A microsatellite-based genetic linkage map for channel catfish, Ictalurus punctatus

A microsatellite genetic map of the turbot (Scophthalmus maximus)

A consensus microsatellite-based linkage map of the turbot (Scophthalmus maximus) was constructed from two unrelated families. The mapping panel was derived from a gynogenetic family of 96 haploid embryos and a biparental diploid family of 85 full-sib progeny with known linkage phase. A total of 242 microsatellites were mapped in 26 linkage groups, six markers remaining unlinked. The consensus map length was 1343.2 cM, with an average distance between markers of 6.5 +/- 0.5 cM. Similar length of female and male maps was evidenced. However, the mean recombination at common intervals throughout the genome revealed significant differences between sexes, approximately 1.6 times higher in the female than in the male. The comparison of turbot microsatellite flanking sequences against the Tetraodon nigroviridis genome revealed 55 significant matches, with a mean length of 102 bp and high sequence similarity (81-100%). The comparative mapping revealed significant syntenic regions among fish species. This study represents the first linkage map in the turbot, one of the most important flatfish in European aquaculture. This map will be suitable for QTL identification of productive traits in this species and for further evolutionary studies in fish and vertebrate species.

Characterization of a BAC library from channel catfish Ictalurus punctatus: indications of high levels of chromosomal reshuffling among teleost genomes

The CHORI-212 bacterial artificial chromosome (BAC) library was constructed by cloning EcoRI/EcoRI partially digested DNA into the pTARBAC2.1 vector. The library has an average insert size of 161 kb, and provides 10.6-fold coverage of the channel catfish haploid genome. Screening of 32 genes using overgo or cDNA probes indicated that this library had a good representation of the genome as all tested genes existed in the library. We previously reported sequencing of approximately 25,000 BAC ends that generated 20,366 high-quality BAC end sequences (BES) and identified a large number of sequences similar to known genes using BLASTX searches. In this work, particular attention was given to identification of BAC mate pairs with known genes from both ends. When identified, comparative genome analysis was conducted to determine syntenic regions of the catfish genome with the genomes of zebrafish and Tetraodon. Of the 141 mate pairs with known genes from channel catfish, conserved syntenies were identified in 34 (24.1%), with 30 conserved in the zebrafish genome and 14 conserved in the Tetraodon genome. Additional analysis of three of the 34 conserved syntenic groups by direct sequencing indicated conserved gene contents in all three species. This indicates that comparative genome analysis may provide shortcuts to genome analysis in catfish, especially for short genomic regions once the conserved syntenies are identified.

A Genetic linkage map of Atlantic halibut (Hippoglossus hippoglossus L.)

A genetic linkage map has been constructed for Atlantic halibut on the basis of 258 microsatellites and 346 AFLPs. Twenty-four linkage groups were identified, consistent with the 24 chromosomes seen in chromosome spreads. The total map distance is 1562.2 cM in the female and 1459.6 cM in the male with an average resolution of 4.3 and 3.5 cM, respectively. Using diploid gynogens, we estimated centromere locations in 19 of 24 linkage groups. Overall recombination in the female was approximately twice that of the male; however, this trend was not consistent along the linkage groups. In the centromeric regions, females had 11-17.5 times the recombination of the males, whereas this trend reversed toward the distal end with males having three times the recombination of the females. Correspondingly, in the male, markers clustered toward the centromeric region with 50% of markers within 20 cM of the putative centromere, whereas 35% of markers in the female were found between 60 and 80 cM from the putative centromere. Limited interspecies comparisons within Japanese flounder and Tetraodon nigroviridis revealed blocks of conservation in sequence and marker order, although regions of chromosomal rearrangement were also apparent.

Genetic linkage map of the loach Misgurnus anguillicaudatus (Teleostei: Cobitidae)

In the present study, the first genetic linkage map of the loach Misgurnus anguillicaudatus was constructed with 164 microsatellite markers and a color locus, and it included 155 newly developed markers. A total of 159 microsatellite markers and a color locus were mapped in 27 linkage groups (LGs). The female map covered 784.5 cM with 153 microsatellite markers and a color locus, whereas the male map covered 662.2 cM with 119 microsatellite markers. The centromeric position in each LG was estimated by marker-centromere mapping based on half-tetrad analysis. In 4 LGs (LG2, LG3, LG4, and LG5), the centromere was estimated at the intermediate region. In LG1, LG11, and LG12, the centromere was estimated to shift from the sub-intermediate region to the end (telomeric). The number of these LGs (7) was identical to the collective number of bi-arm metacentric (5) and sub-metacentric chromosome (2) of the haploid chromosome set (n = 5) of the loach. In the other LGs, the position of the centromere was estimated at the end or outside. These results indicate satisfactory compliance between the linkage map and the chromosome set. Our map would cover approximately almost the entire loach genome because most markers were successfully mapped.

A BAC-based physical map of the channel catfish genome

Catfish is the major aquaculture species in the United States. To enhance its genome studies involving genetic linkage and comparative mapping, a bacterial artificial chromosome (BAC) contig-based physical map of the channel catfish (Ictalurus punctatus) genome was generated using four-color fluorescence-based fingerprints. Fingerprints of 34,580 BAC clones (5.6x genome coverage) were generated for the FPC assembly of the BAC contigs. A total of 3307 contigs were assembled using a cutoff value of 1x10(-20). Each contig contains an average of 9.25 clones with an average size of 292 kb. The combined contig size for all contigs was 0.965 Gb, approximately the genome size of the channel catfish. The reliability of the contig assembly was assessed by both hybridization of gene probes to BAC clones contained in the fingerprinted assembly and validation of randomly selected contigs using overgo probes designed from BAC end sequences. The presented physical map should greatly enhance genome research in the catfish, particularly aiding in the identification of genomic regions containing genes underlying important performance traits.

Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs

Background

EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. While much progress has been made in catfish genomics, large-scale EST resources have been lacking. The objectives of this project were to construct primary cDNA libraries, to conduct initial EST sequencing to generate catfish EST resources, and to obtain baseline information about highly expressed genes in various catfish organs to provide a guide for the production of normalized and subtracted cDNA libraries for large-scale transcriptome analysis in catfish.

Results

A total of 17 cDNA libraries were constructed including 12 from channel catfish (Ictalurus punctatus) and 5 from blue catfish (I. furcatus). A total of 31,215 ESTs, with average length of 778 bp, were generated including 20,451 from the channel catfish and 10,764 from blue catfish. Cluster analysis indicated that 73% of channel catfish and 67% of blue catfish ESTs were unique within the project. Over 53% and 50% of the channel catfish and blue catfish ESTs, respectively, had significant similarities to known genes. All ESTs have been deposited in GenBank. Evaluation of the catfish EST resources demonstrated their potential for molecular marker development, comparative genome analysis, and evaluation of ancient and recent gene duplications. Subtraction of abundantly expressed genes in a variety of catfish tissues, identified here, will allow the production of low-redundancy libraries for in-depth sequencing.

Conclusion

The sequencing of 31,215 ESTs from channel catfish and blue catfish has significantly increased the EST resources in catfish. The EST resources should provide the potential for microarray development, polymorphic marker identification, mapping, and comparative genome analysis.

Definition of the USDA103 strain of channel catfish (Ictalurus punctatus)

Although there are differences in performance between genetic groups of channel catfish, identification and management of these groups is difficult because catfish strains look alike and individuals cannot be tagged efficiently. Thus, US catfish producers have not been able to objectively identify fish from different strains or populations, and it has been difficult for them to maintain the genetic purity of populations on the farm. We have developed a multiplexed microsatellite genotyping system to define catfish populations based on allelic frequency and exclusion. A commercial catfish genotype database was developed using catfish samples collected from 24 processing plants in the four main US catfish-producing states. The utility of the system was tested by the molecular characterization of the USDA103 research strain. Using eight microsatellite loci, the probability of falsely classifying an individual non-USDA103 catfish as a USDA103 was 0.0065. From a sample of 50 fish from a putative USDA103 pond, the probability of falsely including two non-USDA103 fish was 1 x 10(-105), and the conservative probability of falsely excluding two USDA103 fish was 1 x 10(-6). This genotyping system provides channel catfish producers with an objective mechanism for identification and management of genetically selected fish.

Applications of microsatellite markers in studies of genetics and breeding of fish

The microsatellite, or short sequence repeat (SSR), is a powerful genetic marker, useful in many areas of fish genetics and breeding. Polymorphic microsatellite loci have been frequently applied to the analysis of genetic diversity, population genetic structure, and genomic mapping. These co-dominant markers have also been applied to the classification and systematics, parentage identification, germplasm conservation, and breeding programme of food fish.

A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis

Background

Comparative teleost studies are of great interest since they are important in aquaculture and in evolutionary issues. Comparing genomes of fully sequenced model fish species with those of farmed fish species through comparative mapping offers shortcuts for quantitative trait loci (QTL) detections and for studying genome evolution through the identification of regions of conserved synteny in teleosts. Here a comparative mapping study is presented by radiation hybrid (RH) mapping genes of the gilthead sea bream Sparus aurata, a non-model teleost fish of commercial and evolutionary interest, as it represents the worldwide distributed species-rich family of Sparidae.

Results

An additional 74 microsatellite markers and 428 gene-based markers appropriate for comparative mapping studies were mapped on the existing RH map of Sparus aurata. The anchoring of the RH map to the genetic linkage map resulted in 24 groups matching the karyotype of Sparus aurata. Homologous sequences to Tetraodon were identified for 301 of the gene-based markers positioned on the RH map of Sparus aurata. Comparison between Sparus aurata RH groups and Tetraodon chromosomes (karyotype of Tetraodon consists of 21 chromosomes) in this study reveals an unambiguous one-to-one relationship suggesting that three Tetraodon chromosomes correspond to six Sparus aurata radiation hybrid groups. The exploitation of this conserved synteny relationship is furthermore demonstrated by in silico mapping of gilthead sea bream expressed sequence tags (EST) that give a significant similarity hit to Tetraodon.

Conclusion

The addition of primarily gene-based markers increased substantially the density of the existing RH map and facilitated comparative analysis. The anchoring of this gene-based radiation hybrid map to the genome maps of model species broadened the pool of candidate genes that mainly control growth, disease resistance, sex determination and reversal, reproduction as well as environmental tolerance in this species, all traits of great importance for QTL mapping and marker assisted selection. Furthermore this comparative mapping approach will facilitate to give insights into chromosome evolution and into the genetic make up of the gilthead sea bream.

A first generation BAC-based physical map of the channel catfish genome

BACKGROUND

Channel catfish, Ictalurus punctatus, is the leading species in North American aquaculture. Genetic improvement of catfish is performed through selective breeding, and genomic tools will help improve selection efficiency. A physical map is needed to integrate the genetic map with the karyotype and to support fine mapping of phenotypic trait alleles such as Quantitative Trait Loci (QTL) and the effective positional cloning of genes.

