Table 2.
List of 24 primer pairs used by Sanger resequencing of 24 contigs representing polymorphic genomic regions in the 48 Linum accessions, along with the polymorphism and gene annotation information.
| Primer1 | Sequence (5′>3′)1 | Tm (°C)2 | CL2 | Ts2 | Nh2 | π2 | Scaffold|GO2 |
|---|---|---|---|---|---|---|---|
| 031B/A | CTCATCTTCTTCTTCCTTACATCTGACG/AACAGGACGCCCGAATGAATTG | 56.6/58.1 | 346 | 10 | 5 | 0.0064 | sc453|gn |
| 049B/A | TGCAGGTGTGCCTGAATCTGACAT/AACAGGCCTTGGTGGGTCTAATGA | 60.8/60.3 | 334 | 13 | 8 | 0.0078 | sc401|gn |
| 071B/A | AGGACCATTGTGTTGCAAGCATCC/CCAATCATCTTTGGATCTGTCCAGG | 60.2/57.5 | 283 | 15 | 17 | 0.0079 | sc297|g13204 |
| 145B/A | GGACAAGGGTTCATTTCGTGAAAGCG/AGTRGCATCCTCGGAACTTCTCTT | 60.4/58.6 | 364 | 3 | 5 | 0.0033 | sc530|g23272 |
| 151B/A | ACAAAGACACCAATGCTCCCTCCT/TCCRGGCATGGAAAGATATTAAGT | 60.5/55.0 | 363 | 10 | 5 | 0.0077 | sc142|gn |
| 204B/A | TGTTTATTGACATAATTGGACGAAA/AACGCCCTTACGAATGRACAYTA | 51.4/56.5 | 225 | 4 | 5 | 0.0042 | sc181|gn |
| 221B/A | TGTAGGGATAGCGAACGATAGTAAC/CCCTTTCATTCCACGGTAGCAA | 55.6/57.5 | 370 | 12 | 8 | 0.0114 | sc186|gn |
| 242B/A | ACTCTAACAGACAAGGCCACCGAT/GCCATACAAGCATGGATCCTGTCA | 59.9/59.2 | 304 | 4 | 9 | 0.0061 | sc475|g20873 |
| 246B/A | AATTCAGGGAGCGACACAGCCAGA/CAACCGTCGACAAGTTGGCAAGAA | 62.5/60.0 | 259 | 5 | 5 | 0.0029 | sc1078|g37692 |
| 281B/A | AACTCTGCTCTCATTCCTGCCGAA/ACCTCGAGTACATCTCGTTCGCAT | 60.3/59.7 | 285 | 7 | 6 | 0.0060 | sc584|g24349 |
| 316B/A | TGTGATCAATTGTGAAGACGAA/ATAATCTGCGTGCTCCCTCT | 52.4/55.9 | 227 | 10 | 7 | 0.0129 | sc1937|gn |
| 360B/A | CCCAGAAGWCAAACTGATGTATGC/CCAGTGTTAGGTTTAAGCGTGCAG | 55.9/58.2 | 287 | 8 | 14 | 0.0068 | sc741|g29697 |
| 440B/A | ATCGTTCGTGGTCATTGGTTTGCC/ATGTGCGATGGCACCATGGAAATG | 60.2/60.5 | 231 | 27 | 7 | 0.0411 | sc299|g8719 |
| 449B/A | GATTCGTCGTCGTGTCAATG/CCACGGCAAACTTAGCAAAT | 53.8/54.0 | 248 | 2 | 3 | 0.0018 | sc719|g33222 |
| 469B/A | CTGATAGACCGCTATGGAACGTAG/AGGCTGAACTGCGAGAAAGTGGT | 56.4/60.9 | 441 | 15 | 9 | 0.0078 | sc672|g27554 |
| 503B/A | CATCGCCAAGCAACACTTCTCCAT/AGGTTGGAAAGGAGTACGAGCTGA | 59.9/59.6 | 313 | 10 | 17 | 0.0062 | sc983|g36290 |
| 524B/A | GCAAGCCATACATGTGCCAGATTTGC/GCATTGATAGTGTTCTGATGCTGCCG | 61.0/60.1 | 277 | 4 | 7 | 0.0033 | sc689|g27494 |
| 550B/A | TCCATGTTTCTACGCAGTGAGG/TGCTCTGCAAGTGATGTTCATTGT | 56.9/57.4 | 330 | 7 | 5 | 0.0062 | sc1204|g40050 |
| 586B/A | CACTACCTTCTTCGAGGTGTGCAA/TCACAGCAGGATCATCACCGAACA | 58.8/60.3 | 222 | 1 | 2 | 0.0183 | sc67|g3272 |
| 590B/A | GTCAAGTGTATACGATTTCAACAAG/GGAAGGCACCAGTGACTACAAT | 52.3/57.0 | 231 | 8 | 9 | 0.0095 | sc977|g11464 |
| 632B/A | TGGGATAAATCGAAATCTGAGAGGA/GGTGCGTTTCACAGATTTAGCAGTCC | 55.4/60.0 | 256 | 6 | 5 | 0.0151 | sc411|g17731 |
| 676B/A | CCCTGGTTTACTCTCTCTGGTCAA/CCTTCGGCCGTGTTACGTTGTTT | 58.0/60.2 | 257 | 15 | 10 | 0.0104 | sc1159|gn |
| 677B/A | CTGGKATGCTRAATTGTGTTCTGC/GGCCACCTCTTCAAATTCTGCGAT | 56.6/59.8 | 184 | 5 | 10 | 0.0062 | sc1616|gn |
| 712B/A | GTTGAAATATCTAAACATTGCTGCTGA/CGTGGCTCAATTTAATGGTGACGG | 54.3/58.5 | 249 | 2 | 3 | 0.0024 | sc436|g18214 |
| Total | 6886 | 203 | 48 | 0.0079 |
1
The primer set was labeled for the contig, followed by B and A for right and left primers for the contig. More primer information is available in Table S2 of Fu and Peterson (2012).
2
Tm, annealing temperature; CL, contig length flanking by the primer set; Ts, the total number of segregating sites; Nh, the number of haplotypes observed; π, the estimate of nucleotide diversity; Scaffold|GO, the scaffold number and gene annotation number available at http://WWW.linum.ca, and gn means no gene annotation found for the contig.