Genetic linkage mapping of economically important traits in cultivated tetraploid potato (Solanum tuberosum L.)

G3: Genes, Genomes, Genetics

Volumn 5, Issue 11, 2015, Pages 2357-2364

  Massa, Alicia N ^a   Manrique Carpintero, Norma C ^a   Coombs, Joseph J ^a   Zarka, Daniel G ^a   Boone, Anne E ^a   Kirk, William W ^a   Hackett, Christine A ^b   Bryan, Glenn J ^c   Douches, David S ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b BIOMATHEMATICS AND STATISTICS SCOTLAND   (United Kingdom)

^c SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

Author keywords

Autotetraploid; Genetic linkage map; Potato; QTL; Single nucleotide polymorphism

Indexed keywords

AGRONOMIC TRAIT; ALLELE; ARTICLE; CHROMOSOME 5; CHROMOSOME 9; CHROMOSOME ARM; GENE DOSAGE; GENETIC LINKAGE; GENOTYPE; MATURITY; NONHUMAN; PHYTOPHTHORA INFESTANS; PLANT GENETICS; POTATO; POTATO LATE BLIGHT; PROGENY; QUANTITATIVE TRAIT LOCUS; QUANTITATIVE TRAIT LOCUS MAPPING; SINGLE NUCLEOTIDE POLYMORPHISM; DISEASE RESISTANCE; GENETICS; GROWTH, DEVELOPMENT AND AGING; MICROBIOLOGY; PATHOGENICITY; TETRAPLOIDY;

DISEASE RESISTANCE; GENETIC LINKAGE; PHYTOPHTHORA INFESTANS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SOLANUM TUBEROSUM; TETRAPLOIDY;

EID: 84947460389     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.115.019646     Document Type: Article

References (48)

