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

BMC Plant Biology

Volumn 12, Issue , 2012, Pages

  Labate, Joanne A ^a   Robertson, Larry D ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Breeding; Cryptic introgression; DNA sequence; Linkage drag; Solanum species

Indexed keywords

LYCOPERSICON; LYCOPERSICON ESCULENTUM; LYCOPERSICON HIRSUTUM; LYCOPERSICON PENNELLII; LYCOPERSICON PERUVIANUM; LYCOPERSICON PIMPINELLIFOLIUM; SOLANUM;

PLANT DNA;

ALLELE; ARTICLE; CHROMOSOME MAP; CLASSIFICATION; COMPARATIVE STUDY; FRUIT; GENETIC LINKAGE; GENETIC MARKER; GENETIC VARIABILITY; GENETICS; GENOTYPE; HYBRIDIZATION; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PLANT CHROMOSOME; PLANT GENOME; TOMATO;

ALLELES; BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA, PLANT; EVOLUTION, MOLECULAR; FRUIT; GENETIC LINKAGE; GENETIC MARKERS; GENETIC VARIATION; GENOME, PLANT; GENOTYPE; HYBRIDIZATION, GENETIC; LYCOPERSICON ESCULENTUM;

EID: 84864778786     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-12-133     Document Type: Article

References (70)

