Gossypium hirsutum

Overview
Species Name hirsutum
Family Malvaceae
Scientific Name Gossypium hirsutum L.
Synonym Gossypium hirsutum var. palmeri
Common Name 陆地棉 [view all 16]
GRIN Taxonomy GRIN
Geographic Origin Southern Mexico
Genome Group AD
Genome (AD)1
Haploid Chromosome Number 26
Ploidy allotetraploid
Propagation Method N/A
Fertile withGossypium tomentosum [view all 2]
Sterile withGossypium triphyllum [view all 15]
Incompatible withGossypium davidsonii [view all 3]
GermplasmN/A
Library[view all 131]
Sequence [view all 28324543 ]
Publication Wang K, Wendel JF, Hua J. Designations for individual genomes and chromosomes in Gossypium. Journal of Cotton Research. 2018 JUN 29;1:3
Description

Gossypium hirsutum is the most widly cultivated cotton species in the world.   It is native to Central America but cultivated worldwide.  
Alias
Synonym
Gossypium hirsutum var. punctatum
Gossypium jamaicense
Gossypium lanceolatum
Gossypium mexicanum
Gossypium morrillii
Gossypium punctatum
Gossypium purpurascens
Gossypium religiosum
Gossypium schottii
Gossypium taitense
Gossypium tridens
Gossypium tricuspidatum
Gossypium hirsutum var. marie-galante
Gossypium hirsutum var. palmeri


