GENETIC MAPS OF AQUACULTURE SPECIES

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
303	3710	1040	40%
303	3710	1080	10%
304	3710	1040	40%
304	3710	1080	10%

Progress 01/01/98 to 09/30/04

Outputs
We have completed this project by development of several thousand of molecular markers and the construction of the catfish linkage map.

Impacts
The linkage map will be the framework map that can be used for detailed mapping analysis for QTLs. The molecular markers will be useful not only for mapping, but also for genetic resource analysis.

Publications

Liu, Z.J., Kim, S., Kucuktas, H., and Karsi, A. (2001) Multiple isoforms and an unusual cathodic isoform of creatine kinase from channel catfish (Ictalurus punctatus). Gene 275, 207-215.
Liu, Z.J., Li, P., Kocabas, A., Ju, Z., Karsi, A., Cao, D., Patterson, A. (2001) Microsatellite-containing genes from the channel catfish brain: evidence of trinucleotide repeat expansion in the coding region of nucleotide excision repair gene RAD23B, Biochemical and Biophysical Research Communications 289, 317-324.
Liu, Z.J., Kim, S., Karsi, A. (2001) Channel catfish follicle stimulating hormone and luteinizing hormone: cDNA cloning and their expression during ovulation. Marine Biotechnology 3, 590-599.
Liu, Z.J., Feng, J. (2001) Gene mapping and marker-assisted selection in channel catfish (Ictalurus punctatus). Acta Agriculturae Boreali-Occidentalis Sinica 10, 110-114.
Kim, S., Karsi, A., Dunham, R., Liu, Z.J. (2000) The skeletal muscle alpha-actin gene of channel catfish (Ictalurus punctatus) and its association with piscine-specific SINE elements. Gene 252: 173-181.
Tan, G., Karsi, A., Li, P., Kim, S., Zheng, X., Kucuktas, H., Argue, B. J., Dunham, R. A., and Liu, Z. J. (1999) Polymorphic microsatellite markers in Ictalurus punctatus and related catfish species. Molecular Ecology 8: 1758-1760.
Liu, Z. J., Tan, G., Li, P., and Dunham, R. A. (1999) Transcribed dinucleotide microsatellites and their associated genes from channel catfish, Ictalurus punctatus. Biochemical and Biophysical Research Communications 259, 190-194.
Liu, Z.J., Karsi, A., and Dunham, R.A. (1999) Development of polymorphic EST markers suitable for genetic linkage mapping of catfish. Mar. Biotechnol. 1: 437-447.
Liu, Z. J., Tan, G., Kucuktas, H., Li, P., Karsi, A., Yant D. R., and Dunham, R. A. (1999) High levels of conservation at microsatellite loci among Ictalurid catfishes. J. Heredity 90, 307-312.
Liu, Z. J., Li, P., Kucuktas, H., and Dunham, R. A. (1999) Characterization of nonautonomous Tc1-like transposable elements of channel catfish (Ictalurus punctatus). Fish Physiology and Biochemistry 21, 65-72.
Liu, Z. J., Li, P., Argue, B. J., and Dunham, R. A. (1999) Random amplified polymorphic DNA markers: usefulness for gene mapping and analysis of genetic variation of catfish. Aquaculture 174, 59-68.
Liu, Z. J., Li, P., Kucuktas, H., Nichols, A., Tan, G., Zheng, X., Argue, B. J., Yant, R., and Dunham, R. A. (1999) Development of AFLP markers for genetic linkage mapping analysis using channel catfish and blue catfish interspecific hybrids. Trans. Amer. Fish. Soc. 128, 317-327.
Liu, Z. (1999) Gene mapping, marker-assisted selection, gene cloning, genetic engineering, and integrated genetic improvement programs at Auburn University. The Fifth Conference of the International Network on Genetics in Aquaculture Proceedings, Kuala Lumpur, Malaysia. pp. 1-19.
Liu, Z. J. (1999) Gene Mapping and marker-assisted selection in channel catfish (Ictalurus punctatus). Proceedings of Sino-US Symposium on Agricultural Biotechnology. pp. 101-112.