1. Evans PD, Mekel-Bobrov N, Vallender EJ, Hudson RR, Lahn BT. Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage. P Natl Acad Sci USA 2006, 103(48):18178-18183.
2. Randi E. Detecting hybridization between wild species and their domesticated relatives. Mol Ecol 2008, 17(1):285-293. 10.1111/j.1365-294X.2007.03417.x, 18173502.
3. Tosi AJ, Detwiler KM, Clifford SL. X-chromosomal synapomorphies provide a non-invasive test for introgression among Cercopithecus monkeys. Conserv Genet 2006, 7(5):803-805.
4. Hajjar R, Hodgkin T. The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica 2007, 156(1):1-13.
5. Dearing C. Muscadine grape breeding. J Hered 1917, 8(9):409-424.
6. Bremer G. A cytological investigation of some species and species hybrids within the genus Saccharum. Genetica 1923, 5(2):97-148.
7. Prescott-Allen C, Prescott-Allen R. The first resource: Wild species in the North American economy 1986, Yale University, New Haven.
8. Baldo AM, Francis DM, Caramante M, Robertson LD, Labate JA. AlleleCoder: a PERL script for coding codominant polymorphism data for PCA analysis. Plant Genetic Resources: Characterization and Utilization 2011, 10:1-3.
9. Labate JA, Sheffer SM, Balch T, Robertson LD. Diversity and population structure in a geographic sample of tomato accessions. Crop Sci 2011, 51(3):1068-1079.
10. Gardner M. Indiana plant diseases, 1920. Proceedings of the Indiana Academy of Science 1920, 187-208. Fort Wayne Printing Co., Fort Wayne, Indiana, Breeze F.
11. Boswell VR, Pearson OH, Work P, Brown HD, MacGillivray JH, Seaton HL, Starr GE, Bayles JJ, Friend WH, Hawthorn LR, et al. Descriptions of types of principal American varieties of tomatoes. In: Misc Pub No 160 1933, 176-206. USDA, Washington, DC.
12. Porte WS, Walker HB. The Pan American tomato, a new red variety highly resistant to Fusarium wilt 1941, USDA Circ 611, Washington, DC.
13. Rick CM, Chetelat RT. Utilization of related wild species for tomato improvement. Acta Hort 1995, 412:21-38.
14. Zamir D. Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2001, 2(12):983-989. 10.1038/35103589, 11733751.
15. Zamir D. Plant breeders go back to nature. Nat Genet 2008, 40(3):269-270. 10.1038/ng0308-269, 18305476.
16. Foolad MR. Genome mapping and molecular breeding of tomato. Int J of Plant Genomics 2007, 2007:64358.
17. Haanstra JPW, Laugé R, Meijer-Dekens F, Bonnema G, de Wit PJGM, Lindhout P. The Cf-ECP2 gene is linked to, but not part of, the Cf-4/Cf-9 cluster on the short arm of chromosome 1 in tomato. Mol Gen Genet 1999, 262(4/5):839-845.
18. van der Beek JG, Verkerk R, Zabel P, Lindhout P. Mapping strategy for resistance genes in tomato based on RFLPs between cultivars: Cf9 (resistance to Cladosporium fulvum) on chromosome 1. Theor Appl Genet 1992, 84(1/2):106-112.
19. Young ND, Zamir D, Ganal MW, Tanksley SD. Use of isogenic lines and simultaneous probing to identify DNA markers tightly linked to the Tm-2a gene in tomato. Genetics 1988, 120:579-585. 1203534, 17246482.
20. Randhawa HS, Mutti JS, Kidwell K, Morris CF, Chen X, Gill KS. Rapid and targeted introgression of genes into popular wheat cultivars using marker-assisted background selection. PLoS One 2009, 4(6):e5752. 10.1371/journal.pone.0005752, 2684585, 19484121.
21. Klein RR, Mullet JE, Jordan DR, Miller FR, Rooney WL, Menz MA, Franks CD, Klein PE. The effect of tropical Sorghum conversion and inbred development on genome diversity as revealed by high-resolution genotyping. Crop Sci 2008, 48:S12-S26.
22. Rieseberg L, Baird S, Gardner K. Hybridization, introgression, and linkage evolution. Plant Mol Biol 2000, 42:205-224. 10.1023/A:1006340407546, 10688138.
23. Rick CM. The role of natural hybridization in the derivation of cultivated tomatoes of western South America. Econ Bot 1958, 12:346-367.
24. Labate JA, Baldo AM. Tomato SNP discovery by EST mining and resequencing. Mol Breed 2005, 16:343-349.
25. Labate JA, Robertson LD, Baldo AM. Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.). Heredity 2009, 103:257-267. 10.1038/hdy.2009.58, 19436327.
26. Robertson LD, Labate JA. Genetic resources of tomato (Lycopersicon esculentum Mill.) and wild relatives. Genetic improvement of Solanaceous crops 2007, 25-75. Science Publishers, Enfield, NH, Razdan MK, Mattoo AK, Tomato, Volume 2.
27. Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: A test case in the Euasterid plant clade. Genetics 2006, 174(3):1407-1420. 10.1534/genetics.106.062455, 1667096, 16951058.
28. Labate JA, Robertson LD, Wu F, Tanksley SD, Baldo AM. EST, COSII, and arbitrary gene markers give similar estimates of nucleotide diversity in cultivated tomato (Solanum lycopersicum L.). Theor Appl Genet 2009, 118:1005-1014. 10.1007/s00122-008-0957-2, 19153710.
29. Fulton TM, Van der Hoeven R, Eannetta NT, Tanksley S. Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 2002, 14(7):1457-1467. 10.1105/tpc.010479, 150699, 12119367.
30. Jiménez-Gómez JM, Maloof JN. Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biology 2009, 9(1):85. 10.1186/1471-2229-9-85, 3224693, 19575805.
31. Shirasawa K, Asamizu E, Fukuoka H, Ohyama A, Sato S, Nakamura Y, Tabata S, Sasamoto S, Wada T, Kishida Y, et al. An interspecific linkage map of SSR and intronic polymorphism markers in tomato. Theor Appl Genet 2010, 121(4):731-739. 10.1007/s00122-010-1344-3, 2909429, 20431859.
32. Rao ES, Kadirvel P, Symonds RC, Geethanjali S, Ebert AW. Using SSR markers to map genetic diversity and population structure of Solanum pimpinellifolium for development of a core collection. Plant Genetic Resources: Characterization and Utilization 2012,
33. Pitblado RE, Kerr EA. Resistance to bacterial speck (Pseudomonas tomato) in tomato. Acta Hort (ISHS) 1980, 100:379-382.
34. Jukes TH, Cantor CR. Evolution of protein molecules. Mammalian protein metabolism 1969, 21-132. Academic, New York, Munro H.
