An ultra-high-density, transcript-based, genetic map of lettuce

G3: Genes, Genomes, Genetics

Volumn 3, Issue 4, 2013, Pages 617-631

  Truco, Maria José ^a   Ashrafi, Hamid ^a   Kozik, Alexander ^a   Van Leeuwen, Hans ^a,c   Bowers, John ^b   Wo, Sebastian Reyes Chin ^a   Stoffel, Kevin ^a   Xu, Huaqin ^a   Hill, Theresa ^a   Van Deynze, Allen ^a   Michelmore, Richard W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c Nunhems Netherlands BV   (Netherlands)

Author keywords

Lactuca sativa; Linkage analysis; Microarray; Recombination

Indexed keywords

GENOMIC DNA; GENETIC MARKER;

ARTICLE; DENSITY; DNA MICROARRAY; GENE MAPPING; GENETIC DISTANCE; GENETIC LINKAGE; GENETIC POLYMORPHISM; GRAPE; HAPLOTYPE; LACTUCA; LETTUCE; NONHUMAN; PHENOTYPE; RECOMBINANT INBRED STRAIN; SEGREGATION ANALYSIS; UNITED STATES; CHROMOSOMAL MAPPING; GENETIC MARKER; GENETICS; PLANT GENOME;

ASTERACEAE; LACTUCA; LACTUCA SATIVA; LACTUCA SERRIOLA; VITACEAE; VITIS VINIFERA;

CHROMOSOME MAPPING; GENETIC LINKAGE; GENETIC MARKERS; GENOME, PLANT; LETTUCE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE;

EID: 84883215485     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.112.004929     Document Type: Article

References (72)

