The information is arranged in three tables: 1. Primer sequences and amplification conditions 2. PCR product sizes from 6 ecotypes 3. Strain distribution patterns. Table 1. Primer sequences. 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, between other pairs of ecotypes. Most 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. All of them should be available shortly. 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.
This is the sequence of the SSLPs amplified from Columbia DNA.
Locus Forward primer Reverse primer ATHCHIB CTCATATATACAAAGAACTACTATAC ATGAGAAGCTATAATTTTTTCAATA ATEAT1 GCCACTGCGTGAATGATATG CGAACAGCCAACATTAATTCCC ATHACS AGAAGTTTAGACAGGTAC AAATGTGCAATTGCCTTC ATHGENEA ACCATGCATAGCTTAAACTTCTTG ACATAACCACAAATAGGGGTGC ca72 AATCCCAGTAACCAAACACACA CCCAGTCTAACCACGACCAC ATHATPASE CTGGGAACGGTTCGATTCGAGC GTTCACAGAGAGACTCATAAACCA ATHCTR1A TATCAACAGAAACGCACCGAG CCACTTGTTTCTCTCTCTAG nga6 TGGATTTCTTCCTCTCTTCAC ATGGAGAAGCTTACACTGATC nga8 GAGGGCAAATCTTTATTTCGG TGGCTTTCGTTTATAAACATCC nga12 AATGTTGTCCTCCCCTCCTC TGATGCTCTCTGAAACAAGAGC nga32 GGAGACTTTTTGAGATTGGCC CCAAAACAATTAGCTCCCCA nga59 GCATCTGTGTTCACTCGCC TTAATACATTAGCCCAGACCCG nga63 AACCAAGGCACAGAAGCG ACCCAAGTGATCGCCACC nga76 GGAGAAAATGTCACTCTCCACC AGGCATGGGAGACATTTACG nga106 GTTATGGAGTTTCTAGGGCACG TGCCCCATTTTGTTCTTCTC nga111 CTCCAGTTGGAAGCTAAAGGG TGTTTTTTAGGACAAATGGCG nga112 TAATCACGTGTATGCAGCTGC CTCTCCACCTCCTCCAGTACC nga126 GAAAAAACGCTACTTTCGTGG CAAGAGCAATATCAAGAGCAGC nga128 GGTCTGTTGATGTCGTAAGTCG ATCTTGAAACCTTTAGGGAGGG nga129 TCAGGAGGAACTAAAGTGAGGG CACACTGAAGATGGTCTTGAGG nga139 AGAGCTACCAGATCCGATGG GGTTTCGTTTCACTATCCAGG nga151 GTTTTGGGAAGTTTTGCTGG CAGTCTAAAAGCGAGAGTATGATG nga158 TCATTTTGGCCGACTTAGC ACCTGAACCATCCTCCGTC nga162 CATGCAATTTGCATCTGAGG CTCTGTCACTCTTTTCCTCTGG nga168 TCGTCTACTGCACTGCCG GAGGACATGTATAGGAGCCTCG nga172 AGCTGCTTCCTTATAGCGTCC CATCCGAATGCCATTGTTC nga225 GAAATCCAAATCCCAGAGAGG TCTCCCCACTAGTTTTGTGTCC nga248 TACCGAACCAAAACACAAAGG TCTGTATCTCGGTGAATTCTCC nga249 TACCGTCAATTTCATCGCC GGATCCCTAACTGTAAAATCCC nga280 CTGATCTCACGGACAATAGTGC GGCTCCATAAAAAGTGCACC Recommended amplification conditions are as follows: 20 ul reactions containing 1-10 ng genomic DNA 5 picomoles of each primer 200uM deoxyribonucleotides 50 mM KCl 10 mM Tris-Cl pH 9 0.01% gelatin 0.1% Triton X-100 2 units of Taq polymerase. The final concentration of magnesium chloride was usually 2 mM. Standard cycling conditions were: 94C for 15 seconds, 55C for 15 seconds and 72C for 30 seconds, repeated 40 times. Note: Locus ca72 requires an annealing temperature of 61C nga112 requires 3 mM magnesium. Table 2. Allele sizes from 6 common ecotypes. This table shows the the simple tandem repeat sequences (from Columbia), and the expected sizes of PCR products amplified from 6 common ecotypes. This data can be used to decide what kind of separation system (acrylamide versus agarose) to use to score the polymorphisms, and gives some measure of how polymorphic each locus is. Locus Repeat Col-0 Ler Ws-0 No-0 Nd-0 RLD # alleles ATHCHIB (AT)14 84 74 82 72 66 90 6 ATEAT1 (AT)11 172 162 162 164 164 162 3 ATHACS (A)36 259 256 262 259 259 259 3 ATHGENEA (A)39 209 205 211 221 213 217 6 ca72 (CA)18 124 110 110 106 106 106 3 ATHATPASE (AG)18 85 69 69 69 69 77 3 CTR1 (AG)16 159 143 145 143 147 143 4 nga6 (GA)31 143 123 131 147 123 133 5 nga8 (GA)27 154 198 166 168 188 160 6 nga12 (GA)16 247 234 247 n.a. 232 