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

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 resequencing,and highly polymorphic SNPs were screened on the basis of optimized filtering parameters.A total of 14392738 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.

Multiplex PCR Sets of Novel Microsatellite Loci for Iwagaki Oyster Crassostrea nippona and Their Application in Parentage Assignment

Iwagaki oyster,Crassostrea nippona,widely distributes along the seashore of Eastern Asia,and has been considered to be a potential breeding species due to its delicious taste and high commercial value.In order to study its genetic background and population structure,we developed 46 novel polymorphic microsatellite markers using next-generation sequencing technique and characterized them in 30 individuals.The number of alleles ranged from 3 to 22,while the observed and expected heterozygosities varied from 0.133 to 1.000 and 0.455 to 0.949,respectively.Fifteen microsatellite markers were selected and grouped into five highly informative multiplex PCRs for C.nippona.We evaluated and validated these multiplex PCRs in a cultured population including 173 candidate parents and 486 offspring.In actual parentage analysis,80%of the offspring were correctly assigned to their parental pairs using three multiplex PCRs.Furthermore,the success rate of parentage assignment reached 96%when the other two multiplex PCRs were added.These 46 microsatellite loci with high variability and the five multiplex PCRs described here provide a powerful tool for pedigree reconstruction,resource conservation and selective breeding program of C.nippona.

Reducing the Common Environmental Effect on Litopenaeus vannamei Body Weight by Rearing Communally at Early Developmental Stages and Using a Reconstructed Pedigree

Heritability estimates may be severely biased when a large common environmental effect on a family arises from a longlasting separate rearing at early stages(SRES)in traditional selective breeding programs,especially when bred populations have weak genetic ties.Communal rearing at early stages(CRES)may reduce common environmental effect since all families are reared in the same environment immediately after hatching.Here,we compared the effects of CRES and SRES strategies on genetic parameter estimation for harvest body weight in a selective breeding population of Litopenaeus vannamei with a small number of half-sib families.Genetic parameters of each strategy were estimated by using animal models excluding and including the common environmental effect(Model 1 and Model 2,respectively).Heritability estimates for body weight were 0.21±0.06(P<0.05)and 0.69±0.09(P<0.05)for CRES and SRES,respectively,in Model 1,and 0.21±0.06(P<0.05)and 0.52±0.27(P>0.05)in Model 2.The ratio of common environmental variance to phenotypic variance was 0.002±0.000 and 0.071±0.112 for CRES and SRES,respectively.Neither strategy precisely partitioned the common environmental variance according to likelihood ratio test.Lower heritability for body weight in CRES than in SRES implied that a large common environmental variance was confounded with additive genetic variance and was not effectively partitioned in SRES.Moreover,genetic correlation of body weight between the two strategies was 0.75±0.15,indicating that family rankings truly changed.The CRES should be followed in the selective breeding program of shrimp,especially in a population with a shallow pedigree and weak genetic ties between families.