A BAC-based physical map of the Nile tilapia genome

BACKGROUND: Cichlid fishes, particularly tilapias, are an important source of animal protein in tropical countries around the world. To support selective breeding of these species we are constructing genetic and physical maps of the tilapia genome. Physical maps linking collections of BAC clones are a critical resource for both positional cloning and assembly of whole genome sequences. RESULTS: We constructed a genome-wide physical map of the tilapia genome by restriction fingerprinting 35,245 bacterial artificial chromosome (BAC) clones using high-resolution capillary polyacrylamide gel electrophoresis. The map consists of 3,621 contigs and is estimated to span 1.752 Gb in physical length. An independent analysis of the marker content of four contigs demonstrates the reliability of the assembly. CONCLUSION: This physical map is a powerful tool for accelerating genomic studies in cichlid fishes, including comparative mapping among fish species, long-range assembly of genomic shotgun sequences, and the positional cloning of genes underlying important phenotypic traits. The tilapia BAC fingerprint database is freely available at

An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags

<p>Abstract</p> <p>Background</p> <p>Large collections of expressed sequence tags (ESTs) are a fundamental resource for analysis of gene expression and annotation of genome sequences. We generated 116,899 ESTs from 17 normalized and two non-normalized cDNA libraries representing 16 tissues from tilapia, a cichlid fish widely used in aquaculture and biological research.</p> <p>Results</p> <p>The ESTs were assembled into 20,190 contigs and 36,028 singletons for a total of 56,218 unique sequences and a total assembled length of 35,168,415 bp. Over the whole project, a unique sequence was discovered for every 2.079 sequence reads. 17,722 (31.5%) of these unique sequences had significant BLAST hits (e-value < 10^-10) to the UniProt database.</p> <p>Conclusion</p> <p>Normalization of the cDNA pools with double-stranded nuclease allowed us to efficiently sequence a large collection of ESTs. These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.</p

Data from: Quantitative genetic analyses of male color pattern and female mate choice in a pair of cichlid fishes of Lake Malawi, East Africa

The traits involved in sexual selection, such as male secondary sexual characteristics and female mate choice, often co-evolve which can promote population differentiation. However, the genetic architecture of these phenotypes can influence their evolvability and thereby affect the divergence of species. The extraordinary diversity of East African cichlid fishes is often attributed to strong sexual selection and thus this system provides an excellent model to test predictions regarding the genetic architecture of sexually selected traits that contribute to reproductive isolation. In particular, theory predicts that rapid speciation is facilitated when male sexual traits and female mating preferences are controlled by a limited number of linked genes. However, few studies have examined the genetic basis of male secondary sexual traits and female mating preferences in cichlids and none have investigated the genetic architecture of both jointly. In this study, we artificially hybridized a pair of behaviorally isolated cichlid fishes from Lake Malawi and quantified both melanistic color pattern and female mate choice. We investigated the genetic architecture of both phenotypes using quantitative genetic analyses. Our results suggest that 1) many non-additively acting genetic factors influence melanistic color patterns, 2) female mate choice may be controlled by a minimum of 1–2 non-additive genetic factors, and 3) F2 female mate choice is not influenced by male courting effort. Furthermore, a joint analysis of color pattern and female mate choice indicates that the genes underlying these two traits are unlikely to be physically linked. These results suggest that reproductive isolation may evolve rapidly owing to the few genetic factors underlying female mate choice. Hence, female mate choice likely played an important role in the unparalleled speciation of East African cichlid fish

Amh and Dmrta2 Genes Map to Tilapia (Oreochromis spp.) Linkage Group 23 Within Quantitative Trait Locus Regions for Sex Determination

Recent studies have revealed that the major genes of the mammalian sex determination pathway are also involved in sex determination of fish. Several studies have reported QTL in various species and strains of tilapia, regions contributing to sex determination have been identified on linkage groups 1, 3, and 23. Genes contributing to sex-specific mortality have been detected on linkage groups 2, 6, and 23. To test whether the same genes might control sex determination in mammals and fishes, we mapped 11 genes that are considered putative master key regulators of sex determination: Amh, Cyp19, Dax1, Dmrt2, Dmrta2, Fhl3l, Foxl2, Ixl, Lhx9, Sf1, and Sox8. We identified polymorphisms in noncoding regions of these genes and genotyped these sites for 90 individuals of an F(2) mapping family. Mapping of Dax1 joined LG16 and LG21 into a single linkage group. The Amh and Dmrta2 genes were mapped to two distinct regions of LG23. The Amh gene was mapped 5 cM from UNH879 within a QTL region for sex determination and 2 cM from UNH216 within a QTL region for sex-specific mortality. Dmrta2 was mapped 4 cM from UNH848 within another QTL region for sex determination. Cyp19 was mapped to LG1 far from a previously reported QTL region for sex determination on this chromosome. Seven other candidate genes mapped to LG4, -11, -12, -14, and -17

F2 female behavior score

This is the dataset to evaluate time in association, male courting effort on female mate choic

Data for color pattern factor analysis

This is the dataset to calculate number of genetic factors for male color patter

The estimated effective number of factors (standard deviation) influencing scale and fin melanophore counts for a range of allelic effects (C_a = 0 assumes the equivalence of allelic effects; C_a = assumes a normal distribution of allelic effects; C_a = 1 assumes the allelic effects have a negative exponential distribution; C_a = 4 assumes that allelic effects have a leptokurtic distribution).

<p>The estimated effective number of factors (standard deviation) influencing scale and fin melanophore counts for a range of allelic effects (C_a = 0 assumes the equivalence of allelic effects; C_a =  assumes a normal distribution of allelic effects; C_a = 1 assumes the allelic effects have a negative exponential distribution; C_a = 4 assumes that allelic effects have a leptokurtic distribution).</p

The boxplot of melanophore count in fin of the parentals, and F₁, F₂ hybrids and backcrosses.

<p>BZ represents backcross with <i>M. zebra</i>, while BB represents backcross with <i>M. benetos</i>.</p

The estimated effective number of factors influencing cichlid female mate choice for a range of allelic effects (C_a = 0 assumes the equivalence of allelic effects; C_a = 0.25 assumes a normal distribution of allelic effects; C_a = 1 assumes the allelic effects have a negative exponential distribution; C_a = 4 assumes that allelic effects have a leptokurtic distribution).

<p>The estimated effective number of factors influencing cichlid female mate choice for a range of allelic effects (C_a = 0 assumes the equivalence of allelic effects; C_a = 0.25 assumes a normal distribution of allelic effects; C_a = 1 assumes the allelic effects have a negative exponential distribution; C_a = 4 assumes that allelic effects have a leptokurtic distribution).</p

The boxplot of melanophore counts in scale of the parentals, and F₁, F₂ hybrids and backcrosses.

<p>BZ represents backcross with <i>M. zebra</i>, while BB represents backcross with <i>M. benetos</i>.</p