR-National Research Centre on Plant Biotechnology (NRCPB), Pusa, New Delhi, 110 012, India

    Nagendra Kumar Singh

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All laboratory experiments complied with appropriate ethical standards, according to existing rules and regulations of the Indian Council of Agricultural Research (ICAR), Government of India. The article does not pertain to any laboratory experiments involving human participants or animals.

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Communicated by Dacheng Tian.

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The raw Illumina RADseq reads have been deposited in the NCBI Sequence Read Archive (SRA) under the project SRP064554 vide BioProject PRJNA207496 and BioSamples SAMN03097738 to SAMN03097962, with 225 SRX accessions listed in Online Resource 2. RADseq genotype data and other summary statistics are available as a Figshare (https://figshare.com/s/05b13e169a8f5ae8e634) entry doi: https://doi.org/10.6084/m9.figshare.6339518.

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Sarkar, D., Kundu, A., Das, D. et al. Resolving population structure and genetic differentiation associated with RAD-SNP loci under selection in tossa jute (Corchorus olitorius L.). Mol Genet Genomics 294, 479–492 (2019). https://doi.org/10.1007/s00438-018-1526-2

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