Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum × G. barbadense populations

Abstract

A specialized database currently containing more than 2200 QTL is established, which allows graphic presentation, visualization and submission of QTL. In cotton quantitative trait loci (QTL), studies are focused on intraspecific Gossypium hirsutum and interspecific G. hirsutum × G. barbadense populations. These two populations are commercially important for the textile industry and are evaluated for fiber quality, yield, seed quality, resistance, physiological, and morphological trait QTL. With meta-analysis data based on the vast amount of QTL studies in cotton it will be beneficial to organize the data into a functional database for the cotton community. Here we provide a tool for cotton researchers to visualize previously identified QTL and submit their own QTL to the Cotton QTLdb database. The database provides the user with the option of selecting various QTL trait types from either the G. hirsutum or G. hirsutum × G. barbadense populations. Based on the user's QTL trait selection, graphical representations of chromosomes of the population selected are displayed in publication ready images. The database also provides users with trait information on QTL, LOD scores, and explained phenotypic variances for all QTL selected. The CottonQTLdb database provides cotton geneticist and breeders with statistical data on cotton QTL previously identified and provides a visualization tool to view QTL positions on chromosomes. Currently the database (Release 1) contains 2274 QTLs, and succeeding QTL studies will be updated regularly by the curators and members of the cotton community that contribute their data to keep the database current. The database is accessible from http://www.cottonqtldb.org.

Quantitative trait loci analysis of Verticillium wilt resistance in interspecific backcross populations of Gossypium hirsutum × Gossypium barbadense

“…5, Table 2). 7 QTL hotspot regions (c5-VW-Hotspot-2, c7-VW-Hotspot-1, c7-VW-Hotspot-2, c8-VW-Hotspot-1, c19-VW-Hotspot-1, c21-VW-Hotspot-1 and c26-VW-Hotspot-1) were consistent with those identified previously by Zhang et al and Said et al [13, 34] (Table 2), and the other ten were new, unreported hotspot regions. Two QTL hotspot regions were on C5, C7, C9 and C19, respectively.…”

“…5, Table 2). Of them, 7 QTL hotspot regions were consistent with those identified previously by Zhang et al and Said et al [13, 34] (Table 2) and another 10 were new, unreported hotspot regions. 36 (75 %) QTLs from this paper were distributed in 15 hotspot regions, of which 29 QTLs were in 12 hotspot regions and were all from G. barbadense (Table 3).…”

“…of QTLsNo. of QTLs in this paperReported previouslyc3-VW-Hotspot-1C316–28 cM76c5-VW-Hotspot-1C528–43 cM75c5-VW-Hotspot-2C547–68 cM52Zhang et al 2015 [13] and Said et al 2015 [34]c7-VW-Hotspot-1C743–59 cM41Zhang et al 2015 [13]c7-VW-Hotspot-2C764–85 cM53Zhang et al 2015 [13]c8-VW-Hotspot-1C817–34 cM82Zhang et al 2015 [13]c9-VW-Hotspot-1C955–85 cM61c9-VW-Hotspot-2C9124–147 cM50c12-VW-Hotspot-1C1217–26 cM43c14-VW-Hotspot-1C1426–43 cM53c15-VW-Hotspot-1C1542–63 cM63c17-VW-Hotspot-1C1711–36 cM41c19-VW-Hotspot-1C191–26 cM50Zhang et al 2015 [13]c19-VW-Hotspot-2C19120–132 cM41c20-VW-Hotspot-1C201–26 cM41c21-VW-Hotspot-1C2130–44 cM61Zhang et al 2015 [13]c26-VW-Hotspot-1C2654–79 cM93Zhang et al 2015 [13] …”

Genome-Wide SNP Linkage Mapping and QTL Analysis for Fiber Quality and Yield Traits in the Upland Cotton Recombinant Inbred Lines Population

“…Searching for QTLs of upland cotton in a CottonQTLdb database 3 developed by Said et al (2015) and statistical data on cotton QTL previously, there were seven QTLs for FL, two QTLs for FU, two QTLs for MIC, four QTLs for FE, two QTLs for FS, and five QTLs for LP in present work, sharing same genetic position (spacing distance < 5 cM) and physical position with earlier reports (Wu et al, 2008; Tan et al, 2014; Liu et al, 2015; Zhang Z. et al, 2015). In addition, five QTLs for FL, six QTLs for FU, eight QTLs for MIC, four QTLs for FE, seven QTLs for FS, six QTLs for BW, and seven QTLs for LP had been mapped on the same chromosomes but not on the same position as reported in the previous researches.…”

“…In addition, five QTLs for FL, six QTLs for FU, eight QTLs for MIC, four QTLs for FE, seven QTLs for FS, six QTLs for BW, and seven QTLs for LP had been mapped on the same chromosomes but not on the same position as reported in the previous researches. These inconsistencies might be due to different genetic backgrounds and DNA markers (Shappley et al, 1998; Wu et al, 2008; Said et al, 2015). Remaining nine additive QTLs (qFE-Chr17-1, qBW-Chr09-1, qBW-Chr09-2, qBW-Chr23-1, qBW-Chr24-1, qBW-Chr25-1, qLP-Chr20-1, qLP-Chr21-1, and qLP-Chr21-2) might be novel loci, due to unavailability of any reports for these traits on those chromosomes.…”