35. Nesbitt TC, Tanksley SD. Comparative sequencing in the genus Lycopersicon: Implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics 2002, 162(1):365-379. 1462239, 12242247.
36. The Tomato Genome Consortium The tomato genome sequence provides insights into fleshy fruit evolution. Nature 2012, 485(7400):635-641. 10.1038/nature11119, 22660326, The Tomato Genome Consortium.
37. Soltis PS, Soltis DE. Applying the bootstrap in phylogeny reconstruction. Stat Sci 2003, 18:256-267.
38. Zhou YF, Abbott RJ, Jiang ZY, Du FK, Milne RI, Liu JQ. Gene flow and species delimitation: a case study of two pine species with overlapping distributions in southeast China. Evolution 2010, 64(8):2342-2352.
39. Rodriguez F, Wu F, Ané C, Tanksley S, Spooner DM. Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?. BMC Evol Biol 2009, 9(1):191. 10.1186/1471-2148-9-191, 3087518, 19664206.
40. Zuriaga E, Blanca J, Nuez F. Classification and phylogenetic relationships in Solanum section Lycopersicon based on AFLP and two nuclear gene sequences. Genet Resour Crop Ev 2009, 56(5):663-678.
41. Zhu Q, Zheng X, Luo J, Gaut BS, Ge S. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: Severe bottleneck during domestication of rice. Mol Biol Evol 2007, 24(3):875-888.
42. Bai Y, Lindhout P. Domestication and breeding of tomatoes: What have we gained and what can we gain in the future?. Ann Bot 2007, 100(5):1085-1094. 10.1093/aob/mcm150, 2759208, 17717024.
43. Causse M, Caranta C, Saliba-Colombani V, Moretti A, Damidaux R, Rousselle P. Enhancement of tomato genetic resources via molecular markers. Cahiers Agricultures 2000, 9:197-210.
44. Grube RC, Radwanski ER, Jahn M. Comparative genetics of disease resistance within the Solanaceae. Genetics 2000, 155:873-887. 1461130, 10835406.
45. Riaño-Pachón D, Nagel A, Neigenfind J, Wagner R, Basekow R, Weber E, Mueller-Roeber B, Diehl S, Kersten B. GabiPD: the GABI primary database - a plant integrative 'omics'database. Nucleic Acids Res 2009, 37(database issue):D954-D959. 2686513, 18812395.
46. Mutschler MA, Tanksley SD, Rick CM. 1987 Linkage maps of the tomato (Lycopersicon esculentum). TGC Report 1987, 37:5-34.
47. Pillen K, Ganal M, Tanksley S. Construction of a high-resolution genetic map and YAC-contigs in the tomato Tm-2a region. Theor Appl Genet 1996, 93(1-2):228-233.
48. van der Biezen EA, Glagotskaya T, Overduin B, John H, Nijkamp J, Hille J. Inheritance and genetic mapping of resistance to Alternaria alternata f. sp. lycopersici in Lycopersicon pennellii. Mol Gen Genet 1995, 247:453-461. 10.1007/BF00293147, 7770053.
49. Hudson RR, Kreitman M, Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics 1987, 116(1):153-160. 1203113, 3110004.
50. Nakazato T, Housworth EA. Spatial genetics of wild tomato species reveals roles of the Andean geography on demographic history. Am J Bot 2011, 98(1):88-98. 10.3732/ajb.1000272, 21613087.
51. Gao H, Williamson S, Bustamante CD. An MCMC approach for joint inference of population structure and inbreeding rates from multilocus genotype data. Genetics 2007, 176:1635-1651. 10.1534/genetics.107.072371, 1931536, 17483417.
52. Berkman PJ, Lai K, Lorenc MT, Edwards D. Next-generation sequencing applications for wheat crop improvement. Am J Bot 2012, 99(2):365-371. 10.3732/ajb.1100309, 22268223.
53. Islam FMA, Beebe S, Munoz M, Tohme J, Redden RJ, Basford KE. Using molecular markers to assess the effect of introgression on quantitative attributes of common bean in the Andean gene pool. Theor Appl Genet 2004, 108(2):243-252. 10.1007/s00122-003-1437-3, 14657984.
54. Hanson PM, Yang R, Wu J, Chen J, Ledesma D, Tsou SCS, Lee TC. Variation for antioxidant activity and antioxidants in tomato. J Am Soc Hortic Sci 2004, 129(5):704-711.
55. Peralta IE, Knapp S, Spooner D. The taxonomy of tomatoes: a revision of wild tomatoes (Solanum section Lycopersicon) and their outgroup relatives (Solanum sections Juglandifolium and Lycopersicoides). Syst Bot Mngr 2008, 84:1-186.
56. Hall TJ. Resistance at the Tm-2 locus in the tomato to tomato mosaic virus. Euphytica 1980, 29(1):189-197.
57. Tanksley SD, Bernachi D, Beck-Bunn T, Emmatty D, Eshed Y, Inai S, Lopez J, Petiard V, Sayama H, Uhlig J, et al. Yield and quality evaluations on a pair of processing tomato lines nearly isogenic for the Tm-2a gene for resistance to the tobacco mosaic virus. Euphytica 1998, 99:77-83.
58. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186-194.
59. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998, 8:175-185.
60. Staden R. The Staden sequence analysis package. Mol Biotechnol 1996, 5(3):233-241. 10.1007/BF02900361, 8837029.
61. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999, 41:95-98.
62. Schlueter SD, Dong Q, Brendel V. GeneSeqer@ PlantGDB: Gene structure prediction in plant genomes. Nucleic Acids Res 2003, 31(13):3597-3600. 10.1093/nar/gkg533, 168940, 12824374.
63. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
64. Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA. The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res 2011, 39(Database issue):D1149-D1155. 3013765, 20935049.
65. Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-425.
66. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007, 24:1596-1599. 10.1093/molbev/msm092, 17488738.
67. Felsenstein J. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166.
68. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006, 23:254-267.
69. Huson DH, Klopper T, Lockhart PJ, Steel MA. Reconstruction of reticulate networks from gene trees. Research in computational biology, Lecture notes in computer science 2005, 233-249. Springer, Berlin, Miyano JM S, Kasif S, Istrail S, Pevzner P, Waterman M.
70. Librado P, Rozas J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451-1452. 10.1093/bioinformatics/btp187, 19346325.