A High-density Genetic Linkage Map and QTL Mapping for Growth and Sex of Yellow Drum (Nibea Albiflora)

Overview

Journal Sci Rep

Specialty Science

Date 2018 Nov 24

PMID 30467365

Citations 17

Authors

Changliang Qiu

Zhaofang Han

Wanbo Li

Kun Ye

Yangjie Xie

Zhiyong Wang

Affiliations

Soon will be listed here.

Abstract

A high-density genetic linkage map is essential for the studies of comparative genomics and gene mapping, and can facilitate assembly of reference genome. Herein, we constructed a high-density genetic linkage map with 8,094 SNPs selected from 113 sequenced fish of a F1 family. Ultimately, the consensus map spanned 3818.24 cM and covered nearly the whole genome (99.4%) with a resolution of 0.47 cM. 1,457 scaffolds spanning 435.15 Mb were anchored onto 24 linkage groups, accounting for 80.7% of the draft genome assembly of the yellow drum. Comparative genomic analyses with medaka and zebrafish genomes showed superb chromosome-scale synteny between yellow drum and medaka. QTL mapping and association analysis congruously revealed 22 QTLs for growth-related traits and 13 QTLs for sex dimorphism. Some important candidate genes such as PLA2G4A, BRINP3 and P2RY1 were identified from these growth-related QTL regions. A gene family including DMRT1, DMRT2 and DMRT3 was identified from these sex-related QTL regions on the linkage group LG9. We demonstrate that this linkage map can facilitate the ongoing marker-assisted selection and genomic and genetic studies for yellow drum.

Citing Articles

QTL Mapping-Based Identification of Visceral White-Nodules Disease Resistance Genes in .

Li Q, Zhu J, Liu S, Liu H, Zhang T, Ye T Int J Mol Sci. 2024; 25(20).

PMID: 39456653 PMC: 11507142. DOI: 10.3390/ijms252010872.

Construction of a high-density genetic map and QTL localization of body weight and wool production related traits in Alpine Merino sheep based on WGR.

Zhang W, Lu Z, Guo T, Yuan C, Liu J BMC Genomics. 2024; 25(1):641.

PMID: 38937677 PMC: 11212225. DOI: 10.1186/s12864-024-10535-4.

Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in Takifugu fasciatus.

Zhang Y, Li J, Chu P, Shang R, Yin S, Wang T BMC Genomics. 2023; 24(1):645.

PMID: 37891474 PMC: 10604518. DOI: 10.1186/s12864-023-09740-4.

Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome.

Zhu C, Liu H, Pan Z, Cheng L, Sun Y, Wang H DNA Res. 2022; 29(4).

PMID: 35861402 PMC: 9358014. DOI: 10.1093/dnares/dsac028.

DMRT2 Interacts With FXR and Improves Insulin Resistance in Adipocytes and a Mouse Model.

Tao J, Yu X, Yuan Y, Shen X, Liu J, Gu P Front Endocrinol (Lausanne). 2022; 12:723623.

PMID: 35250844 PMC: 8891600. DOI: 10.3389/fendo.2021.723623.

References

Shirak A, Seroussi E, Cnaani A, Howe A, Domokhovsky R, Zilberman N . Amh and Dmrta2 genes map to tilapia (Oreochromis spp.) linkage group 23 within quantitative trait locus regions for sex determination. Genetics. 2006; 174(3):1573-81. PMC: 1667067. DOI: 10.1534/genetics.106.059030. View

Johnston S, Berenos C, Slate J, Pemberton J . Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep (Ovis aries). Genetics. 2016; 203(1):583-98. PMC: 4858801. DOI: 10.1534/genetics.115.185553. View

Young W, Wheeler P, Coryell V, Keim P, Thorgaard G . A detailed linkage map of rainbow trout produced using doubled haploids. Genetics. 1998; 148(2):839-50. PMC: 1459819. DOI: 10.1093/genetics/148.2.839. View

Fu B, Liu H, Yu X, Tong J . A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis). Sci Rep. 2016; 6:28679. PMC: 4921863. DOI: 10.1038/srep28679. View