n.a. 3 nga32 (GA)13 260 256 260 250 260 252 4 nga59 (CT)19 111 115 83 141 111 111 4 nga63 (GA)23 111 89 91 89 91 89 3 nga76 (GA)22 231 >250 199 n.a. 203 n.a. 4 nga106 (GA)26 157 123 123 131 123 123 3 nga111 (GA)16 128 162 146 140 128 130 5 nga112 (GA)16 197 189 189 189 n.a. 189 2 nga126 (AG)31 119 147 119 131 149 103 5 nga128 (AG)16 180 190 172 180 186 188 5 nga129 (GA)20 177 179 165 165 165 165 3 nga139 (AG)29 174 132 132 132 182 136 4 nga151 (CT)31 150 120 102 150 110 120 4 nga158 (GA)13 108 104 120 106 112 124 6 nga162 (GA)21 107 89 85 87 97 91 6 nga168 (GA)25 151 135 135 135 135 135 2 nga172 (GA)29 162 136 138 162 164 180 5 nga225 (CT)18 119 189 119 123 131 97 5 nga248 (CT)24 143 129 133 125 133 135/115 6 nga249 (TC)15 125 115 115 115 135 115 3 nga280 (AG)15 105 85 85 85 85 85 2 Table 3. Strain Distribution Patterns. This table contains raw data generated by scoring 48, or in some cases, 96 recombinant inbred stains for Landsberg or Columbia alleles. Heterozygotes were scored as U (unknown). The first section lists the strain numbers. This is followed by the data for each locus: the locus name and the alleles scored (L or C) for each inbred strain. This data can be pasted into spreadsheets or entered into mapping programs with minor modifications. RI lines 4 5 13 14 17 19A 19B 25 29 30 32 33 34 35 36 37 46 52 53 54 59 62 67 68 71 79 84 90 107 113 115 123 125 131 160 161 166 167 173 175 177 179 180 181 182 188 190 191 193 194 199 209 214 217 231 232 235 237 238 240 242 245 253 257 259 263 264 266 267 279 283 284 288 295 296 297 302 303 311 321 332 342 345 349 350 351 356 358 359 363 367 370 377 378 386 390 394 395 397 398 400 7
ACC2 L C C L L C U L C C C L L L L C C L U C C C L L L C U C L L L C C L L L C L L C L L C L C L L L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga59 L C U L L C U L C C C L L L L U U L U C C C U L L C C C L L L C C L L L C L L C L L C L C L L L C C U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U ATEAT1 L C C L L C U U C C C L C L L C U L U C C C L U L C C C L L L C C L L C C L L C L L L L C L L L U L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga63 L C U L L C U L C C C L C L C C U L U C C C L L L C C C L L L C C L L C C L L C L L C L C C L L U C U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga248 L L L L L C U L L L L L L L C L C L U C U U L L L C C C L L C C C C L C C C C L C C C L L C L C L L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga280 C C L C L L U L C C L C C C C C C L U C L C C L L C C C C L C C L L C C C C L L C C C L C C L L C L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga128 C C L C L L U L C C L C C C C C C L U C L C C L L C C C C L C C L L C C C C L L C C C L C C L L C L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U ATHGENEA C C C C L L U L C C L C C C C C U L U C L C C L L C C C C U L C C L C C C C L U U C C L C C L L C L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga111 C C C C C C U L C L C L C C L C C C U L L C C L C C C L C C C C L L C C C C L C C C C L C C L L C L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U ATHATPASE L C C C C C U L C L C U C C L C C C U L L C C C C C C L C C C U U L C C C C L L C C C L C C U U C L C U L C C C C U C C U C C C C L C L C C C C C L L C C L L C C C C C C L C L L L L L U L U U C C C L L U nga168 L C C C C L U L U C L C L C C C C L U L C C L L L C C L C C C C L C L