BNL3474, BNL3474 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL3474
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL3474_orig
Source Typegenomic
Repeat Motif(CA)16
PCR ConditionAnnealing temperature: 55
Primer 1BNL3474_F: AAGGTAATGCAGTGCGGTTC
Primer 2BNL3474_R: ATAATGGCATTGATTATAGAGTGTG
PolymorphismP_ BNL3474
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
BNL3474_FBNL3474_FGossypium hirsutumprimer
BNL3474_RBNL3474_RGossypium hirsutumprimer


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

Feature NameUnique NameSpeciesType
fiber elongationqFEL.Y7-RIL_ch24.bb12Gossypium hirsutumQTL
fiber strengthqFS.Y7-RIL_ch24.bb12Gossypium hirsutumQTL
fiber uniformityqFU.Y7-RIL_ch24.bb12Gossypium hirsutumQTL


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

Feature NameUnique NameSpeciesType
BNL3474BNL3474Gossypium hirsutummarker_locus
BNL3474aBNL3474aGossypium hirsutummarker_locus
BNL3474bBNL3474bGossypium hirsutummarker_locus
BNL3474-195BNL3474-195Gossypium hirsutummarker_locus
BNL3474-200BNL3474-200Gossypium hirsutummarker_locus
BNL3474-175BNL3474-175Gossypium hirsutummarker_locus
BNL3474-193BNL3474-193Gossypium hirsutummarker_locus
BNL3474-170BNL3474-170Gossypium hirsutummarker_locus
BNL3474_193BNL3474_193Gossypium hirsutummarker_locus
BNL3474BNL3474-68.114Gossypium hirsutummarker_locus


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

Feature NameUnique NameSpeciesType
BNL3474_origBNL3474_origGossypium hirsutumsequence_feature


