SSLP Primers

Each primer pair amplifies a unique segment of genomic DNA containing a simple tandem repeat. The PCR products differ in length between Columbia and Landsberg erecta, and often, other ecotypes. All of these primers are available at low cost from Research Genetics Inc., 2130 Memorial Parkway, Huntsville, Alabama 35801. Telephone 800-533-4363. FAX 205-536-9016. We have no connection with Research Genetics Inc., other than as a customer. Unrestricted use of these sequences and free transfer of the information between laboratories is encouraged.

Suggested PCR conditions.


The SSLP markers are mapped on the NASC RI map.


 

Chromosome 1

SSLPs Primer Sequence Size of
Columbia		 Size of
Landsberg		 Map position
T7I23-77816 T7I23-77816-F CATGCACGTACGATTTGTTTAAC 199 bp < than Col 0.59
T7I23-77816-R GTGTCCTTTTTTCTCAACGATG
nga59 nga59-F GCATCTGTGTTCACTCGCC 111 115 0.79
nga59-R TTAATACATTAGCCCAGACCCG
ATHACS ATHACS-F AGAAGTTTAGACAGGTAC 259 256 1.20
ATHACS-R AAATGTGCAATTGCCTTC
ATEAT1 ATEAT1-F GCCACTGCGTGAATGATATG 172 162 1.75
ATEAT1-R CGAACAGCCAACATTAATTCCC
F21B7-1334 F21B7-13341-F CACGATATGATCAAGCTTTAACG 199 bp < than Col 1.28
F21B7-13341-R TGACTACATGGAGATTATGGCC
F20D22-5521 F20D22-55210-F CCCAAGTGACGTCTGGTTTC 201 bp < than Col 1.98
F20D22-55210-R AACAAAATGAGTTTCTCTGCATG
F19P19-75410 F19P19-75410-F CCACGTAGGTCAAGAAGAAGAAG 202 bp < than Col 2.59
F19P19-75410-R TGTCTGCTGCGATAGAGAGAG
T1G11-89778 T1G11-89778-F GAAGACAAAGCTCTGCAGTAATG 206 bp < than Col 2.58
T1G11-89778-R AATTGCATAAGGCACTTGAAAG
F7G19-92589 F7G19-92589-F TTCAAAAATCGTGAGATGAAATG 197 bp > than Col 8.24
F7G19-92589-R TCGTTGAAAACGATTAGATTGG
nga63 nga63-F AACCAAGGCACAGAAGCG 111 89 9.37
nga63-R ACCCAAGTGATCGCCACC
F21M12-99139 F21M12-99139-F GGCTTTCTCGAAATCTGTCC 200 bp < than Col 9.37
F21M12-99139-R TTACTTTTTGCCTCTTGTCATTG
AthSRP54A AthSRP54A-F TGAATTATGGAATCAATGTTCG 247 245 16.80
AthSRP54A-R AAAAGGAACCCTACCAAAAACA
F19G10-23714 F19G10-23714-F AGTTGGTCCTCGAGCTCTCC 197 bp < than Col N/A
F19G10-23714-R AAGAACTTAATTTCTCTCACCCG
F21J9-83201 F21J9-83201-F CAGATTTCTTGCCAAGTTTCATC 189 bp < than Col 34.66
F21J9-83201-R GAGACGAAGAAGATGGATTCTG
AthZFPG AthZFPG-F TTGCGTTTCCACATTTGTTT 143 139 35.25
AthZFPG-R TGGGTCAATTCACATGTAGAGA
AthS0392 AthS0392-F TTTGGAGTTAGACACGGATCTG 142 156 44.60
AthS0392-R GTTGATCGCAGCTTGATAAGC
nga392 nga392-F TTGAATAATTTGTAGCCATG 170 162 39.52
nga392-R GGTGTTAAATGCGGTGTTC
nga248 nga248-F TACCGAACCAAAACACAAAGG 143e 129 40.06
nga248-R TCTGTATCTCGGTGAATTCTCC
T27K12-Sp6 T27K12-Sp6-F GGACAACGTCTCAAACGGTT 146 152 59.1
T27K12-Sp6-R GGAGGCTATACGAATCTTGACA
nga128 nga128-F GGTCTGTTGATGTCGTAAGTCG 180 190 81.21
nga128-R ATCTTGAAACCTTTAGGGAGGG
nga280 nga280-F CTGATCTCACGGACAATAGTGC 105 85 81.71
nga280-R GGCTCCATAAAAAGTGCACC
F19K23-438 F19K23-438-F GGTCTAATTGCCGTTGTTGC 200 bp < than Col 84.25
F19K23-438-R GAATTCTGTAACATCCCATTTCC
AthGENEA ATHGENEA-F ACCATGCATAGCTTAAACTTCTT 209 205 84.25
ATHGENEAe-R ACATAACCACAAATAGGGGTG
F5I14-49495 F5I14-49495-F CTGCCTGAAATTGTCGAAAC 195 bp > than Col 89.97
F5I14-49495-R GGCATCACAGTTCTGATTCC
F11P17-4615 F11P17-4615-F CGCAATCGATTTTATTTAAATCC 209 bp < than Col N/A
F11P17-4615-R TTTCAGTTTGATGATTTATTCGC
yUP8H12R-28733 yUP8H12R-28733-F GTGTTGCGTGTCGACCC 202 bp < than Col 118.38
yUP8H12R-28733-R AAATTTCAAAATGCGTATCC
AthATPASE AthATPASE-F CTGGGAACGGTTCGATTCGAGC 85 69 115.75
AthATPASE-R GTTCACAGAGAGACTCATAAACCA
nga692 nga692-F TTTAGAGAGAGAGAGCGCGG 119 115 117.14
nga692-R AGCGTTTAGCTCAACCCTAGG
F22K20-9034 F22K20-9034-F TTTTTGGTGAGATTTTAAGCCC 206 bp > than Col 117.37
F22K20-9034-R ATATCTCCATCGCTGCAACC


