Development of genomic predictions for harvest and carcass weight in channel catfish

Authors: GARCIA, ANDRE - University Of Georgia; Bosworth, Brian; Waldbieser, Geoffrey - Geoff; TSURUTA, SHOGO - University Of Georgia; MISZTAL, IGNACY - University Of Georgia; LOURENCO, DANIELA - University Of Georgia

Submitted to: Genetics Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/29/2018
Publication Date: 12/14/2018
Citation: Garcia, A., Bosworth, B.G., Waldbieser, G.C., Tsuruta, S., Misztal, I., Lourenco, D. 2018. Development of genomic predictions for harvest and carcass weight in channel catfish. Genetics Selection Evolution. 50:66.

Interpretive Summary: Catfish farming is the largest segment of US aquaculture and research is being conducted to improve production efficiency, including genetic selection to improve important traits of catfish. The breeding program at the Warmwater Aquaculture Research Unit, USDA-ARS, is focused on developing catfish with faster growth and higher carcass yield (the amount of edible meat) with the goal of releasing genetically improved catfish to U.S. farmers. Genetic selection works by choosing genetically better animals as parents that will produce genetically better, superior performing offspring. Parents are selected based on estimates of their genetic merit for targeted traits. Traditionally, genetic merit was estimated based on an animal’s performance and the performance of related individuals in the population. In this research scientists used a relatively new approach, referred to as genomic selection to improve the accuracy of genetic merit estimates for growth rate and carcass yield of catfish. Genomic selection uses DNA marker information to more accurately estimate genetic merit and was shown in this study to improve the accuracy of genetic merit estimates for growth rate and carcass yield of catfish by about 30%. This research will result in more rapid development of catfish with improved growth and carcass yield, and release of superior performing catfish to U.S. farmers will benefit catfish producers, processors and consumers.

Technical Abstract: Catfish farming is the largest segment of US aquaculture and research is being conducted to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives of this study were to investigate use of genomic selection to improve breeding value accuracy and to identify major SNP associated with harvest weight and residual carcass weight in a channel catfish population. Phenotypes were available for harvest weight (n=27,160) and residual carcass weight (n=6,020), and the number of pedigree records was 36,365. After quality control, genotypes on 54,837 SNPs were available for 2,911 fish. Estimated breeding values (EBV) were estimated with traditional pedigree based BLUP and genomic estimated breeding values (GEBV) were estimated with single-step genomic BLUP (ssGBLUP). EBV and GEBV prediction accuracies were evaluated using different validation strategies. The ability to predict future performance was calculated as the correlation between EBV or GEBV and adjusted phenotypes. Compared to the pedigree BLUP, ssGBLUP increased predictive ability up to 28% and 36% for harvest weight and residual carcass weight, respectively; and GEBV were superior to EBV for all validation strategies tested. Breeding value inflation was assessed as the regression coefficient of adjusted phenotypes on breeding values, and results indicated genomic information reduced breeding value inflation. Genome wide association studies based on 20 SNP windows indicated both harvest weight and residual carcass weight have a polygenic architecture with no major SNP (largest SNP explained 1.4 and 1.2% of variation for harvest weight and residual carcass weight respectively). Genomic evaluation has improved ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families.