Integrating haplotype-specific linkage maps in tetraploid species using SNP markers

Theoretical and Applied Genetics

Volumn 129, Issue 11, 2016, Pages 2211-2226

  Bourke, Peter M ^a   Voorrips, Roeland E ^a   Kranenburg, Twan ^a   Jansen, Johannes ^a   Visser, Richard G F ^a   Maliepaard, Chris ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

FREQUENCY ESTIMATION; GENES; MAPPING; PLANTS (BOTANY);

BIVALENT PAIRING; GENETIC LINKAGE MAPS; INTENSITY VALUES; MAXIMUM LIKELIHOOD ESTIMATE; OPTIMAL STRATEGIES; RECOMBINATION FREQUENCIES; SOLANUM TUBEROSUM; TETRAPLOID SPECIES;

MAXIMUM LIKELIHOOD ESTIMATION;

GENETIC MARKER;

CHROMOSOMAL MAPPING; CLUSTER ANALYSIS; GENETIC LINKAGE; GENETIC MARKER; GENETICS; GENOTYPE; HAPLOTYPE; POTATO; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL; TETRAPLOIDY;

CHROMOSOME MAPPING; CLUSTER ANALYSIS; GENETIC LINKAGE; GENETIC MARKERS; GENOTYPE; HAPLOTYPES; LIKELIHOOD FUNCTIONS; POLYMORPHISM, SINGLE NUCLEOTIDE; SOLANUM TUBEROSUM; TETRAPLOIDY;

EID: 84983393978     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-016-2768-1     Document Type: Article

References (41)

1. Bertioli DJ et al (2014) The use of SNP markers for linkage mapping in diploid and tetraploid peanuts. G3 Genes| Genomes| Genet 4:89–96
2. Bourke PM, Voorrips RE, Visser RGF, Maliepaard C (2015) The double reduction landscape in tetraploid potato as revealed by a high-density linkage map. Genetics 201:853–863
3. Brent R (1973) Algorithms for minimizing without derivatives. Prentice-Hall, Englewood Cliffs
4. Brouwer D, Osborn T (1999) A molecular marker linkage map of tetraploid alfalfa (Medicago sativa L.). Theor Appl Genet 99:1194–1200
5. Csardi G, Nepusz T (2006) The igraph software package for complex network research. InterJ Complex Syst 1695:1–9
6. de Bakker PI, Yelensky R, Pe’er I, Gabriel SB, Daly MJ, Altshuler D (2005) Efficiency and power in genetic association studies. Nat Genet 37:1217–1223
7. Endelman JB (2011) New algorithm improves fine structure of the barley consensus SNP map. BMC Genomics 12:407
8. Endelman JB, Plomion C (2014) LPmerge: an R package for merging genetic maps by linear programming. Bioinformatics 30:1623–1624
9. Felcher KJ et al (2012) Integration of two diploid potato linkage maps with the potato genome sequence. PLoS One 7:e36347
10. Hackett CA, McLean K, Bryan GJ (2013) Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population. PLoS One 8:e63939
11. Hackett CA, Bradshaw JE, Bryan GJ (2014) QTL mapping in autotetraploids using SNP dosage information. Theor Appl Genet 127:1885–1904
12. Hirsch CD et al (2014) Spud DB: a resource for mining sequences, genotypes, and phenotypes to accelerate potato breeding. Plant Genome 7. doi:10.3835/plantgenome2013.12.0042
13. Koning-Boucoiran C et al (2012) The mode of inheritance in tetraploid cut roses. Theor Appl Genet 125:591–607
14. Leach LJ, Wang L, Kearsey MJ, Luo Z (2010) Multilocus tetrasomic linkage analysis using hidden Markov chain model. Proc Natl Acad Sci U. S. A. 107(9):4270–4274
15. Leal-Bertioli S et al (2015) Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis. Genetics 199:1093–1105
16. Luo ZW, Zhang Z, Leach L, Zhang RM, Bradshaw JE, Kearsey MJ (2006) Constructing genetic linkage maps under a tetrasomic model. Genetics 172:2635–2645. doi:10.1534/genetics.105.052449
17. Maliepaard C, Jansen J, Van Ooijen J (1997) Linkage analysis in a full-sib family of an outbreeding plant species: overview and consequences for applications. Genet Res 70:237–250
18. Massa AN et al (2015) Genetic linkage mapping of economically important traits in cultivated tetraploid potato (Solanum tuberosum L.). G3 Genes| Genomes| Genet 5:2357–2364
19. Meyer R, Milbourne D, Hackett C, Bradshaw J, McNichol J, Waugh R (1998) Linkage analysis in tetraploid potato and association of markers with quantitative resistance to late blight (Phytophthora infestans). Mol Gen Genet 259:150–160
20. Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195
21. R Core Team (2016) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
22. Rajapakse S, Byrne D, Zhang L, Anderson N, Arumuganathan K, Ballard R (2001) Two genetic linkage maps of tetraploid roses. Theor Appl Genet 103:575–583
23. Ramsey J, Schemske DW (2002) Neopolyploidy in flowering plants. Annu Rev Ecol Syst 33:589–639
24. Ripol M, Churchill G, Da Silva J, Sorrells M (1999) Statistical aspects of genetic mapping in autopolyploids. Gene 235:31–41
25. Robins JG, Hansen JL, Viands DR, Brummer EC (2008) Genetic mapping of persistence in tetraploid alfalfa. Crop Sci 48:1780–1786
26. Schie S, Chaudhary R, Debener T (2014) Analysis of a complex polyploid plant genome using molecular markers: strong evidence for segmental allooctoploidy in garden dahlias. Plant Genome 7. doi:10.3835/plantgenome2014.01.0002
27. Serang O, Mollinari M, Garcia AAF (2012) Efficient exact maximum a posteriori computation for Bayesian SNP genotyping in polyploids. PLoS One 7:e30906
28. Sharma SK et al (2013) Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps. G3 Genes| Genomes| Genet 3:2031–2047
29. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: Join Map. Plant J 3:739–744
30. Stebbins G (1947) Types of polyploids: their classification and significance. Adv Genet 1:1939
31. Swaminathan MS, Howard H (1953) Cytology and genetics of the potato (Solanum tuberosum) and related species. Bibliogr Genet 16:1–192
32. Sybenga J (1996) Chromosome pairing affinity and quadrivalent formation in polyploids: do segmental allopolyploids exist? Genome 39:1176–1184
33. ® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen 33
34. Van Ooijen JW, Jansen J (2013) Genetic mapping in experimental populations. Cambridge University Press, Cambridge
35. Vigna BB et al (2016) Evidence of allopolyploidy in Urochloa humidicola based on cytological analysis and genetic linkage mapping. PLoS One 11:e0153764
36. Voorrips R (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78
37. Voorrips RE, Maliepaard CA (2012) The simulation of meiosis in diploid and tetraploid organisms using various genetic models. BMC Bioinform 13:248
38. Voorrips RE, Gort G, Vosman B (2011) Genotype calling in tetraploid species from bi-allelic marker data using mixture models. BMC Bioinform 12:172
39. Vos PG, Uitdewilligen JG, Voorrips RE, Visser RG, van Eck HJ (2015) Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history. Theor Appl Genet 128:2387–2401
40. Wolfram Research Inc. (2014) Mathematica version 10.0. Champaign, Illinois
41. Yu C, Luo L, Pan H, Guo X, Wan H, Zhang Q (2015) Filling gaps with construction of a genetic linkage map in tetraploid roses. Front Plant Sci 5:796