High resolution physical map of porcine chromosome 7 QTL region and comparative mapping of this region among vertebrate genomes

Demars, Julie; Riquet, Juliette; Feve, Katia; Gautier, Mathieu; Morisson, Mireille; Demeure, Olivier; Renard, Christine; Chardon, Patrick; Milan, Denis

doi:10.1186/1471-2164-7-13

Table 1 Porcine markers developed for RH mapping and BAC contig construction

From: High resolution physical map of porcine chromosome 7 QTL region and comparative mapping of this region among vertebrate genomes

STS-EST	Sequence up	Sequence on	Size of PCR fragment	% Retention on IMNpRH2	Position (cR)	N° INRA Contig	Human Location (Mb)
*Arrow number 1 on figure 2*
bI0149A04F	CTCTCCTTCAAAGGCCTCCT	ATGCCTCAGGCGATCTAATG	233				33.03
COL11A2	CTCCCACCTGGAGCCTGT	CAGTGTCCTTTCTCTTCTCTTCC	154	48%			33.24
RXRB	TCCAGAGTCCCCTCTCACAC	CCAAATACCACCTCCACCAC	247	41%			33.27
HKE4	CCGCTCTCTGCTCCAGAT	AAGAAAGGCGACAATTCCAC	487	42%	0		33.28
HSD17B8	CTCAAGGACCCTGGACTCTG	GGAATTTATTAGGGTCACAAGCA	186	45%	15		33.28
bI0392F02R	AAGATGCCCTTGAGCTGCTA	GCAGCAGCACATTGAGAGAA	136
RING1	GCCACTTGTTCTCATTTGTGTC	ATCCAAAGTGACCCCACAAG	150	48%			33.28
*Arrow number 4 on figure 2*
bI0149A04R	CTTGGATCAAACCCACATCC	CGGCGTGTAGTGATTGCTTA	282				55.93
bI0248H04R	AGGGAATGACAACAGCAACC	TGGAGCAGATTTAGGATTTGG	163			5174	55.80
bI0123E02R	CCGAGTGGAATCATATGCTCTT	TCCTCGACGAAGTTCTCCAT	153			5174	55.78
bE276E04SP6	GTAGGGTTAGCCTGCTGTGG	TGTCGAAACTTGGCCTCTCT	127				55.77
BMP5	ACAGCAAAAAGCAAAGACCA	GTAAGTAGGTTGTCAGGCTTGC	230	41%	32		55.73
bI0895F12R	GGCAAAGCAATTCCACAGAT	CCGAAACCTCATGGTTCCTA	198	33%	59	5174	55.71
bI0123E02F	GAGACCCAGAAACCAACCAA	GCAGGCTTGTCTCCAATGAC	249			5174	55.67
bI0474F10F	CAAGTGAAGCAAATCCACCA	ACTCCTGCACTGGCCATATT	232
bI0474F10R	CATGCTTGCTAACACCAGGA	AGTGGCTCTCAGCCTCAAAA	176
bI0187D03R	AGAAACACCAGCCTCCTCAA	CCACAGCACAGTGCAGAAAT	256	43%	82	5488	55.51
bI0187D03F	CGACACCCACAAAGGAAAGT	GTGATGCATTTTGCCACATC	169			5488
bI0773C07R	AGAAAGGTGGGGAGAGCATT	GCACTGGAGCACAGCAAATA	132				55.36
bI0136E09F	CTGCTTGTGGGGATACCATT	TCCTCACCTGATTCGCTACA	158	35%	89	5488	55.30
bI0773C07F	GGCATGTTGAAAGCCAAGAT	TTTGGCTTAAGGGAATGTCG	213
bE0164A10SP6	GCACCTGGACTGGAGGAATA	AGGGCCTAGGTCCACTCAAT	115				55.23