Common Name
American cotton
American upland cotton
Bourbon cotton
cotton
upland cotton
Mian Hua [Chinese]
Lu Di Mian [Chinese]
coton velu [French]
cotonnier américain [French]
amerikanische Baumwolle [German]
Uplandbaumwolle [German]
algodoeiro-americano [Portuguese]
algodn [Spanish]
algodonero Americano [Spanish]
American Tetraploid
陆地棉
Maps
Map Name Map Details
(SM3 x SM12) x (X4133 x 8891), 4WC (2008)
Population Type : 4WC
Genome Group : AD
Map Type : genetic
7235 x TM-1, RIL (2007)
Software : MapMaker v3.0b
Population Type : RIL
Genome Group : AD
Map Type : genetic
Deltapine-61 x Texas-701, F2 (2007)
Population Type : F2
Genome Group : AD
Map Type : genetic
DES 119-5 x MD51ne, F2:3 (2002)
Population Type : F2.3
Genome Group : AD
Map Type : genetic
HQ95-6 x MD51ne, F2:3 (2002)
Population Type : F2.3
Genome Group : AD
Map Type : genetic
HS-46 x MARCABUCAG8US-1-88, F2:3 (1998)
Population Type : F2.3
Genome Group : AD
Map Type : genetic
HS-46 x MARCABUCAG8US-1-88, RIL (2009)
Population Type : RIL
Genome Group : AD
Map Type : genetic
MD-5678ne x Prema, F2:3 (2000)
Population Type : F2.3
Genome Group : AD
Map Type : genetic
Yumian-1 x T586, F2:3 (2005)
Population Type : F2:3
Genome Group : AD
Map Type : genetic
Yumian-1 x T586, F2:7 (2008)
Population Type : RIL
Genome Group : AD
Map Type : genetic
Zhongmiansuo-12 x 8891, RIL (2007)
Population Type : RIL
Genome Group : AD
Map Type : genetic
MCU-5 x Siokra 1-4, RIL (2015 SNP)
Genome Group : AD
Map Type : genetic
Baimian 1 x TM-1 , F2:3 (2014)
Map Type : genetic
Population Type : F2:3
Genome Group : AD
Yumian-1 x 7235, RIL (2015)
Software : JoinMap 4.0
Map Type : genetic
Population Type : RIL
Population Size : 180
Genome Group : AD
HS-46 x MARCABUCAG8US-1-88, RIL (2016)
Analysis Method : inclusive composite interval mapping
Software : JoinMap 4.0
Map Type : genetic
Population Type : RIL
Population Size : 188
Genome Group : AD
DH962 X Ji Mian 5, F2 (2015)
Analysis Method : composite interval mapping
Software : MapChart V2.2, JoinMap V3.0, Windows QTL Cartographer 2.5
Map Type : genetic
Population Type : F2
Genome Group : AD
Phytogen 72 x Stoneville 474, F2 (2015 SNP)
Population Type : F2
Population Size : 93
Genome Group : AD
Map Type : genetic
CCRI-35 x Yumian-1, RIL (2017)
Analysis Method : composite interval mapping
Software : Joinmap 4.0
Map Type : genetic
Population Type : RIL
Population Size : 180
Genome Group : AD
TM-1 x (TX-0256 + TX-1046), CSIL (2016)
Analysis Method : likelihood ratio test based on stepwise regression
Software : JoinMap 3.0
Map Type : genetic
Population Type : CSIL
Population Size : 115
Genome Group : AD
W10 x TM-1, F2:3 (2015)
Map Type : genetic
Population Type : F2:3
Genome Group : AD
GX1135 x GX100-2, F2 (2013)
Analysis Method : composite interval mapping
Software : MapMaker 3.0b
Map Type : genetic
Population Type : F2
Population Size : 173
Genome Group : AD
GX1135 x GX100-2, RIL (2015)
Analysis Method : composite interval mapping
Software : MapMaker 3.0
Map Type : genetic
Population Type : RIL
Population Size : 177
Genome Group : AD
GX1135 x GX100-2, RIL (2016)
Analysis Method : composite interval mapping
Software : MapMaker 3.0
Map Type : genetic
Population Type : RIL
Population Size : 177
Genome Group : AD
GX1135 x VGX100-2, RIL (2016)
Map Type : genetic
Population Type : RIL
Population Size : 180
Genome Group : AD
CCRI-35 x NH, F2:3 (2018)
Analysis Method : composite interval mapping
Software : JoinMap 4.1
Map Type : genetic
Population Type : F2:3
Population Size : 277
Genome Group : AD
Yumian-1 x T586, RIL (2006)
Software : JoinMap v3.0
Map Type : genetic
Population Type : RIL
Population Size : 270
Genome Group : AD
H16 x T586, F2 (2009)
Analysis Method : chi squared test
Software : JoinMap v3.0
Map Type : genetic
Population Type : F2
Population Size : 1259
Genome Group : AD
H16 x T586, F2sel (2009)
Analysis Method : chi squared test
Software : JoinMap v3.0
Map Type : genetic
Population Type : F2sel
Population Size : 237
Genome Group : AD
Yumian-1 x T586, RIL (2009)
Software : JoinMap 3.0
Map Type : genetic
Population Type : RIL
Population Size : 270
Genome Group : AD
(YM1 x CCRI35) x (YM1 x 7235), 4WC (2012)
Analysis Method : LOD scores
Software : JoinMap 4.0
Map Type : genetic
Population Type : 4WC
Population Size : 172
Genome Group : AD
Li2 x DP5690, F2 (2011)
Map Type : genetic
Population Type : F2
Population Size : 136
