BNL3971, BNL3971 (genetic_marker) Gossypium hirsutum

Marker Overview


Name	BNL3971
Genbank ID	N/A
Type	SSR
Species	Gossypium hirsutum
Germplasm	Deltapine 90
Source Sequence	BNL3971_orig
Source Type	genomic
Repeat Motif	(TC)15
PCR Condition	Annealing temperature: 55
Primer 1	BNL3971_F: CACATATTTTTGCCTCACGC
Primer 2	BNL3971_R: TGTGGACCCAAAAAGGAAGA
Polymorphism	P_ BNL3971
Comment	Primer data obtained in 2000

Germplasm


Stock Name	Type
Deltapine 90	obsolete_cultivar

Relationships

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


Feature Name	Unique Name	Species	Type
BNL3971_F	BNL3971_F	Gossypium hirsutum	primer
BNL3971_R	BNL3971_R	Gossypium hirsutum	primer

This genetic_marker is contained in the following chromosome_arm feature(s):


Feature Name	Unique Name	Species	Type
2 Long	2 Long	Gossypium hirsutum	chromosome_arm

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


Feature Name	Unique Name	Species	Type
short fiber content	qSFC.PA-F2_ch02-1.pop04-06	Gossypium hirsutum x mustelinum	QTL

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


Feature Name	Unique Name	Species	Type
BNL3971	BNL3971	Gossypium hirsutum	marker_locus
BNL3971b	BNL3971b	Gossypium hirsutum	marker_locus
BNL3971-140	BNL3971-140	Gossypium hirsutum	marker_locus
BNL3971	BNL3971-60.192	Gossypium hirsutum	marker_locus
BNL3971	BNL3971-4.7	Gossypium hirsutum	marker_locus

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


Feature Name	Unique Name	Species	Type
BNL3971_orig	BNL3971_orig	Gossypium hirsutum	sequence_feature

Alignments

The following features are aligned


Aligned Feature	Feature Type	Alignment Location
A02	chromosome	A02:46448807..46448950 +
CM018203.1	chromosome	CM018203.1:44548619..44548738 +
Chr3	chromosome	Chr3:57632671..57632808 -
Chr01_CRI-A2_v1.0.a1	chromosome	Chr01_CRI-A2_v1.0.a1:81706028..81706165 -
At_chr3	chromosome	At_chr3:92099615..92099758 -
A02	chromosome	A02:43443417..43443560 +
Ghir_A02	chromosome	Ghir_A02:47376646..47376788 +
A02	chromosome	A02:45601400..45601543 +
D03	chromosome	D03:33425628..33425771 -
A02	chromosome	A02:45953545..45953687 +
A02	chromosome	A02:45404755..45404898 +
scaffold11147	supercontig	scaffold11147:172978..173097 -
Gbar_A02	chromosome	Gbar_A02:45047359..45047478 +
A02	chromosome	A02:45506048..45506167 +
CM017611.1	chromosome	CM017611.1:44813655..44813798 +
CM017637.1	chromosome	CM017637.1:47998689..47998840 +
CM017689.1	chromosome	CM017689.1:45321119..45321238 +

Sequence

>BNL3971 ID=BNL3971|Name=BNL3971|organism=Gossypium hirsutum|type=genetic_marker|length=144bp
CACATATTTTTGCCTCACGCTCTCCCTCTTATGTCAGTTTCTCCCCTTCT
CTTTCAAGGTTTCAGATTTTGATTTCTCTCTCTCTCTCTCTCTCTCTCTC
TCTCTTTCTCCTTTGATTTTCTTTTCTTCCTTTTTGGGTCCACA