RESULTS

A genome-wide physical map of the channel catfish was constructed by High-Information-Content Fingerprinting (HICF) of 46,548 Bacterial Artificial Chromosomes (BAC) clones using the SNaPshot technique. The clones were assembled into contigs with FPC software. The resulting assembly contained 1,782 contigs and covered an estimated physical length of 0.93 Gb. The validity of the assembly was demonstrated by 1) anchoring 19 of the largest contigs to the microsatellite linkage map 2) comparing the assembly of a multi-gene family to Restriction Fragment Length Polymorphism (RFLP) patterns seen in Southern blots, and 3) contig sequencing.

CONCLUSION

This is the first physical map for channel catfish. The HICF technique allowed the project to be finished with a limited amount of human resource in a high throughput manner. This physical map will greatly facilitate the detailed study of many different genomic regions in channel catfish, and the positional cloning of genes controlling economically important production traits.

A microsatellite linkage map of the blacklip abalone, Haliotis rubra

There is considerable scope for genetic improvement of cultured blacklip abalone Haliotis rubra in Australia using molecular marker-assisted, selective-breeding practices. Such improvement is dependent on the availability of primary genetic resources, such as a genetic linkage map. This study presents a first-generation linkage map of H. rubra, containing 122 microsatellite markers typed in a single full-sib family. These loci mapped to 17 and 20 linkage groups for the male and female respectively, and when aligned, the consensus map represented 18 linkage groups. The male linkage map contained 102 markers (one unlinked) covering 621 cM with an average intermarker spacing of 7.3 cM, and the female map contained 98 markers (eight unlinked) covering 766 cM with an average intermarker spacing of 9.8 cM. Analysis of markers informative in both parents showed a significantly higher recombination rate in the female parent, with an average male-to-female recombination ratio of 1:1.45 between linked pairs of markers. This linkage map represents a significant advancement in the genetic resource available for H. rubra and provides a framework for future quantitative trait loci mapping and eventual implementation of marker-assisted selection.

A microsatellite linkage map of Barramundi, Lates calcarifer

Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its compact genome (approximately 700 Mb) is among the smallest genomes of food fish species. We established a first-generation genetic linkage map of Barramundi with a mapping panel containing three parents (two males and one female) and 93 progeny. A total of 240 microsatellite markers were mapped into 24 linkage groups. Among these markers, 10 were located in ESTs and known genes. The total lengths of the female and male maps were 873.8 and 414.5 cM with an average marker spacing of 6.20 and 4.70 cM, respectively. Comparing the flanking sequences of the 240 Barramundi microsatellites with the assembled whole-genome sequences of Tetraodon nigrovidiris revealed 55 homologous sequences located in 19 of the 21 chromosomes of T. nigrovidiris. The map will not only enable the mapping of quantitative trait loci, but also provide new resources for understanding the evolution of fish genomes.

A genetic linkage map of Pacific white shrimp (Litopenaeus vannamei): sex-linked microsatellite markers and high recombination rates

Pacific white shrimp (Litopenaeus vannamei) is the leading species farmed in the Western Hemisphere and an economically important aquaculture species in China. In this project, a genetic linkage map was constructed using amplified fragment length polymorphism (AFLP) and microsatellite markers. One hundred and eight select AFLP primer combinations and 30 polymorphic microsatellite markers produced 2071 markers that were polymorphic in either of the parents and segregated in the progeny. Of these segregating markers, 319 were mapped to 45 linkage groups of the female framework map, covering a total of 4134.4 cM; and 267 markers were assigned to 45 linkage groups of the male map, covering a total of 3220.9 cM. High recombination rates were found in both parental maps. A sex-linked microsatellite marker was mapped on the female map with 6.6 cM to sex and a LOD of 17.8, two other microsatellite markers were also linked with both 8.6 cM to sex and LOD score of 14.3 and 16.4. The genetic maps presented here will serve as a basis for the construction of a high-resolution genetic map, quantitative trait loci (QTLs) detection, marker-assisted selection (MAS) and comparative genome mapping.

Genetic Polymorphism of Microsatellite DNA in Two Populations of Northern Sheatfish (Silurus soldatovi)

In this article, population variations and genetic structures of two populations of northern sheatfish (Silurus soldatovi) were analyzed using 24 microsatellite loci enriched from southern catfish (S. meriaionalis Chen) by magnetic beads. Gene frequency (P), observed heterozygosity (Ho), expected heterozygosity (He), polymorphism information contents (PIC), and number of effective alleles (Ne) were determined. One population was wild, ripe individuals collected from Heilongjiang River (HNS); the other was cultured fry collected from Songhuajiang River (SNS). The Hardy-Weinberg equilibrium (HWE) was tested by the genetic departure index (d). The coefficient of gene differentiation G(ST) and Phi(ST) by AMOVA (Analysis of Molecular Variety) was imputed using Arlequin software in this study. In addition, a phylogenetic tree was constructed by UPGMA method based on the pairwise Nei's standard distances using PHYLIP. A total of 1,357 fragments with sizes ranging between 102 bp and 385 bp were acquired by PCR amplifications. The average number of alleles of the two populations was 8.875. Results indicated that these microsatellite loci were highly polymorphic and could be used as genetic markers. The mean values of the parameters P, Ho, He, PIC, and Ne were 0.165, 0.435, 0.758, 0.742, and 5.019 for HNS and 0.147, 0.299, 0.847, 0.764, and 5.944 for SNS, respectively. Although there were differences, there were no significant differentiations except for the locus HLJcf37. These populations to a certain extent deviated from HWE, such as excessive and deficient heterozygote numbers. The value of G(ST) was 0.078 and above 98% of the variation were differences among individuals within the population, so the variation between populations was insignificant. Cluster analysis also showed that the relationships among individuals were very close. In conclusion, the microsatellite markers that were developed through this study are useful for genetic analysis and the genetic culture that was proposed in this study has no significant impact on S. soldatovi.