Genome Group : AD
Yumian-1 x T586, F2:3 (2005.v0)
Analysis Method : MapChart v2.1
Software : JoinMap 3.0
Map Type : genetic
Population Type : F2:3
Population Size : 230
Genome Group : AD
H18 x TM-1, F2 (2005)
Software : MapMaker v3.0b
Map Type : genetic
Population Type : F2
Population Size : 345
Genome Group : AD
DH962 x Jinmian-6, F2 (2009)
Software : Mapmaker v3.0
Map Type : genetic
Population Type : F2
Population Size : 137
Genome Group : AD
NemX x SJ-2, RIL (2005)
Analysis Method : SAS CORR procedure
Software : SAS
Map Type : genetic
Population Type : RIL
Population Size : 69
Genome Group : AD
ST-474 x Auburn 634 RNR, F2 (2007)
Map Type : genetic
Population Type : F2
Population Size : 200
Genome Group : AD
GB713 x Nem-X, F2 (2011)
Map Type : genetic
Population Type : F2
Genome Group : AD
7235 x TM-1, F2:3 (2005)
Analysis Method : Composite interval mapping
Software : MapMaker v3.0b
Map Type : genetic
Population Type : F2:3
Genome Group : AD
HS427-10 x TM-1, F2:3 (2005)
Analysis Method : Composite interval mapping
Software : MapMaker v3.0b
Map Type : genetic
Population Type : F2:3
Genome Group : AD
PD6992 x SM3, F2:3 (2005)
Analysis Method : Composite interval mapping
Software : MapMaker v3.0b
Map Type : genetic
Population Type : F2:3
Genome Group : AD
60182 x Jun Mian 1, F2:3 (2007)
Analysis Method : Joint analysis method
Software : JoinMap v3.0
Map Type : genetic
Population Type : F2:3
Population Size : 229
Genome Group : AD
Yumian-1 x T586, RIL (2015)
Map Type : genetic
Population Type : RIL
Population Size : 270
Genome Group : AD
Prema x 86-1, RIL (2015)
Map Type : genetic
Population Type : RIL
Population Size : 179
Genome Group : AD
0-153 x sGK9708, RIL (2016)
Analysis Method : composite interval mapping
Software : JoinMap 4.0
Map Type : genetic
Population Type : RIL
Population Size : 196
Genome Group : AD
0-153 x sGK9708, RIL (2015)
Analysis Method : composite interval mapping
Software : JoinMap 4.0
Map Type : genetic
Population Type : RIL
Population Size : 196
Genome Group : AD
DH962 x Ji Mian 5, RIL (2015)
Analysis Method : composite interval mapping
Software : JoinMap 3.0
Map Type : genetic
Population Type : RIL
Population Size : 178
Genome Group : AD
CCRI-35 x Yumian-1, RIL (2015)
Software : JoinMap 4.0
Map Type : genetic
Population Type : RIL
Population Size : 180
Genome Group : AD
Phytogen 72 x Stoneville 474, consbin (2017)
Analysis Method : 3824 bin markers out of the 7244 markers mapped on a consensus map, the consensus map was JoinMap derived from 3 populations: a) Phytogen 72 x Stoneville 474 F2, b) Phytogen 72 x Stoneville 474 RIL, and c) Stoneville 474 x Phytogen 72 RIL
Software : JoinMap 4.1
Map Type : genetic
Population Type : RIL
Genome Group : AD
0-153 x sGK9708, RIL (2017)
Analysis Method : composite interval mapping
Map Type : genetic
Population Type : RIL
Population Size : 196
Genome Group : AD
Yumian-1 x Acala Maxxa, RIL (2018)
Software : JoinMap 4.0
Map Type : genetic
Population Type : RIL
Population Size : 180
Genome Group : AD
LMY28 x XLZ24, RIL (2018)
Map Type : genetic
Population Size : 231
Population Type : RIL
HS-46 x MARCABUCAG8US-1-88, RIL (2018)
Map Type : genetic
CCRI-35 x TX-41, F2 (2020)
Map Type : genetic
Population Type : F2
Population Size : 392
901-001 x sGK156, F2 (2019)
Map Type : genetic
Population Type : F2
Population Size : 250
LMY22 x LY343, RIL (2016)
Map Type : genetic
Population Type : RIL
Population Size : 282
LMY22 x LY343, RIL (2020)
Map Type : genetic
Population Type : RIL
Population Size : 239
4133B x Suyuan04-3, F2 (2021)
Software : Joinmap 4.0
Map Type : genetic
Population Type : F2
Population Size : 271
4133B x J02-247, F2 (2021)
Software : Joinmap 4.0
Map Type : genetic
Population Type : F2
Population Size : 248
SGK9708 x J02-247, F2 (2021)
Software : Joinmap 4.0
Map Type : genetic
Population Type : F2
Population Size : 276
SGK9708 x 4133B, F2 (2021)
Software : Joinmap 4.0
Map Type : genetic
Population Type : F2
Population Size : 304
Germplasm
NameType
0020-31 neaccession
0023-11 neaccession
0028-1accession
0028-16 neaccession
0033-6accession
0042-3-7accession
0043-28 -1accession
0044-29accession
0045-14 -5accession
0045-14 -8accession
0050-3accession
00 U-82accession
00 WA-103accession
00 WA-104accession
010001Gaccession
0110-1 neaccession
0110-2 neaccession
0141-14 neaccession
0141-15 neaccession
0147-22 neaccession

