Genome-Wide Association Study Identifies Genomic Loci Of Sex Determination And Reproductive Trait In Larimichthys Crocea And Takifugu Bimaculatus

Larimichthys crocea is one of the traditional marculture fishes in China,widely distributed in South China Sea,East Sea,and southern Yellow Sea.Sex dimorphism is evident in this species that females present a substantial growth strength than males,suggesting breeding an all-female population could obtain more economic benefits in L.crocea aquaculture industry.Takifugu bimaculatus shows a great tolerance to high temperature,which makes it the main culturing fugu species in southern China.Its consumption market and production module are still immature due to previous constraints of national policies,indicating remarkable development potential it owns.The testis of pufferfish is non-toxic and contains valuable nutrients.Breeding male individuals helps to provide high-quality high-end aquatic products for consumers and enhance the industrial value of pufferfish.However,there is little gender difference in appearance and no heteromorphic sex chromosome has been found by karyotype analysis in L.crocea or T.bismaculatus.In this study,we performed association mapping in L.crocea and T.culatus at the genome-wide scale,aiming to develop the sex-linked molecular sites and provide solid genetic research support for molecular marker-assisted selection and exploration of the financial value of farmed fish.The main results are as below:1.Genome-wide association analysis(GWAS)of sex was conducted among 905 individuals from a random breeding population,with variants collected by double digestion restriction-site association DNA(ddRAD)sequencing.21 significant single nucleotide polymorphisms(SNP)in chromosome(Chr)22 were identified and the sexassociated region was narrowed down further to 2.4 Mb through fixation index(Fst)scanning.Surrounding these SNPs,we founded several candidate genes,including dmrtl,fam102a and odf2.These genes are involved in spermatogenesis,testis development and sex hormone metabolism.2.3 SNPs in the supposed sex-determining region on Chr22 were identified as highly associated with gonad differentiation through GWAS on gonadosomatic index(GSI)in 350 males and 231 females.Besides,GWAS on male GSI identified an SNP on Chr18 showing genome-wide significant association and three genes axl,cyp2a10 and cyp2g1 involved in spermatogenesis and hormone synthesis.3.Based on the resequencing data of 71 T.bismaculatus from a full-sib family,we conducted a genome-wide association analysis and Fst scanning.As a result,a 12.4Mb region on Chr7 displayed great gender difference in the genome sequence.Combined with linkage disequilibrium analysis,we locked a 1.4Mb highly associated region as the sex-determining region of T.bismaculatus.After comparing the male and female genome sincerely,we screened and characterized a sex-linked SNP marker for identification of the genetic sex in this family.