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Estimating breeding values for juvenile body weight using trait associated SNP assisted BLUP in turbot (Scophthalmus maximus)

Lyu, Ding, Hu, Yulong, Wu, Huanhuan, Sun, Song, Wang, Weiji
Aquaculture 2019
Scophthalmus maximus, body weight, breeding value, economic valuation, genotype, genotyping, juveniles, least squares, linear models, mariculture, marker-assisted selection, quantitative trait loci, single nucleotide polymorphism, t-test, turbot
Turbot is an important marine aquaculture species with great economic value. Marker-assisted selection is an attractive breeding technique to improve economic traits in turbot. The objective of this study was 1) to validate SNPs associated with juvenile turbot body weight (BW) on a population scale and 2) to evaluate the performance of a marker-assisted BLUP (MA-BLUP) method to estimate breeding values for BW. Based on a previous study, four SNPs associated to candidate QTLs for juvenile BW were genotyped in a breeding population consisting of 926 individuals from 40 full-sib families. General linear models (GLM) and mixed linear models (MLM) were applied to identify associations between SNPs and juvenile BW. Individual breeding values were estimated by MA-BLUP based on associated SNP and traditional BLUP. Thereafter, we compared the accuracy of both estimators by cross validation. Both GLM and MLM obtained similar results, with SNP105 showing significant effect on juvenile BW. Least squares mean of genotypes AA, GA and GG at SNP105 were 10.635 ± 0.454 g, 9.953 ± 0.449 g and 9.897 ± 0.497 g, respectively. Cross validation revealed that the accuracy of estimated breeding values was 0.573 with MA-BLUP and 0.565 with traditional BLUP, and t-test suggested that the accuracy of both methods differed significantly (P < .001), which indicated that accuracy of estimators based on MA-BLUP was better than traditional method. The results suggested MA-BLUP was a feasible approach to apply trait associated markers in turbot breeding.