Page of 643
Libraries
The following libraries are associated with this organism.
Library NameType
Gossypium hirsutum cloned into Strata clone blunt end pSC-B- amp/kan vectorgenomic
Lambda gt11cDNA
Cotton embryocDNA
Cotton drought tolerant genotype, leafcDNA
Cotton Boll Abscission Zone cDNA LibrarycDNA
Gossypium hirsutum 24 days postanthesis secondary-stage fiberscDNA
Six-day Cotton fibercDNA
Cotton fiber and embryo Lambda Zap Express LibrarycDNA
Gossypium hirsutum cotyledoncDNA
Gossypium hirsutum ovule first day the flower openscDNA
pARcDNA
pGHcDNA
Pst1-M fragmentcDNA
Pst1-P fragmentcDNA
pVNCcDNA
cotton leaf cDNA (differential display PCR)cDNA
Cotton fiber subtracted cDNA librarycDNA
Cotton ovules of 0DPAcDNA
Cotton fiber of 18DPAcDNA
Cotton Root and Hypocotyl tissues infected with Fusarium oxysporum f.sp. vasinfectum (Fov) Lambda ZIPLOX Library (CFUS)cDNA
Cotton Root and Hypocotyl Lambda ZIPLOX Library (CRH)cDNA
Cotton fiber DDRTcDNA
Wilt ResistancecDNA
A suppression subtractive hybridization cDNA library from bacterial-blight-resistant cottoncDNA
G.h.fbr-swcDNA
Cultured cotton cellscDNA
Cotton leaf tissuecDNA
cotton fibercDNA
PCR amplified cotton stem cDNAcDNA
Cotton somatic embryogenesis subtracted cDNA librarycDNA
cDNA from CotyledonscDNA
3 week old cold stressed seedlingcDNA
5 week old drought stressed seedlingcDNA
15-20 DAA bolls from drought stressed plantscDNA
15-20 DAA bolls from irrigated plantscDNA
8-10 DAA cotton bolls from drought stressed plantscDNA
8-10 DAA cotton bolls from irrigated plantscDNA
3 and 5 week old seedlingscDNA
Leaf cDNA 8,14 hrs post inoculation with Xanthomonas campestris pv. malvacearum 3631cDNA
Leaf cDNA 20,30 hrs post inoculation with Xanthomonas campestris pv. malvacearum 3631cDNA
Leaf cDNA 45, 60 hrs post inoculation with Xanthomonas campestris pv. malvacearum 3631cDNA
Gossypium hirsutum 5-25 dpa fiber librarycDNA
cotton fiber suppression subtractive hybridization LibrarycDNA
Cotton Lambda Zap Express LibrarycDNA
Gossypium hirsutum (AD)2 embryoid one month after subculturecDNA
Gossypium hirsutum embryoid one month after subculturecDNA
Gossypium hirsutum cv. TM-1 embryoid one month after subculturecDNA
Fiber and Ovule of Xu-142 Lambda Zap Express LibrarycDNA
GH_CHXcDNA
Cotton anther cDNA(differential display PCR) annotation.cDNA
GH_ONcDNA
GH_OCFcDNA
GH_TMOcDNA
LambdaGem 12 of G.Galauunassigned
Gossypium hirsutum cv. TM-1 embryoid calluscDNA
A suppression subtractive hybridization cDNA library from developmental senescence cotyledonscDNA
GH_LSLcDNA
Young Fiber 1-3 days after anthesiscDNA
fiber-five days after anthesiscDNA
Fiber - 3 days after anthesiscDNA
Stem - 7 weeks after plantingcDNA
Stem - 3 weeks after plantingcDNA
Fiber - 1 day after anthesiscDNA
Ovules - day of anthesis from a fiberless mutantcDNA
Ovules - day of anthesiscDNA
Root (free) - 7-10 weeks after plantingcDNA
Root (mb) - 3 weeks after plantingcDNA
Root (free) - 3 weeks after plantingcDNA
Stem (mb) - 7-10 weeks after plantingcDNA
Stem - 3-5 weeks after plantingcDNA
Stem (mb) 3-5 weeks after plantingcDNA
Stem (norm) - 3-5 weeks after plantingcDNA
Gossypium hirsutum fiber cellcDNA
Cotton Normalized Library random primedcDNA
Cotton Normalized Library dT primedcDNA
GH_SFcDNA
Gossypium hirsutum cotton fibercDNA
Cotton fiber suppression subtractive hybridization cDNA librarycDNA
Gossypium hirsutum Fiber SSH cDNA LibrarycDNA
cotton leaves expressed sequencescDNA
Cotton fiber 0-10 day post anthesiscDNA
Cotton 1-14 day post anthesis Lambda Zap Express LibrarycDNA
Gossypium hirsutum D8 restoration anther cDNAcDNA
Subtracted cDNA library of cotton between cold acclimation and normal onescDNA
Cotton ovule and fiber 3-5 days post anthesiscDNA
Library for cotton induced by herbivorescDNA
suppression subtractive hybridization library of cell wall regeneration from protoplastcDNA
SSH library of differentially expressed genes response to medium changes during cotton somatic embryogenesiscDNA
