Development of SNP parentage assignment techniques in the yellowfin seabream Acanthopagrus latus

Abstract

Acanthopagrus latus is an essential aquaculture species on the south coast of China. However, there is a lack of systematic breeding of A. latus, which considerably limits the sustainable development of A. latus. As a result, genetic improvements are urgently needed to breed new strains of A. latus with rapid growth and strong resistance to disease. During selective breeding, it is necessary to estimate the genetic parameters of the target trait, which in turn depends on an accurate disentangled pedigree for the selective population. Therefore, it is necessary to establish the parentage assignment technique for A. latus. In this study, 95 individuals selected from their parents and their 14 families were used as experimental material. SNPs were developed by genome re-sequencing, and highly polymorphic SNPs were screened on the basis of optimized filtering parameters. A total of 14 392 738 SNPs were discovered and 205 SNPs were selected for parentage assignment using the CERVUS software. In the model where the gender of the parents is known, the assignment success rate is 98.61% for the male parent, 97.22% for the female parent, and 95.83% for the parent pair. In the model where the gender of the parents is unknown, the assignment success rate is 100% for a single parent and 90.28% for the parent pair. The results of this study were expected to serve as a reference for the breeding of new varieties of A.latus.