BNL3627, BNL3627 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL3627
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL3627_orig
Source Typegenomic
Repeat Motif(TC)17
PCR ConditionAnnealing temperature: 55
Primer 1BNL3627_F: TATGGGCCTGTCCACCTAAG
Primer 2BNL3627_R: CAAAGCAACATGCACACACA
PolymorphismP_ BNL3627
CommentPrimer data obtained in 2000
Germplasm
Stock NameType
Deltapine 90obsolete_cultivar
Relationships

This genetic_marker is adjacent to the following primer feature(s):

Feature NameUnique NameSpeciesType
BNL3627_FBNL3627_FGossypium hirsutumprimer
BNL3627_RBNL3627_RGossypium hirsutumprimer


This genetic_marker is adjacent to the following QTL feature(s):

Feature NameUnique NameSpeciesType
fiber strengthqFS.HP-ch8.2Gossypium spp.QTL
micronaireqMIC.HP-ch8Gossypium spp.QTL


This genetic_marker is located in the following QTL feature(s):

Feature NameUnique NameSpeciesType
seed indexqSI.TTT-CSIL_ch08.nj13Gossypium hirsutumQTL


The following marker_locus feature(s) are an instance of this genetic_marker:

Feature NameUnique NameSpeciesType
BNL3627BNL3627Gossypium hirsutummarker_locus
BNL3627aBNL3627aGossypium hirsutummarker_locus
BNL3627bBNL3627bGossypium hirsutummarker_locus
BNL3627-180BNL3627-180Gossypium hirsutummarker_locus
BNL3627_180BNL3627_180Gossypium hirsutummarker_locus
BNL3627BNL3627-46.336Gossypium hirsutummarker_locus
BNL3627bBNL3627b-101.3Gossypium hirsutummarker_locus
BNL3627aBNL3627a-5.8Gossypium hirsutummarker_locus


The following sequence_feature feature(s) derives from this genetic_marker:

Feature NameUnique NameSpeciesType
BNL3627_origBNL3627_origGossypium hirsutumsequence_feature


