Genetic evaluation of feed efficiency in the breeding population of Fenneropenaeus chinensis “Huanghai No. 2” using phenotypic, pedigree and genomic information

Abstract

Genetic evaluation of feed efficiency for Fenneropenaeus chinensis was implemented in the breeding population of “Huanghai No. 2” using phenotypic, pedigree and genomic information via a single-step genomic best linear unbiased prediction method (ssGBLUP). Feed efficiency ratio (FER) and average daily gain (ADG) were recorded individually during the grow-out period in 51 full-sib families from the breeding population. High level of inter-individual variation (0.055–0.593) existed in FER. Marginal means of families for FER (0.115–0.388) displayed large inter-family variation. A total of 123 individuals in the pedigree were genotyped with 14,165 single nucleotide polymorphism (SNP) markers, which were used to construct a genomic relationship matrix. Heritability estimate of FER based on pedigree and genomic information reached a moderate level (0.259 ± 0.101), which was not significantly different from that based on only pedigree (P > 0.05). FER exhibited strong and positive genetic and phenotypic correlations (> 0.80) with ADG. ssGBLUP and the pedigree-based method were found to be consistent in predicting breeding values. No clear differences in accuracy were observed between the two methods through cross-validation. Although the heritability estimate of FER highlights the potential to implement breeding programs for feed efficiency in Huanghai No. 2, indirect selection for FER through increased growth may be a better choice considering the difficulty of measuring individual FER in shrimps.