1. Bormann, C. A., A. M. Rickert, R. A. Castillo Ruiz, J. Paal, J. Lübeck et al., 2004 Tagging quantitative trait loci for maturity-corrected late blight resistance in tetraploid potato with PCR-based candidate gene markers. Mol. Plant Microbe Interact. 17: 1126-1138.
2. Bradshaw, J., G. Bryan, A. Lees, K. McLean, and R. Solomon-Blackburn, 2006 Mapping the R10 and R11 genes for resistance to late blight (Phytophthora infestans) present in the potato (Solanum tuberosum) R-gene differentials of Black. Theor. Appl. Genet. 112: 744-751.
3. Cleveland, W. S., 1979 Robust locally weighted regression and smoothing scatterplots. J. Am. Stat. Assoc. 74: 829-836.
4. De Jong, H., T. R. Tarn, A. M. Murphy, G. C. C. Tai, R. H. Bagnall et al., 1995 Ac chaleur: a new early-maturing cultivar with excellent table quality. Am. Potato J. 72: 393-399.
5. Douches, D., J. Coombs, K. Felcher, and W. Kirk, 2004 Foliar reaction to Phytophthora infestans in inoculated potato field trials in Michigan. Am. J. Potato Res. 81: 443-448.
6. Douches, D., C. N. Hirsch, N. C. Manrique-Carpintero, A. N. Massa, J. Coombs et al., 2014 The contribution of the solanaceae coordinated agricultural project to potato breeding. Potato Res. 57: 215-224.
7. Douches, D. S., K. Jastrzebski, J. Coombs, W. W. Kirk, K. K. Felcher et al., 2001 Jacqueline Lee: a late-blight-resistant tablestock variety. Am. J. Potato Res. 78: 413-419.
8. Driscoll, J., J. Coombs, R. Hammerschmidt, W. Kirk, L. Wanner et al., 2009 Greenhouse and field nursery evaluation for potato common scab tolerance in a tetraploid population. Am. J. Potato Res. 86: 96-101.
9. 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.
10. Foster, S., T. Park, M. Pel, G. Brigneti, J. Sliwka et al., 2009 Rpi-vnt1.1, a Tm-22 homolog from Solanum venturii, confers resistance to potato late blight. Mol. Plant Microbe Interact. 22: 589-600.
11. 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.
12. Gebhardt, C., A. Ballvora, B. Walkemeier, P. Oberhagemann, and K. Schüler, 2004 Assessing genetic potential in germplasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Mol. Breed. 13: 93-102.
13. Grunwald, N. J., M. A. Cadena Hinojosa, O. R. Covarrubias, A. R. Pena, J. S. Niederhauser et al., 2002 Potato cultivars from the Mexican National Program: sources and durability of resistance against late blight. Phytopathology 92: 688-693.
14. Hackett, C., J. Bradshaw, and G. Bryan, 2014 QTL mapping in autotetraploids using SNP dosage information. Theor. Appl. Genet. 127: 1885-1904.
15. Hackett, C. A., J. E. Bradshaw, R. C. Meyer, J. W. McNicol, D. Milbourne et al., 1998 Linkage analysis in tetraploid species: a simulation study. Genet. Res. 71: 143-153.
16. Hackett, C. A., K. McLean, and G. J. Bryan, 2013 Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population. PLoS One 8: e63939.
17. Hamilton, J., C. Hansey, B. Whitty, K. Stoffel, A. Massa et al., 2011 Single nucleotide polymorphism discovery in elite north american potato germplasm. BMC Genomics 12: 302.
18. Hein, I., P. J. Birch, S. Danan, V. Lefebvre, D. Achieng Odeny et al., 2009 Progress in mapping and cloning qualitative and quantitative resistance against Phytophthora infestans in potato and its wild relatives. Potato Res. 52: 215-227.
19. Hirsch, C. D., J. P. Hamilton, K. L. Childs, J. Cepela, E. Crisovan et al., 2014 Spud DB: A resource for mining sequences, genotypes, and phenotypes to accelerate potato breeding. Plant Genome 7: 1-12.
20. Hirsch, C. N., C. D. Hirsch, K. Felcher, J. Coombs, D. Zarka et al., 2013 Retrospective view of North American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries. G3 (Bethesda) 3: 1003-1013.
21. Huang, S., E. A. G. Van Der Vossen, H. Kuang, V. G. A. A. Vleeshouwers, N. Zhang et al., 2005 Comparative genomics enabled the isolation of the R3a late blight resistance gene in potato. Plant J. 42: 251-261.
22. Jelihovschi, E. G., J. C. Faria, and I. Bezerra Allaman, 2014 ScottKnott: a package for performing the Scott-Knott clustering algorithm in R. TEMA 15: 3-7.
23. Jo, K. R., M. Arens, T. Y. Kim, M. Jongsma, R. F. Visser et al., 2011 Mapping of the S. demissum late blight resistance gene R8 to a new locus on chromosome IX. Theor. Appl. Genet. 123: 1331-1340.
24. Jo, K. R., R. F. Visser, E. Jacobsen, and J. Vossen, 2015 Characterisation of the late blight resistance in potato differential MaR9 reveals a qualitative resistance gene, R9a, residing in a cluster of Tm-2 (2) homologs on chromosome IX. Theor. Appl. Genet. 128: 931-941.