RAYMOND C, Murphy M, OSullivan M, Bardwell V, Zarkower D . Dmrt1, a gene related to worm and fly sexual regulators, is required for mammalian testis differentiation. Genes Dev. 2000; 14(20):2587-95. PMC: 316999. DOI: 10.1101/gad.834100. View

Tian M, Li Y, Jing J, Mu C, Du H, Dou J . Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus. Sci Rep. 2015; 5:14852. PMC: 4594301. DOI: 10.1038/srep14852. View

Crawford A, Dodds K, Ede A, Pierson C, Montgomery G, Garmonsway H . An autosomal genetic linkage map of the sheep genome. Genetics. 1995; 140(2):703-24. PMC: 1206646. DOI: 10.1093/genetics/140.2.703. View

Cheng Y, Xu T, Jin X, Wang R . Complete mitochondrial genome of the yellow drum Nibea albiflora (Perciformes, Sciaenidae). Mitochondrial DNA. 2011; 22(4):80-2. DOI: 10.3109/19401736.2011.624602. View

Hong C, Park B, Saint-Jeannet J . The function of Dmrt genes in vertebrate development: it is not just about sex. Dev Biol. 2007; 310(1):1-9. DOI: 10.1016/j.ydbio.2007.07.035. View

10.

Hedgecock D, Shin G, Gracey A, van den Berg D, Samanta M . Second-Generation Linkage Maps for the Pacific Oyster Crassostrea gigas Reveal Errors in Assembly of Genome Scaffolds. G3 (Bethesda). 2015; 5(10):2007-19. PMC: 4592983. DOI: 10.1534/g3.115.019570. View

11.

Xia J, Liu F, Zhu Z, Fu J, Feng J, Li J . A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs. BMC Genomics. 2010; 11:135. PMC: 2838847. DOI: 10.1186/1471-2164-11-135. View

12.

RAYMOND C, Kettlewell J, Hirsch B, Bardwell V, Zarkower D . Expression of Dmrt1 in the genital ridge of mouse and chicken embryos suggests a role in vertebrate sexual development. Dev Biol. 1999; 215(2):208-20. DOI: 10.1006/dbio.1999.9461. View

13.

Han Z, Xiao S, Li W, Ye K, Wang Z . The identification of growth, immune related genes and marker discovery through transcriptome in the yellow drum (Nibea albiflora). Genes Genomics. 2018; 40(8):881-891. DOI: 10.1007/s13258-018-0697-x. View

14.

Houston R, Davey J, Bishop S, Lowe N, Mota-Velasco J, Hamilton A . Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon. BMC Genomics. 2012; 13:244. PMC: 3520118. DOI: 10.1186/1471-2164-13-244. View

15.

Rastas P, Calboli F, Guo B, Shikano T, Merila J . Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example. Genome Biol Evol. 2015; 8(1):78-93. PMC: 4758246. DOI: 10.1093/gbe/evv250. View

16.

Jones M, Blahna M, Kozlowski E, Matsuura K, Ferrari J, Morris S . Zcchc11 uridylates mature miRNAs to enhance neonatal IGF-1 expression, growth, and survival. PLoS Genet. 2012; 8(11):e1003105. PMC: 3510031. DOI: 10.1371/journal.pgen.1003105. View

17.

Broman K, Murray J, Sheffield V, White R, Weber J . Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am J Hum Genet. 1998; 63(3):861-9. PMC: 1377399. DOI: 10.1086/302011. View

18.

Kopp A . Dmrt genes in the development and evolution of sexual dimorphism. Trends Genet. 2012; 28(4):175-84. PMC: 3350790. DOI: 10.1016/j.tig.2012.02.002. View

19.

Wu S, Yang J, Huang Y, Li Y, Yin T, Wullschleger S . An improved approach for mapping quantitative trait Loci in a pseudo-testcross: revisiting a poplar mapping study. Bioinform Biol Insights. 2010; 4:1-8. PMC: 2832300. DOI: 10.4137/bbi.s4153. View

20.

Moen T, Hayes B, Baranski M, Berg P, Kjoglum S, Koop B . A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics. 2008; 9:223. PMC: 2405805. DOI: 10.1186/1471-2164-9-223. View