1. Argyris, J., M. J. Truco, O. Ochoa, S. J. Knapp, D. W. Still et al., 2005 Quantitative trait loci associated with seed and seedling traits in Lactuca. Theor. Appl. Genet. 111: 1365-1376.
2. Argyris, J. M., P. Dahal, E. Hayashi, D. W. Still, and K. J. Bradford, 2008 Genetic variation for lettuce seed thermoinhibition is associated with temperature-sensitive expression of abscisic acid, gibberellins, and ethylene biosynthesis, metabolism, and response genes. Plant Physiol. 148: 926-947.
3. Argyris, J., M. J. Truco, O. Ochoa, L. McHale, P. Dahal et al., 2010 A gene encoding an abscisic acid biosynthetic enzyme (LsNCED4) colocates with the high temperature germination locus Htg6.1 in lettuce (Lactuca sp.). Theor. Appl. Genet. 122: 95-108.
4. Banks, T. W., M. C. Jordan, and D. J. Somers, 2009 Single-feature polymorphism mapping in bread wheat. Plant Genome 2: 167-178.
5. Barker, M. S., N. C. Kane, M. Matvienko, A. Kozik, and R. W. Michelmore, 2008 Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol. Biol. Evol. 25: 2445-2455.
6. Bernardo, A. N., P. J. Bradbury, H. Ma, S. Hu, R. L. Bowden et al., 2009 Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays. BMC Genomics 10: 251.
7. Borevitz, J. O., D. Liang, D. Plouffe, H. S. Chang, T. Zhu et al., 2003 Largescale identification of single-feature polymorphisms in complex genomes. Genome Res. 13: 513-523.
8. Borevitz, J. O., S. P. Hazen, T. P. Michael, G. P. Morris, I. R. Baxter et al., 2007 Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 104: 12057-12062.
9. Bowers, J. E., E. Bachlava, R. L. Brunick, L. H. Rieseberg, S. J. Knapp et al., 2012 Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses. G3 (Bethesda) 2: 721-729.
10. Cartwright, D. A., M. Troggio, R. Velasco, and A. Gutin, 2007 Genetic mapping in the presence of genotyping errors. Genetics 176: 2521-2527.
11. Crute, I. R., 1988 The impact of breeding on pest and disease control in lettuce. Asp. Appl. Biol. 17: 305-312.
12. Davey, J. W., P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen et al., 2011 Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12: 499-510.
13. de Vries, I. M., 1997 Origin and domestication of Lactuca sativa L. Genet. Resour. Crop Evol. 44: 165-174.
14. Drost, D. R., E. Novaes, C. Boaventura-Novaes, C. I. Benedict, R. S. Brown et al., 2009 A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence. Plant J. 58: 1054-1067.
15. Edwards, J. D., J. Janda, M. T. Sweeney, A. B. Gaikwad, B. Liu et al., 2008 Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice. Plant Methods 4: 13.
16. Elshire, R. J., J. C. Glaubitz, J. A. Poland, K. Kawamoto, E. S. Buckler et al., 2011 A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6: e19379.
17. Fu, H. H., Z. W. Zheng, and H. K. Dooner, 2002 Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc. Natl. Acad. Sci. USA 99: 1082-1087.
18. Hartman, Y., D. A. P. Hooftman, B. Uwimana, C. C. M. van de Wiel, M. J. M. Smulders et al., 2012 Genomic regions in crop-wild hybrids of lettuce are affected differently in different environments: implications for crop breeding. Evol. Appl. 5:629-640.
19. Hayashi, E., N. Aoyama, and D. W. Still, 2008 Quantitative trait loci associated with lettuce seed germination under different temperature and light environments. Genome 51: 928-947.
20. Hill, T., H. Ashrafi, S. Reyes-Chin-Wo, J. Yao, K. Stoffel et al., 2013 Genome-wide analysis of Capsicum annuum germplasm reveals marked changes in diversity from pungent to non-pungent pepper. PLoS ONE 8: e56200.
21. Hill, W. G., and A. Robertson, 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38: 226-231.
22. Hu, T. T., P. Pattyn, E. G. Bakker, J. Cao, J. F. Cheng et al., 2011 The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43: 476-481.
23. Huang, X., Q. Feng, Q. Qian, Q. Zhao, L.Wang et al., 2009 High-throughput genotyping by whole-genome resequencing. Genome Res. 19: 1068-1076.
24. Irizarry, R. A., B. Hobbs, F. Collin, Y. D. Beazer-Barclay, K. J. Antonellis et al., 2003 Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
25. Isobe, S. N., H. Hisano, S. Sato, H. Hirakawa, K. Okumura et al., 2012 Comparative genetic mapping and discovery of linkage disequilibrium across linkage groups in white clover (Trifolium repens L.). G3 (Bethesda) 2: 607-617.