25. Jupe, F., L. Pritchard, G. Etherington, K. MacKenzie, P. Cock et al., 2012 Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics 13: 75.
26. Kirk, W. W., F. M. Abu-El Samen, J. B. Muhinyuza, R. Hammerschmidt, D. S. Douches et al., 2005 Evaluation of potato late blight management utilizing host plant resistance and reduced rates and frequencies of fungicide applications. Crop Prot. 24: 961-970.
27. Kloosterman, B., J. A. Abelenda, M. M. Carretero-Gomez, M. Oortwijn, J. M. de Boer et al., 2013 Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature 495: 246-250.
28. Li, J., H. Lindqvist-Kreuze, Z. Tian, J. Liu, B. Song et al., 2012 Conditional QTL underlying resistance to late blight in a diploid potato population. Theor. Appl. Genet. 124: 1339-1350.
29. Li, X., Y. Wei, A. Acharya, Q. Jiang, J. Kang et al., 2014 A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome. G3 (Bethesda) 4: 1971-1979.
30. Luo, Z. W., R. M. Zhang, and M. J. Kearsey, 2004 Theoretical basis for genetic linkage analysis in autotetraploid species. Proc. Natl. Acad. Sci. USA 101: 7040-7045.
31. Nelson, R. R., 1972 Stabilizing racial populations of plant pathogens by use of resistance genes. J. Environ. Qual. 1: 220-227.
32. Nettleton, D., and R. W. Doerge, 2000 Accounting for variability in the use of permutation testing to detect quantitative trait loci. Biometrics 56: 52-58.
33. Pel, M. A., S. J. Foster, T. H. Park, H. Rietman, G. van Arkel et al., 2009 Mapping and cloning of late blight resistance genes from Solanum venturii using an interspecific candidate gene approach. Mol. Plant Microbe Interact. 22: 601-615.
34. Ramakrishnan, A., C. Ritland, R. Blas Sevillano, and A. Riseman, 2015 Review of potato molecular markers to enhance trait selection. Am. J. Pot Res. 92: 455-472.
35. Rezvoy, C., D. Charif, L. Gueguen, and G. A. B. Marais, 2007 MareyMap: an R-based tool with graphical interface for estimating recombination rates. Bioinformatics 23: 2188-2189.
36. Rietman, H., G. Bijsterbosch, L. M. Cano, H. R. Lee, J. H. Vossen et al., 2012 Qualitative and quantitative late blight resistance in the potato cultivar Sarpo Mira is determined by the perception of five distinct RXLR effectors. Mol. Plant Microbe Interact. 25: 910-919.
37. Rojas, J. A., W. W. Kirk, E. Gachango, D. S. Douches, and L. E. Hanson, 2014 Tuber blight development in potato cultivars in response to different genotypes of Phytophthora infestans. J. Phytopathol. 162: 33-42.
38. Schwarz, G., 1978 Estimating the dimension of a model. Ann. Stat. 6: 461-464.
39. Scott, A. J., and M. Knott, 1974 A cluster analysis method for grouping means in the analysis of variance. Biometrics 30: 507-512.
40. Sharma, S. K., D. Bolser, J. de Boer, M. Sønderkær, W. Amoros et al., 2013 Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps. G3 (Bethesda) 3: 2031-2047.
41. Smilde, W. D., G. Brigneti, L. Jagger, S. Perkins, and J. D. G. Jones, 2005 Solanum mochiquense chromosome IX carries a novel late blight resistance gene Rpi-moc1. Theor. Appl. Genet. 110: 252-258.
42. Tan, M. Y. A., R. C. B. Hutten, R. G. F. Visser, and H. J. van Eck, 2010 The effect of pyramiding Phytophthora infestans resistance genes R Pi-mcd1 and R Pi-ber in potato. Theor. Appl. Genet. 121: 117-125.
43. Tiwari, J. K., S. Siddappa, B. P. Singh, S. K. Kaushik, S. K. Chakrabarti et al., 2013 Molecular markers for late blight resistance breeding of potato: an update. Plant Breed. 132: 237-245.
44. Vleeshouwers, V. G. A. A., S. Raffaele, J. H. Vossen, N. Champouret, R. Oliva et al., 2011 Understanding and exploiting late blight resistance in the age of effectors. Annu. Rev. Phytopathol. 49: 507-531.
45. Voorrips, R. E., 2002 MapChart: software for the graphical presentation of linkage maps and QTLs. J. Hered. 93: 77-78.
46. Vossen, J. H., K. R. Jo, and B. Vosman, 2014 Mining the genus Solanum for increasing disease resistance, pp. 27-46 in Genomics of Plant Genetic Resources, edited by Tuberosa, R., E. Frison, and A. Graner. Springer, Dordrecht.
47. Young, G. K., L. R. Cooke, W. W. Kirk, P. Tumbalam, F. M. Perez et al., 2009 Influence of competition and host plant resistance on selection in Phytophthora infestans populations in Michigan, USA and in Northern Ireland. Plant Pathol. 58: 703-714.
48. Zhang, C., L. Liu, X. Wang, J. Vossen, G. Li et al., 2014 The Ph-3 gene from Solanum pimpinellifolium encodes CC-NBS-LRR protein conferring resistance to Phytophthora infestans. Theor. Appl. Genet. 127: 1353-1364.