Channel catfish BAC-end sequences for marker development and assessment of syntenic conservation with other fish species

In the present study, 25 195 BAC ends for channel catfish (Ictalurus punctatus) were sequenced, generating 20 366 clean BAC-end sequences (BES), with an average read length of 557 bp after trimming. A total of 11 414 601 bp were generated, representing approximately 1.2% of the catfish genome. Based on this survey, the catfish genome was found to be highly AT-rich, with 60.7% A+T and 39.3% G+C. Approximately 12% of the catfish genome consisted of dispersed repetitive elements, with the Tc1/mariner transposons making up the largest percentage by base pair (4.57%). Microsatellites were detected in 17.5% of BES. Catfish BACs were anchored to the zebrafish and Tetraodon genome sequences by BLASTN, generating 16% and 8.2% significant hits (E < e(-5)) respectively. A total of 1074 and 773 significant hits were unique to the zebrafish and Tetraodon genomes, respectively, of which 417 and 406, respectively, were identified as known genes in other species, providing a major genome resource for comparative genomic mapping.

Segregation and linkage analysis of 75 novel microsatellite DNA markers in pair crosses of Japanese abalone (Haliotis discus hannai) using the 5'-tailed primer method

We present novel microsatellite markers of the Japanese abalone (Haliotis discus hannai) for general mapping studies in this species. A total of 75 microsatellite markers were developed, and the allele-transmission patterns of these markers were studied in three families generated by pair crosses. For allele scoring, we employed the 5'-tailed primer polymerase chain reaction (PCR) technique, which substantially reduces the cost for fluorescent labeling of primers. Of the 225 possible marker-family combinations (75 markers x 3 families), 18 cases of informative null-allele segregation were inferred. When such null-allele segregations were allowed, more than 70% of the 75 markers in the families turned out to be markers with an expected segregation ratio of 1:1:1:1, allowing maximal exploitation of the codominant nature of microsatellite markers. There were 16 instances of segregation distortion at the 5% significance level. The test for independence of segregation assigned the 75 markers into 17 linkage groups, which is in close agreement with the haploid chromosome number of H. discus hannai (n = 18). Six markers could not be placed into any linkage group. We suggest that these markers could help construct a H. discus hannai linkage map.

A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L

The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60-90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal.

A preliminary genetic linkage map of the Pacific abalone Haliotis discus hannai Ino

Preliminary genetic linkage maps were constructed for the Pacific abalone (Haliotis discus hannai Ino) using amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA (RAPD), and microsatellite markers segregating in a F(1) family. Nine microsatellite loci, 41 RAPD, and 2688 AFLP markers were genotyped in the parents and 86 progeny of the mapping family. Among the 2738 markers, 384 (including 365 AFLP markers, 10 RAPD markers, and 9 microsatellite loci) were polymorphic and segregated in one or both parents: 241 in the female and 146 in the male. The majority of these markers, 232 in the female and 134 in the male, segregated according to the expected 1:1 Mendelian ratio (alpha = 0.05). Two genetic linkage maps were constructed using markers segregating in the female or the male parent. The female framework map consisted of 119 markers in 22 linkage groups, covering 1773.6 cM with an average intermarker space of 18.3 cM. The male framework map contained 94 markers in 19 linkage groups, spanning 1365.9 cM with an average intermarker space of 18.2 cM. The sex determination locus was mapped to the male map but not to the female map, suggesting a XY-male determination mechanism. Distorted markers showing excess of homozygotes were mapped in clusters, probably because of their linkage to a gene that is incompatible between two parental populations.

Assignment of immune-related genes to the channel catfish, Ictalurus punctatus, genetic map

Eighteen new genes, adenosine A1 receptor (ADORA1), complement component 4-beta (C4b), complement component 8-beta (C8b), chemokine ligand 19 (CCL19), chemokine ligand 21 (CCL21), chemokine ligand 25 (CCL25), chemokine receptor 2 (CCR2), chemokine receptor 5 (CCR5), chemokine receptor 4 (CCR4), chemokine receptor 7 (CCR7), chemokine receptor 9 (CCR9), interleukin 1-beta (IL1B), integrin II-beta (ITGB2), novel immune type receptor 2 (NITR2), novel immune type receptor 4 (NITR4), natural killer cell lysin (NKLYSIN), nucleotide excision repair (RAD23B) and tumour necrosis factor-alpha (TNF), were assigned to the channel catfish (Ictalurus punctatus) genetic linkage map. Polymorphic microsatellite markers were developed for NITR2, NITR4 and RAD23B from short-tandem repeats in the available sequence. Polymorphic microsatellite markers were developed for the remaining 15 genes by short-tandem repeat-anchored primer sequencing of catfish bacterial artificial chromosomes. Two gene clusters (MYOG-NRAMP-ADORA1) and (CCR4-CCR2-CCR5) displayed conservation of synteny between catfish and mammals. Assignment of 18 new genes to the catfish linkage map will further advance integration of genetic and physical maps and comparative mapping between channel catfish and map rich species.

