A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus)
Background: A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most...
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BIOMED CENTRAL LTD
2018
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ftchinacadsciihb:oai:ir.ihb.ac.cn:342005/29603 2023-05-15T15:33:07+02:00 A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus) Feng, Xiu Yu, Xiaomu Fu, Beide Wang, Xinhua Liu, Haiyang Pang, Meixia Tong, Jingou 2018-04-02 http://ir.ihb.ac.cn/handle/342005/29603 https://doi.org/10.1186/s12864-018-4613-1 英语 eng BIOMED CENTRAL LTD BMC GENOMICS http://ir.ihb.ac.cn/handle/342005/29603 doi:10.1186/s12864-018-4613-1 Genetic map QTL mapping Growth-related traits Sex Candidate gene Cyprinus carpio Haematopterus Biotechnology & Applied Microbiology Genetics & Heredity ATLANTIC SALMON PROVIDES INSIGHTS DRAFT GENOME BODY-WEIGHT EVOLUTION LOCUS DNA FISHES CONSTRUCTION SEQUENCE 期刊论文 2018 ftchinacadsciihb https://doi.org/10.1186/s12864-018-4613-1 2019-07-12T00:03:47Z Background: A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain. Results: A high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C. c. haematopterus). The length of the map was 4586.56 cM with an average marker interval of 0.57 cM. Comparative genome mapping revealed that a high proportion (70%) of markers with disagreed chromosome location was observed between C. c. haematopterus and another common carp strain (subspecies) C. c. carpio. A clear 2:1 relationship was observed between C. c. haematopterus linkage groups (LGs) and zebrafish (Danio rerio) chromosomes. Based on the genetic map, 21 QTLs for growth-related traits were detected on 12 LGs, and contributed values of phenotypic variance explained (PVE) ranging from 16.3 to 38.6%, with LOD scores ranging from 4.02 to 11.13. A genome-wide significant QTL (LOD = 10.83) and three chromosome-wide significant QTLs (mean LOD = 4.84) for sex were mapped on LG50 and LG24, respectively. A 1.4 cM confidence interval of QTL for all growth-related traits showed conserved synteny with a 2. 06 M segment on chromosome 14 of D. rerio. Five potential candidate genes were identified by blast search in this genomic region, including a well-studied multi-functional growth related gene, Apelin. Conclusions: We mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a high-density genetic linkage map using SNP and microsatellite markers for Yangtze River common carp. Several candidate growth genes were also identified from the QTL regions by comparative mapping. This genetic map would provide a basis for genome assembly and comparative genomics studies, and those QTL-derived candidate genes and genetic markers are useful genomic resources for marker-assisted selection (MAS) of growth-related traits in the Yangtze River common carp. Report Atlantic salmon Institute of Hydrobiology, Chinese Academy of Sciences: IHB OpenIR BMC Genomics 19 1 |
institution |
Open Polar |
collection |
Institute of Hydrobiology, Chinese Academy of Sciences: IHB OpenIR |
op_collection_id |
ftchinacadsciihb |
language |
English |
topic |
Genetic map QTL mapping Growth-related traits Sex Candidate gene Cyprinus carpio Haematopterus Biotechnology & Applied Microbiology Genetics & Heredity ATLANTIC SALMON PROVIDES INSIGHTS DRAFT GENOME BODY-WEIGHT EVOLUTION LOCUS DNA FISHES CONSTRUCTION SEQUENCE |
spellingShingle |
Genetic map QTL mapping Growth-related traits Sex Candidate gene Cyprinus carpio Haematopterus Biotechnology & Applied Microbiology Genetics & Heredity ATLANTIC SALMON PROVIDES INSIGHTS DRAFT GENOME BODY-WEIGHT EVOLUTION LOCUS DNA FISHES CONSTRUCTION SEQUENCE Feng, Xiu Yu, Xiaomu Fu, Beide Wang, Xinhua Liu, Haiyang Pang, Meixia Tong, Jingou A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus) |
topic_facet |
Genetic map QTL mapping Growth-related traits Sex Candidate gene Cyprinus carpio Haematopterus Biotechnology & Applied Microbiology Genetics & Heredity ATLANTIC SALMON PROVIDES INSIGHTS DRAFT GENOME BODY-WEIGHT EVOLUTION LOCUS DNA FISHES CONSTRUCTION SEQUENCE |
description |
Background: A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain. Results: A high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C. c. haematopterus). The length of the map was 4586.56 cM with an average marker interval of 0.57 cM. Comparative genome mapping revealed that a high proportion (70%) of markers with disagreed chromosome location was observed between C. c. haematopterus and another common carp strain (subspecies) C. c. carpio. A clear 2:1 relationship was observed between C. c. haematopterus linkage groups (LGs) and zebrafish (Danio rerio) chromosomes. Based on the genetic map, 21 QTLs for growth-related traits were detected on 12 LGs, and contributed values of phenotypic variance explained (PVE) ranging from 16.3 to 38.6%, with LOD scores ranging from 4.02 to 11.13. A genome-wide significant QTL (LOD = 10.83) and three chromosome-wide significant QTLs (mean LOD = 4.84) for sex were mapped on LG50 and LG24, respectively. A 1.4 cM confidence interval of QTL for all growth-related traits showed conserved synteny with a 2. 06 M segment on chromosome 14 of D. rerio. Five potential candidate genes were identified by blast search in this genomic region, including a well-studied multi-functional growth related gene, Apelin. Conclusions: We mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a high-density genetic linkage map using SNP and microsatellite markers for Yangtze River common carp. Several candidate growth genes were also identified from the QTL regions by comparative mapping. This genetic map would provide a basis for genome assembly and comparative genomics studies, and those QTL-derived candidate genes and genetic markers are useful genomic resources for marker-assisted selection (MAS) of growth-related traits in the Yangtze River common carp. |
format |
Report |
author |
Feng, Xiu Yu, Xiaomu Fu, Beide Wang, Xinhua Liu, Haiyang Pang, Meixia Tong, Jingou |
author_facet |
Feng, Xiu Yu, Xiaomu Fu, Beide Wang, Xinhua Liu, Haiyang Pang, Meixia Tong, Jingou |
author_sort |
Feng, Xiu |
title |
A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus) |
title_short |
A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus) |
title_full |
A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus) |
title_fullStr |
A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus) |
title_full_unstemmed |
A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus) |
title_sort |
high-resolution genetic linkage map and qtl fine mapping for growth-related traits and sex in the yangtze river common carp (cyprinus carpio haematopterus) |
publisher |
BIOMED CENTRAL LTD |
publishDate |
2018 |
url |
http://ir.ihb.ac.cn/handle/342005/29603 https://doi.org/10.1186/s12864-018-4613-1 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
BMC GENOMICS http://ir.ihb.ac.cn/handle/342005/29603 doi:10.1186/s12864-018-4613-1 |
op_doi |
https://doi.org/10.1186/s12864-018-4613-1 |
container_title |
BMC Genomics |
container_volume |
19 |
container_issue |
1 |
_version_ |
1766363585690206208 |