CottonGVD: A Comprehensive Genomic Variation Database for Cultivated Cottons

作者：棉花生物学国家重点实验室 日期：2022-08-30 访问量：

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

Frontiers in Plant Science

Doi: 10.3389/fpls.2021.803736

Abstract：

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.