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).
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).
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DOI：
10.1186/s12864-018-4613-1
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发表时间：
2018-04-02
期刊：
影响因子：
4.4
通讯作者：
Tong J
中科院分区：
文献类型：
--
作者：
Feng X;Yu X;Fu B;Wang X;Liu H;Pang M;Tong J
构建高密度遗传连锁图对于水产养殖物种QTL精细定位、比较基因组分析、候选基因的鉴定和经济性状的分子标记辅助选择至关重要。长江鲤鱼（Cyprinus carpio haematopterus）是我国重要的水产养殖品种之一。然而，用于经济性状遗传改良的遗传学和基因组学资源非常有限。利用7820个2b-RAD和295个微卫星标记构建了长江鲤F2家系的高分辨率遗传连锁图谱。C.血蝠属）。地图长度为4586.56 cM，平均标记间隔为0.57 cM。比较基因组图谱显示，在C. C. haematopterus和另一个鲤鱼品系（亚种）C. C. carpio。C. C.血鳍鱼连锁群（LGs）和斑马鱼（Danio rerio）染色体。在12个群体上共检测到21个与生长相关的QTL，其表型方差解释贡献率（PVE）为16.3 ~ 38.6%，LOD值为4.02 ~ 11.13。在LG 50和LG 24上分别定位了1个全基因组显著性QTL（LOD = 10.83）和3个全染色体显著性QTL（平均LOD = 4.84）。所有生长相关性状的QTL的置信区间为1.4cM，与D的第14染色体上的2.06M片段保守共线性。雷里奥。在该基因组区域中通过blast搜索鉴定出5个潜在的候选基因，包括一个已被充分研究的多功能生长相关基因Apelin。利用SNP标记和微卫星标记构建了长江鲤高密度遗传连锁图谱，定位了一组对生长相关性状和性别具有重要意义的QTL。通过比较作图，从QTL区域中还鉴定出几个候选生长基因。该遗传图谱为长江鲤的基因组组装和比较基因组学研究奠定了基础，所获得的QTL候选基因和遗传标记为长江鲤生长相关性状的标记辅助选择（MAS）提供了有用的基因组资源。本文的在线版本（10.1186/s12864-018-4613-1）包含补充材料，可供授权用户使用。
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. 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. 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. The online version of this article (10.1186/s12864-018-4613-1) contains supplementary material, which is available to authorized users.
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影响因子：
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