CottonGVD: A Comprehensive Genomic Variation Database for Cultivated Cottons

文献类型： 外文期刊

第一作者： Peng, Zhen

作者： Peng, Zhen;Li, Hongge;Dai, Panhong;Geng, Xiaoli;Wang, Xiao;Zhang, Xiaomeng;Wang, Zhengzhen;Jia, Yinhua;Pan, Zhaoe;Chen, Baojun;Du, Xiongming;He, Shoupu;Peng, Zhen;Li, Hongge;Du, Xiongming;He, Shoupu;Sun, Gaofei

作者机构：

关键词： Gossypium; genomics; genetics; variation; eGWAS; database

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：6.627； 五年影响因子：7.255 ）

ISSN： 1664-462X

年卷期： 2021 年 12 卷

页码：

收录情况： SCI

摘要： Cultivated cottons are the most important economic crop, which produce natural fiber for the textile industry. In recent years, the genetic basis of several essential traits for cultivated cottons has been gradually elucidated by decoding their genomic variations. Although an abundance of resequencing data is available in public, there is still a lack of a comprehensive tool to exhibit the results of genomic variations and genome-wide association study (GWAS). To assist cotton researchers in utilizing these data efficiently and conveniently, we constructed the cotton genomic variation database (CottonGVD; http://120.78.174.209/ or http://db.cngb.org/cottonGVD). This database contains the published genomic information of three cultivated cotton species, the corresponding population variations (SNP and InDel markers), and the visualized results of GWAS for major traits. Various built-in genomic tools help users retrieve, browse, and query the variations conveniently. The database also provides interactive maps (e.g., Manhattan map, scatter plot, heatmap, and linkage disequilibrium block) to exhibit GWAS and expression GWAS results. Cotton researchers could easily focus on phenotype-associated loci visualization, and they are interested in and screen for candidate genes. Moreover, CottonGVD will continue to update by adding more data and functions.

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