HCRTR2	TGTGTCGGTGTCTGTGTCTG	CGATCCAGATGATGACGATG	131	44%	101		55.15
bE0164A10T7	AATCTTTGGGCAGTGAGTCG	CATGGAATCACCGAAATGTG	230				55.01
bI0759D02R	TTTTAACGCAATCTGCTTGG	CAGCTCCCTCATTTTGAAGC	151	45%	121	6382	54.90
bI0699B10R	TGTTGGTTTGGGTGTTGAGA	TCTTGAGGCAGTGTGCATTC	262			6382
bE0047O02T7	CTCACCTCCATCCACAACCT	GCTGGTGCCAAGATCCTAAG	235				54.83
RPCI44_0470A18F	CCTAAGTGCCATTCTCCTCCT	AAAGCAGGCCACTCGAAGTA	241				54.82
bI0131F01R	CACCACACACAGCAACATCA	TCAGGAGCTCCCAGGAATAA	103	41%	138	1178
bI0131F01F	CCTCTCTGGTCTCTGCATCC	CTCCTGTCTTCCAGCTCCTG	157			1178	54.78
SW2019	ATGATGCGAACCTGGAACTC	TATGTGTAACTTGGTCCCATGC		30%	153
bI0444G09F	GGCAATCATTTCCACCTTGT	AGAACTGGAGGCAGTGGAGA	231			1178
bI0704C03F	CGGCCCTATTTTTCACTTCA	CTCCCTGGTGCCAAATAGAA	172			1178	54.55
bI0295F03F	CCCACCCAAGGTTGACTAGA	GGAACTCCCAACGTGAACTC	129			5990	54.41
bI0704C03R	AACCCAGGACCCAAGGATAC	ACTCTCCTTCCACAGCCAGA	232	33%		1178	54.31
TINAG	ATTCCTGGGGAAAGTCATGG	AAGGCATGACCTTATGGAAAT	157	33%	175		54.28
bI0295F03R	GTGGTGCAGAGGGTTAAGGA	TAGGGCTTTGCTTGTCTCGT	269	47%		5990
bI0716B06F	TCCATTTGTTGGGGGTTTTA	ATAAGCCTCAGCCTCCATGA	177			5990	54.19
bI0355A07F	GGCCAGATGGAAATCTTTGA	CCAGCGGATGTGTCCTATTT	252	29%	196	3302	54.17
bI0615F10R	TCTGTTTCCCATTTGCACCT	CCACTGCAGTCAAGGTCTCA	186			3302	0.00
bI0872D06F	TCATGCTGGCAAATGGTAAA	ATTTCTGGCAGAGCGGATAA	116	33%		3302	53.78
bI0438F07R	CGGGTGGAAGGAGATCACTA	TTCAAAGAAGGCATGGTTCC	244				53.77
LANO	GGGATGCTGAATGTGGTATTT	TTTTCTCTTTTTGTGCTTTTCTG	287	38%	235		53.77
bI1044F02R	TACATGCACAGTTGGGGAAA	ACCCCTTTGGTGGTGTTGTA	144
bI0547G12F	ATCTCTGAGCAGGTCGCAGT	ATCTTCCCTGATCCCCACTT	188			2270
bI0547G12R	TGTCAGGGTGTCGGTTGTAG	GTCCTAACCCATGCAGCAGT	174			2270
bI0285E03R	AATTCCTCCGCTCACTCTGA	TCAGGAGGGGAAGCTGACTA	174			2270
GCLC	ACCATCCTACCCTTTGGAGA	TTTCCCCCAGTAAAGACGTG	150	37%	268		53.47
bI0879H07F	CTGGACGTGGAGTCTGGTTT	TTGCCCTTGATGCTAAATCC	300	38%	324	2270
*Arrow number 6 on figure 2*
bE251O22T7	TGGCAGCTTGACATCAGTTC	AATGTGCCAGAGGGTTTGAG	210				62.48
bI0879H07R	GAGCCTGTTAGCGCATTTCT	ATGCCAAACCATCTGTCCTC	189			2270	62.51
bT79E18SP6	TGTGGTATGAACCCAGGACA	AAGGGGATTTTCCCCATGTA	211				62.60
bE235D14SP6	TCGGAAGATTGCCTATTTGG	TGAAGATGACTGCTGCCTTG	192				62.67
