Genomic dissection of maternal, additive and non-additive genetic effects for growth and carcass traits in Nile tilapia

Abstract

23Background: 24 The availability of both pedigree and genomic sources of information for animal 25 breeding and genetics has created new challenges in understanding how best they 26 may be utilized and how they may be interpreted. This study computed the variance 27 components obtained using genomic information and compared these to the variances 28 obtained using pedigree in a population generated to estimate non-additive genetic 29 variance. Further, the impact of assumptions concerning Hardy-Weinberg Equilibrium 30 (HWE) on the component estimates was examined. The magnitude of inbreeding 31 depression for important commercial traits in Nile tilapia was estimated for the first 32 time, here using genomic data. 33 Results 34The non-additive genetic variance in a Nile tilapia population was estimated from full- 35 sib families and, where present, was found to be almost entirely additive by additive 36 epistatic variance, although in pedigree studies this source is commonly assumed to 37 arise from dominance. For body depth (BD) and body weight at harvest (BWH), the 38 estimates of the additive by additive epistatic ratio (P<0.05) were found to be 0.15 and 39 0.17 in the current breeding population using genomic data. In addition, we found 40 maternal variance (P<0.05) for BD, BWH, body length (BL) and fillet weight (FW), 41 explaining approximately 10% of the observed phenotypic variance, which are 42 comparable to the pedigree-based estimates. This study also disclosed detrimental 43 effects of inbreeding in commercial traits of tilapia, which were estimated to cause 44 1.1%, 0.9%, 0.4% and 0.3% decrease in the trait value with 1% increase in the 45 individual homozygosity for FW, BWH, BD and BL, respectively. The inbreeding 46 3 depression and lack of dominance variance was consistent with an infinitesimal 47 dominance model 48 Conclusions: 49 An eventual utilisation of non-additive genetic effects in breeding schemes is not 50 evident or straightforward from our findings, but inbreeding depression suggests for 51 cross-breeding, although commercially this conclusion will depend on cost structures. 52 However, the creation of maternal lines in Tilapia breeding schemes may be a 53 possibility if this variation is found to be heritable. 54 55 56 non-additive genetic effects, reciprocal, heritability, inbreeding depression 57 58 4 Background 59This paper is a part of a wider study on the non-additive genetic effects in Nile tilapia 60 and their potential utilization in tilapia breeding programs. A previous study [1] used 61 the classical approach to partition the variance observed from a diallel mating design 62 into additive, non-additive and maternal components using pedigree information to 63 generate the additive and dominance relationship matrixes. These variance 64 components are inferred from the variances within and between full-sib families, where 65 the latter is also decomposed among sires and among dams. 66These pedigree based selection methods have been gradu...