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

Sarkar, Debabrata, Kundu, Avijit, Das, Debajeet, Chakraborty, Avrajit, Mandal, Nur Alam, Satya, Pratik, Karmakar, Pran Gobinda, Kar, Chandan Sourav, Mitra, Jiban, Singh, Nagendra Kumar
Molecular genetics and genomics 2019 v.294 no.2 pp. 479-492
Corchorus olitorius, DNA, abiotic stress, biotic stress, center of origin, genetic variance, genetic variation, germplasm exchange, jute, loci, natural selection, population structure, provenance, India
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.