Chromosome 2

SSLPs Primer Sequence Size of
Columbia		 Size of
Landsberg		 Map position Contact
nga1145 nga1145-F CCTTCACATCCAAAACCCAC 213 217 9.60
nga1145-R GCACATACCCACAACCAGAA
AthGPA1 AthGPA1-F ATCTCTTATCGTCACGAGAGGC 101 99 48.90
AthGPA1-R TAAGCAAAGGGGAAGACGAA
nga1126 nga1126-F CGCTACGCTTTTCGGTAAAG 191 199 50.65
nga1126-R GCACAGTCCAAGTCACAACC
nga361 nga361-F AAAGAGATGAGAATTTGGAC 114 120 63.02
nga361-R ACATATCAATATATTAAAGTAGC
nga168 nga168-F TCGTCTACTGCACTGCCG 151135 73.77
nga168-R GAGGACATGTATAGGAGCCTCG
AthBIO2b AthBIO2b-F TGACCTCCTCTTCCATGGAG 141 209 76.11
AthBIO2b-R TTAACAGAAACCCAAAGCTTTC
AthUBIQUE AthUBIQUE-F AGGCAAATGTCCATTTCATTG 146 148 82.20
AthUBIQUE-R ACGACATGGCAGATTTCTCC


Chromosome 3

SSLPs Primer Sequence Size of
Columbia		 Size of
Landsberg		 Map position
nga32 nga32-F GGAGACTTTTTGAGATTGGCC 260 256 5.87
nga32-R CCAAAACAATTAGCTCCCCA
nga172 nga172-F AGCTGCTTCCTTATAGCGTCC 162 136 6.91
nga172-R CATCCGAATGCCATTGTTC
nga126 nga126-F GAAAAAACGCTACTTTCGTGG 119 147 16.35
nga126-R CAAGAGCAATATCAAGAGCAGC
AthCHIB AthCHIB-F CTCATATATACAAAGAACTACTATAC 84 74 19.10
AthCHIB-R ATGAGAAGCTATAATTTTTTCAATA
nga162 nga162-F CATGCAATTTGCATCTGAGG 107 89 20.56
nga162-R CTCTGTCACTCTTTTCCTCTGG
AthGAPAb AthGAPAb-F CACCATGGCTTCGGTTACTT 142 150 43.77
AthGAPAb-R TCCTGAGAATTCAGTGAAACCC
AthCDC2BG AthCDC2BG-F GGGAAAAACGAAGTGACGTG 131 129 76.14
AthCDC2BG-R ATTGAACTGTGTTGGTTTCTGG
nga707 nga707-F TGAATGCGTCCAGTGAGAAG 132 128 78.25
nga707-R CTCTCTGCCTCTCGCTGG
AthFUS6 AthFUS6-F TCGTTACACTGGCTTGCTTG ~280 bp > than Col 81.64
AthFUS6-R TTCCTTGATCAGATTTGGTCG
nga6 nga6-F TGGATTTCTTCCTCTCTTCAC 143 123 86.41
nga6-R ATGGAGAAGCTTACACTGATC
nga112 nga112-F TAATCACGTGTATGCAGCTGC 197 189 87.88
nga112-R CTCTCCACCTCCTCCAGTACC