Progress 01/01/02 to 12/31/02

Outputs
A large number of type II polymorphic markers have been developed from catfish and their applications in catfish have been evaluated. Over 600 RAPD markers have been developed. Several thousand of AFLP markers have been identified. Over 250 microsatellite markers have been developed. Over 100 type I markers including microsatellite-containing gene markers, intronic microsatellites, and expressed single nucleotide (eSNPs) have been developed. Resource families have been developed using both the channel catfish resource families and the channel catfish x blue catfish resource families. The advantage of using the channel catfish resource families is that it can be used in breeding programs attempting improving traits where phenotypic variation exist among different lines of channel catfish. The interspecific hybrid resource families are advantageous in that it provide an experiment system where maximum marker polymorphism can be created. Practically, because blue catfish is different and superior to channel catfish in resistance to the major bacterial disease enteric septicemia (ESC) and in processing yield, while channel catfish is different and superior to blue catfish in growth rate, feed conversion efficiency, and resistance to the most common bacterial disease columnaris, the interspecific hybrid system will allow mapping of these traits related genes for construction of synthetic breeds through introgression. DNA of the resource families is available for mapping. Genetic linkage maps have been made. 418 AFLP markers have been mapped using the interspecific hybrid resource families at Auburn University. Efforts have been devoted to QTL analysis of growth rate, feed conversion efficiency, disease resistance, and processing yield. Several putative markers have been identified related to growth and feed conversion efficiency at Auburn University. A few markers that appear to be linked to disease resistance are under further study. Genomic resources have been developed in catfish including lambda DNA library and BAC large insert libraries, 15 cDNA libraries from 14 tissues of channel catfish. John Liu's group has sequenced over 11,000 ESTs from channel catfish. A total of over 1000 blue catfish ESTs have also been sequenced at Auburn.

Impacts
This is the first genetic linkage map constructed using the channel catfish x blue catfish hybrid system. Although more markers are needed to be mapped, the framework map will be the start point for QTL analysis. Because both channel catfish and blue catfish are rich in genetic variation causing significant differences in performance, mapping of QTLs will undoubtedly improve genetic brood stocks that will overcome much of the disease problems today. Our ultimate goal is to construct synthetic breeds by introgression. Also, because the F1 hybrid is perhaps the best genotype that exist for catfish, this work and continue genome work will eventually provide hints to how to produce F1 in mass quantities to meet the industry needs. Genomic resource development is very important for genomics research. The ESTs will serve as the basic reagents and tools for comparative mapping, physical mapping, and functional genomics.

Publications

Dunham, R., and Liu, Z.J. 2002. Gene mapping, isolation and genetic improvement in catfish. In N.Shimizu, T Aoki, I. Hirono and F.Takashima (eds.) Aquatic Genomics: Steps Toward a Great Future. Springer-Verlag, New York pp. 45-60.
Karsi, A., Cao, D., Li, P., Patterson, A., Kocabas, A., Feng, J., Ju, Z., Mickett, K., and Liu, Z.J. 2002. Transcriptome analysis of channel catfish (Ictalurus punctatus): Initial analysis of gene expression and microsatellite-containing cDNAs in the skin, Gene 285, 157-168.
Kocabas, A., Kucuktas, H., Dunham, R. A. and Liu, Z.J. 2002. Molecular characterization and differential expression of the myostatin gene in channel catfish (Ictalurus punctatus). Biochimica et Biophysica Acta 1575, 99-107.
Liu, Z.J., Karsi, A., Li, P., Cao, D., and R. Dunham. 2003. An AFLP-Based Genetic Linkage Map of Channel catfish (Ictalurus punctatus) Constructed by Using an Interspecific Hybrid Resource Family. Genetics, in press.
Ju, Z., Dunham, R., and Liu, Z.J. 2002. Differential gene expression in the brain of channel catfish (Ictalurus punctatus) in response to cold acclimation. Molecular Genetics and Genomics 268:87-95.
Karsi, A., Patterson, A., Feng, J., and Liu, Z.J. 2002. Translational machinery of channel catfish: I. A transcriptomic approach to the analysis of 32 40S ribosomal protein genes and their expression. Gene 291, 177-186.