Alignments
The following features are aligned
Aligned FeatureFeature TypeAlignment Location
D08chromosomeD08:44974531..44974710 -
A08chromosomeA08:88094233..88094404 -
CM018222.1chromosomeCM018222.1:41778180..41778359 -
CM018209.1chromosomeCM018209.1:83413171..83413362 -
D5_08chromosomeD5_08:38512127..38512308 -
Chr3chromosomeChr3:11974717..11974896 -
Chr08_CRI-A2_v1.0.a1chromosomeChr08_CRI-A2_v1.0.a1:91321165..91321344 -
scaffold197supercontigscaffold197:1008080..1008261 +
D10_08chromosomeD10_08:22798339..22798504 +
CM016621.1chromosomeCM016621.1:77255183..77255370 -
At_chr4chromosomeAt_chr4:68302854..68303025 -
D08chromosomeD08:41391461..41391640 -
A08chromosomeA08:69114633..69114804 -
Ghir_D08chromosomeGhir_D08:44314753..44314932 -
Ghir_A08chromosomeGhir_A08:86753701..86753888 -
D08chromosomeD08:45348169..45348348 -
A08chromosomeA08:90245720..90245891 -
D08chromosomeD08:44185066..44185245 -
A08chromosomeA08:89707587..89707758 -
D08chromosomeD08:41467944..41468123 -
A08chromosomeA08:86930464..86930653 -
Dt08chromosomeDt08:41592081..41592258 -
scaffold1394supercontigscaffold1394:277844..278033 +
scaffold6048supercontigscaffold6048:53142..53319 -
Gbar_D08chromosomeGbar_D08:41725193..41725372 -
Gbar_A08chromosomeGbar_A08:84225258..84225449 -
D08chromosomeD08:43858442..43858629 -
A08chromosomeA08:85281265..85281454 -
CM017630.1chromosomeCM017630.1:43208039..43208218 -
CM017617.1chromosomeCM017617.1:84187319..84187506 -
CM017656.1chromosomeCM017656.1:44896043..44896218 -
CM017708.1chromosomeCM017708.1:42409571..42409752 -
CM017695.1chromosomeCM017695.1:84741942..84742133 -
scaffold197supercontigBNL3474:1..613 .
scaffold197:1007653..1008270 +
Chr04chromosomeBNL3474:1..613 .
Chr04:38653712..38654329 -
Sequence
>BNL3474 ID=BNL3474|Name=BNL3474|organism=Gossypium hirsutum|type=genetic_marker|length=190bp
AAGGTAATGCAGTGCGGTTCAAATGGAAGGATCATACCCTTTTTTCTACC
CAGCTCATCTTTTGACTTCAATTGTTCTGCTCAAATATTTTAGTAGGTGC
ATTAGATACCGAAATGAGCTGATTCGGCATTTGCTTCCACACACACACAC
ACACACACACACACACACACTCTATAATCAATGCCATTAT
Map Positions
#Map NameLinkage GroupBinChromosomePositionLocus
17235 x TM-1, RIL (2007)7235 x TM-1, RIL (2007).7T-RIL_D08N/AAD_chr.2445.7BNL3474
2Guazuncho-2 x VH8-4602, consensus (2009)Guazuncho-2 x VH8-4602, consensus (2009).GV-cons_c24N/AAD_chr.2475.9BNL3474
3Guazuncho-2 x VH8-4602, consensus (2009)Guazuncho-2 x VH8-4602, consensus (2009).GV-cons_c08N/AAD_chr.08118.27BNL3474
4Handan-208 x Pima-90, F2:3 (2007)Handan-208 x Pima-90, F2:3 (2007).HP-F2:3_chr24/lgD03N/AAD_chr.2498.8BNL3474
5Monsanto SSR Bin Map, (2009)Monsanto SSR Bin Map, (2009).BIN-SSR_chr08N/AAD_chr.08110BNL3474
6AD-genome wide Reference Map (2009)AD-genome wide Reference Map (2009).Ref-chr08N/AAD_chr.08134BNL3474
7TM-1 x 3-79, RIL (2012)TM-1 x 3-79, RIL (2012).T3-RIL.12_c08N/AAD_chr.0857.66BNL3474
8Yumian-1 x T586, F2:3 (2005)Yumian-1 x T586, F2:3 (2005).YT-F2:3_A02/D03N/AAD_chr.087.4BNL3474
9Yumian-1 x T586, F2:3 (2005)Yumian-1 x T586, F2:3 (2005).YT-F2:3_A02/D03N/AAD_chr.247.4BNL3474
10Yumian-1 x T586, F2:7 (2008)Yumian-1 x T586, RIL (2008).YT-RIL_chr08N/AAD_chr.080BNL3474
11CCRI-36 x Hai-7124, F2 (2007)CCRI-36 x Hai-7124, F2 (2007).CH-F2_D03N/AAD_chr.2495BNL3474
12AD-genome wide Reference Map (2009)AD-genome wide Reference Map (2009).Ref-chr24N/AAD_chr.24116BNL3474
13Yumian-1 x T586, RIL (2006)YT-RIL_chr08-3N/AAD_chr.0820.1BNL3474
147235 x TM-1, F2:3 (2005)7T-F2:3_chr24/LGD03N/AAD_chr.2413.7BNL3474
15Yumian-1 x T586, RIL (2015)YT-RIL.15_chr08N/AAD_chr.0870.3BNL3474
16TM-1 x 3-79, RIL (2014)T3-RIL.14_chr08N/AAD_chr.0868.1BNL3474
17CCRI 12-4 x (AD)5-7, F2 (2015)CAD5-F2_chr24N/ADt.0865BNL3474
18Guazuncho-2 x VH8-4602, BC1 (2005)Guazuncho-2 x VH8-4602, BC1 (2005).GV-BC1_chr08/lgA02N/AAD_chr.08170.6BNL3474a
19Yumian-1 x 7235, RIL (2015)Y7-RIL_chr08N/AAD_chr.0869.8BNL3474a
20Guazuncho-2 x VH8-4602, BC1 (2005)Guazuncho-2 x VH8-4602, BC1 (2005).GV-BC1_chr24/lgD03N/AAD_chr.24110.6BNL3474b
21Yumian-1 x 7235, RIL (2015)Y7-RIL_chr24N/AAD_chr.2447BNL3474b
22TM-1 x Hai-7124, BC1 (2007)TM-1 x Hai-7124, BC1 (2007).TH-BC1_chr08N/AAD_chr.0847.8BNL3474-195
23TM-1 x Hai-7124, BC1 (2008)TM-1 x Hai-7124, BC1 (2008).TH-BC1.08_chr08/A8N/AAD_chr.0879.31BNL3474-195
24TM-1 x Hai-7124, BC1 (2008)TM-1 x Hai-7124, BC1 (2008).TH-BC1.08_chr24/D8N/AAD_chr.2497.04BNL3474-200
25TM-1 x Hai-7124, BC1 (2007)TM-1 x Hai-7124, BC1 (2007).TH-BC1_chr24N/AAD_chr.2414.7BNL3474-200
26TM-1 x Hai-7124, BC1 (2008)TM-1 x Hai-7124, BC1 (2008).TH-BC1.08_chr24/D8N/AAD_chr.2492.4BNL3474-175
27TM-1 x Hai-7124, BC1 (2007)TM-1 x Hai-7124, BC1 (2007).TH-BC1_chr24N/AAD_chr.2418.2BNL3474-175
28Vsg x (TM-1 x Hai-7124), DH (2005)Vsg x (TM-1 x Hai-7124), DH (2005).VTH-DH.05_lgD03N/AAD_chr.2478.3BNL3474-175
29Vsg x (TM-1 x Hai-7124), DH (2005)Vsg x (TM-1 x Hai-7124), DH (2005).VTH-DH.05_lgA02.1N/AAD_chr.080BNL3474-193
30Vsg x (TM-1 x Hai-7124), DH (2005)Vsg x (TM-1 x Hai-7124), DH (2005).VTH-DH.05_lgA02.1N/AAD_chr.085.3BNL3474-170
31TM-1 x Hai-7124, BC1S1 (2007)TH-BC1S1_chr08N/AAD_chr.0826.1BNL3474_193
32TM-1 x 3-79, RIL (2012.v3)T3-RIL.12v3_chr.08N/AAD_chr.0868.11BNL3474