High-resolution linkage and quantitative trait locus mapping aided by genome survey sequencing: Building up an integrative genomic framework for a bivalve mollusc

文献类型: 外文期刊

第一作者: Jiao, Wenqian

作者: Jiao, Wenqian;Fu, Xiaoteng;Dou, Jinzhuang;Li, Hengde;Su, Hailin;Mao, Junxia;Yu, Qian;Zhang, Lingling;Hu, Xiaoli;Huang, Xiaoting;Wang, Yangfan;Wang, Shi;Bao, Zhenmin;Li, Hengde

作者机构:

关键词: 2b-RAD genotyping;bivalve;genome sequencing;linkage mapping;quantitative trait locus mapping

期刊名称:DNA RESEARCH ( 影响因子:4.458; 五年影响因子:5.371 )

ISSN:

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收录情况: SCI

摘要: Genetic linkage maps are indispensable tools in genetic and genomic studies. Recent development of genotyping-by-sequencing (GBS) methods holds great promise for constructing high-resolution linkage maps in organisms lacking extensive genomic resources. In the present study, linkage mapping was conducted for a bivalve mollusc (Chlamys farreri) using a newly developed GBS method-2b-restriction site-associated DNA (2b-RAD). Genome survey sequencing was performed to generate a preliminary reference genome that was utilized to facilitate linkage and quantitative trait locus (QTL) mapping in C. farreri. A high-resolution linkage map was constructed with a marker density (3806) that has, to our knowledge, never been achieved in any other molluscs. The linkage map covered nearly the whole genome (99.5%) with a resolution of 0.41 cM. QTL mapping and association analysis congruously revealed two growth-related QTLs and one potential sex-determination region. An important candidate QTL gene named PROP1, which functions in the regulation of growth hormone production in vertebrates, was identified from the growth-related QTL region detected on the linkage group LG3. We demonstrate that this linkage map can serve as an important platform for improving genome assembly and unifying multiple genomic resources. Our study, therefore, exemplifies how to build up an integrative genomic framework in a non-model organism.

分类号: Q75

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