26. Jaillon, O., J.-M. Aury, B. Noel, A. Policriti, C. Clepet et al., 2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-476.
27. Jeuken, M., R. van Wijk, J. Peleman, and P. Linhout, 2001 An integrated interspecific AFLP map of lettuce (Lactuca) based on two L. sativa x L. saligna F2 populations. Theor. Appl. Genet. 103: 638-647.
28. Johnson, W. C., L. E. Jackson, O. Ochoa, R. van Wijk, J. Peleman et al., 2000 Lettuce, a shallow-rooted crop, and Lactuca serriola, its wild progenitor, differ at QTL determining root architecture and deep soil water exploitation. Theor. Appl. Genet. 101: 1066-1073.
29. Kesseli, R. V., O. Ochoa, and R. W. Michelmore, 1991 Variation at RFLP loci in Lactuca spp. and the origin of cultivated lettuce (L. sativa). Genome 34: 430-436.
30. Kesseli, R. V., I. Paran, and R. W. Michelmore, 1994 Analysis of a detailed genetic linkage map of Lactuca sativa (lettuce) constructed from RFLP and RAPD markers. Genetics 136: 1435-1446.
31. Landry, B. S., R. V. Kesseli, B. Farrara, and R. W. Michelmore, 1987 A genetic map of lettuce (Lactuca sativa L.) with restriction fragment length polymorphism, isozyme, disease resistance and morphological markers. Genetics 116: 331-337.
32. Lavelle, D. O., 2009 Genetics of candidate genes for developmental and domestication- related traits in lettuce. Ph.D. dissertation in Genetics, U. C. Davis.
33. Li, H., A. Kilian, M. Zhou, P. Wenzl, E. Huttner et al., 2010 Construction of a high-density composite map and comparative mapping of segregation distortion regions in barley. Mol. Genet. Genomics 284: 319-331.
34. Lindqvist, K., 1960 Inheritance studies in lettuce. Hereditas 46: 387-470.
35. Lysak, M. A., A. Berr, A. Pecinka, R. Schmidt, K. McBreen et al., 2006 Mechanisms of chromosome number reduction in Arabdiopsis thaliana and related Brassicaceae species. Proc. Natl. Acad. Sci. USA 103: 5224-5229.
36. MacDaniel, S. F., and W. J. H. Shaw, 2007 A linkage map reveals a complex basis for segregation distortion in an interpopulation cross in the moss Ceratodon pupureus. Genetics 176: 2489-2500.
37. McHale, L. K., M. J. Truco, A. Kozik, T. Wroblewski, O. E. Ochoa et al., 2009 The genomic architecture of disease resistance in lettuce. Theor. Appl. Genet. 118: 565-580.
38. Michelmore, R. W., and B. C. Myers, 1998 Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res. 8: 1113-1130.
39. Michelmore, R. W., I. Paran, and R. V. Kesseli, 1991 Identification of markers linked to disease-resistance genes by bulked segregant analysis-a rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl. Acad. Sci. USA 88: 9828-9832.
40. Moyle, L. C., and E. B. Graham, 2006 Genome-wide associations between hybrid sterility QTL and marker transmission ratio distortion. Mol. Biol. Evol. 23: 973-980.
41. National Agricultural Statistics Service, 2012 National Statistics for Lettuce. Available at: http://www.nass.usda.gov/Statistics_by_Subject/index.php? sector=CROPS.
42. Neves, L. G., E. M. C. Mamani, A. C. Alfenas, M. Kirst, and D. Grattapaglia, 2011 A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based single feature polymorphisms (SFP) in Eucalyptus. BMC Genomics 12: 189.
43. Poland, J. A., P. J. Brown, M. E. Sorrells, and J.-L. Jannink, 2012 Development of high-density genetic maps for barley and wheat using a novel twoenzyme genotyping-by-sequencing approach. PLoS ONE 7: e32253.
44. Rebollo, R., M. T. Romanish, and D. L. Mager, 2012 Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu. Rev. Genet. 46: 21-42.
45. Salomé, P. A., K. Bomblies, J. Fitz, R. A. E. Laitinen, N. Warthmann et al., 2011 The recombination landscape in Arabidopsis thaliana F2 populations. Heredity 108: 447-455.
46. Singer, T., Y. Fan, H. S. Chang, T. Zhu, S. P. Hazen et al., 2006 A highresolution map of Arabidopsis recombinant inbred lines by wholegenome exon array hybridization. PLoS Genet. 2: e144.
47. Sourdille, P., S. Singh, T. Cadalen, G. L. Brown-Guedira, G. Gay et al., 2004 Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.). Funct. Integr. Genomics 4: 12-25.
48. Stoffel, K., H. van Leeuwen, A. Kozik, D. Caldwell, H. Ashrafi et al., 2012 Development and application of a 6.5 million feature Affymetrix GeneChip for massively parallel discovery of single-position polymorphisms in lettuce (Lactuca spp.). BMC Genomics 13: 185.