Progress 01/01/01 to 12/31/01

Outputs
In the last three years, large numbers of molecular markers have been developed and evaluated for application in catfish. We have evaluated many types of markers and concluded that AFLP, microsatellites, and SNPs are most suitable for applications in catfish. In the last year, we developed type I markers using a comparative cDNA analysis approach. It is an efficient approach for identification of type I markers. We are continuing our efforts in developing more type I markers, particularly the expressed SNP markers. All 53 AFLP primer combinations that were highly reproducible in catfish (Liu et al., 1999d) were genotyped in two half-sib families with 73 fish and 56 fish. A LOD score of 3.5 was used for the construction of the genetic linkage map. 453 AFLP markers were mapped belonging to 43 linkage groups. We have cloned, sequenced and characterized all 79 ribosomal protein mRNAs and their expression including 47 60S ribosomal protein genes and 32 40S ribosomal protein genes. Together, with exception of the human, mouse, and rat genes, the 79 channel catfish ribosomal protein mRNAs represent the most complete set of ribosomal protein gene sequences from a single organism that should be useful for phylogenetic and comparative genomic studies. To understand the genomic landscape of catfish, we have identified a family of repetitive elements known as the Xba elements. The Xba elements are arranged in head-to-tail tandem arrays, is highly A/T-rich (67%), 327-331 bp in size, and is highly similar, but not identical to one another in sequence. It has high copy numbers and accounts for over 5% of the catfish genome. We have characterized multi-family of Tc1 transposable elements. One family, named Tip1, is 1.6-kb long, low copy numbers, and is similar to Tc1 elements from other teleost fish. The second family named Tip2 is 1.0-kb in size and is more similar to Tc1 elements from invertebrates. The third family named Tipnon, is 0.5-kb in size and does not harbor transposase-related coding capacity and therefore, is non-autonomous family of transposons. Tipnon has high copy numbers and accounts for 1.6% of the catfish genome. We have also characterized several families of SINE elements, particularly the Mermaid and Merman elements that are specifically associated with aquatic genomes.

Impacts
This project is expected: for the first time, to generate a detailed genetic linkage map of channel catfish; to produce information for markers that are linked to important economic traits. The catfish genetic linkage map will fill the genomic research gap in the most important cultured fish in the US. Such a map will be useful for catfish breeding programs. Markers identified to be linked to economic traits will be immediately useful for marker-assisted selection and for introgression of genes for combined benefits.

Publications

2001 Liu, Z.J., Li, P., Kocabas, A., Ju, Z., Karsi, A., Cao, D., Patterson, A. Microsatellite-containing genes from the channel catfish brain: evidence of trinucleotide repeat expansion in the coding region of nucleotide excision repair gene RAD23B, Biochemical and Biophysical Research Communications 289, 317-324.
2001 Liu, Z.J., Kim, S., Karsi, A. Channel catfish follicle stimulating hormone and luteinizing hormone: cDNA cloning and their expression during ovulation. Marine Biotechnology 3, 590-599.
2001 Liu, Z.J., Feng, J. Gene mapping and marker-assisted selection in channel catfish (Ictalurus punctatus). Acta Agriculturae Boreali-Occidentalis Sinica 10, 110-114.
2001 Liu, Z.J., Kim, S., Kucuktas, H., and Karsi, A. Multiple isoforms and an unusual cathodic isoform of creatine kinase from channel catfish (Ictalurus punctatus). Gene 275, 207-215.
2001 Cao, D., Kocabas, A., Ju, Z., Karsi, A., Li, P., Patterson, A., and Liu, Z.J. Transcriptome of channel catfish (Ictalurus punctatus): initial analysis of genes and expression profiles from the head kidney. Animal Genetics 32, 169-188.
2001 Karsi,A., Moav,B., Hackett, P., Liu , Z.J. Effects of insert size on transposition efficiency of the Sleeping Beauty transposon in mouse cells. Marine Biotechnology 3, 241-245.
2001. Altinok, I., Grizzle, J., and Liu, Z.J. Detection of Yersinia ruckeri in rainbow trout blood by use of polymerase chain reaction. Disease of Aquatic Organisms 44, 29-34.

