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Table 2 Tomato markers tested for cryptic introgression

From: Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles

Marker SGN gene model, predicted protein Chromosome location (MB) Divergent line or accession Genetic-distance based clustering resultsa Observations
Introgression from crop improvement
220_1 Solyc09g014280, hydroxycinnamoyl transferase ch09, 5.77 TA496 TA496 intermediate between LA1537 and S. pennelli Major disease resistance genes on ch09 include:
Ve2, 0.05 MB, (11.002 cMb), from Peru Wild
2486_1 Solyc09g014350, glycerol-3-phosphate acyltransferase 6 ch09, 5.90 TA496 low bootstrap values overall except {TA496, LA1537}
Ve1, 0.06 MB, (11.002 cM), from Peru Wild
2534_1b Solyc09g018790, succinic semialdehyde reductase isofom1 ch09, 17.00 TA496 TA496 clustered with two S. peruvianum accessions Cm9.1, (4.0 – 24.0 cM), from S. peruvianum
Frl, (27.0 – 37.0 cM), from S. peruvianum
437_2 Solyc09g061440, uncharacterized protein ch09, 54.71 TA496 TA496 intermediate between {S. peruvianum, S. arcanum, Peru Wild, S. pimpinellifolium, Tomate} and {S. pennellii, S. habrochaites}
Tm2a, 13.62 MB, (32.002 cM), from S. peruvianum
Sw-5, 67.30 MB, (78.001 cM), from S. peruvianum
Ph-3, 66.71 – 66.78 MB, (63.0 – 78.0 cM), from S. pimpinellifolium
Introgression from natural hybridization with S. pimpinellifolium
2325_3c Solyc01g073640, alcohol dehydrogenase-3 ch01, 70.26 TA496 red-fruited clade was supported PI 258478 was collected from Peru in 1959, highly variable, fasciated fruit.
PI 258478
C2_At1g44575 Solyc06g060340, chloroplast photosystem II-associated protein ch06, 34.71 PI 258478 red-fruited clade was supported Introgressions on ch06 include:
Cyc-B, 42.29 MB, (106 cM), from S. habrochaites
2819_5c Solyc06g082670, ribosomal protein L10 ch06, 44.70 PI 258478 red-fruited clade was split into {Peru Wild-1, Tomate, TA496} and {Peru Wild-2, S. pimpinellifolium, PI 258478}  
U146140 Solyc06g083360, DNA-directed RNA polymerase II subunit ch06, 45.08 PI 109834 red-fruited clade was split into {PI 109834, S. pimpinellifolium} and {TA496, Peru Wild, Tomate} PI 109834 Merville des Marchés was collected from France in 1935.
C2_At1g73180 Solyc08g014060, eukaryotic translation initiation factor 3 subunit 9-like protein ch08, 3.57 PI 129026 {PI 196297, PI 390510} were divergent from other members of red-fruited clade PI 196297 was collected in Nicaragua in 1951, fasciated fruit, reported as introgressed by Rick [23]; carries same allele as PI 129026 (from Ecuador, 1938, fasciated fruit), PI 129128 (from Panama, 1938, fasciated fruit), PI 258474 (from Ecuador, 1959, fasciated fruit). PI 390510 was collected in Ecuador in 1974, described as a wild cherry tomato.
PI 129128
PI 196297
PI 258474
    PI 390510   
  1. Nine tomato markers previously identified as carrying highly divergent alleles within Solanum lycopersicum.
  2. a (Additional file 2: Figure S1).
  3. b Genetic linkage map positions from [45] or [46].
  4. c Sequence mapped to two locations, see Results and discussion.