| A genetic map with sufficient density and resolution is a critical and indispensable tool,which has been used in a wide range of genetic and genomic research,such as fine mapping of quantitative trait loci(QTL),positioning of candidate genes,marker-assisted selection(MAS),comparative analysis of genomic synteny and assembly of chromosome-level reference genomes.Yellow drum,Nibea albiflora,is an economically important marine fish species.However,very limited genetic and genomic resources about this species have been documented,and no study has performed about the genetic linkage map,which severely impeded the study of genetic breeding programs of this species.In this study,we constructed a genetic linkage map for the yellow drum with the SNP markers developed from a sequenced F1 family through whole-genome resequencing.Subsequently,with this high-density linkage map,we conducted the chromosome-level assembly of the genome reference sequences and performed the comparative genomic analyses between the yellow drum and model fishes,such as medaka and zebrafish.Finally,we located QTL loci on the linkage map and identified candidate genes in the corresponding QTL regions for growth-related traits and sex dimorphism.The main results are as follows:1.In this study,we sequenced a F1 family(2 parents and 111 offspring)through whole-genome resequencing to develop the SNP markers(the sequencing depth for male and female parent is 34.2 × and 32.8 ×,respectively;the average sequencing depth for the offspring is 6.5 ×).After filtration with stringent criterion(SNP calling rate > 95% and minor allele frequency > 5%),approximately 1.2 million SNPs were retained for further analysis.We further selected 153,722 and 158,825 SNPs,which were heterozygous only in female and male parent based on segregation and after filtering of non-Mendelian inheritance sites(P<0.01).2.In this study,we constructed the female and male sex-specific linkage map with double pseudo-testcross strategy,and the consensus map was integrated with shared markers.The consensus genetic map was comprised of 8,094 SNPs,including 3,826 female-specific markers,3,735 male-specific markers and 533 shared markers in 24 LGs with a total genetic length of 3,818.24 cM and an average marker interval of 0.47 cM.The expected map length is 3,843.02 cM,therefore,the map coverage of our consensus map is 99.4% based on the expected map length,suggesting our genetic map is close to complete.3.In this study,a total of 7,776 SNPs have been successfully mapped onto the draft genome assembly and anchored 1,457 scaffolds with total length of 435.2 Mb to our high-density linkage map,accounting for 80.7% of the genome assembly.4.In this study,we performed the comparative genomic analyses between the yellow drum and two model fishes,revealing superb chromosome-scale synteny between yellow drum and medaka and suggesting that intensive chromosome rearrangements have occurred post the divergence of zebrafish and yellow drum.5.In this study,we performed QTL mapping and association analysis of the four growth-related traits,including body weight,body length,body height and body width.In total,22 QTLs associated with growth surpassed chromosome-wide significance.Subsequently,we identified a series of candidate genes including PLA2G4 A,BRINP3 and P2RY1 in these QTLs,which might regulate the growth of yellow drum.6.In this study,we performed QTL mapping and association analysis of the sex dimorphism.As a result,QTLs for sex dimorphism were mapped on LG9,and a series of candidate genes including DMRT1,DMRT2 and DMRT3 were identified in the most significant QTL region,which might regulate the sex of yellow drum. |
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