Progress 01/01/00 to 12/31/00

Outputs
In the last three years, large numbers of molecular markers have been developed and evaluated for application in catfish. We have evaluated many types of markers and concluded that AFLP, microsatellites, and SNPs are most suitable for applications in catfish. In the last year, we developed type I markers using a comparative cDNA analysis approach. It is an efficient approach for identification of type I markers. We are continuing our efforts in developing more type I markers, particularly the SNP markers. All 53 AFLP primer combinations that were highly reproducible in catfish (Liu et al., 1999d) were genotyped in two half-sib families with 73 fish and 56 fish. A LOD score of 3.5 was used for the construction of the genetic linkage map. 418 AFLP markers were mapped belonging to 43 linkage groups. This framework map has a genomic coverage of 2450 cM. Recently, we also genotyped all the 129 fish with 100 microsatellites and map construction with Mapmaker will shortly be completed. We used the same resource family for construction of the genetic linkage map and QTL analysis. Collected data on growth and body conformation include body weight, body length, body width, body depth, head length, head width, head depth, caudal width, and caudal depth. We are in the processes of regression analysis for body conformation data to normalize all data based on fish size (Dunham et al., 1984; 1985; Elsherbini, 1990). Computer analysis using Mapmaker QTL will be completed in the next few months. Our major objective in QTL analysis was to test the system by using a "model trait" in which accurate phenotypic evaluation can be determined. We used growth rate as the model trait since growth can be measured by weight, which can be obtained accurately. We have collected growth (body weight) data on 454 fish and genotyped 129 of the 454 fish.

Impacts
This project is expected: for the first time, to generate a detailed genetic linkage map of channel catfish; to produce information for markers that are linked to important economic traits. The catfish genetic linkage map will fill the genomic research gap in the most important cultured fish in the US. Such a map will be useful for catfish breeding programs. Markers identified to be linked to economic traits will be immediately useful for marker-assisted selection and for introgression of genes for combined benefits.

Publications

Ju, Z., Karsi, A., Kocabas, A., Patterson, A., Li, P., Cao, D., Dunham, R., and Liu, Z.J. (2001) Transcriptome analysis of channel catfish (Ictalurus punctatus): genes and expression profile from the brain. Gene 261, 373-382.
Liu, Z.J., Feng, J. (2000) DNA marker technologies and marker-assisted selection. Acta Agriculturae Boreali-Occidentalis Sinica 9, 413-421.
Liu, Z.J., Tan, G., Kucuktas, H., Li, P., Karsi, A., Yant D. R., and Dunham, R. A. (1999) High levels of conservation at microsatellite loci among Ictalurid catfishes. J. Heredity 90, 307-312.
Liu, Z.J., Li, P., Argue, B. J., and Dunham, R. A. (1999) Random amplified polymorphic DNA markers: usefulness for gene mapping and analysis of genetic variation of catfish. Aquaculture 174, 59-68.
Liu, Z.J., Li, P., Kucuktas, H., Nichols, A., Tan, G., Zheng, X., Argue, B. J., Yant, R., and Dunham, R. A. (1999) Development of AFLP markers for genetic linkage mapping analysis using channel catfish and blue catfish interspecific hybrids. Trans. Amer. Fish. Soc. 128, 317-327.
Tan, G., Karsi, A., Li, P., Kim, S., Zheng, X., Kucuktas, H., Argue, B. J., Dunham, R. A., and Liu, Z.J. (1999) Polymorphic microsatellite markers in Ictalurus punctatus and related catfish species. Mol. Ecol. 8, 1758-1760.
Liu, Z.J., Tan, G., Li, P., and Dunham, R. A. (1999) Transcribed dinucleotide microsatellites and their associated genes from channel catfish, Ictalurus punctatus. Biochem. Biophys. Res. Comm. 259, 190-194.
Liu, Z.J., Karsi, A., and Dunham, R.A. (1999) Development of polymorphic EST markers suitable for genetic linkage mapping of catfish. Mar. Biotechnol. 1, 437-447.
Kim, S., Karsi, A., Dunham, R., Liu, Z.J. (2000) The skeletal muscle a-actin gene of channel catfish (Ictalurus punctatus) and its association with piscine-specific SINE elements. Gene 252, 173-181.
Liu, Z.J., Li, P., Kucuktas, H., and Dunham, R. A. (1999) Characterization of nonautonomous Tc1-like transposable elements of channel catfish (Ictalurus punctatus). Fish Physiol. Biochem. 21, 65-72.
Liu, Z.J. (1999) Gene mapping, marker-assisted selection, gene cloning, genetic engineering, and integrated genetic improvement programs at Auburn University. The Fifth Conference of the International Network on Genetics in Aquaculture Proceedings, Kuala Lumpur, Malaysia. pp. 1-19.
Liu, Z.J. (1999) Gene Mapping and marker-assisted selection in channel catfish (Ictalurus punctatus). Proceedings of Sino-US Symposium on Agricultural Biotechnology. Pp. 101-112.

