BNL3259, BNL3259 (genetic_marker) Gossypium hirsutum

Marker Overview


Name	BNL3259
Genbank ID	N/A
Type	SSR
Species	Gossypium hirsutum
Germplasm	Deltapine 90
Source Sequence	BNL3259_orig
Source Type	genomic
Repeat Motif	(AC)11
PCR Condition	Annealing temperature: 55
Primer 1	BNL3259_F: TTTTGAAATTCCAGCGAAGG
Primer 2	BNL3259_R: GTCAATACCTGCTTCTCCACG
Polymorphism	P_ BNL3259
Comment	Primer data obtained in 2000

Alignments

The following features are aligned


Feature Name	Type	Location	Analysis	Reference
D02	chromosome	D02:68047607..68047810 +	Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1	n/a
A03	chromosome	A03:105688615..105688824 +	Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1	n/a
CM018216.1	chromosome	CM018216.1:64398181..64398398 +	Gossypium barbadense (AD2) '3-79' genome HGS_v1.1	n/a
D5_03	chromosome	D5_03:2548338..2548557 -	Gossypium raimondii (D5) 'D5-4' genome NSF_v1	n/a
KI_03	chromosome	KI_03:39758162..39758383 +	Gossypioides kirkii genome ISU_v3	n/a
Chr03_CRI-A2_v1.0.a1	chromosome	Chr03_CRI-A2_v1.0.a1:132723191..132723406 +	Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1	n/a
D10_03	chromosome	D10_03:2484837..2485046 -	Gossypium turneri (D10) genome NSF_v1_a2	n/a
CM016616.1	chromosome	CM016616.1:3494950..3495147 -	Gossypium australe (G2) genome CRI_v1.1	n/a
Dt_chr5	chromosome	Dt_chr5:9848526..9848729 +	Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1	n/a
scaffold1147.1	supercontig	scaffold1147.1:541937..542146 -	Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1	n/a
D02	chromosome	D02:64670518..64670721 +	Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1	n/a
A03	chromosome	A03:97427110..97427319 +	Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1	n/a
Ghir_D02	chromosome	Ghir_D02:67145013..67145216 +	Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1	n/a
Ghir_A03	chromosome	Ghir_A03:110075714..110075923 +	Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1	n/a
D02	chromosome	D02:67181520..67181723 +	Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1	n/a
A03	chromosome	A03:108753777..108753986 +	Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1	n/a
D02	chromosome	D02:68470118..68470321 +	Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1	n/a
A03	chromosome	A03:107182927..107183136 +	Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1	n/a
D02	chromosome	D02:65584287..65584492 +	Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1	n/a
A03	chromosome	A03:102458213..102458422 +	Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1	n/a
A03	chromosome	A03:102434244..102434453 +	Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1	n/a
scaffold10232	supercontig	scaffold10232:169607..170412 +	Gossypium barbadense (AD2) '3-79' genome HAU_v1	n/a
Gbar_D02	chromosome	Gbar_D02:64999764..64999983 +	Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1	n/a
Gbar_A03	chromosome	Gbar_A03:102374500..102374727 +	Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1	n/a
D02	chromosome	D02:66216502..66216723 +	Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1	n/a
A03	chromosome	A03:104705242..104705471 +	Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1	n/a
CM017624.1	chromosome	CM017624.1:67304022..67304249 +	Gossypium tomentosum (AD3) genome HGS_v1.1	n/a
CM017612.1	chromosome	CM017612.1:104080773..104080982 +	Gossypium tomentosum (AD3) genome HGS_v1.1	n/a
CM017650.1	chromosome	CM017650.1:68925533..68925744 +	Gossypium mustelinum (AD4) genome JGI_v1.1	n/a
CM017638.1	chromosome	CM017638.1:111196570..111196771 +	Gossypium mustelinum (AD4) genome JGI_v1.1	n/a
CM017702.1	chromosome	CM017702.1:65814166..65814385 +	Gossypium darwinii (AD5) genome HGS_v1.1	n/a
CM017690.1	chromosome	CM017690.1:105188573..105188796 +	Gossypium darwinii (AD5) genome HGS_v1.1	n/a
D02	chromosome	D02:69480429..69480632 +	Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1	n/a
A03	chromosome	A03:110755672..110755881 +	Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1	n/a
Chr03	chromosome	Chr03:2914082..2914291 -	Gossypium herbaceum (A1) 'Mutema' genome WHU_v1	n/a
Chr03	chromosome	Chr03:2983477..2983692 -	Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1	n/a
Chr03	chromosome	Chr03:60528029..60528248 +	Gossypium raimondii (D5) 'Grai D502' genome HAU_v1	n/a
B_03	chromosome	B_03:3017395..3017614 -	Gossypium anomalum (B1) genome NSF_v1	n/a
Chr05	chromosome	Chr05:63558677..63558888 +	Gossypium thurberi (D1-5) genome CRI_v1	n/a
chr05	chromosome	chr05:48059346..48059666 +	Gossypium armourianum (D2-1) genome ISU_v1	n/a
Chr_05	chromosome	Chr_05:41402478..41402697 +	Gossypium harknessii (D2-2) genome ISU_v1	n/a
Chr05	chromosome	Chr05:65042649..65042858 +	Gossypium davidsonii (D3d-8) genome CRI_v1	n/a
Chr05	chromosome	Chr05:42199900..42200109 +	Gossypium aridum (D4) genome ISU_v1	n/a
Chr05	chromosome	Chr05:35646082..35646440 +	Gossypium gossypioides (D6) genome ISU_v1	n/a
Chr05	chromosome	Chr05:43786423..43786630 +	Gossypium lobatum (D7) genome ISU_v1	n/a
E03	chromosome	E03:122729380..122729581 +	Gossypium stocksii (E1) genome NSF_v1	n/a
F03	chromosome	F03:107697563..107697785 +	Gossypium longicalyx (F1) genome NSF_v1	n/a
Chr03	chromosome	Chr03:3440988..3441185 -	Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1	n/a
Chr05	chromosome	BNL3259:9..530 . Chr05:61607204..61607736 +		n/a
Chr10	chromosome	BNL3259:9..530 . Chr10:4321824..4322356 +		n/a

