Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps

G3: Genes, Genomes, Genetics

Volumn 3, Issue 11, 2013, Pages 2031-2047

  Sharma, Sanjeev Kumar ^a   Bolser, Daniel ^b,t   de Boer, Jan ^c   Sønderkær, Mads ^d   Amoros, Walter ^e   Carboni, Martin Federico ^f   D'Ambrosio, Juan Martín ^g   de la Cruz, German ^g   Di Genova, Alex ^h   Douches, David S ⁱ   Eguiluz, Maria ^j   Guo, Xiao ^k   Guzman, Frank ^j,u   Hackett, Christine A ^l   Hamilton, John P ⁱ   Li, Guangcun ^k   Li, Ying ^m   Lozano, Roberto ^j   Maass, Alejandro ^h   Marshall, David ^a   Martinez, Diana ^j   McLean, Karen ^a   Mejía, Nilo ⁿ   Milne, Linda ^a   Munive, Susan ^e   Nagy, Istvan ^o,v   Ponce, Olga ^j   Ramirez, Manuel ^j   Simon, Reinhard ^e   Thomson, Susan J ^m   Torres, Yerisf ^j   Waugh, Robbie ^a   Zhang, Zhonghua ^m   Huang, Sanwen ^m   Visser, Richard G F ^c   Bachem, Christian W B ^c   Sagredo, Boris ^q,r   Feingold, Sergio E ^f   Orjeda, Gisella ^j   Veilleux, Richard E ^s   Bonierbale, Merideth ^e   Jacobs, Jeanne M E ^p   Milbourne, Dan ^o   Martin, David Michael Alan ^b   Bryan, Glenn J ^a   more..

^a SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^b UNIVERSITY OF DUNDEE   (United Kingdom)

^c WAGENINGEN UNIVERSITY   (Netherlands)

^d AALBORG UNIVERSITY   (Denmark)

^e INTERNATIONAL POTATO CENTER   (Peru)

^f INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA INTA   (Argentina)

^g UNIVERSIDAD NACIONAL DE SAN CRISTÓBAL DE HUAMANGA   (Peru)

^h UNIVERSITY OF CHILE   (Chile)

ⁱ MICHIGAN STATE UNIVERSITY   (United States)

^j UNIVERSIDAD PERUANA CAYETANO HEREDIA   (Peru)

^k SHANDONG PEANUT RESEARCH INSTITUTE   (China)

^l BIOMATHEMATICS AND STATISTICS SCOTLAND   (United Kingdom)

^m INSTITUTE OF PLANT PROTECTION   (China)

ⁿ INSTITUTO DE INVESTIGACIONES AGROPECUARIAS   (Chile)

^o TEAGASC   (Ireland)

^p THE NEW ZEALAND INSTITUTE FOR PLANT AND FOOD RESEARCH LIMITED   (New Zealand)

^q Crops Environment and Land Use Programme ^*  (Chile)

^r UNIVERSIDAD DE LA FRONTERA   (Chile)

^s VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^t EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^u FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^v AARHUS UNIVERSITY   (Denmark)

more..

Author keywords

Anchoring scaffold; Genetic map; Orientation; Physical map; Pseudomolecules potato; Sequencetagged sites; Solanaceae genome

Indexed keywords

GENOMIC DNA; PLANT DNA;

ARTICLE; CENTROMERE; CHROMOSOME 4; CHROMOSOME INVERSION; COMPUTER MODEL; DIPLOIDY; GENE MAPPING; GENETIC LINKAGE; GENETIC MARKER; GENOTYPE; MOLECULE; NONHUMAN; PLANT CHROMOSOME; PLANT GENETICS; PLANT GENOME; POTATO; SEGREGATION DISTORTION; SEQUENCE TAGGED SITE; SPECIES DIFFERENCE; TOMATO;

GENETIC MAP; GENOME ANCHORING; PHYSICAL MAP; POTATO; PSEUDOMOLECULES; SCAFFOLD ORIENTATION; SEQUENCE-TAGGED SITES; SOLANACEAE;

BIOLOGICAL MARKERS; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENOME, PLANT; INTERNET; SOLANUM TUBEROSUM; USER-COMPUTER INTERFACE;

EID: 84889019837     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.113.007153     Document Type: Article

References (46)