Chromosome 4

SSLPs Primer Sequence Size of
Columbia		 Size of
Landsberg		 Map position
nga12 nga12-F AATGTTGTCCTCCCCTCCTC 247 234l 22.92
nga12-R TGATGCTCTCTGAAACAAGAGC
nga8 nga8-F GAGGGCAAATCTTTATTTCGG 154 198 26.56
nga8-R TGGCTTTCGTTTATAAACATCC
nga1111 nga1111-F GGGTTCGGTTACAATCGTGT 148 154 29.64
nga1111-R AGTTCCAGATTGAGCTTTGAGC
AthDET1 AthDET1-F TTCAAACACCAATATCAGGCC-F 138 136 31.44
AthDET1-R GGTGAAAATGGAGGAGACGA
nga1139 nga1139-F TAGCCGGATGAGTTGGTACC 114 118 83.41
nga1139-R TTTTTCCTTGTGTTGCATTCC
nga1107 nga1107-F GCGAAAAAACAAAAAAATCCA 150 140 104.73
nga1107-R CGACGAATCGACAGAATTAGG


Chromosome 5

SSLPs Primer Sequence Size of
Columbia		 Size of
Landsberg		 Map position
nga225 nga225-F GAAATCCAAATCCCAGAGAGG 119 189 14.31
nga225-R TCTCCCCACTAGTTTTGTGTCC
nga158 nga158-F TCATTTTGGCCGACTTAGC 108 104 18.12
nga158-R ACCTGAACCATCCTCCGTC-R
AthEMC AthEMC-F AATGACGACGAGACGCTCTT 131 135 22.30
AthEMC-R AACAGATCGGAAAATCGTCG
nga249 nga249-F TACCGTCAATTTCATCGCC 125 115 23.72
nga249-R GGATCCCTAACTGTAAAATCCC
nga151 nga151-F GTTTTGGGAAGTTTTGCTGG 150 120 29.62
nga151-R CAGTCTAAAAGCGAGAGTATGATG
ca72 ca72-F AATCCCAGTAACCAAACACACA 124 110 29.60
ca72-R CCCAGTCTAACCACGACCAC
nga106 nga106-F GTTATGGAGTTTCTAGGGCACGF 157 123 33.35
nga106-R TGCCCCATTTTGTTCTTCTC
AthCDPK9 AthCDPK9-F TCAATCATTGTCCAAAACTTGG 106 104 44.55
AthCDPK9-R GAAACTGACTTGGAGAAGGCA
nga139 nga139-F AGAGCTACCAGATCCGATGG 174 132 50.48
nga139-R GGTTTCGTTTCACTATCCAGG
AthS0262 AthS0262-F TTGCTTTTTGGTTATATTCGGA 145 159 65.20
AthS0262-R ATCATCTGCCCATGGTTTTT
nga76 nga76-F GGAGAAAATGTCACTCTCCACC 231 >250 68.40
nga76-R AGGCATGGGAGACATTTACG
AthPHYC AthPHYC-F CTCAGAGAATTCCCAGAAAAATCT 207 222 71.13
AthPHYC-R AAACTCGAGAGTTTTGTCTAGATC
AthS0191 AthS0191-F TGATGTTGATGGAGATGGTCA 148 156 N/A
AthS0191-R CTCCACCAATCATGCAAATG
nga129 nga129-F TCAGGAGGAACTAAAGTGAGGG 177 179 105.41
nga129-R CACACTGAAGATGGTCTTGAGG


ATGC June 29,1999
E-Mail Address: atgc@atgenome.bio.upenn.edu