bE251O22SP6	ATCTGGCCCCTGTTCTCTTT	GAAAATTTCTCTCCCCTGTGC	232				62.73
bI0052D02F	ACAGCATTATGCCGATTTCT	CCTACAAGAACCTTACAGCATTAGA	100			137	62.78
bI0052D02R	TGGCTTTATAATTATGTGCTAATGAC	CCTACATGGGAAAAGAATTTGAA	169	27%		137
bI0137B12F	GCATGGAGTTTGGTGTTGTG	TTAGGTGAAAGGCCTGATGG	165			137
bI0137B12R	CCAAACCCAAACTCCCTGTA	TCAGCAACATGGATGCAACT	218			137
bI0666E01F	GCATGCAAAGGCACTCAGTA	CAAGAGCAAATGCATTCCAA	171	35%		236	62.91
bI0455F01R	CAAGAGCAAATGCATTCCAA	GCATGCAAAGGCACTCAGTA	171	35%		137	62.91
bI0415F05R	TCTGAGCTGCATTTGTGACC	GCTGGTTCTGAATCCCCATA	249			236	62.98
bI0688H06R	GCATCTTTGCATGAGCCATA	CATTGGCTAGAGAGAAGAGAAACA	189			236	63.02
bI0666E01R	CCTCCGGACACTACTTCCAA	CAAAGACACACGCTGAGGAA	221			236	63.05
bI0374A03R	CAAATGCCAGGTGGTGAAAT	CCATTTTCTGAGAAGGGGTCT	192			236
bI0415F05F	AGCAATGGAAAAGCAACTGG	CGGGAACTCCTCTGCTGTT	212			236
bI0688H06F	ATGTTTGCACATTATGCCTTT	ACTGCAGGCCATTCTGACTT	234			236	63.67
SW1856	TTGTATGGTATCCTGTGATGCC	TCATTCCAAACACACAGAGTCC		42%	361
bI0586C11R	GCTGAGTTGATGCTTGACCA	CCCACTTGGGCAAAGTAAAG	193			236	63.70
bI0222C06F	TCCCGACTACAGACCAAAGG	GCATTCGATAGCAATTTGGAA	199			236	63.70
bI0374A03F	TGGGTGCAAAAAGTTTCCAG	AGAGCGACCCAAGAAAGTGA	151			236
bI0834F10R	AGGCTCCAGGCAAGAGAAG	GAGAGGAGGTTTGCCAGAGA	247			236
bI0492A07R	GGCATTTGATGCTGACACAC	CATTCGGGGATAGCGTTTTA	153			236	63.70
bI0834F10F	AACTCTGCTTCCCAGTGCAT	TAGGCTGCAGGCCTTTTCTA	222			236
bI0586C11F	ACCTTGGACGAAGTCCCTCT	GACATCCAGCATCAGCTCAA	207			236
*Arrow number 5 on figure 2*
bI0223C10R	CTTGGGCAAGGCTGATAGAC	CATTCCATAGTCGGGTGTTTTT	168			236	58.03
bI0762H12R	TGGCCCTAAAAAGACCAAAA	TGGACTGGGAAACAACTTCC	176			236	57.78
bI0492A07F	GGGCATCATCGTGTTCTTTT	GGCACAACTTTGACCTCATGT	240			236	57.69
bI0392B02R	GATGGCCTGGTGGTTAAAGA	AGTGAAAAATGCCACCAACC	180			236	57.67
bI0223C10F	TGTTCCAAAGGAAAATAGAACAAA	AAAGCAGAAGTGACCCAGCTA	227			236	57.65
bI0186F03R	GGTGCGGTCAAAAATGAAAA	TAAAAATCCAGGGCCACTCA	187			236	57.58
RPCI44_0334P20R	CCTCTGCCAGCCTCATTTAC	GCTTCAGGGAAGGGGATTAG	144				57.56
bI0392B02F	CTCCCTTGTGTCCACTTGCT	AGAGCACCACCCTTGAGAGA	206	32%		236	57.55
bI0877E01R	CTCCCCCTCCTCAGCTAAAT	TGAGGTTCACCGGATCTTTC	195	34%	412	7444	57.52
bI0877E01F	GGCCATTTGCAGTGTCTTTT	AAGCCTCAGGAACAATGCTG	164			7444	57.39
RPCI44_0334P20F	TCCCCCTTTGTTTCTTCCTT	CACGCAAATCAGAAGATGGA	195				57.38
