Validation of Simple Sequence Length Polymorphism Regions of Commonly Used Mouse Strains for Marker Assisted Speed Congenics Screening

Table 3

The markers that yielded PCR bands but could not be included in the panel due to their not meeting the set criteria.

(a) Category 1: markers that yielded the same size bands in all the strains

Marker	cM	Primer F	Primer R	Lab code
D2Mit74	103.43	CCAAGCTTGCAGTTTGTTAGC	AGGTGTTATTGAGCCCTGTATAGC	2-6A
D10Mit88	28.64	AAGATGAGAAGATAACATGTCAGGC	TTCTGAATTAAGTTCATCTGAACCC	10-2C
D11Mit226	5.64	AGGTGAACTCTTTTGAAGTTTGTG	AAAGGAGTGACTGAGAAAGACACC	11-1
D11Mit60	42.86	AGAGAGGCAAAAATTCCAAGC	CTTCCTGATGGTAGGATTTAGGC	11-60
D16Mit51	53.78	CCTCAGGTCAGTCAGGATTTAA	CCTGTTCACCCTCTCCACAT	16-5
DXMit57	16.24	AGTAGCAAGTAGACTCTCAAAGAGGG	TCTGGCATACATGGGCACT	X-57
DXMit81	20.59	GAGGAGCATCAACCTTCTCG	GAGGTGGGGAGAAACAGAGG	X-81
DXMit63	41.51	TTATAAATTAGTGTTACCACATGCAGC	AACATTTTTTTCCTAGCATGTGTG	X-63
DXMit186	76.75	ATCAATGCATAGTATTTGGGCC	AATTTGTCACTGCGGGTAGG	X-186

(b) Category 2: markers that failed to amplify a PCR band in some strains

Marker	cM	Primer F	Primer R	Lab code
D1Mit375	23.18	TAAATCCATAGATGATAGATCAGTGTG	GTGGAAAAAAAACCTAAGACACC	1-2C
D1Mit76	33.31	ACAAAGGAAACTAAACAGACTCGG	CTCCCTCAAATACATCTTTGGC	1-3C
D1Mit308	50.78	GAGGCTATGAGTCAAATGGACC	TTTATGAGGTGCTGAGATGCA	1-5
D2Mit448	65.66	TACTGTTTGCATTTGAGTGCG	AAAAAGTAATGGTTGGGGCC	2-4B
D3Mit278	32.59	TCTAATATTGGAAAATGAATTTCTCTC	TATGCCCACATGCACACC	3-3P
D5Mit309	42.22	TAGAGCCTATTTCAAACCCCC	GTTGCATCCATAGCAAGCAA	5-4
D10Mit49	1.91	GGAATTTACACTGGAATACAACCC	GTGGGCATTTGCACTGTG	10-1
D11Mit168	78.74	CAGGGATTTGACTTTTAACCTCC	GAAATGGCTCCTACAACCTCC	11-168
D14Mit132	6.03	GAACAGCACCATCCACACAC	GTGGGGTTATATGCAGATACTCG	14-1
D15Mit147	46.85	GATGTGTGAAAAATTTTGTTTCTTG	GTCTCAAAGGAATAAGAAAGAGATGG	15-5
D17Mit3	34.9	GATCTTTTCTTATTCTGGTT	GCAAAGTCATGTACTCTGAG	17-3B
D17Mit39	45.64	CCTCTGAGGAGTAACCAAGCC	CACAGAGTTCTACCTCCAACCC	17-5
D18Mit48	51.89	TTGCACTCACAGGGCACAT	TCAGAGTTTCCAGAAGACACCA	18-6
D18Mit25	59.05	CTGGAAATAAAACCTGGGCA	TTTAGCCTAACTGAGTTCCAGACC	18-7
D19Mit31	8.84	CAATACAGAGTAATGATTGCCTGA	TTCACATTTTGGGATGCTCA	19-1B
D19Mit41	13.18	AGCCCTCCACCCAGTTTC	TCTGGGGAAAAAGGATGAGA	19-2
DXMit124a	4.25	AAGGAGAAGTAGAAGAAAGAAAAGAGG	GGTGTAGCCTCAAAAAAGATGG	X-124a
DXMit68	29.49	TCCTTTGGCCTCCTGCATAT	TGTTCTTACAATGAGCCTCATAGG	X-68
DXMit114	42.82	ATGGCATCCACAGTACCACA	GTAAAATCAATTTGTGAATAAGGAAGC	X-114
DXMit95	45.86	CTGTCAATCTAATTCTCTATGTCTGTG	CTTTCCTGGGTGGCAGTG	X-95
DXMit155	67.49	TGTGCACCACCACCATTC	AGGATCTGAGTGCCCAACC	X-155

(c) Category 3: markers that amplified multiple PCR products in most (or all) strains

Marker	cM	Primer F	Primer R	Lab code
D11Mit86	32.13	TTGACATTGTGACAAAGACTTTCA	AAGGCATCATGAGGTTTTTAGTG	11-3
D12Mit118	44.93	CATCTTCAATAAAATGGAGATGTACA	CGCTTTCCCTTCATGTACTAGC	12-4
D13Mit107	50.2	CAACTGAGCCACATTCCTAGC	CAGCCACAGGATGATGAGG	13-4
DXMit98	72.38	GAGAGCAGGACTATGACTTG	ACACACCAGTTCGCACACAT	X-98
DXMit222	78.31	TTGGTTTGGGGTTTTTTTTG	ATTCCTGATAATGTCTTCTGGACA	X-222