Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs

Ma, Junwu; Iannuccelli, Nathalie; Duan, Yanyu; Huang, Weibing; Guo, Beili; Riquet, Juliette; Huang, Lusheng; Milan, Denis

doi:10.1186/1471-2164-11-159

Table 1 Locations of all markers on the different porcine maps and comparison with those on the human physical map

From: Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs

Ord.¹	Marker name²	SSC-X cyto-genetic map	Blast matched clones on pig genome³	IMpRH map_Carthagene (cR)⁴	IMpRH map_INRA2005 (cR)⁵	SSC-X clone map (Mb)⁶	HSA-X physical map (Mb)⁷	INRA genetic map (Kosabi; cM)	JXAU genetic map (Kosabi; cM)⁸	USDA-MARC genetic map at NCBI (cM)⁹
1	SW949	Xp24/Yp	CH242-231E5	58	2126	0			0	0
2	SW980	Xp24-23	CH242-336E9	285	1861	7.65	11.38	0	16	11.9
3	SW1903	Xp21	CH242-273O11	523	1588	21.28	25.47	23.7	46.6	33
4	SW2456	Xp12	CH242-31B7	864	1345	38.46	42.14	46	65.5	55.4
5	UMNP1174	Xp11.2	CH242-69I19	976	1253	42.25	47.22	56.5	76.1
6	SW2476	Xp11.2	CH242-24N13	985	1250	42.70	48.32			77.6
7	SWR1861			992	1211			59.5	78.7	65.7
8	UMNP448		CH242-147G7	1027	1200	43.78	50.42
9	BE102J23.0003R1		CH242-102J23			44.30	50.94
10	SW259	Near centro-mere	CH242-225C1	1293	1045	54.21	63.35	62.7	79.9	74.4
11	MCSE3F14		CH242-3F14	1301	1093	55.27	65.30
12	BE145J20.0597R1	Xq12	CH242-145J20			58.94	69.06
13	MCST2J13	Xq13	PigE-2J13	1480		63.85	74.74
14	SW1994	Xq13	CH242-123K13	1547	1007	67.72	79.92	62.8	80.1	74.4
15	MCSE58H4	Xq13	CH242-58H4	1596	983	70.38	83.46
16	BE8B11.0679Y1	Xq21	CH242-8B11			77.85	97.31
17	MCSE65L7	Xq21	CH242-65L7	1768	932	82.80	91.66
18	UMNP71	Xq21	CH242-203F13	1797	905	84.83	93.18	62.8	80.2
19	UMNP374	Xq21	CH242-74J23	1840	840	77.38	97.00
20	UMNP1218	Xq21	CH242-166I17	1884	800	80.02	99.84	62.8	80.4
21	BE497I6FB48R	Xq22	CH242-497I6			88.52	103.76
22	BE218F2FB67K	Xq22	CH242-218F2			89.33	104.46	63.2
23	SERPINA7E2B114M	Xq22	CH242-427M6			89.90	105.02		80.9
24	BE151D17.0014Y1	Xq22	CH242-151D17			90.42	105.88
25	SW1426	Xq22	CH242-264N4	1991	710	91.73	107.08	65.7	83.5	71.7
26	BE32D24.0584R1	Xq22	CH242-32D24			91.73	107.03
27	BE276J1FB107R	Xq22	CH242-276J1		700	91.87	107.20
28	BE206D8.0949R1	Xq22	CH242-206D8			92.18	107.47
29	BE386O15.1136R1	Xq22	CH242-386O15			92.27	107.86
30	IRS4.Y1	Xq22	CH242-477D6			93.33	107.86		85.9
31	MCSE313H19.0244	Xq22	CH242-313H19			93.72	108.38	67.5
32	ACSL4I3B259R	Xq22	CH242-17O13		687	93.87	108.58
33	*ACSL4I3B359M*	Xq22	CH242-17O13		687	93.87	108.58	67.9	87
34	MCSE231M24	Xq22	CH242-231M24		682	92.48	109.41	69.8	88.1
35	MCSE12P4.1041	Xq22	CH242-12P4			92.78	109.65	70.1
36	MCSE12P4.0112	Xq22	CH242-12P4					71.2
37	MCST96O22	Xq22	PigE-96O22		658	92.99	110.22	72.8	90.5
38	UMNP891			2050	656			73.4	90.9
39	BE95P6.0900R1	Xq22	CH242-95P6			94.38	110.48
40	MCSE347J6	Xq22	CH242-347J6		646	94.52	110.63	74.5	92.3
41	BE412O5B120R	Xq22	CH242-412O5			95.59	111.90
42	BE80C18FB136W	Xq22	CH242-80C18			95.76		77
43	BE504J7.0664Y1	Xq22	CH242-504J7			97.03
44	SW1522	Xq22	CH242-408J11	2168	595	97.35	113.73	77.5	95.2	55.4
45	HTR2CI3B151R	Xq22	CH242-135K13			97.56	113.90		95
46	BE371L5.0001Y1	Xq22	CH242-371L5			97.88	114.30
47	BE185O8FB63S	Xq22	CH242-185O8			98.02	114.48	78.3
48	BE219E21.0003M1	Xq22	CH242-219E21			98.16	114.79
49	UMNP93			2214	540			79.1	96.5
50	BE28B16.0529Y1	Xq23	CH242-28B16			99.34
51	UMNP870	Xq23	CH242-141A6	2246	522	102.50	117.67
52	MCSI0244D12			2261	506		118.15	81.6	98.8
53	*SLC25A5I2B103DE*	Xq23	CH242-78C24			102.00	118.36	82.5	99.5
54	UMNP1008	Xq23	CH242-458G8	2300	475	101.68	118.75
55	SW1943	Xq24	CH242-105E5	2454	440	107.17	126.14	85	101.5	87.4
56	SW1608	Xq24	CH242-238J16	2650	304	112.30	132.31	98.4	114.1	101.9
57	SW707			2672	286				120.8	107.9
58	SW2137			2694	273					108.1
59	S0218	Xq25	CH242-1I19	2765	211	117.02		111.4		114.4
60	SW2588	Xq26	CH242-394H2	3117	0	125.93	150.01		159.7	128.4

¹The most likely marker order was determined as the common order shared by most of maps.
²Markers placed on both INRA and JXAU genetic maps are indicated in bold letter, while gene-based markers are shown in italics.
³Pig clones were picked if their available sequences matched marker sequences through blast analysis at Sanger Center's website http://www.sanger.ac.uk.
⁴IMpRH1 (7000-rad) map was constructed by using Cathagene software.
⁵Positions of markers were determined by using the reference map of INRA2006 http://rhdev.toulouse.inra.fr/Do=Maps. This map was not oriented, and 0 cR corresponds the the last marker at the end of Xq arm.
⁶Locations of pig clones have been provided by UCSC Genome Browser http://pre.ensembl.org/Sus_scrofa_map/Location/Genome
⁷Placement information about homologous human sequences for porcine BAC end sequences is available at Sanger Center's website.
⁸Bold numbers indicate that the marker orders in two segments (UMNP71-UMNP1218 and ACSL4I3B359M-MCST96O22) on SSC-X clone map are inconsistent with those on the RH map, genetic maps and HSA-X physical map.
⁹Bold numbers indicate that the markers (SW2476, SW259, SW1994, SW1426 and SW1522) were in reverse order on the USDA-MARC map versus the current genetic maps or other maps.

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ISSN: 1471-2164

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