Tags

Type your tag names separated by a space and hit enter

A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer.
BMC Genomics. 2011 Apr 02; 12:174.BG

Abstract

BACKGROUND

High density linkage maps are essential for comparative analysis of synteny, fine mapping of quantitative trait loci (QTL), searching for candidate genes and facilitating genome sequence assembly. However, in most foodfish species, marker density is still low. We previously reported a first generation linkage map with 240 DNA markers and its application to preliminarily map QTL for growth traits in Asian seabass (Lates calcarifer). Here, we report a high-resolution linkage map with 790 microsatellites and SNPs, comparative analysis of synteny, fine-mapping of QTL and the identification of potential candidate genes for growth traits.

RESULTS

A second generation linkage map of Asian seabass was developed with 790 microsatellite and SNP markers. The map spanned a genetic length of 2411.5 cM, with an average intermarker distance of 3.4 cM or 1.1 Mb. This high density map allowed for comparison of the map with Tetraodon nigroviridis genome, which revealed 16 synteny regions between the two species. Moreover, by employing this map we refined QTL to regions of 1.4 and 0.2 cM (or 400 and 50 kb) in linkage groups 2 and 3 in a population containing 380 progeny; potential candidate genes for growth traits in QTL regions were further identified using comparative genome analysis, whose effects on growth traits were investigated. Interestingly, a QTL cluster at Lca371 underlying growth traits of Asian seabass showed similarity to the cathepsin D gene of human, which is related to cancer and Alzheimer's disease.

CONCLUSIONS

We constructed a high resolution linkage map, carried out comparative mapping, refined the positions of QTL, identified candidate genes for growth traits and analyzed their effects on growth. Our study developed a framework that will be indispensable for further identification of genes and analysis of molecular variation within the refined QTL to enhance understanding of the molecular basis of growth and speed up genetic improvement of growth performance, and it also provides critical resource for future genome sequence assembly and comparative genomics studies on the evolution of fish genomes.

Authors+Show Affiliations

Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

21457569

Citation

Wang, Chun Ming, et al. "A High-resolution Linkage Map for Comparative Genome Analysis and QTL Fine Mapping in Asian Seabass, Lates Calcarifer." BMC Genomics, vol. 12, 2011, p. 174.
Wang CM, Bai ZY, He XP, et al. A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer. BMC Genomics. 2011;12:174.
Wang, C. M., Bai, Z. Y., He, X. P., Lin, G., Xia, J. H., Sun, F., Lo, L. C., Feng, F., Zhu, Z. Y., & Yue, G. H. (2011). A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer. BMC Genomics, 12, 174. https://doi.org/10.1186/1471-2164-12-174
Wang CM, et al. A High-resolution Linkage Map for Comparative Genome Analysis and QTL Fine Mapping in Asian Seabass, Lates Calcarifer. BMC Genomics. 2011 Apr 2;12:174. PubMed PMID: 21457569.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer. AU - Wang,Chun Ming, AU - Bai,Zhi Yi, AU - He,Xiao Ping, AU - Lin,Grace, AU - Xia,Jun Hong, AU - Sun,Fei, AU - Lo,Loong Chueng, AU - Feng,Felicia, AU - Zhu,Ze Yuan, AU - Yue,Gen Hua, Y1 - 2011/04/02/ PY - 2010/12/15/received PY - 2011/04/02/accepted PY - 2011/4/5/entrez PY - 2011/4/5/pubmed PY - 2011/8/24/medline SP - 174 EP - 174 JF - BMC genomics JO - BMC Genomics VL - 12 N2 - BACKGROUND: High density linkage maps are essential for comparative analysis of synteny, fine mapping of quantitative trait loci (QTL), searching for candidate genes and facilitating genome sequence assembly. However, in most foodfish species, marker density is still low. We previously reported a first generation linkage map with 240 DNA markers and its application to preliminarily map QTL for growth traits in Asian seabass (Lates calcarifer). Here, we report a high-resolution linkage map with 790 microsatellites and SNPs, comparative analysis of synteny, fine-mapping of QTL and the identification of potential candidate genes for growth traits. RESULTS: A second generation linkage map of Asian seabass was developed with 790 microsatellite and SNP markers. The map spanned a genetic length of 2411.5 cM, with an average intermarker distance of 3.4 cM or 1.1 Mb. This high density map allowed for comparison of the map with Tetraodon nigroviridis genome, which revealed 16 synteny regions between the two species. Moreover, by employing this map we refined QTL to regions of 1.4 and 0.2 cM (or 400 and 50 kb) in linkage groups 2 and 3 in a population containing 380 progeny; potential candidate genes for growth traits in QTL regions were further identified using comparative genome analysis, whose effects on growth traits were investigated. Interestingly, a QTL cluster at Lca371 underlying growth traits of Asian seabass showed similarity to the cathepsin D gene of human, which is related to cancer and Alzheimer's disease. CONCLUSIONS: We constructed a high resolution linkage map, carried out comparative mapping, refined the positions of QTL, identified candidate genes for growth traits and analyzed their effects on growth. Our study developed a framework that will be indispensable for further identification of genes and analysis of molecular variation within the refined QTL to enhance understanding of the molecular basis of growth and speed up genetic improvement of growth performance, and it also provides critical resource for future genome sequence assembly and comparative genomics studies on the evolution of fish genomes. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/21457569/A_high_resolution_linkage_map_for_comparative_genome_analysis_and_QTL_fine_mapping_in_Asian_seabass_Lates_calcarifer_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-174 DB - PRIME DP - Unbound Medicine ER -