Germplasm


Stock Name	Type
Deltapine 90	accession

Relationships

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


Feature Name	Unique Name	Species	Type
BNL3259_orig	BNL3259_orig	Gossypium hirsutum	sequence_feature

Image


File Name	Legend
48_FISH_TAG-115-675.jpg	Twenty-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]

Map Positions


#	Map Name	Linkage Group	Bin	Position	Locus	MapViewer
1	CCRI-36 x Hai-7124, F2 (2007)	AD_ch03_At.03	N/A	73.3	BNL3259a	View
2	Guazuncho-2 x VH8-4602, BC1 (2005)	AD_ch03_At.03	N/A	109.2	BNL3259a	View
3	Guazuncho-2 x VH8-4602, BC2 (2005)	AD_ch14_Dt.02	N/A	136.7	BNL3259a	View
4	TM-1 x 3-79, RIL (2012)	AD_ch14_Dt.02	N/A	29.37	BNL3259a	View
5	TM-1 x 3-79, RIL (2014)	AD_ch14_Dt.02	N/A	97	BNL3259a	View
6	Monsanto SSR Bin Map, (2009)	AD_ch14_Dt.02	N/A	41	BNL3259a	View
7	CCRI-36 x Hai-7124, F2 (2007)	AD_ch14_Dt.02	N/A	167	BNL3259b	View
8	Guazuncho-2 x VH8-4602, BC1 (2005)	AD_ch14_Dt.02	N/A	160.6	BNL3259b	View
9	Guazuncho-2 x VH8-4602, BC2 (2005)	AD_ch03_At.03	N/A	96.9	BNL3259b	View
10	TM-1 x 3-79, RIL (2012)	AD_ch03_At.03	N/A	20.59	BNL3259b	View
11	TM-1 x 3-79, RIL (2014)	AD_ch03_At.03	N/A	95.8	BNL3259b	View
12	Guazuncho-2 x VH8-4602, consensus (2009)	AD_ch14_Dt.02	N/A	99.62	BNL3259	View
13	Guazuncho-2 x VH8-4602, consensus (2009)	AD_ch03_At.03	N/A	91.2	BNL3259	View
14	Guazuncho-2 x VH8-4602, RIL (2009)	AD_ch14_Dt.02	N/A	81.01	BNL3259	View
15	Guazuncho-2 x VH8-4602, RIL (2009)	AD_ch03_At.03	N/A	61.12	BNL3259	View
16	AD-genome wide Reference Map (2009)	AD_ch14_Dt.02	N/A	188	BNL3259	View
17	Xinluzao-1 x Hai-7124, F2 (2008)	AD_chU	N/A	22.3	BNL3259	View
18	Handan-208 x Pima-90, F2:3 (2007)	AD_ch03_At.03	N/A	154.7	BNL3259	View
19	AD-genome wide Reference Map (2009)	AD_ch03_At.03	N/A	184	BNL3259	View
20	(YM1 x CCRI35) x (YM1 x 7235), 4WC (2012)	AD_ch14_Dt.02	N/A	45.1	BNL3259	View
21	T582 x Hai-7124, F2 (2010)	AD_ch03_At.03	N/A	0	BNL3259	View
22	Yumian-1 x T586, RIL (2015)	AD_ch14_Dt.02	N/A	139.6	BNL3259	View
23	Yumian-1 x 7235, RIL (2015)	AD_ch14_Dt.02	N/A	91.9	BNL3259	View
