Abstract
Rohu (Labeo rohita) is a significant freshwater aquaculture species with approximately 1.8 Mt produced annually. Fin clips obtained from the founders of a newly established Bangladesh-based breeding population (∼140 fish from each of the Halda, Jamuna, and Padma rivers) were used to identify 9157 SNPs and 14 411 silicoDArT markers using the Diversity Arrays Technology (DArT) genotyping-by-sequencing platform known as DArTseq. After quality control, 1985 SNPs were retained and used to examine population structure within and among river systems. Examination of genomic relationships revealed evidence of full- and half-sibling relationships among founders. Accordingly, sibship and dummy parents were assigned within each river population using a maximum likelihood approach with COLONY software. Founders that had no dummy parents in common were then identified for population genetic analyses. Only 40 unique dummy parents and 17 founders with no common dummy parents were identified from the Halda river, compared with 206 (96) from the Jamuna and 184 (83) from the Padma. Overall pairwise FST estimates among rivers were low (<0.005) and the optimum number of clusters using unsupervised K-means clustering was one, indicating little genetic divergence among the river populations in our SNPs. These results suggest that observed sibship among founders should be accounted for in future pedigree-based analyses and it cannot be assumed that fertilized spawn collections are representative samples of river populations.
Highlights
Rohu (Labeo rohita Hamilton) is a member of the Indian major carps and has a natural distribution encompassing rivers in Bangladesh, Myanmar, Nepal, and Pakistan, as well as the tributaries and branches of the Ganges river in northern India (Jhingran and Pullin, 1985)
In 2012, fish were collected as fertilized spawn from three Bangladeshi rivers – the Halda, Jamuna, and Padma – as part of a USAID funded project implemented by WorldFish known as Aquaculture for Income and Nutrition (AIN)
Fish in the breeding population are managed in accordance with the Guiding Principles of the Animal Care, Welfare and Ethics Policy of the WorldFish Center (Worldfish, 2004)
Summary
Rohu (Labeo rohita Hamilton) is a member of the Indian major carps and has a natural distribution encompassing rivers in Bangladesh, Myanmar, Nepal, and Pakistan, as well as the tributaries and branches of the Ganges river in northern India (Jhingran and Pullin, 1985) It is a globally significant freshwater aquaculture species with approximately 1.8 Mt produced annually (FAO, 2017). Sibship in Labeo rohita Founders has resulted in the widespread dissemination of seed exhibiting poor performance attributed to inbreeding, negative selection and interspecific hybridization (Penman et al, 2005; Das Mahapatra et al, 2016; Khan et al, 2018) To address these issues, in 2012, fish were collected as fertilized spawn from three Bangladeshi rivers – the Halda, Jamuna, and Padma – as part of a USAID funded project implemented by WorldFish known as Aquaculture for Income and Nutrition (AIN). All three rivers are important natural breeding grounds for rohu and have historically been important sources of rohu seed for aquaculture (Penman et al, 2005; Khan et al, 2018)
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