The catfish liver-expressed antimicrobial peptide 2 (LEAP-2) gene is expressed in a wide range of tissues and developmentally regulated

Antimicrobial peptides (AMPs) are important components of the host's innate immune response against microbial invasion. The cysteine-rich AMPs such as defensin and hepcidin have been extensively studied, but the recently identified cysteine-rich liver-expressed antimicrobial peptide 2 (LEAP-2) has been characterized from only a few organisms. Here we cloned and sequenced the LEAP-2 cDNAs from both Channel catfish and Blue catfish. The LEAP-2 gene from Channel catfish was also sequenced and characterized. Channel catfish LEAP-2 gene consists of two introns and three exons that encode a peptide of 94 amino acids with a 28 amino acid signal peptide and a mature peptide of 41 amino acids. The amino acid sequences and gene organization were conserved between catfish and other organisms. The Channel catfish LEAP-2 gene is expressed in a wide range of tissues except brain and stomach. Its expression is developmentally regulated with no detection of mature mRNA in early stages of development. It appears that the catfish LEAP-2 gene is regulated at the level of splicing; it is constitutively transcribed, but remains unspliced until 6 days after hatching. The expression of LEAP-2 was induced in a tissue-specific manner. Its expression was upregulated in the spleen, but not in the liver and head kidney, after challenge with Edwardsiella ictaluri, the causative agent of enteric septicemia of catfish (ESC).

Isolation and enrichment of abundant microsatellites from a channel catfish (Ictalurus punctatus) brain cDNA library

Efforts to construct a genetic linkage map of channel catfish have involved identification of random genomic microsatellite markers, as well as anchored Type I loci (expressed genes) from channel catfish. To identify Type I markers we constructed a directional cDNA library from brain tissue to obtain expressed catfish sequences that could be used for single nucleotide polymorphism (SNP) marker development. These cDNA sequences surprisingly contained a high proportion of microsatellites (about 14%) in noncoding regions of expressed sequence tags (ESTs), many of which were not associated with known sequences. To further identify cDNAs with microsatellites and reduce the number of sequencing reactions needed for marker development, we enriched this library for repeat sequences and sequenced clones from both directions. A total of 1644 clones from seven repeat-enriched captures (CA, GT, CT, GA, MTT, TAG, and TAC) were sequenced from both ends, and 795 nonredundant clones were assembled. Thirty-seven percent of the clones contained microsatellites in the trimmed sequence. After assembly in the TIGR Catfish Gene Index (CfGI), 154 contigs matched known vertebrate genes and 92 contigs contained microsatellites. When BLAST-matched orthologues were available for similarity alignments, 28% of these contigs contained repeats in the 5'-UTR, 72% contained repeats in the 3'-UTR, and 8% contained repeats at both ends. Using biotinylated repeat oligonucleotides coupled with streptavidin-coated magnetic beads, and rapid; single-pass hybridization, we were able to enrich our plasmid library greater than two-fold for repeat sequences and increase the ability to link these ESTs with known sequences greater than six-fold.

Genomic organisation and expression of the natural killer cell enhancing factor (NKEF) gene in channel catfish, Ictalurus punctatus (Rafinesque)

The gene encoding Natural Killer Cell Enhancing Factor (NKEF) was identified in clones from a gynogenetic channel catfish BAC library. NKEF gene sequence (5.2 kb) was obtained by direct sequencing of BAC clones. The catfish NKEF gene contains one non-coding exon, five coding exons and five introns. A putative TATA box and other transcription factor binding sites were identified in the promoter region. The NKEF amino acid sequence is highly conserved between fish and mammals. Gene expression, measured by real-time quantitative PCR, was detected in all major tissues with the highest level of expression in stomach and heart and lowest levels in gonad and pituitary gland. Catfish NKEF mRNA levels were slightly upregulated 8 and 24 h after injection of lipopolysaccharide. A TAA-repeat microsatellite was identified in a BAC clone containing the NKEF gene, and this locus contained at least 12 alleles in a random-bred catfish population. Multipoint linkage analysis in two reference families placed the NKEF gene on linkage group U18, 5.1 cM from locus IpCG0177 (r=0.05; LOD=45.8), 6.0 cM from a novel immune type receptor, syntenic (40 cM) with T-cell receptor alpha, and not linked with MHC loci.

Molecular characterization of the insulin-like growth factor-I (IGF-I) gene in channel catfish (Ictalurus punctatus)

The insulin-like growth factor I (IGF-I) gene was characterized in channel catfish. Partial cDNA sequence, missing exon 1 and part of exon 2, was obtained in 5'- and 3'-RACE experiments. Direct sequencing of two bacterial artificial chromosome clones revealed gene structure and provided sequence from 640 bp upstream of the initiator methionine to 136 bp beyond the polyadenylation site. Genomic sequence contained a putative TATA box 506 bp upstream of the initiator methionine. The 477-bp reading frame within five exons encoded a 159-amino acid (aa) pre-propeptide highly similar to IGF-I in higher vertebrates. The sequence encoding the signal peptide was unique in catfish and contained 70% G+C content with the potential for a stable stem-loop structure. Full-length cDNA was only maintained in recombination-deficient (DH10B) strain E. coli. Levels of IGF-I mRNA were highest in liver, followed by brain and muscle, then heart and kidney (P<0.05). A CT/GA dinucleotide microsatellite in intron 1 was highly polymorphic in commercial channel catfish, and permitted placement of the IGF-I gene on the catfish genetic map. However, specific IGF-I alleles were not correlated with differences in growth rate from 100 to 130 days post-hatch in USDA103 line catfish.