24	DH962 X Ji Mian 5, F2 (2015)	AD_ch14_Dt.02	N/A	51.84	BNL3259	View
25	DH962 x Ji Mian 5, RIL (2015)	AD_ch14_Dt.02	N/A	9.9	BNL3259	View
26	SG 747 x Giza 75, BIL (2013)	AD_ch03_At.03	N/A	16.9	BNL3259	View
27	CCRI-35 x Yumian-1, RIL (2015)	AD_ch14_Dt.02	N/A	15.4	BNL3259	View
28	HS-46 x MARCABUCAG8US-1-88, RIL (2009)	AD_ch14_Dt.02	N/A	50	BNL3259-200	View
29	TM-1 x Hai-7124, BC1 (2007)	AD_ch03_At.03	N/A	0	BNL3259-210	View
30	Vsg x (TM-1 x Hai-7124), DH (2005)	AD_ch03_At.03	N/A	115.4	BNL3259-210	View
31	TM-1 x Hai-7124, BC1 (2012)	AD_ch03_At.03	N/A	0	BNL3259-210	View
32	TM-1 x Hai-7124, BC1 (2007)	AD_ch03_At.03	N/A	24.3	BNL3259-295	View
33	TM-1 x Hai-7124, BC1 (2008)	AD_ch03_At.03	N/A	25.48	BNL3259-295	View
34	TM-1 x Hai-7124, BC1 (2012)	AD_ch03_At.03	N/A	24.2	BNL3259-295	View
35	Vsg x (TM-1 x Hai-7124), DH (2005)	AD_ch03_At.03	N/A	110	BNL3259-225	View
36	Vsg x (TM-1 x Hai-7124), DH (2005)	AD_ch14_Dt.02	N/A	115.8	BNL3259-222	View
37	Vsg x (TM-1 x Hai-7124), DH (2005)	AD_ch14_Dt.02	N/A	119.6	BNL3259-205	View
38	Vsg x (TM-1 x Hai-7124), DH (2005)	AD_ch14_Dt.02	N/A	157.3	BNL3259-227	View
39	Zhongmiansuo-12 x 8891, RIL (2007)	AD_ch14_Dt.02	N/A	0	BML3259	View
40	Yumian-1 x T586, F2:3 (2005.v0)	AD_ch08_At.08	N/A	11	BNL3259(C3,C14)	View
41	Yumian-1 x T586, F2:3 (2005.v0)	AD_ch24_Dt.08	N/A	11	BNL3259(C3,C14)	View
42	CCRI-35 x Yumian-1, RIL (2017)	AD_ch14_Dt.02	N/A	127.29	BNL3259	View
43	TM-1 x 3-79, RIL (2012.v3)	AD_ch03_At.03	N/A	95.78	BNL3259b	View
44	TM-1 x 3-79, RIL (2012.v3)	AD_ch14_Dt.02	N/A	97.05	BNL3259a	View
45	PD 94042 x (AD)4-08, F2 (2016)	AD_ch14_Dt.02	N/A	40.9	BNL3259	View
46	TM-1 x Hai-7124, BC1 (2012)	AD_ch14_Dt.02	N/A	120	BNL3259-255	View

Sequence

>BNL3259 ID=BNL3259; Name=BNL3259; organism=Gossypium hirsutum; type=genetic_marker; length=210bp
TTTTGAAATTCCAGCGAAGGGAGAGGAGACACACACACACACACACACAC
AGAGATCTTCAAATTTCATCAATGGATCATTCAAAGGTTCAAGAGGTAAC
TTCAATGATAAACCCTTAAGCTTTCCATTTTGGATCTTTAATTTGTCTTC
TGAATTTATTTATATAAATATTTCGATTCTTGTCCAGATCGTGGAGAAGC
AGGTATTGAC

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BNL3259, BNL3259 (genetic_marker) Gossypium hirsutum