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In 2017, the base population of a family-based silver carp (Hypophthalmichthys molitrix) genetic improvement program was spawned in Bangladesh. This program aims to improve the growth rate of silver carp under polyculture production systems, through direct selection on the primary trait of harvest-age weight. The objective of this study was to quantify genetic variation in, and genetic correlations between, harvest-age weight (assessed on 8012 fish from 184 families) and a set of secondary traits (assessed on 1603 fish from 175 families). Secondary traits examined included feeding and digestive system traits (i.e. gill raker sponginess and gut length as a ratio of standard length), a morphometric trait (i.e. extent of overlap of pectoral and pelvic fins) and health traits (i.e. presence of Lernaea and prevalence of red spots — sites of inflammation/haemorrhaging). Despite not being under direct selection, genetic change in secondary traits is possible across generations in closed genetic improvement populations as a result of a correlated response to selection for the primary trait (i.e. indirect selection), adaptation to culture conditions, inbreeding and/or genetic drift. It was found that the additive genetic variance within genetic groups was significantly different from zero for all but the studied health traits. Heritability estimates for harvest-age weight and pectoral/pelvic fin overlap were moderate (0.24 and 0.22, respectively) but were low for gill raker score and relative gut length (0.12 and 0.09, respectively). Genetic correlations between harvest-age weight and secondary traits were not significantly different from zero, indicating that selection for harvest-age weight will not result in a correlated response to selection in the studied secondary traits. [ABSTRACT FROM AUTHOR]

Nile tilapia (Oreochromis niloticus) is among the most important finfish in aquaculture, particularly in Asia. Numerous genetically improved strains of Nile tilapia have been developed and disseminated through formal and informal channels to hatcheries, many of which operate at a relatively small scale in developing countries. The primary objective of this study was to assess the extent to which molecular genetic tools can identify different and interrelated strains of Nile tilapia in Bangladesh and the Philippines, two globally significant producers. A tool was developed using a low-density panel of single-nucleotide polymorphisms (SNPs), genotyping-by-sequencing and discriminant analysis of principal components (DAPC). When applied to 2,057 samples from 205 hatcheries in Bangladesh and the Philippines, for hatcheries where the hatchery-identified strain was one of the sampled core populations used to develop the tool, hatchery-identified and DAPC-assigned hatchery-level strains were in agreement in 74.1% of cases in Bangladesh and 80.6% of cases in the Philippines. The dominant hatchery-identified and DAPC-assigned strains were GIFT, in Bangladesh, and GET-ExCEL—a composite strain partially derived from GIFT—in the Philippines. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Catla catla (Hamilton) fertilised spawn was collected from the Halda, Jamuna and Padma rivers in Bangladesh from which approximately 900 individuals were retained as 'candidate founders' of a breeding population. These fish were fin-clipped and genotyped using the DArTseq platform to obtain, 3048 single nucleotide polymorphisms (SNPs) and 4726 silicoDArT markers. Using SNP data, individuals that shared no putative parents were identified using the program COLONY, i.e. 140, 47 and 23 from the Halda, Jamuna and Padma rivers, respectively. Allele frequencies from these individuals were considered as representative of those of the river populations, and genomic relationship matrices were generated. Then, half-sibling and full-sibling relationships between individuals were assigned manually based on the genomic relationship matrices. Many putative half-sibling and full-sibling relationships were found between individuals from the Halda and Jamuna rivers, which suggests that catla sampled from rivers as spawn are not necessarily representative of river populations. This has implications for the interpretation of past population genetics studies, the sampling strategies to be adopted in future studies and the management of broodstock sourced as river spawn in commercial hatcheries. Using data from individuals that shared no putative parents, overall multi-locus pairwise estimates of Wright's fixation index (FST) were low (≤ 0.013) and the optimum number of clusters using unsupervised K-means clustering was equal to 1, which indicates little genetic divergence among the SNPs included in our study within and among river populations. [ABSTRACT FROM AUTHOR]