Progress 01/01/99 to 12/31/99

Outputs
Catfish is the most important cultured aquaculture species accounting for over 50% of the aquacultural production in the US. Important performance traits include growth rate, disease resistance to enteric septicemia of catfish (ESC) and columnaris disease, feed conversion efficiency, processing yields, tolerance to low dissolved oxygen, tolerance to high ammonia, and harvestability, with the growth rate and disease resistance as the most important traits. The aim of this work was to construct a genetic linkage map containing QTLs for the most important performance traits. To date, 607 AFLP markers have been genotyped in 71 fish derived from F1 hybrid (channel catfish x blue catfish) backcrossed with blue catfish female. The segregating markers thus were channel catfish markers heterozygous in the F1 hybrid catfish. Over 94% of the markers were linked markers and were able to be assigned into linkage groups. It appears that a large proportion of AFLP markers is highly clustered. With the large numbers of AFLP marker (607) analyzed, however, we were able to have a broad genomic coverage. It appears several AFLP markers are linked to the performance traits of growth rate, resistance to ESC, and resistance to columnaris. However, additional fish are being tested to evaluate the linkage and chromosomal regions containing quantitative trait loci (QTLs) responsible for the performance traits. Genotyping of reciprocal backcross (F1 backcrossed with channel catfish male) progenies has also been conducted to construct the linkage map of blue catfish, which can be anchored by the shared markers with the channel catfish. This will provide information concerning genomic evolution and conservation, difference between the male and the female linkage maps, and more importantly, the QTLs from the blue catfish such as resistance to ESC. Blue catfish is much more resistant to ESC disease than channel catfish. Therefore, analysis of QTLs with relation to the linkage map is the first step to identify the blue catfish genomic regions for genetic improvement through introgression.

Impacts
(N/A)

Publications

Tan, G., Karsi, A., Li, P., Kim, S., Zheng, X., Kucuktas, H., Argue, B. J., Dunham, R. A., and Liu, Z. J. (1999) Polymorphic microsatellite markers in Ictalurus punctatus and related catfish species. Molecular Ecology 8: 1758-1760.
Liu, Z. J., Tan, G., Li, P., and Dunham, R. A. (1999) Transcribed dinucleotide microsatellites and their associated genes from channel catfish, Ictalurus punctatus. Biochemical and Biophysical Research Communications 259, 190-194.
Liu, Z.J., Karsi, A., and Dunham, R.A. (1999) Development of polymorphic EST markers suitable for genetic linkage mapping of catfish. Mar. Biotechnol. 1: 437-447.
Liu, Z. J., Tan, G., Kucuktas, H., Li, P., Karsi, A., Yant D. R., and Dunham, R. A. (1999) High levels of conservation at microsatellite loci among Ictalurid catfishes. J. Heredity 90, 307-312.
Liu, Z. J. (1999) Gene Mapping and marker-assisted selection in channel catfish (Ictalurus punctatus). Proceedings of Sino-US Symposium on Agricultural Biotechnology. pp. 101-112.
Liu, Z. J., Li, P., Kucuktas, H., and Dunham, R. A. (1999) Characterization of nonautonomous Tc1-like transposable elements of channel catfish (Ictalurus punctatus). Fish Physiology and Biochemistry 21, 65-72.
Liu, Z. J., Li, P., Argue, B. J., and Dunham, R. A. (1999) Random amplified polymorphic DNA markers: usefulness for gene mapping and analysis of genetic variation of catfish. Aquaculture 174, 59-68.
Liu, Z. J., Li, P., Kucuktas, H., Nichols, A., Tan, G., Zheng, X., Argue, B. J., Yant, R., and Dunham, R. A. (1999) Development of AFLP markers for genetic linkage mapping analysis using channel catfish and blue catfish interspecific hybrids. Trans. Amer. Fish. Soc. 128, 317-327.
Liu, Z. (1999) Gene mapping, marker-assisted selection, gene cloning, genetic engineering, and integrated genetic improvement programs at Auburn University. The Fifth Conference of the International Network on Genetics in Aquaculture Proceedings, Kuala Lumpur, Malaysia. pp. 1-19.