1. Buntjer, J. B., 1999 Cross Checker, Vol. 291. Department of Plant Breeding, Wageningen University and Research Centre, Wageningen.
2. Creste, S., A. T. Neto, and A. Figueira, 2001 Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining. Plant Mol. Biol. Rep. 19: 299-306.
3. de Boer, J. M., T. J. A. Borm, T. Jesse, B. Brugmans, L. Wiggers-Perebolte et al.,2012 A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome (vol 12, 594, 2011). BMC Genomics 13: 423.
4. Fan, J. B., A. Oliphant, R. Shen, B. G. Kermani, F. Garcia et al., 2003 Highly parallel SNP genotyping. Cold Spring Harb. Symp. Quant. Biol. 68: 69-78.
5. Feingold, S., J. Lloyd, N. Norero, M. Bonierbale, and J. Lorenzen, 2005 Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.). Theor. Appl. Genet. 111: 456-466.
6. Felcher, K. J., J. J. Coombs, A. N. Massa, C. N. Hansey, J. P. Hamilton et al.,2012 Integration of two diploid potato linkage maps with the potato genome sequence. PLoS ONE 7: e36347.
7. Fulton, T. M., R. Van der Hoeven, N. T. Eannetta, and S. D. Tanksley, 2002 Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 1457-1467.
8. Gebhardt, C., E. Ritter, A. Barone, T. Debener, B. Walkemeier et al.,1991 RFLP maps of potato and their alignment with the homoeologous tomato genome. Theor. Appl. Genet. 83: 49-57.
9. Ghislain, M., J. Núñez, M. R. Herrera, J. Pignataro, F. Guzman et al.,2009 Robust and highly informative microsatellite-based genetic identity kit for potato. Mol. Breed. 23: 377-388.
10. Gong, Z., Y. Wu, A. Koblízková, G. A. Torres, K. Wang et al.,2012 Repeatless and repeat-based centromeres in potato: implications for centromere evolution. Plant Cell 24: 3559-3574.
11. Green, E. D., and P. Green, 1991 Sequence-tagged site (STS) content mapping of human chromosomes: theoretical considerations and early experiences. PCR Methods Appl. 1: 77-90.
12. Hamilton, J. P., and C. R. Buell, 2012 Advances in plant genome sequencing. Plant J. 70: 177-190.
13. Hamilton, J. P., C. N. Hansey, B. R. Whitty, K. Stoffel, A. N. Massa et al.,2011 Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genomics 12: 302.
14. Herrera, M. R., and M. Ghislain, 2000 Molecular Biology Laboratory Protocols:Plant Genotyping, Ed. 3. Crop Improvement and Genetic Resources Department, International Potato Center (CIP), Lima, Peru.International Rice Genome Sequencing Project, 2005 The map-based sequence of the rice genome. Nature 436: 793-800.
15. Iovene, M., S. M. Wielgus, P. W. Simon, C. R. Buell, and J. M. Jiang,2008 Chromatin structure and physical mapping of chromosome 6 of potato and comparative analyses with tomato. Genetics 180: 1307-1317.
16. Istrail, S., G. G. Sutton, L. Florea, A. L. Halpern, C. M. Mobarry et al.,2004 Whole-genome shotgun assembly and comparison of human genome assemblies. Proc. Natl. Acad. Sci. USA 101: 1916-1921.
17. Jaccoud, D., K. Peng, D. Feinstein, and A. Kilian, 2001 Diversity arrays:a solid state technology for sequence information independent genotyping.Nucleic Acids Res. 29: E25.
18. Kloosterman, B., J. A. Abelenda, M. M. C. Gomez, M. Oortwijn, J. M. de Boer et al., 2013 Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature 495: 246-250.
19. Kurtz, S., A. Phillippy, A. L. Delcher, M. Smoot, M. Shumway et al.,2004 Versatile and open software for comparing large genomes.Genome Biol. 5: R12.
20. Levy, D., W. K. Coleman, and R. E. Veilleux, 2013 Adaptation of potato to water shortage: irrigation management and enhancement of tolerance to drought and salinity. Am. J. Potato Res. 90: 186-206.
21. Lindhout, P., D. Meijer, T. Schotte, R. C. B. Hutten, R. G. F. Visser et al.,2011 Towards F 1 hybrid seed potato breeding. Potato Res. 54: 301-312.
22. Margulies, M., M. Egholm, W. E. Altman, S. Attiya, J. S. Bader et al.,2006 Genome sequencing in microfabricated high-density picolitre reactors (vol 437, pg 376, 2005). Nature 441: 120-120.
23. Milbourne, D., R. C. Meyer, A. J. Collins, L. D. Ramsay, C. Gebhardt et al.,1998 Isolation, characterisation and mapping of simple sequence repeat loci in potato. Mol. Gen. Genet. 259: 233-245.