Molecular evolution of minisatellites in hemiascomycetous yeasts

Minisatellites are DNA tandem repeats exhibiting size polymorphism among individuals of a population. This polymorphism is generated by two different mechanisms, both in human and yeast cells, "replication slippage" during S-phase DNA synthesis and "repair slippage" associated to meiotic gene conversion. The Saccharomyces cerevisiae genome contains numerous natural minisatellites. They are located on all chromosomes without any obvious distribution bias. Minisatellites found in protein-coding genes have longer repeat units and on the average more repeat units than minisatellites in noncoding regions. They show an excess of cytosines on the coding strand, as compared to guanines (negative GC skew). They are always multiples of three, encode serine- and threonine-rich amino acid repeats, and are found preferably within genes encoding cell wall proteins, suggesting that they are positively selected in this particular class of genes. Genome-wide, there is no statistically significant association between minisatellites and meiotic recombination hot spots. In addition, minisatellites that are located in the vicinity of a meiotic hot spot are not more polymorphic than minisatellites located far from any hot spot. This suggests that minisatellites, in S. cerevisiae, evolve probably by strand slippage during replication or mitotic recombination. Finally, evolution of minisatellites among hemiascomycetous yeasts shows that even though many minisatellite-containing genes are conserved, most of the time the minisatellite itself is not conserved. The diversity of minisatellite sequences found in orthologous genes of different species suggests that minisatellites are differentially acquired and lost during evolution of hemiascomycetous yeasts at a pace faster than the genes containing them.

A microsatellite linkage map of the European sea bass Dicentrarchus labrax L

A genetic linkage map of the European sea bass (Dicentrarchus labrax) was constructed from 174 microsatellite markers, including 145 new markers reported in this study. The mapping panel was derived from farmed sea bass from the North Adriatic Sea and consisted of a single family including both parents and 50 full-sib progeny (biparental diploids). A total of 162 microsatellites were mapped in 25 linkage groups. Eleven loci represent type I (coding) markers; 2 loci are located within the peptide Y (linkage group 1) and cytochrome P450 aromatase (linkage group 6) genes. The sex-averaged map spans 814.5 cM of the sea bass genome. The female map covers 905.9 cM, whereas the male map covers only 567.4 cM. The constructed map represents the first linkage map of European sea bass, one of the most important aquaculture species in Europe.

Linkage maps of microsatellite DNA markers for the Pacific oyster Crassostrea gigas

We constructed male and female consensus linkage maps for the Pacific oyster Crassostrea gigas, using a total of 102 microsatellite DNA markers typed in 11-day-old larvae from three families. We identified 11 and 12 linkage groups in the male and female consensus maps, respectively. Alignment of these separate maps, however, suggests 10 linkage groups, which agrees with the haploid chromosome number. The male linkage map comprises 88 loci and spans 616.1 cM, while the female map comprises 86 loci and spans 770.5 cM. The male and the female maps share 74 loci; 2 markers remain unlinked. The estimated coverages for the consensus linkage maps are 79% for the male and 70-75% for the female, on the basis of two estimates of genome length. Ninety-five percent of the genome is expected to lie within 16 and 21 cM of markers on the male and female maps, respectively, while 95% of simulated minimum distances to the male and female maps are within 10.1 and 13.6 cM, respectively. Females have significantly more recombination than males, across 118 pairs of linked markers in common to the parents of the three families. Significant differences in recombination and orders of markers are also evident among same-sex parents of different families as well as sibling parents of opposite sex. These observations suggest that polymorphism for chromosomal rearrangements may exist in natural populations, which could have profound implications for interpreting the evolutionary genetics of the oyster. These are the first linkage maps for a bivalve mollusc that use microsatellite DNA markers, which should enable them to be transferred to other families and to be useful for further genetic analyses such as QTL mapping.

Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs

Genomic resources for peach, a model species for Rosaceae, are being developed to accelerate gene discovery in other Rosaceae species by comparative mapping. Simple sequence repeats (SSRs) are an important tool for comparative mapping because of their high polymorphism and transportability. To accelerate the development of SSR markers, we analyzed publicly available Rosaceae expressed sequence tags (ESTs) for SSRs. A total of 17,284 ESTs from almond, peach and rose were assembled into putatively non-redundant EST sets. For comparison, 179,099 ESTs from Arabidopsis were also used in the analysis. About 4% of the assembled ESTs contained SSRs in Rosaceae, which was higher than the 2.4% found in Arabidopsis. About half of the SSRs were found in the putative UTR, and the estimated average distance between SSRs in the UTR was 5.5 kb in rose, 5.1 kb in almond, 7 kb in peach and 13 kb in Arabidopsis. In the putative coding region, the estimated average distance was two to four times longer than in the UTR. Rosaceae ESTs containing SSRs were functionally annotated using the GenBank nr database and further classified using the gene ontology terms associated with the matching sequences in the SwissProt database. The detailed data including the sequences and annotation results are available from http://www.genome.clemson.edu/gdr/rosaceaessr/.