Map Positions


#	Map Name	Linkage Group	Bin	Chromosome	Position	Locus	MapViewer
1	3-79 x NM24016, RIL (2008)	3-79 x NM24016, RIL (2008).3N-RIL_chr02	N/A	AD_chr.02	29.1	BNL3971	View
2	CCRI-36 x Hai-7124, F2 (2007)	CCRI-36 x Hai-7124, F2 (2007).CH-F2_chr02	N/A	AD_chr.02	53.1	BNL3971	View
3	Guazuncho-2 x VH8-4602, BC1 (2005)	Guazuncho-2 x VH8-4602, BC1 (2005).GV-BC1_chr02	N/A	AD_chr.02	84.3	BNL3971	View
4	Guazuncho-2 x VH8-4602, consensus (2009)	Guazuncho-2 x VH8-4602, consensus (2009).GV-cons_c02	N/A	AD_chr.02	45.54	BNL3971	View
5	Guazuncho-2 x VH8-4602, RIL (2009)	Guazuncho-2 x VH8-4602, RIL (2009).GV-RIL_ch02	N/A	AD_chr.02	36.49	BNL3971	View
6	Handan-208 x Pima-90, F2:3 (2007)	Handan-208 x Pima-90, F2:3 (2007).HP-F2:3_chr02	N/A	AD_chr.02	2.5	BNL3971	View
7	Jiang-Ling-Zhong-Mian x Zhe-Jiang-Xiao-Shan-Lu-Shu, F2 (2008)	Jiang-Ling-Zhong-Mian x Zhe-Jiang-Xiao-Shan-Lu-Shu, F2 (2008).JZ-F2_A02	N/A	A_chr.02	41.2	BNL3971	View
8	Monsanto SSR Bin Map, (2009)	Monsanto SSR Bin Map, (2009).BIN-SSR_chr02	N/A	AD_chr.02	70	BNL3971	View
9	Palmeri x K-101, F2 (2007)	Palmeri x K-101, F2 (2007).PK-F2_chr02	N/A	AD_chr.02	88.7	BNL3971	View
10	AD-genome wide Reference Map (2009)	AD-genome wide Reference Map (2009).Ref-chr17	N/A	AD_chr.17	72	BNL3971	View
11	TM-1 x 3-79, RIL (2006)	TM-1 x 3-79, RIL (2006).T3-RIL_chr.02	N/A	AD_chr.02	48.3	BNL3971	View
12	TM-1 x 3-79, RIL (2012)	TM-1 x 3-79, RIL (2012).T3-RIL.12_c02	N/A	AD_chr.02	59.5	BNL3971	View
13	Xinluzao-1 x Hai-7124, F2 (2008)	Xinluzao-1 x Hai-7124, F2 (2008).XH-F2_lg6/chr02	N/A	AD_chr.02	117.3	BNL3971	View
14	Emian-22 x 3-79, BC1 (2011)	Emian-22 x 3-79, BC1 (2011).E3-BC1_chr02	N/A	AD_chr.02	78.32	BNL3971	View
15	AD-genome wide Reference Map (2009)	AD-genome wide Reference Map (2009).Ref-chr02	N/A	AD_chr.02	96	BNL3971	View
16	TM-1 x 3-79, RIL (2014)	T3-RIL.14_chr02	N/A	AD_chr.02	60.2	BNL3971	View
17	CCRI 12-4 x (AD)5-7, F2 (2015)	CAD5-F2_chr02	N/A	At.02	96.2	BNL3971	View
18	SG 747 x Giza 75, BIL (2013)	SG-BIL_chr02	N/A	AD_chr.02	56.2	BNL3971	View
19	Handan-208 x Pima-90, F2:3 (2007)	Handan-208 x Pima-90, F2:3 (2007).HP-F2:3_chr17	N/A	AD_chr.17	141.1	BNL3971b	View
20	TM-1 x Hai-7124, BC1 (2007)	TM-1 x Hai-7124, BC1 (2007).TH-BC1_chr02	N/A	AD_chr.02	59.6	BNL3971-140	View
21	TM-1 x Hai-7124, BC1 (2008)	TM-1 x Hai-7124, BC1 (2008).TH-BC1.08_chr02/A2	N/A	AD_chr.02	48.12	BNL3971-140	View
22	Vsg x (TM-1 x Hai-7124), DH (2005)	Vsg x (TM-1 x Hai-7124), DH (2005).VTH-DH.05_chr02	N/A	AD_chr.02	83	BNL3971-140	View
23	TM-1 x 3-79, RIL (2012.v3)	T3-RIL.12v3_chr.02	N/A	AD_chr.02	60.19	BNL3971	View
24	PD 94042 x (AD)4-08, F2 (2016)	PA-F2_chr02-1	N/A	At.02	4.7	BNL3971	View

Image


File Name	Legend
45_FISH_GEN-178-1117_fig2.jpg	BAC 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.jpg	Two 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]
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]

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BNL3971, BNL3971 (genetic_marker) Gossypium hirsutum