L L L L L L L L L L C L L L L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga32 L C C C L L U L C C L U C C L L L C U C L L C L C C L L C U C L C L L C L L C L C C L L L C C L L C U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga172 L C C C L L U C C C L U C C L L L C U C L L C L C C L L C L C L C L L C L L C L C C L L L C C L L C L U C L C L C U L C U C C C C C L C L C C L C L C L L C C L C C L C L C C L L L U L U L U C L L C C C U nga126 L C C C L C U C C C L U L C L L L C U C L L C L C C L L C L C L L L U U L L C L C C L L L C C L C L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U ATHCHIB L C C C L L U C C C L U L C L L L C U C L L C L L C L L C L C L L L L C L L C U C C L L L C C U U L L U C L C L C U L C U C C C C C C C L C C L C C C C L L C L C C L C L C C L L L U L U C U C L L L C C U nga162 L C C C L C U C C C L C L C L L L C U C L L C L L C L L C L C L L L L C L L C L C C L L L C C L L L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga6 C L C L C C U L L C L C L C C C L C U L C C L L C C L L C L L L L C L C L C L C L C L C C C L C L C U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga112 C L L L C C U U U C L C L U C C L C U L C C C L C C L L C L L L L C L C L C L C L C L C C C L C L C U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga12 C L L C C C U C L C L L L C C C L L U C L C C L L L L C C C U L L C L L C L C L C C L C L L C L U L C U C L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga8 C L L C C C U C C C L L L C C L L L U C C C C L L U L C C C L L L C L L C L C L C C L U L L C L L L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U CTR1 C C L C L L U L L C L C C L L C L U U C C L C L C L L C L C L L L L L L L L L C C L L L L C L L U C U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga225 C C L C L L U L L C L C C L L C C L U C C L C L C L L C L C L L L L L L L L L C C L L L L L L L C C U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga158 C C L L L L U L L C L C C L L C C L U C C L C L C L L C L C L L L L U L U U C L L L L L L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga249 C C L L L L U L L C L C C L L C C L U C C L C L C L L C L L L L L L L L L L L C L L L L L L L L C C U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga151 C C L L L C U L L C L C C L L C C C U C C L C L C L L C L L L L L L L L L L L C L L L L L L L L C C U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U ca72 C C L L L C U L L C L U C L L C L C U C C U U U C L L C L L L L U U L L L L L C L L U L L L L U U C L U L L L C L U C L U L L L L L L U C C L L L L L L L L L C L L L C C L C C C C U L L U U L C L C C L U nga106 C C U L L L U L L L L C C C L C C C U C C L C L C L L C L L L L L L L L L L L C L L L L U L L C C C U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga139 C L C L L C U L C L L C C C L C C C U C L L C L C L L L L L L L L L L L L U L L L C L L L L C C C C U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U nga76 L L C L L C U L C L L C C C C C L C U C L C C L L L L L C L L L L L L U C C C L L C L L L L C U C L L U L C L L C U C L U C L C L C L U C C L L L C L L L L L C L L L C C L L C L C U L U U U L C L C C C U nga129 L C L L C C U L C C L C L C L L L C U L L C C L L U L L C C C C L C L C C L L C C L C L L L C L C L U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U U UIf you have questions or comments, please contact the ATGC.