Location: Cool and Cold Water Aquaculture Research
2017 Annual Report
Accomplishments
1. A reference genome assembly for rainbow trout. A high-quality reference physical genome map is important for facilitating meaningful genetic analyses and enhancing research on the physiology of fish. ARS researchers at Leetown, West Virginia, have provided leadership and worked closely with national and international cooperators to generate a reliable and high-quality reference genome for rainbow trout. In an effort to improve the rainbow trout reference genome assembly, we used recent improvements in DNA sequencing technology and sophisticated new bioinformatics. This new reference genome assembly aligns with 88% of the assembly chromosome sequences of rainbow trout. The NIH National Center for Biotechnology Information (NCBI) has made the new reference genome coding available for browsing through the NCBI online interactive databases. The new rainbow trout genome assembly and chromosome sequences provide major improvements for rainbow trout aquaculture genetics research, and for all aspects of fish quality improvement.
2. Development of a fast-growth rainbow trout line. Fast-growth is one of the most important economic traits in rainbow trout aquaculture, that can be improved by selective breeding of the fastest-growing fish. ARS researchers at Leetown, West Virginia selectively bred a pedigreed, commercial-scale rainbow trout population to market weight for five generations. Compared to the unselected control line, body weight in the growth-selected line increased by approximately 12% per generation through 13 months of age. Thus, the selection breeding practiced by ARS researchers resulted in a line that grows approximately 60% faster to and beyond standard market weight. The improvement growth over commercial lines was consistent when fish were reared in different environments. This genetically-improved and highly characterized rainbow trout germplasm is available for release to stakeholders for commercial propagation.
Review Publications
Nezafatiana, E., Zadmajid, V., Cleveland, B.M. 2017. Short-term effects of genistein on gamete quality, steroidogenesis and histological changes in gonads in gibel carp, Carassius auratus gibelio. Journal of the World Aquaculture Society. doi:10.1111/jwas.12399.
Vallejo, R.L., Leeds, T.D., Gao, G., Parsons, J.E., Martin, K.E., Evenhuis, J., Fragomeni, B.O., Wiens, G.D., Palti, Y. 2017. Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture. Genetics Selection Evolution. 49(17):1-33. doi: 10.1186/s12711-017-0293-6.
Gonazlez-Pena, D., Gao, G., Baranski, M., Moen, T., Cleveland, B.M., Kenney, B., Vallejo, R.L., Palti, Y., Leeds, T.D. 2016. Genome-wide association study for identifying loci that affect fillet yield, carcass, and body weight traits in rainbow trout (Oncorhynchus mykiss). Frontiers in Genetics. 7(203):1-14. doi:10.3389/fgen.2016.00203.
Kutyrev, I., Cleveland, B.M., Leeds, T.D., Wiens, G.D. 2016. Proinflammatory cytokine and cytokine receptor gene expression kinetics following challenge with Flavobacterium psychrophilum in resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss). Fish and Shellfish Immunology. 58:542-553. doi: 10.1016/j.fsi.2016.09.053.
Koganti, P., Wang, J., Cleveland, B.M., Ma, H., Weber, G.M., Yao, J. 2016. Estradiol regulates expression of miRNAs associated with myogenesis in rainbow trout. Molecular and Cellular Endocrinology. 443:1-14. doi:10.1016/j.mce.2016.12.014.
Kutyrev, I., Cleveland, B.M., Leeds, T.D., Wiens, G.D. 2017. Dataset of proinflammatory cytokine and cytokine receptor gene expression in rainbow trout (Oncorhynchus mykiss) measured using a novel GeXP multiplex, RT-PCR assay. Data in Brief. 11:192-196.
Cleveland, B.M., Weber, G.M., Raatz, S.K., Rexroad III, C.E., Picklo, M.J. 2017. Fatty acid partitioning varies across fillet regions during sexual maturation in female rainbow trout (Oncorhynchus mykiss). Aquaculture. 475:52-60.
Koganti, P., Wang, J., Cleveland, B.M., Yao, J. 2017. 17ß-Estradiol increases non-CpG methylation in exon 1 of the rainbow trout (Oncorhynchus mykiss) MyoD gene. Marine Biotechnology. 19:1-7. doi:10.1007/s10126-017-9756-6.
Leeds, T.D., Vallejo, R.L., Weber, G.M., Gonzalez-Pena, D., Silverstein, J. 2016. Response to five generations of selection for growth performance traits in rainbow trout (Oncorhynchus mykiss). Aquaculture. 465:341-351.
Gatrell, S.K., Silverstein, J., Barrows, F., Grimmett, J., Cleveland, B.M., Blemings, K.P. 2016. Effect of dietary lysine and genetics on growth and indices of lysine catabolism in rainbow trout. Aquaculture Nutrition. doi: 10.1111/anu.12459.
Weber, G.M., Martin, K., Kretzer, J.D., Ma, H., Dixon II, D. 2016. Effects of incubation temperatures on embryonic and larval survival in rainbow trout, Oncorhynchus mykiss. Journal of Applied Aquaculture. 28:285-297. doi:10.1080/10454438.2016.1212447.
Cleveland, B.M., Leeds, T.D., Rexroad III, C.E., Summerfelt, S., Good, C., Davidson, J., May, T., Crouse, C., Wolters, W.R., Plemmons, B., Kenney, P. 2017. Genetic line by environment interaction on rainbow trout growth and processing traits. North American Journal of Aquaculture. 79:140-154. doi:10.1080/15222055.2016.1271846.
Liu, S., Palti, Y., Martin, K.E., Parsons, J.E., Rexroad, III, C.E. 2016. Assessment of genetic differentiation and genetic assignment of commercial rainbow trout strains using a SNP panel. Aquaculture. 468(1):120-125. doi: 10.1016/j.aquaculture.2016.10.004.
Ma, H., Weber, G.M., Gao, G., Wei, H., Yao, J. 2016. Identification of mitochondrial genome-encoded small RNAs related to egg deterioration caused by postovulatory aging in rainbow trout. Marine Biotechnology. 18(5):584-597. doi:10.1007/s10126-016-9719-3.
