Abstract
The bay scallop (Argopecten irradians irradians) is one of the most important shellfish species in China. Since their introduction into China, only mass selection has been used in bay scallop breeding. With its gradual expansion and shortage of mate selection, population homozygosity increased, and fitness decreased. To investigate the effects of inbreeding and provide reference for improving breeding strategies and mating management, the variance components of the growth traits of the bay scallop were decomposed with genomic relationship matrices. The results indicated that the genetic variations in shell height and length were mainly accounted for by the additive effects. The genetic variation in shell width was mainly caused by dominance or dominance-by-dominance epistasis. The genetic variation in body weight was accounted for by dominance. No significant directional dominances were detected for all growth traits. Cross-validation for genomic prediction showed that including insignificant inbreeding in the genomic prediction model is not necessary, and we suggest that the genomic prediction model should be optimized with both likelihood ratio tests and cross-validation before utilization in practice.
Highlights
China is the largest shellfish producer globally (FAO, 2018)
For shell height (Table 1), the likelihoods of models A, AD, and ADE were nearly the same, indicating that no variances of dominance and epistasis existed, and the genetic variation was mainly caused by additive effects
As for shell height, the comparison between the likelihoods of these models showed that dominance and epistatic variance components were not significant, likewise indicating that the main genetic variance was caused by additive effects
Summary
China is the largest shellfish producer globally (FAO, 2018). The bay scallop (Argopecten irradians irradians) was introduced into China from North America in 1982 (Zhang et al, 1986). Mass selection began to be utilized in bay scallop breeding, and the growth traits of the scallops were genetically improved (Zheng et al, 2004; Wang et al, 2020). The expansion of bay scallop aquaculture and shortage of mate selection has led to its remarkable decrease in survival rate in hatcheries in the last decade. This is thought to be a result of consecutive generations of inbreeding (Zheng et al, 2007, 2012), which increased the homozygosity of the population and decreased the fitness and trait values of this species (Charlesworth and Charlesworth, 1987). Inbreeding increased the segregation distortion of genetic markers (Wang et al, 2012)
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