Genetic Evaluation Of Germplasm And Selection Breeding Of Growth Traits In Rock Bream Based On Genomic Information

Rock Bream(Oplegnathus fasciatus),belonging to the Oplegnathidae family and Oplegnathus genus,is a subtropical carnivorous teleost,which mainly distributed in China,South Korea and Japan,and was one of the most economically important marine fish in East Asia.Due to its beautiful appearance and high nutritional value,it had a huge potential market demand.With farming techniques improving and aquaculture structures optimizing,this marine species had become an excellent candidate for intensive aquaculture.At present,the artificial breeding of O.fasciatus was still in infancy,and the in-depth genetic research work was still very scarce.Based on the above background,this paper constructed the genome assembly of the female O.fasciatus,and identified genomic regions selected during the artificial domestication process through population genetic analysis between wild population and cultured population.The loci associated with growth traits were examined and the potential of genomic selection to improve growth traits was further assessed.In addition,O.fasciatus exhibits sexual dimorphism in growth performance,in which males growed faster than females.Lack of rapid and cost-effective sex molecular markers hindered research on the mechanisms of sex determination and applications in breeding.In this paper,the sex-determining regions of O.fasciatus were identified by genome resequencing,and the molecular markers were developed.The main findings were as follows:(1)Assembly and annotation of O.fasciatus genomeThe chromosome-level reference genome of female O.fasciatus was constructed by the Illumina,PacBio and Hi-C technologies.The genome was assembled into 120 contigs with a total length of 732.95 Mb and N50 length of 27.33 Mb.After chromosome-level scaffolding,24 chromosomes with a total length of 723.22 Mb were constructed.Moreover,a total of 27,015 protein-coding genes and 5,880 ncRNAs were annotated in the reference genome.This reference genome of O.fasciatus will provide an important resource not only for basic ecological and population genetic studies,but also for dissect artificial selection mechanisms in marine aquaculture.(2)Identification genomic signatures of artificial domestication in O.fasciatusThe samples of O.fasciatus in this study were obtained from six wild populations in different geographical locations along the coast of China,and one cultured population collected from Ningde,Fujian.Based on the analysis of whole-genome resequencing data,there was not obvious genetic differentiation and genetic structure among six wild geographic populations of O.fasciatus in three sea areas.However,there was a large genetic differentiation between domesticated population and wild population,which the genetic diversity of domesticated population is lower than that of wild population.Although recent domestication conditions had not caused significant phenotypic variation in cultured populations of O.fasciatus,the selection process has left important signals in the genomes.Three genome scanning methods including fixation index(Fst),the ratio of nucleotide polymorphism(Pi),and minor allele frequency(Maf)were utilized to detect the selected genome regions in domesticated populations where genes present in these regions may be associated with behavior,memory,growth,and immune responses.Overall,these results contributed to the detection of variations that may underlie important traits of practical interest for aquaculture and to fully understanding the early patterns and effect of domestication in O.fasciatus.(3)Genetic analysis of growth traits in O.fasciatusIn this study,28,700 SNPs and 455 samples of O.fasciatus were adopted to carry out genome-wide association studies(GWAS)to dissect the genetic architecture of growth-related traits(body weight,total length,body length,body depth and body thickness).25 genome-wide significant SNPs were identified to be associated with different growth-related traits by four GWAS methods.Surrounding these SNPs,17 growth-related candidate genes including GDF10,GDF6,BMP5 and RSPO2 were identified.The results of GWAS also showed a polygenic architecture for these growth traits,which indicated that the implementation of genomic selection instead of MAS is necessary in the present rock bream population.(4)Genomic selection for growth traits in O.fasciatusThe purposes of the study were to explore the performance of genomic selection based on GBLUP and five statistic Bayesian models in the O.fasciatus population.Six statistic models showed similar performance for the predictability of genomic estimated breeding value(GEBV).Heritabilities were estimated to be moderate for the five growth traits.The low SNP density(around 1 K selected SNPs based on GWAS)was sufficient for accurate prediction on the breeding value for the five growth-related traits in the current studied population,which will provide a good compromise between genotyping costs and predictability.By evaluating the calculation time for each method,the efficiency of GBLUP method was significantly better than Bayesian methods.These consequences illustrate that the employment of genomic selection in O.fasciatus breeding could provide advantages for the selection of breeding candidates to facilitate complex economic growth traits.(5)Sex-specific genomic region identifcation and molecular sex marker developmentSex-specifc genomic regions/loci for sex determination were discovered on Chr2 and Chr6 by genome-wide association analysis,sequencing depth,and heterozygosity comparison between females and males O.fasciatus.Candidate sex-determining genes(CCDC63,ITR,WNT4)were furtherly detected in transcriptome data of testes and ovaries.Taken together,a male-specifc 34-bp deletion on the Chr2 was identifed and developed into sex molecular marker based on PCR method for rapid accurately and cost-efcient genetic sex identifcation in this species,which is of great practical signifcance for sex control breeding strategies in O.fasciatus.