Cloning and characterization of myogenic regulatory genes in three Ictalurid species

We report sequence, tissue expression and map-position data for myogenin, MYOD1, myostatin and follistatin in three Ictalurid catfish species: channel catfish (Ictalurus punctatus), blue catfish (I. furcatus) and white catfish (Ameiurus catus). These genes are involved in muscle growth and development in mammals and may play similar roles in catfish. Amino acid sequences were highly conserved among the three Ictalurid species (>95% identity), moderately conserved among catfish and zebrafish (approximately 80% identity), and less conserved among catfish and humans (approximately 40-60% identity) for all four genes. Gene structure (number of exons and introns and exon-intron boundaries) was conserved between catfish and other species for all genes. Myogenin and MYOD1 expression was limited to skeletal muscle in juvenile channel catfish, similar to expression patterns for these genes in other fish and mammalian species. Myostatin was expressed in a variety of tissues in juvenile channel catfish, a pattern common in other fish species but contrasting with data from mammals where myostatin is primarily expressed in skeletal muscle. Follistatin was expressed in juvenile catfish heart, testes and spleen. All four genes contained polymorphic microsatellite repeats in non-coding regions and linkage analysis based on inheritance of these microsatellite loci was used to place the genes on the channel catfish linkage map. Information provided in this study will be useful in further studies to determine the role these genes play in muscle growth and development in catfish.

A second-generation genetic linkage map of tilapia (Oreochromis spp.)

We constructed a second-generation linkage map of tilapia from the F(2) progeny of an interspecific cross between Oreochromis niloticus and Oreochromis aureus. The map reported here contains 525 microsatellite and 21 gene-based markers. It spans 1311 cM in 24 linkage groups, for an average marker spacing of 2.4 cM. We detected associations of sex and red color with markers on linkage group 3. This map will enable mapping and selective breeding of quantitative traits important to the economic culture of tilapia as a food fish and will contribute to the study of closely related cichlids that have undergone explosive adaptive radiation in the lakes of East Africa.

First-generation linkage map of the gray, short-tailed opossum, Monodelphis domestica, reveals genome-wide reduction in female recombination rates

The gray, short-tailed opossum, Monodelphis domestica, is the most extensively used, laboratory-bred marsupial resource for basic biologic and biomedical research worldwide. To enhance the research utility of this species, we are building a linkage map, using both anonymous markers and functional gene loci, that will enable the localization of quantitative trait loci (QTL) and provide comparative information regarding the evolution of mammalian and other vertebrate genomes. The current map is composed of 83 loci distributed among eight autosomal linkage groups and the X chromosome. The autosomal linkage groups appear to encompass a very large portion of the genome, yet span a sex-average distance of only 633.0 cM, making this the most compact linkage map known among vertebrates. Most surprising, the male map is much larger than the female map (884.6 cM vs. 443.1 cM), a pattern contrary to that in eutherian mammals and other vertebrates. The finding of genome-wide reduction in female recombination in M. domestica, coupled with recombination data from two other, distantly related marsupial species, suggests that reduced female recombination might be a widespread metatherian attribute. We discuss possible explanations for reduced female recombination in marsupials as a consequence of the metatherian characteristic of determinate paternal X chromosome inactivation.

Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus)

Gene-derived markers are pivotal to the analysis of genome structure, organization, and evolution and necessary for comparative genomics. However, gene-derived markers are relatively difficult to develop. This project utilized the genomic resources of channel catfish expressed sequence tags (ESTs) to identify simple sequence repeats (SSRs), or microsatellites. It took the advantage of ESTs for the establishment of gene identities, and of microsatellites for the acquisition of high polymorphism. When microsatellites are tagged to genes, the microsatellites can then be used as gene markers. A bioinformatic analysis of 43,033 ESTs identified 4855 ESTs containing microsatellites. Cluster analysis indicated that 1312 of these ESTs fell into 569 contigs, and the remaining 3534 ESTs were singletons. A total of 4103 unique microsatellite-containing genes were identified. The dinucleotide CA/TG and GA/TC pairs were the most abundant microsatellites. AT-rich microsatellite types were predominant among trinucleotide and tetranucleotide microsatellites, consistent with our earlier estimation that the catfish genome is highly AT-rich. Our preliminary results indicated that the majority of the identified microsatellites were polymorphic and, therefore, useful for genetic linkage mapping of catfish. Mapping of these gene-derived markers is under way, which will set the foundation for comparative genome analysis in catfish.

Complete sequence and characterization of the channel catfish mitochondrial genome

In order to support analysis of channel catfish populations and genetic improvement programs, the channel catfish, Ictalurus punctatus, mitochondrial genome was completely sequenced and revealed gene structure and gene order common to vertebrates. Nucleotide sequence comparisons of cytochrome b (Cytb) and cytochrome c oxidase subunit 1 (COI) demonstrated genetic separation of the genera Ictalurus, Pylodictis and Ameiurus consistent with the taxonomic classification within Ictaluridae. The ictalurid Cytb nucleotide sequences were significantly different from a putative channel catfish Cytb sequence in GenBank. Genetic relationships based on mitochondrial DNA sequences indicated the value of channel catfish in genomic comparisons between teleosts. Pairwise alignment of DNA sequences revealed conservation of regulatory sequences in the D-loop region with other vertebrates. Analysis of D-loop sequences in commercial populations and a research strain revealed 28 polymorphic sites and 33 D-loop haplotypes. Sequence analysis revealed clustering of haplotypes within commercial farms and the USDA103 research line, but D-loop haplotypes were not sufficient to discriminate the USDA103 fish from commercial catfish.

