CottonGen: a genomics, genetics and breeding database for cotton research

Abstract

CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST.

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

“…XinHai-21 (NAU, version 2.1) were retrieved from the CottonGen website (Yu et al 2014) and the CottonFGD website (Zhu et al 2017).…”

Distribution and evolution of cotton fiber development genes in the fibreless Gossypium raimondii genome

“…Cotton ESTs have been systamatically collected, assembled, clustered into Unigenes, formatted and deposited into the cotton genome database, CottonGen (http://www.cottongen.org/). Of 442,954 ESTs, most have been assembled into 21,698 contigs leaving 128,218 singletons [40].…”

“…Fiber development Unigenes were anchored to recombination hotspot regions among the tetraploid At and Dt subgenomes, and the sequenced diploid D genome. We accomplished this study by using cotton EST Unigenes, the sequenced D genome, BAC-end sequences from USDA-ARS, College Station, Texas, and all marker sequences that were publicly available for the development of simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), single nucleotide polymorphism (SNP) markers in cotton http://www.cottongen.org [40].…”

Optimal use of SSR markers for varietal identification of upland cotton

“…These SSR loci are summarized in Table 1 according to information available at the CottonGen database (Yu et al, 2014 (2000) CIR203 ( The amplification reaction for the BNL primers was performed by an initial denaturation at 95°C for 12 min, followed by 30 cycles at 93°C for 1 min, 55°C for 2 min, and 72°C for 3 min, with a final extension at 72°C for 7 min. For the CIR, JESPR, and NAU primers, the initial denaturation was at 94°C for 5 min, followed by 35 cycles at 94°C for 30 s, annealing temperature recommended for each primer pair (Table 1) at 1 min, and 72°C for 1 min, with a final extension at 72°C for 8 min.…”