Detecting Deleterious Recessive Variants in Large Yellow Croaker Using Data from 7337 Individuals

In diploid organisms, deleterious recessive alleles represent a significant component of genetic mutations and often result in lethal effects when in a homozygous state. Large yellow croaker (Larimichthys crocea), a critical marine aquaculture species in China, has shown signs of inbreeding depression due to its limited natural distribution along the coasts of Fujian, Guangdong, and Zhejiang provinces, combined with intensive artificial propagation practices. Identifying loci with deleterious recessive homozygous genotypes is therefore crucial for sustainable industry development. In this study, 1844 large yellow croaker across three consecutive generations were analyzed, resulting in the preliminary identification of 131 loci with missing recessive homozygous genotypes. After excluding false positives through parentage analysis, large-scale validation was conducted using genotype data from 4663 individuals from the MinDong population and 830 individuals from the Daqu population. Ultimately, 22 loci with complete absence of homozygous recessive genotypes were identified across 7337 individuals. The average minor allele frequency (MAF) of these loci was 0.16. Except for LG17_2296176 and LG17_4414232, which exhibited moderate linkage disequilibrium, the remaining 20 loci were largely independent with no observed linkage disequilibrium. Annotation of the 22 loci identified 12 associated genes, including vegfa, sntg2, tcf7, kif2a, lage3, ano10, mpdu1, and others. These genes are involved in key biological processes such as signal transduction regulation, cytoskeletal organization, neural function, and glycan synthesis. To further verify the reliability of the loci with missing recessive homozygous genotypes, heterozygous parental fish carrying 6 randomly selected loci were paired to establish independent families. None of the offspring exhibited recessive homozygous genotypes at these loci, supporting the accuracy of the prior identification. By analyzing genotype data from large yellow croaker populations, this study identifies key loci with missing recessive homozygous genotypes. These findings may offer guidance for selective breeding strategies aimed at minimizing lethal mutations, thereby enhancing population fitness and supporting the sustainable development of the aquaculture industry.