Dataset Information

Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus).

ABSTRACT: The Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite of genomic resources has been developed for this species, including genetic maps and ESTs. Here we analyze BAC end-sequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species.We obtained sequence from one or both ends of 106,259 tilapia BACs. BLAST analysis against the genome assemblies of stickleback, medaka and pufferfish allowed identification of homologies for approximately 25,000 BACs for each species. We calculate that rearrangement breakpoints between tilapia and these species occur about every 3 Mb across the genome. Analysis of 35,000 clones previously assembled into contigs by restriction fingerprints allowed identification of longer-range syntenies.Our data suggest that chromosomal evolution in recent teleosts is dominated by alternate loss of gene duplicates, and by intra-chromosomal rearrangements (~one per million years). These physical maps are a useful resource for comparative positional cloning of traits in cichlid fishes. The paired BAC end sequences from these clones will be an important resource for scaffolding forthcoming shotgun sequence assemblies of the tilapia genome.

SUBMITTER: Soler L

PROVIDER: S-EPMC3018143 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature

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Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus).

Soler Lucile L Conte Matthew A MA Katagiri Takayuki T Howe Aimee E AE Lee Bo-Young BY Amemiya Chris C Stuart Andrew A Dossat Carole C Poulain Julie J Johnson Jeremy J Di Palma Federica F Lindblad-Toh Kerstin K Baroiller Jean-Francois JF D'Cotta Helena H Ozouf-Costaz Catherine C Kocher Thomas D TD

BMC genomics 20101116

<h4>Background</h4>The Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite of genomic resources has been developed for this species, including genetic maps and ESTs. Here we analyze BAC end-sequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species.<h4>Results</h4 ...[more]

PMID: 21080946

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Project description:BACKGROUND:Fish species often exhibit significant sexual dimorphism for commercially important traits. Accordingly, the control of phenotypic sex, and in particular the production of monosex cultures, is of particular interest to the aquaculture industry. Sex determination in the widely farmed Nile tilapia (Oreochromis niloticus) is complex, involving genomic regions on at least three chromosomes (chromosomes 1, 3 and 23) and interacting in certain cases with elevated early rearing temperature as well. Thus, sex ratios may vary substantially from 50%. RESULTS:This study focused on mapping sex-determining quantitative trait loci (QTL) in families with skewed sex ratios. These included four families that showed an excess of males (male ratio varied between 64% and 93%) when reared at standard temperature (28°C) and a fifth family in which an excess of males (96%) was observed when fry were reared at 36°C for ten days from first feeding. All the samples used in the current study were genotyped for two single-nucleotide polymorphisms (rs397507167 and rs397507165) located in the expected major sex-determining region in linkage group 1 (LG 1). The only misassigned individuals were phenotypic males with the expected female genotype, suggesting that those offspring had undergone sex-reversal with respect to the major sex-determining locus. We mapped SNPs identified from double digest Restriction-site Associated DNA (ddRAD) sequencing in these five families. Three genetic maps were constructed consisting of 641, 175 and 1,155 SNPs from the three largest families. QTL analyses provided evidence for a novel genome-wide significant QTL in LG 20. Evidence was also found for another sex-determining QTL in the fifth family, in the proximal region of LG 1. CONCLUSIONS:Overall, the results from this study suggest that these previously undetected QTLs are involved in sex determination in the Nile tilapia, causing sex reversal (masculinisation) with respect to the XX genotype at the major sex-determining locus in LG 1.

Project description:Nile tilapia (Oreochromis niloticus) is a globally significant aquaculture species rapidly gaining status as a farmed commodity. In West Africa, wild Nile tilapia genetic resources are abundant yet knowledge of fine-scale population structure and patterns of natural genetic variation are limited. Coinciding with this is a burgeoning growth in tilapia aquaculture in Ghana and other countries within the region underpinned by locally available genetic resources. Using 192 single nucleotide polymorphism (SNP) markers this study conducted a genetic survey of Nile tilapia throughout West Africa, sampling 23 wild populations across eight countries (Benin, Burkina Faso, Côte d'Ivoire, Ghana, Togo, Mali, Gambia and Senegal), representing the major catchments of the Volta, Niger, Senegal and Gambia River basins. A pattern of isolation-by-distance and significant spatial genetic structure was identified throughout West Africa (Global FST = 0.144), which largely corresponds to major river basins and, to a lesser extent, sub-basins. Two populations from the Gambia River (Kudang and Walekounda), one from the western Niger River (Lake Sélingué) and one from the upper Red Volta River (Kongoussi) showed markedly lower levels of diversity and high genetic differentiation compared to all other populations, suggesting genetically isolated populations occurring across the region. Genetic structure within the Volta Basin did not always follow the pattern expected for sub-river basins. This study identifies clear genetic structuring and differentiation amongst West African Nile tilapia populations, which concur with broad patterns found in previous studies. In addition, we provide new evidence for fine-scale genetic structuring within the Volta Basin and previously unidentified genetic differences of populations in Gambia. The 192 SNP marker suite used in this study is a useful tool for differentiating tilapia populations and we recommend incorporating this marker suite into future population screening of O. niloticus. Our results form the basis of a solid platform for future research on wild tilapia genetic resources in West Africa, and the identification of potentially valuable germplasm for use in ongoing breeding programs for aquaculture.

Project description:A 12-wk trial was conducted to compare the tolerance of tilapia to high carbohydrate and high lipid diets. Three isonitrogenous and isoenergetic diets, whose carbohydrate and lipid levels were the following: 35.0% and 8% (control), 44.2% and 4% (D1, high carbohydrate), and 25.8% and 12% (D2, high lipid), respectively. Three hundred tilapias (27 ± 0.11 g) were fed the diets for 10 wk (4 replicates per group); 72 fish from the D1 group were continually fed the D1 (D1D1) and 72 fish from the D2 were continually fed the D2 (D2D2) diet for 2 wk (3 replicates each group) to evaluate the tilapia's capacity to tolerate high carbohydrate and high lipid diets, respectively. Another 36 fish from D1 group were continually fed D2 (D1D2) for comparison with D1D1 and D2D2 groups. In phase 1, hepatosomatic index, liver triglycerides (TG), glucose tolerance (GT) and crude protein in the whole body in D1 group were higher than those in D2 group (P < 0.05). During phase 2, D1D1 group had lower feed intake and weight gain, as well as lower serum total protein and albumin than that of D2D2 group (P < 0.05), while its liver glycogen was significantly higher than that in D1D2 and D2D2 groups (P < 0.05). Moreover, serum glucose and GT were higher in D1D1 and D1D2 groups than those in D2D2 group (P < 0.05). By contrast, D2D2 group had significantly higher intraperitoneal fat, subcutaneous adipose tissue (SCAT) and liver TG than those in D1D1 group (P < 0.05). The mRNA expression of brain npy, hepatic nrf2, gst1 and hepatic transcriptomic data showed that immune-related genes (gama, mrc2, mhc2 and cd163), were downregulated in D1D1 group compared to D2D2 and D1D2 groups. Taken together: 1) tilapia have higher tolerance to a high lipid diet than high carbohydrate diet; 2) despite retention of glucose tolerance, the continuous feeding of D1 diet impaired tilapia's appetite, weight gain rate and host immune response; 3) specific distribution of fat in intraperitoneal regions, SCAT and liver may be a risk-avoidance strategy in tilapia in response to a continuous D2 diet.

Dataset Information

Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus).

Publications

Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus).

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