An AFLP-Based Genetic Linkage Map of Channel Catfish (Ictalurus punctatus) Constructed by Using an Interspecific Hybrid Resource Family

Catfish is the major aquaculture species in the United States. The hybrid catfish produced by crossing channel catfish females with blue catfish males exhibit a number of desirable production traits, but their mass production has been difficult. To introduce desirable genes from blue catfish into channel catfish through introgression, a genetic linkage map is helpful. In this project, a genetic linkage map was constructed using amplified fragment length polymorphism (AFLP). A total of 607 AFLP markers were analyzed using 65 primer combinations and an interspecific backcross resource family. A total of 418 AFLP markers were assigned to 44 linkage groups. Among the remaining 189 markers, 101 were not used because of significant segregation distortion, 29 were unlinked, and 59 were eliminated because they span very large distances. The 418 AFLP markers covered 1593 cM Kosambi. The AFLP markers showed a high level of clustering that appears to be related to certain primer combinations. This linkage map will serve as the basis for mapping a greater number of markers to provide a map with high enough resolution for it to be useful for selective breeding programs using introgression.

Genetic linkage map of the eastern oyster Crassostrea virginica Gmelin

Amplified fragment length polymorphisms (AFLPs), along with some microsatellite and Type I markers, were used for linkage analysis in Crassostrea virginica Gmelin, the eastern oyster. Seventeen AFLP primer combinations were selected for linkage analysis with two parents and their 81 progeny. The 17 primer combinations produced 396 polymorphic markers, and 282 of them were segregating in the two parents. Chi-square analysis indicated that 259 (91.8%) markers segregated in Mendelian ratio, while the other 23 (8.2%) showed significant (P < 0.05) segregation distortion, primarily for homozygote deficiency and probably due to deleterious recessive genes. Moderately dense linkage maps were constructed using 158 and 133 segregating markers (including a few microsatellite and Type I markers) from male and female parents, respectively. The male framework map consisted of 114 markers in 12 linkage groups, covering 647 cM. The female map had 84 markers in 12 linkage groups with a length of 904 cM. The estimated genome length was 858 cM for the male map and 1296 cM for the female map. The observed genome coverage was 84% for the male and female map when all linked markers were considered. Genetic maps observed in this study are longer than the cytogenetic map, possibly because of low marker density.

Gene mapping in fishes: a means to an end

Genetic research in fishes is poised to contribute a vast amount of information on the structural organization and function of vertebrate genomes. Recent advances in molecular biology have made possible the widescale characterization of genomes in all living organisms. This includes defining chromosomes at the cytological level down to their linear composition at individual nucleotide base pairs. Pioneering gene mapping studies into the genomes of fishes will only serve as the starting point for more detailed studies into the function of these genomes. Future research directed at understanding the mechanisms of gene actions and interactions will benefit all areas of biology, including ecology, ethology, evolution, and physiology. Gene mapping data from brown trout and rainbow trout are used to exemplify how basic information on gene transmission in a species may help to localize centromeres onto a genetic map and identify chromosomal regions possessing a high degree of segregation distortion. Genetic maps may also be used to identify differences in recombination levels among individuals and between the sexes when multiple mapping families are utilized in studies. Observations of this type are the antecedents to more complex biological investigations on the genetic architecture underlying these phenomena.

Isolation and characterization of channel catfish natural resistance associated macrophage protein gene

Natural resistance associated macrophage protein 1 (Nramp1) affects the ability of macrophages to kill pathogens. We cloned Nramp cDNA of channel catfish to identify potential molecular markers for disease resistance. Three different Nramp transcripts were identified: NrampCa-2912 nucleotides (nt), NrampCb-3245 nt, and NrampCc-3721 nt. At the 5' end, the transcripts have a common 2263 nt sequence containing the open reading frame. The differences are in the 3' untranslated region resulting from alternative splicing and polyadenylation. NrampCc is the predominant form expressed. The deduced 550 amino acid sequence of the channel catfish Nramp (NrampC) has high homology to Nramp from other vertebrates and a predicted conserved structure. The NrampC contains the 12 transmembrane domains, and the consensus transport motif. Post-transcriptional processing is also conserved. Phylogenetic analysis grouped NrampC with other fish Nramps and closer to Nramp2 than to Nramp1 of mammals. However, the catfish transcript does not contain an iron-responsive regulatory-protein binding site, a characteristic of Nramp2, and, like Nramp1, NrampC expression is induced in macrophage-rich tissues after exposure to lipopolysaccharide and in a macrophage cell line when stimulated. Thus NrampC is structurally closer to mammalian Nramp2 but may function similar to Nramp1.

Molecular characterization and differential expression of the myostatin gene in channel catfish (Ictalurus punctatus)

Myostatin is a recently discovered gene that inhibits muscle growth. In the present study, we characterized the myostatin locus and its expression in channel catfish (Ictalurus punctatus). The genomic DNA and cDNA encoding the channel catfish myostatin were cloned and sequenced. The myostatin gene has three exons encoding a protein of 389 amino acids. Comparison of the genomic sequences with those of the cDNA revealed that the myostatin cDNA was 1673 base pair (bp) long with a 5'-untranslated region (UTR) and 3'-UTR of 180 and 323 bp, respectively. The deduced amino acid sequences of the catfish myostatin is highly conserved with those of other organisms. The myostatin locus is highly polymorphic in channel catfish because of the presence of several microsatellites and single nucleotide polymorphic sites. The myostatin gene was expressed in various tissues and developmental stages at differential levels, suggesting complex regulation of this gene and perhaps roles for myostatin in addition to those originally suggested.