49. Sun, Z., Z. Wang, J. Tu, J. Zhang, F. Yu et al., 2007 An ultradense genetic recombination map for Brassica napus, consisting of 13551 SRAP markers. Theor. Appl. Genet. 114: 1305-1317.
50. Syed, N. H., A. P. Sorensen, R. Antonise, C. van de Wiel, C. G. van der Linden et al., 2006 A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers. Theor. Appl. Genet. 112: 517-527.
51. Tanksley, S. D., M. W. Ganal, and G. B. Martin, 1995 Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. Trends Genet. 11: 63-68.
52. The Tomato Genome Consortium, 2012 The tomato genome sequence provides insights into fleshy fruit evolution. Nature 31: 635-641.
53. Troggio, M., G. Malacarne, G. Coppola, C. Segala, D. A. Cartwright et al., 2007 A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs. Genetics 176: 2637-2650.
54. Truco, M. J., R. Antonise, D. Lavelle, O. Ochoa, A. Kozik et al., 2007 A high-density, integrated genetic linkage map of lettuce (Lactuca spp.). Theor. Appl. Genet. 115: 735-746.
55. Truong, H. T., A. M. Ramos, F. Yalcin, M. de Ruiter, H. J. A. van der Poel et al., 2012 Sequence-based genotyping for marker discovery and codominant scoring in germplasm and populations. PLoS ONE 7: e37565.
56. United States Department of Agriculture, 2011 U.S. lettuce statistics. Available at: http://usda.mannlib.cornell.edu/MannUsda/viewDocumentInfo. do?documentID=1576. Accessed: February 18, 2013.
57. Uwimana, B., M. J. M. Smulders, D. A. P.Hooftman, Y. Hartman, P. H. van Tienderen et al., 2012 Hybridization between crops and wild relatives: the contribution of cultivated lettuce to the vigour of crop-wild hybrids under drought, salinity and nutrient deficiency conditions. Theor. Appl. Genet. 125: 1097-1111.
58. Van Berloo, R., 2008 Computer note: GGT 2.0: versatile software for visualization and analysis of genetic data. J. Hered. 99: 232-236.
59. Van Ooijen, J. W., 2006 Software for the Calculation of Genetic Linkage Maps. Kyazma B. V., Wageningen, the Netherlands.
60. van Os,H., P. Stam, R.G. F. Visser, andH. J. van Eck, 2005 RECORD: a novel method for ordering loci on a genetic linkage map. Theor. Appl. Genet. 112: 30-40.
61. van Os, H., S. Andrzejewski, E. Bakker, I. Barrena, G. J. Bryan et al., 2006 Construction of a 10,000-marker ultradense genetic recombination map of potato: Providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173: 1075-1087.
62. Wade, M. J., R. G. Winther, A. F. Agrawal, and C. J. Goodnight, 2001 Alternative definitions of epistasis: dependence and interaction. Trends Ecol. Evol. 16: 498-504.
63. Wang, G., J. P. Xu, Y. P. Tang, L. L. Zhou, F. Wang et al., 2011 Molecular characterization of a genomic interval with highly uneven recombination distribution on maize chromosome 10. L. Genetica 139: 1109-1118.
64. Waycott, W., S. B. Fort, E. J. Ryder, and R. W. Michelmore, 1999 Mapping morphological genes relative to molecular markers in lettuce (Lactuca sativa L.). Heredity 82: 245-251.
65. Werner, J. D., J. O. Borevitz, N. H. Uhlenhaut, J. R. Ecker, J. Chory et al., 2005 FRIGIDA-independent variation in flowering time of natural Arabidiopsis thaliana accessions. Genetics 170: 1197-1207.
66. West,M. A. L., H. van Leeuwen, A. Kozik, D. J. Kliebenstein, R. W. Doerge et al., 2006 High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Res. 16: 702-712.
67. Wu, Y., P. R. Bhat, T. J. Close, and S. Lonardi, 2008 Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet. 4: e1000212.
68. Wu, J., J. N. Jenkins, J. C. McCarty, and X.-Y. Lou, 2011 Comparisons of four approximation algorithms for large-scale linkage map construction. Theor. Appl. Genet. 123: 649-655.
69. Xie,W., Q. Feng, H. Yua, X. Huang, Q. Zhao et al., 2010 Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc. Natl. Acad. Sci. USA 107: 10578-10583.
70. Yogeeswaran, K., A. Frary, T. L. York, A. Amenta, A. H. Lesser et al., 2005 Comparative genome analyses of Arabidopsis spp.: Inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Res. 15: 505-515.
71. Zhang, F. Z., C.Wagstaff,A.M.Rae,A.K. Sihota,C. W. Keevil et al., 2007 QTLs for shelf life in lettuce co-locate with those for leaf biophysical properties but not with those for leaf developmental traits. J. Exp. Bot. 58: 1433-1449.
72. Zhao, K., C. W. Tung, G. C. Eizenga, M. H. Wright, M. L. Ali et al., 2011 Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Comm. 2: 467.