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.
Highlights
The cotton genus (Gossypium) contains four major cultivated species: two diploids, such as G. herbaceum (A1) and G. arboreum (A2), and two tetraploids, such as G. hirsutum [(AD)1] and G. barbadense [(AD)2]
Understanding the genomic basis of phenotypic variations of cotton is essential for guiding molecular breeding practice
Based on these reference genomes, researchers exhibited the landscape of CottonGVD: A Cotton Database genomic variation during domestication of cultivated tetraploid cottons (Yuan et al, 2021) and discovered the population differentiation within cultivated upland cotton (He et al, 2019, 2020; Dai et al, 2020)
Summary
The cotton genus (Gossypium) contains four major cultivated species: two diploids, such as G. herbaceum (A1) and G. arboreum (A2), and two tetraploids, such as G. hirsutum [(AD)1] and G. barbadense [(AD)2]. All these databases lack modules to exhibit genome-wide association study (GWAS) results that can show the phenotypic traits (various types) of multiple populations of different cotton species.
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