| Large yellow croaker(Larimichthys crocea)is an important representative fish of the family Sciaenidae,Perciformes,and Larimichthys.It was one of the most important fishing objects in the southeastern coastal area of China,and once ranked as the "flagship species" of fishery resources in the east China sea.However,the extensive and rapid development of the large yellow croaker aquaculture industry has accumulated a large number of bottlenecks restricting the healthy development of the industry,such as the depletion of wild yellow croaker resources,lack of germplasm resources,attenuation of genetic diversity of aquaculture population,degeneration of germplasm.High aquaculture density and large proportion of feed for chilled hybrid fish lead to deterioration of water quality and frequent occurrence of diseases in aquaculture waters,which greatly restrict the sustainable development of the yellow croaker industry.Among various diseases,"white spot disease" caused by Cryptocaryon irritans is the most threatening disease to the breeding industry of large yellow croakers in Fujian,causing significant economic losses every year.The sustainable development of the large yellow croaker aquaculture largely relies germplasm innovation and disease resistance breeding.In addition,due to the degradation of germplasm resources,the body shape of large yellow croaker also changed greatly.Compared with the slender and fusiform body shape of the wild population,the breeding population tends to be stout.Body shape is an important economic trait for this species,because consumers prefer to purchase fish that have a slender shape.Therefore,it has seriously affected the economic benefits of the large yellow croaker industry.Furthermore,investigating the genetic basis of this trait may be useful for understanding the evolution of fish body shape in general.We will employ the genomic resources and genetic tools of large yellow croaker,and perform precise pest resistance phenotype,phenotype data measurement of basal growth somatotype,genome-wide association analysis,quantitative trait loci analysis to identify the genomic loci and genes which are closely linked to the resistant traits and body shape traits.Our study provides theoretical support and working basis for genome-wide marker assisted breeding of disease resistance and body shape traits in large yellow croaker.1 Constructing a high-density genetic linkage map for large yellow croaker(Larimichthys crocea)and mapping resistance trait against ciliate parasite Cryptocaryon irritansFor better understanding the genetic basis of parasite infection and disease resistance to C.irritans,it's vital to map the traits and localize the underlying candidate genes in L.crocea genome.Linkage map construction and quantitative trait loci(QTL)mapping have been widely and successfully used for complex traits localization in the genomes and subsequently applying for molecular assistant breeding in economically important species.Therefore,we constructed a high-density genetic linkage map using ddRAD-based high throughput SNP genotyping data of a F1 mapping family of L.crocea,which had been challenged with C.irritans for resistant trait measure.A total of 5,261 SNPs was grouped and oriented into 24 LGs,representing 24 chromosomes of L.crocea.The total genetic map length was 1885.67 cM with an average inter-locus distance of 0.36 cM.Both QTL mapping and genome association analysis consistently identified 7 significant QTLs in 4 LGs linked to C.irritans disease resistance.Candidate genes underlying disease resistance were identified from the reference genome,including interferon alpha/beta receptor 1a(ifnar1),interferon gamma receptor 2 precursor(ifngr2),inhibitor of nuclear factor kappa-B kinase subunit epsilon(ikbke)and nectin-2(CD112).Comparative genomic analysis between large yellow croaker and the four closely related species revealed high evolutionary conservation of chromosomes,though inter-chromosomal rearrangements do exist.Especially,the croaker genome structure was closer to medaka genome than stickleback,indicating that the croaker genome might retain the teleost ancestral genome structure.The high-density genetic linkage map provides an important tool and resource for fine mapping,comparative genome analysis and molecular selective breeding of large yellow croaker.2 Genome-wide association study of body shape related traits in large yellow croaker(Larimichthys crocea)Body shape is an important economic trait for L.crocea,which playing a significant role in swimming,ingesting and avoiding predators.Moreover,due to the market preference of slender L.crocea,body shape has seriously impacted the economic benefits of the breeding industry.Thus,it's vital to understand the genetic basis of body shape differentiation.Here,a total of 281 individuals from multiple families were genotyped using double-digest restriction-site associated DNA(ddRAD)strategies and retained 51928 SNPs after quality control.We then performed genome-wide association study to identify SNP and genes potentially associated with body shape related traits including head length/body length ratio(HBR),body thickness/body length ratio(TLR),caudal peduncle depth/caudal peduncle length ratio(CPLHR),body mass index(BMI),body length/body height ratio(LHR),and body height/body thickness ratio(HTR).Twenty-seven SNPs on 11 LGs were identified to be significantly associated with body shape traits in GWAS.Candidate genes underlying body shape traits were identified surrounding the significant SNPs,including start5,apt2,igfbps,ac1,which identified with potential functions on lipid metabolism,energy metabolism,bone and other important regulatory pathways.Our results may provide insights into the genetic basis of body shape evolution and facilitate the molecular marker-assisted selection design of slender population large yellow croaker. |
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