bI0297A11R	CAGAATGCCAAGAGGGAGAG	CAGAATGCCAAGAGGGAGAG	161			7444	57.36
PRIM2A	CATAGCTTCGGAAAGGAAGG	CTTGGTGGATTGGTGAGGAT					57.29
bI0297A11F	CCACTGCCACTGACTCTTCA	TCAATGCAATCCCTGTCAAA	266		425	7444	0.00
bI0229F01F	CTGAGGGGAAGCCTAGACAG	CAGGAATACAGCCCCTACCA	227	41%		1421	57.12
BAG2	CGCCTGTTCTTCCGAGGT	GCATTTCTACGCCATTATTTCAAG	255	39%	432		57.15
bI0229F01R	TGCCACGGCATATATTTTCA	CTACACCAGAGCCACAGCAA	202			1421
bI0192A07F	CCGACTAGGATCCATGAGGA	CCTTTTTAGGGCTGCACTTG	198			1421
bI0192A07R	ACCCACTGATCGACGTTAGG	GTGGTTGGAATTTGGCACTT	209			1421	56.86
bI0783E01R	GAGGGCCTCTTAGATGCTGA	CACCCATAAGGCTTCCTCTG	260	38%	458	1421
bI0697C09R	TTATCACTGCTGTGGCTTGG	TCCCTCCCTATTGCTTCCTT	213	35%	479
bI0697C09F	ATGAGGCGAAACGAAATGAC	CAATGACTCGTGCTGGTTTG	191	25%	507	1421	56.67
bI0135F11R	CCCTCTGACAACCACCAGTT	GCAACATGGAGGGACCTAGA	163				56.68
bI0135F11F	TTGACCCTGTCGACTGCTTT	CAACACAGTGGTTGAACGTTTT	185
bT220O06SP6	TGAGAGGCCTCGTGGATTAC	TTGGAGGTGGCTCAGAACTT	155				56.58
DST	TGTCAGGTTTTCTTTTGCTTGA	GGGACACGTTTTATTTCATAGCTT	106	32%	538		56.58
bI0105B03F	TCAGGGCACTTTCTGCTGTA	GCTGGGAGTTTGGGGTTAGT	183
bI0105B03R	TCAGTTGGAGCTGAAAAACTCA	AAACCACAAAAGCCAAACCA	226				56.47
bT220O06T7	GAATGGGAGGAGGAAGTGGT	CAGCTAAAGGACGGACGAAC	228				56.44
bI0032D02F	TCTGTGTACCACCCCACTCA	CCATGGCTGGTATTTGAACC	257				56.15
bI0032D02R	AGGGGCCTGTTTACGTCTTT	CACCTTGACGTCTCATCAGC	120
COL21A1	TGCATGCTTTCATTTTCCAT	TGTTCCTTAACAACGAAGCATT	204	37%			56.03
*Arrow number 2 on figure 2*
VPS52	CAAGAAGCACAAGCCCAACT	GGGACCCAGCTTATCCTGA	190	39%	557		33.33
RPS18	CTGCAGCCATGGTAAGAGTT	GTCTTCACGACACAACACGA	350	38%			33.35
RAB2L	AAGTGTCATCANGTCGTGTCC	GCCCAGCGTAGCAGTAGAG	314	54%	578	33.37

Markers in bold belong to the framework RH map, whereas markers in italic are positioned at the most likely location. Other markers have been developed in the frame of the contig building. The arrows on the side represent the fragments conserved between the pig and human genomes. Primer sequences, retention fraction, RH map location on porcine map and human location are indicated.

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ISSN: 1471-2164

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