Probabilistic multilocus haplotype reconstruction in outcrossing tetraploids

Genetics

Volumn 203, Issue 1, 2016, Pages 119-131

  Zheng, Chaozhi ^a   Voorrips, Roeland E ^a   Jansen, Johannes ^a   Hackett, Christine A ^b   Ho, Julie ^c   Bink, Marco C A M ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b BIOMATHEMATICS AND STATISTICS SCOTLAND   (United Kingdom)

^c Forage Genetics International Inc   (United States)

Author keywords

Ancestral inference; Double reduction; Outbred population; Polyploidy; Preferential pairing

Indexed keywords

ARTICLE; CENTROMERE; CHROMOSOME 1; CHROMOSOME 2; CHROMOSOME 3; CHROMOSOME 4; CHROMOSOME PAIRING; COMPARATIVE STUDY; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; GAMETE; GENE LOCUS; GENE MAPPING; GENETIC ALGORITHM; GENETIC LINKAGE; HAPLOTYPE; MEIOSIS; MULTILOCUS HAPLOTYPE RECONSTRUCTION; MULTILOCUS SEQUENCE TYPING; NEXT GENERATION SEQUENCING; NONHUMAN; OUTCROSSING; PLANT GENETICS; POTATO; PRIORITY JOURNAL; PROGENY; SINGLE NUCLEOTIDE POLYMORPHISM; TETRAPLOIDY; ZYGOTE; ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; CROSS BREEDING; GENE DOSAGE; GENETICS; MOLECULAR EVOLUTION; PROBABILITY; QUANTITATIVE TRAIT LOCUS;

ALGORITHMS; CHROMOSOME PAIRING; COMPUTER SIMULATION; CROSSES, GENETIC; EVOLUTION, MOLECULAR; GENE DOSAGE; GENETIC LINKAGE; HAPLOTYPES; MODELS, GENETIC; PROBABILITY; QUANTITATIVE TRAIT LOCI; SOLANUM TUBEROSUM; TETRAPLOIDY; ZYGOTE;

EID: 84979955952     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.185579     Document Type: Article

References (26)

1. Bourke, P. M., R. E. Voorrips, R. G. F. Visser, and C. Maliepaard, 2015 The double reduction landscape in tetraploid potato as revealed by a high-density linkage map. Genetics 201: 853–863.
2. Broman, K. W., H. Wu, S. Sen, and G. A. Churchill, 2003 R/qtl: Qtl mapping in experimental crosses. Bioinformatics 19: 889–890.
3. Fisher, R. A., 1947 The theory of linkage in polysomic inheritance. Philos. Trans. R. Soc. Lond. B Biol. Sci. 233: 55–87.
4. Garcia, A. A. F., M. Mollinari, T. G. Marconi, O. R. Serang, R. R. Silva et al., 2013 Snp genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids. Sci. Rep. 3: 3399.
5. Gelman, A., J. Carlin, H. Stern, and D. Rubin, 2004 Bayesian Data Analysis. Chapman & Hall/CRC, Boca Raton, FL.
6. Hackett, C. A., J. E. Bradshaw, and J. W. McNicol, 2001 Interval mapping of quantitative trait loci in autotetraploid species. Genetics 159: 1819–1832.
7. 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.
8. Leach, L. J., L. Wang, M. J. Kearsey, and Z. W. Luo, 2010 Multilocus tetrasomic linkage analysis using hidden Markov chain model. Proc. Natl. Acad. Sci. USA 107: 4270–4274.
9. 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 4: 1971–1979.
10. Liu, E. Y., Q. Zhang, L. McMillan, F. Pardo-Manuel de Villena, and W. Wang, 2010 Efficient genome ancestry inference in complex pedigrees with inbreeding. Bioinformatics 26: i199–i207.
11. Luo, Z. W., C. A. Hackett, J. E. Bradshaw, J. W. McNicol, and D. Milbourne, 2001 Construction of a genetic linkage map in tetraploid species using molecular markers. Genetics 157: 1369–1385.
12. 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.
13. Luo, Z. W., Z. Zhang, L. Leach, R. M. Zhang, J. E. Bradshaw et al., 2006 Constructing genetic linkage maps under a tetrasomic model. Genetics 172: 2635–2645.
14. Mather, K., 1935 Reductional and equational separation of the chromosomes in bivalents and multivalents. J. Genet. 30: 53–78.
15. Mather, K., 1936 Segregation and linkage in autotetraploids. J. Genet. 32: 287–314.
16. Mott, R., C. J. Talbot, M. G. Turri, A. C. Collins, and J. Flint, 2000 A method for fine mapping quantitative trait loci in outbred animal stocks. Proc. Natl. Acad. Sci. USA 97: 12649–12654.
17. Rabiner, L., 1989 A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE 77: 257–286.
18. Stam, P., 1993 Construction of integrated genetic-linkage maps by means of a new computer package—joinmap. Plant J. 3: 739–744.
19. Stift, M., R. Reeve, and P. H. van Tienderen, 2010 Inheritance in tetraploid yeast revisited: segregation patterns and statistical power under different inheritance models. J. Evol. Biol. 23: 1570–1578.
20. Sybenga, J., 1972 General cytogenetics. North-Holland, Amsterdam.
21. Sybenga, J., 1994 Preferential pairing estimates from multivalent frequencies in tetraploids. Genome 37: 1045–1055.
22. Voorrips, R. E., and C. A. Maliepaard, 2012 The simulation of meiosis in diploid and tetraploid organisms using various genetic models. BMC Bioinformatics 13: 248.
23. Voorrips, R. E., G. Gort, and B. Vosman, 2011 Genotype calling in tetraploid species from bi-allelic marker data using mixture models. BMC Bioinformatics 12: 172.
24. Wolfram Research, 2012 Mathematica, v9.0 edn. Wolfram Research, Inc., Champaign, IL.
25. Xie, C. G., and S. H. Xu, 2000 Mapping quantitative trait loci in tetraploid populations. Genet. Res. 76: 105–115.
26. Zheng, C. Z., M. P. Boer, and F. A. van Eeuwijk, 2015 Reconstruction of genome ancestry blocks in multiparental populations. Genetics 200: 1073–1087.