Alignments
The following features are aligned
Aligned FeatureFeature TypeAlignment Location
D08chromosomeD08:4877498..4877663 +
A08chromosomeA08:4201049..4201231 +
CM018222.1chromosomeCM018222.1:3970933..3971097 +
CM018209.1chromosomeCM018209.1:4225969..4226143 +
D5_08chromosomeD5_08:4056882..4057047 +
KI_08chromosomeKI_08:3440021..3440191 +
Chr3chromosomeChr3:38170814..38171004 -
Chr08_CRI-A2_v1.0.a1chromosomeChr08_CRI-A2_v1.0.a1:4471818..4472008 +
Chr4chromosomeChr4:23497147..23497312 +
D10_08chromosomeD10_08:58311604..58311771 -
CM016621.1chromosomeCM016621.1:138530769..138530939 -
scaffold417.1supercontigscaffold417.1:1130605..1130787 +
Dt_chr4chromosomeDt_chr4:31394680..31394845 +
D08chromosomeD08:4253462..4253627 +
A08chromosomeA08:3731681..3731863 +
Ghir_D08chromosomeGhir_D08:4221789..4221954 +
Ghir_A08chromosomeGhir_A08:4186904..4187086 +
D08chromosomeD08:4006356..4006521 +
A08chromosomeA08:4276807..4276989 +
D08chromosomeD08:4217810..4217975 +
A08chromosomeA08:4580569..4580750 +
D08chromosomeD08:4291407..4291572 +
A08chromosomeA08:4162173..4162355 +
At08chromosomeAt08:3790338..3790502 +
scaffold11030supercontigscaffold11030:137402..137566 +
scaffold1102supercontigscaffold1102:261611..261775 -
Gbar_D08chromosomeGbar_D08:4161359..4161523 +
Gbar_A08chromosomeGbar_A08:4553087..4553259 +
D08chromosomeD08:4117579..4117743 +
A08chromosomeA08:4396556..4396730 +
CM017630.1chromosomeCM017630.1:4305198..4305363 +
CM017617.1chromosomeCM017617.1:4446841..4447011 +
CM017656.1chromosomeCM017656.1:4309799..4309963 +
CM017643.1chromosomeCM017643.1:4596272..4596456 +
CM017708.1chromosomeCM017708.1:4293763..4293927 +
CM017695.1chromosomeCM017695.1:4370270..4370450 +
Sequence
>BNL3627 ID=BNL3627|Name=BNL3627|organism=Gossypium hirsutum|type=genetic_marker|length=183bp
TATGGGCCTGTCCACCTAAGAAAGGAGAAGATTATATCTTCTATTTCCAC
CCAGAGATTCAGAAAATACCGAAGTCTGATAAGCTGAGGCAGTGGTCTCT
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTGTCACATATCTCTTATAC
ATGCATGTCTTTATGTGTGTGCATGTTGCTTTG
Map Positions
#Map NameLinkage GroupBinChromosomePositionLocus
13-79 x NM24016, RIL (2008)3-79 x NM24016, RIL (2008).3N-RIL_chr03-2N/AAD_chr.030BNL3627
2Guazuncho-2 x VH8-4602, BC2 (2005)Guazuncho-2 x VH8-4602, BC2 (2005).GV-BC2_chr24/lgD03N/AAD_chr.2466.7BNL3627
3Guazuncho-2 x VH8-4602, consensus (2009)Guazuncho-2 x VH8-4602, consensus (2009).GV-cons_c24N/AAD_chr.2499.34BNL3627
4Guazuncho-2 x VH8-4602, consensus (2009)Guazuncho-2 x VH8-4602, consensus (2009).GV-cons_c03N/AAD_chr.0337.25BNL3627
5Guazuncho-2 x VH8-4602, consensus (2009)Guazuncho-2 x VH8-4602, consensus (2009).GV-cons_c08N/AAD_chr.08109.66BNL3627
6Guazuncho-2 x VH8-4602, RIL (2009)Guazuncho-2 x VH8-4602, RIL (2009).GV-RIL_ch08/lgA02N/AAD_chr.0836.06BNL3627
7Guazuncho-2 x VH8-4602, RIL (2009)Guazuncho-2 x VH8-4602, RIL (2009).GV-RIL_ch24/lgD03N/AAD_chr.2482.32BNL3627
8Handan-208 x Pima-90, F2:3 (2007)Handan-208 x Pima-90, F2:3 (2007).HP-F2:3_chr08/lgA02N/AAD_chr.08164.9BNL3627
9Palmeri x K-101, F2 (2007)Palmeri x K-101, F2 (2007).PK-F2_chr08/lgA02N/AAD_chr.08128.3BNL3627
10AD-genome wide Reference Map (2009)AD-genome wide Reference Map (2009).Ref-chr08N/AAD_chr.08200BNL3627
11TM-1 x 3-79, RIL (2006)TM-1 x 3-79, RIL (2006).T3-RIL_chr.08N/AAD_chr.0827.9BNL3627
12TM-1 x 3-79, RIL (2012)TM-1 x 3-79, RIL (2012).T3-RIL.12_c08N/AAD_chr.0836.72BNL3627
13Xinluzao-1 x Hai-7124, F2 (2008)Xinluzao-1 x Hai-7124, F2 (2008).XH-F2_lg37/chr08N/AAD_chr.0816BNL3627
14Emian-22 x 3-79, BC1 (2011)Emian-22 x 3-79, BC1 (2011).E3-BC1_chr08N/AAD_chr.08126.71BNL3627
15AD-genome wide Reference Map (2009)AD-genome wide Reference Map (2009).Ref-chr24N/AAD_chr.2443BNL3627
16AD-genome wide Reference Map (2009)AD-genome wide Reference Map (2009).Ref-chr03N/AAD_chr.03109BNL3627
17TM-1 x 3-79, RIL (2014)T3-RIL.14_chr08N/AAD_chr.0846.3BNL3627
18TM-1 x (TX-0256 + TX-1046), CSIL (2016)TTT-CSIL_chr08N/AAD_chr.0896.9BNL3627
19CCRI 12-4 x (AD)5-7, F2 (2015)CAD5-F2_chr08N/AAt.0875.4BNL3627
20SG 747 x Giza 75, BIL (2013)SG-BIL_chr08N/AAD_chr.0845BNL3627
21CCRI-36 x Hai-7124, F2 (2007)CCRI-36 x Hai-7124, F2 (2007).CH-F2_A02N/AAD_chr.08148.9BNL3627a
22Guazuncho-2 x VH8-4602, BC1 (2005)Guazuncho-2 x VH8-4602, BC1 (2005).GV-BC1_chr24/lgD03N/AAD_chr.24136.5BNL3627a
23Monsanto SSR Bin Map, (2009)Monsanto SSR Bin Map, (2009).BIN-SSR_chr08N/AAD_chr.08150BNL3627a
24CCRI-36 x Hai-7124, F2 (2007)CCRI-36 x Hai-7124, F2 (2007).CH-F2_D03N/AAD_chr.2468.6BNL3627b
25Guazuncho-2 x VH8-4602, BC1 (2005)Guazuncho-2 x VH8-4602, BC1 (2005).GV-BC1_chr03N/AAD_chr.0341BNL3627b
26Handan-208 x Pima-90, F2:3 (2007)Handan-208 x Pima-90, F2:3 (2007).HP-F2:3_chr26N/AAD_chr.2622.5BNL3627b
27Monsanto SSR Bin Map, (2009)Monsanto SSR Bin Map, (2009).BIN-SSR_chr24N/AAD_chr.24110BNL3627b
28TM-1 x Hai-7124, BC1 (2007)TM-1 x Hai-7124, BC1 (2007).TH-BC1_chr08N/AAD_chr.0845.3BNL3627-180
29TM-1 x Hai-7124, BC1 (2008)TM-1 x Hai-7124, BC1 (2008).TH-BC1.08_chr08/A8N/AAD_chr.0883.72BNL3627-180
30Vsg x (TM-1 x Hai-7124), DH (2005)Vsg x (TM-1 x Hai-7124), DH (2005).VTH-DH.05_lgA02.2N/AAD_chr.0811BNL3627-180
31TM-1 x Hai-7124, BC1S1 (2007)TH-BC1S1_chr08N/AAD_chr.0814.6BNL3627_180
32TM-1 x 3-79, RIL (2012.v3)T3-RIL.12v3_chr.08N/AAD_chr.0846.34BNL3627
33PD 94042 x (AD)4-08, F2 (2016)PA-F2_chr08N/AAt.08101.3BNL3627b
34PD 94042 x (AD)4-08, F2 (2016)PA-F2_chr24N/ADt.085.8BNL3627a
Image
File NameLegend
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]
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]