24. Miller, J. R., S. Koren, and G. Sutton, 2010 Assembly algorithms for nextgeneration sequencing data. Genomics 95: 315-327.
25. Ning, Z. M., A. J. Cox, and J. C. Mullikin, 2001 SSAHA: a fast search method for large DNA databases. Genome Res. 11: 1725-1729.
26. Ovchinnikova, A., E. Krylova, T. Gavrilenko, T. Smekalova, M. Zhuk et al.,2011 Taxonomy of cultivated potatoes (Solanum section Petota: Solanaceae).Bot. J. Linn. Soc. 165: 107-155.
27. Park, T. H., J. B. Kim, R. C. Hutten, H. J. van Eck, E. Jacobsen et al.,2007 Genetic positioning of centromeres using half-tetrad analysis in a 4x-2x cross population of potato. Genetics 176: 85-94.
28. Paz, M. M., and R. E. Veilleux, 1999 Influence of culture medium and in vitro conditions on shoot regeneration in Solanum phureja monoploids and fertility of regenerated doubled monoploids. Plant Breed. 118:53-57.
29. Peters, S. A., J. W. Bargsten, D. Szinay, J. van de Belt, R. G. Visser et al.,2012 Structural homology in the Solanaceae: analysis of genomic regions in support of synteny studies in tomato, potato and pepper. Plant J.71: 602-614.
30. Potato Genome Sequencing Consortium, 2011 Genome sequence and analysis of the tuber crop potato. Nature 475: 189-195.
31. Rezvoy, C. M., D. Charif, L. Gue'guen, and G. A. B. Marais, 2007 MareyMap: an R-based tool with graphical interface for estimating recombination rates. Bioinformatics 23: 2188-2189.
32. Sliwka, J., H. Jakuczun, M. Chmielarz, A. Hara-Skrzypiec, I. Tomczyn'ska et al., 2012 A resistance gene against potato late blight originating from Solanum x michoacanum maps to potato chromosome VII. Theor. Appl.Genet. 124: 397-406.
33. Spooner, D. M., J. Núñez, G. Trujillo, M. D. Herrera, F. Guzmán et al.,2007 Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification.Proc. Natl. Acad. Sci. USA 104: 19398-19403.
34. Tang, J. F., S. J. Baldwin, J. M. E. Jacobs, C. G. van der Linden, R. E. Voorrips et al., 2008a Large-scale identification of polymorphic microsatellites using an in silico approach. BMC Bioinformatics 9: 374.
35. Tang, X., D. Szinay, C. Lang, M. S. Ramanna, E. A. van der Vossen et al.,2008b Cross-species bacterial artificial chromosome-fluorescence in situ hybridization painting of the tomato and potato chromosome 6 reveals undescribed chromosomal rearrangements. Genetics 180: 1319-1328.
36. Tang, X., J.M.deBoer, H. J. vanEck,C.Bachem,R.G. Visser et al., 2009 Assignment of genetic linkage maps to diploid Solanum tuberosum pachytene chromosomes by BAC-FISH technology. Chromosome Res. 17: 899-915.
37. Tanksley, S. D., M. W. Ganal, J. P. Prince, M. C. Devicente, M. W. Bonierbale et al., 1992 High-density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141-1160.
38. The Arabidopsis Genome Initiative, 2000 Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
39. The French-Italian Public Consortium for Grapevine Genome Characterization,2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467.
40. The Tomato Genome Sequencing Consortium, 2012 The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641.
41. Uitdewilligen, J. G., A. M. Wolters, B. B. D'hoop, T. J. Borm, R. G. Visser et al., 2013 A next-generation sequencing method for genotyping-bysequencing of highly heterozygous autotetraploid potato. PLoS ONE 8:e62355.
42. Van Ooijen, J. W., 2006 Joinmap 4: Software for the Calculation of Genetic Linkage Maps. Kyazma B. V., Wageningen, The Netherlands.
43. 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.
44. Veilleux, R. E., L. Y. Shen, and M. M. Paz, 1995 Analysis of the genetic composition of anther-derived potato by randomly amplified polymorphic DNA and simple sequence repeats. Genome 38: 1153-1162.
45. Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. Vandelee et al., 1995 AFLP:a new technique for DNA-fingerprinting. Nucleic Acids Res. 23: 4407-4414.
46. Wenzl, P., J. Carling, D. Kudrna, D. Jaccoud, E. Huttner et al.,2004 Diversity arrays technology (DArT) for whole-genome profiling of barley. Proc. Natl. Acad. Sci. USA 101: 9915-9920.