SSH library of cotton somatic embryogenesiscDNA
Cotton resistant to Meloidogyne incognitacDNA
Cotton susceptible to Meloidogyne incognitacDNA
Gossypium hirsutum leaf blade of M1 progenycDNA
Differential display of COTTON GENOTYPE, leaf, one month of infectioncDNA
Gossypium hirsutum cv. Emian 22 at fiber initiation stage 5-20dpacDNA
Gossypium hirsutum cv. Emian 22 at fiber initiation stagecDNA
Cotton root NaCl treated suppression subtractive hybridization cDNA librarycDNA
cotton shoot apical meristems, buds and flowerscDNA
Differential display of Cotton Genotype, ovule (3 day post anthesis)cDNA
Subtracted cDNA library from Gossypium hirsutum L. variety Bikaneri NarmacDNA
Suppression subtractive hybridization library of cellular dedifferentiationcDNA
Brown cotton fiber 5-25 days post anthesis librarycDNA
Brown cotton seedlings in response to low temperature librarycDNA
Heat stress treated cotton (G.hirsutum L.) librarycDNA
Gossypium hirsutum differential display cDNA librarycDNA
Gossypium hirsutum RAPD markergenomic
Gossypium hirsutum DNAgenomic
Gossypium hirsutum L.genomic
CM Cotton SSR markersgenomic
Maxxagenomic
Palgenomic
BAC and BIBAC libraries from Upland cotton genetic standard TM-1genomic
Cotton methylation filtered library (Cotton_F)genomic
Cotton methylation unfiltered library (Cotton_U)genomic
Cotton methylation filtered library (LibID: 205)genomic
Cotton methylation filtered library (LibID: 124)genomic
Cotton methylation unfiltered library (LibID: 125)genomic
Gossypium hirsutum BAC librarygenomic
Plasmid, BAC and BIBAC libraries from upland cotton genetic standard TM-1genomic
GH_MBbgenomic
Gossypium hirsutum BAC ends (Wang K)genomic
The original maize BAC library (ZMMBBb) is contaminated with Gossypium hirsutum cv Maxxa cotton.genomic
Differentially expressed transcript derived fragments (TDFs) upon water deficit stress in Gossypium hirsutum L.cDNA
Gossypium hirsutum BIBAC Librarygenomic
Lambda cottongenomic
EZAPcDNA
Upland cotton TM-1genomic
Sau3I cotton microsatellite enriched librarygenomic
Uni-ZapcDNA
Genomic in lambda Charon 35genomic
Cotton BAC Librarygenomic
NAU_CottonSNP80KSNP_chip
Image
File NameLegend
39_FISH_AJB-85-1364.jpgFISH photomicrographs of Gossypium hirsutum repetitive elements hybridized to metaphase chromosomes of G. hirsutum, G. arboreum, G. raimondii, and an A2D5 synthetic diploid. [Image from Hanson et al., 1998, AJB-85-1364]
45_FISH_GEN-178-1117_fig2.jpgBAC clones and their corresponding genetic markers of the 22 probes according to FISH signal patterns in Figure 1. [Image from Wang et al., 2008, GEN-178-1117]
46_FISH_GEN-178-1117_fig3.jpgTwo BAC translocations involving two chromosome pairs of At2 and A3 and At4 and A5 between G. arboreum and A-subgenome of G. hirsutum. [Image from Wang et al., 2008, GEN-178-1117]
47_FISH_TAG-113-73.jpgEight chromosomespecific BAC clones of cotton identification and chromosomal and subchromosomal location by FISHing to Gossypium hirsutum NTs. [Image from Wang et al., 2006, TAG-113-73]
48_FISH_TAG-115-675.jpgTwenty-six individual cotton mitotic chromosomes with FISH signals derived from the chromosome-speciWc BACs, and comparisons of linkage and FISH maps. [Image from Wang 2007, TAG-115-675]
sp_draw_gh_china.jpgG. hirsutum - illustration
53_Gh_leaves.jpgG. hirsutum - leaves and open bolls
51_Gh_TX-0139_leaves.jpgG. hirsutum - leaves
55_Gh_SA-0097-1.02_flower.jpgG. hirsutum cultivar - flower
54_Gh_SA-0097-1.02_boll.jpgG. hirsutum cultivar - boll
Transcripts

Below is a list of transcript assemblies that are available for Gossypium hirsutum. Click the assembly name for further details.

 
Assembly  Name Analysis Name Date Constructed Stats

 

Gossypium hirsutum CottonGen RefTrans V1

 

G. hirsutum CottonGen RefTrans V1

 

 

2016-10-25

 Reads: 2.75 billion
Contigs:93,449

 

Gossypium hirsutum unigene V1.0

 

G. hirsutum unigene V1

 

2012-09-27

 Reads: 442,954
Contigs:21,698
Singlets:128,218