Progress 01/01/98 to 12/31/98

Outputs
We have made two major progress for this project: development of large numbers of molecular markers and development of resource families. 1. Molecular marker development: We have developed over 300 AFLP markers, over 200 microsatellite markers, over 600 RAPD markers, 11 EST markers, and several hundreds of non-polymorphic ESTs. This would provide the first and also most important element for mapping: sufficient markers. 2. Development of resource and reference families: Although channel catfish is the major cultured catfish, channel catfish x blue catfish hybrid system offers great advantages. The F1 hybrid is fertile and in fact we have produced F2, F3, and various backcrosses. They are a major resource for QTL mapping and for MAS. We have successfully produced backcross progeny designed for this QTL mapping project. Sixteen backcross families (8 from channel and 8 from blue backcrossed with the heterozygous F1) have been produced. These families are reared in 0.1-acre ponds ready for QTL evaluation. The interspecific hybrid system for gene mapping of catfish is advantageous because: (1) high rates of polymorphic markers are assured to exist between blue and channel catfish; (2) several important ETLs are possessed by blue catfish, mainly the disease resistance gene(s) to enteric septicemia of catfish (ESC), carcass yield genes, and the genes controlling better seinability (Dunham et al., 1993a). Mapping these important genes is of great importance by itself; (3) mapping ETLs in blue catfish is important to selective breeding programs using backcrossing to introgress beneficial genes from blue catfish into channel catfish; and (4) Drastic phenotypic variation of the hybrid system offers tools to be exploited for easy QTL evaluation and segregation. 3. Genotyping. Genotyping is in progress now using AFLP and microsatellite markers. It is reasonable to assume that in about a year we should have produced a linkage map for catfish.

Impacts
(N/A)

Publications

Liu, Z. J. and Dunham R. 1998 Genetic linkage and QTL mapping of ictalurid catfish. Alabama Agricultural Experiment Station Circular Bulletin 321, 1-19.
Liu, Z. J., Li, P., and Dunham, R. 1998a Characterization of an A/T-rich family of sequences from the channel catfish (Ictalurus punctatus). Molecular Marine Biology and Biotechnology 7, 232-239.
Liu, Z. J., Li, P., Argue, B. J., and Dunham, R. A. 1999a Random amplified polymorphic DNA markers: usefulness for gene mapping and analysis of genetic variation of catfish. Aquaculture, in press.
Liu, Z. J., Li, P., Argue, B., and Dunham, R. 1998b Inheritance of RAPD markers in channel catfish (Ictalurus punctatus), blue catfish (I. furcatus) and their F1, F2 and backcross hybrids. Animal Genetics 29, 58-62.
Liu, Z. J., Li, P., Kucuktas, H., and Dunham, R. A. 1999b Nonautonomous Tc1-like transposable elements of channel catfish (Ictalurus punctatus) contain sequence blocks similar to the para-type sodium channel proteins. Fish Physiology and Biochemistry, in press.
Liu, Z. J., Li, P., Kucuktas, H., Nichols, A., Tan, G., Zheng, X., Argue, B. J., Yant, R., and Dunham, R. A. 1999 Development of AFLP markers for genetic linkage mapping analysis using channel catfish and blue catfish interspecific hybrids. Trans. Amer. Soc. Fish, in press.
Liu, Z. J., Nichols, A., Li, P., and Dunham, R. 1998c Inheritance and usefulness of AFLP markers in channel catfish (Ictalurus punctatus), blue catfish (I. furcatus) and their F1, F2 and backcross hybrids. Molecular and General Genetics 258, 260-268.
Liu, Z. J., Tan, G., Kucuktas, H., Li, P., Karsi, A., Yant D. R., and Dunham, R. A. 1999d High levels of conservation at microsatellite loci among Ictalurid catfishes. J. Heredity, in press.
Liu, Z.J., Karsi, A., and Dunham, R.A. 1999e Development of polymorphic EST markers suitable for genetic linkage mapping of catfish. Mar. Biotechnol., in press.