TetraploidSNPMap: Software for linkage analysis and QTL mapping in autotetraploid populations using SNP dosage data

Journal of Heredity

Volumn 108, Issue 4, 2017, Pages 438-442

  Hackett, Christine A ^a,b   Boskamp, Bram ^a,b   Vogogias, Athanasios ^a,b   Preedy, Katharine F ^a,b   Milne, Iain ^c  

^a BIOMATHEMATICS AND STATISTICS SCOTLAND   (United Kingdom)

^b EDINBURGH NAPIER UNIVERSITY   (United Kingdom)

^c SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

Author keywords

linkage mapping; quantitative trait loci; tetraploids

Indexed keywords

ALLELE; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; GENETIC LINKAGE; GENOTYPE; HETEROZYGOTE; HIDDEN MARKOV MODEL; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; QUANTITATIVE TRAIT LOCUS MAPPING; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE; TETRAPLOIDY;

EID: 85020225111     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esx022     Document Type: Article

References (21)

1. Brainerd WS, Goldberg CH, Adams JC. 1996. Programmer's Guide to Fortran 90. 3rd ed. New York (NY): Springer.
2. Cheng R, Milligan GW. 1995. Hierarchical-clustering algorithms with influence detection. Educ Psychol Meas. 55:237-244.
3. Felcher KJ, Coombs JJ, Massa AN, Hansey CN, Hamilton JP, Veilleux RE, Buell CR, Douches DS. 2012. Integration of two diploid potato linkage maps with the potato genome sequence. PLoS One. 7:e36347.
4. Green BF. 1963. Digital computers in research. New York: McGraw-Hill.
5. Green BF. 1977. FORTRAN subroutines for random sampling without replacement. Beh Res Meth Instrum. 9:559.
6. Hackett CA, Bradshaw JE, Bryan GJ. 2014. QTL mapping in autotetraploids using SNP dosage information. Theor Appl Genet. 127:1885-1904.
7. 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.
8. Hackett CA, Milne I, Bradshaw JE, Luo Z. 2007. TetraploidMap for Windows: Linkage map construction and QTL mapping in autotetraploid species. J Hered. 98:727-729.
9. Lau C. 1980. Algorithm 147: A simple series for the incomplete gamma integral. J R Stat Soc Series C Appl Stat. 29:113-114.
10. Macleod AJ. 1989. Algorithm AS 245: A robust and reliable algorithm for the logarithm of the gamma function. J R Stat Soc Series C Appl Stat. 38:397-402.
11. Miller AJ. 1992. Algorithm AS 274: Least squares routines to supplement those of Gentleman. J R Stat Soc Series C Appl Stat. 41:458-478.
12. Miller AJ. 2002. Subset selection in regression. 2nd ed. Boca Raton (FL): Chapman & Hall/CRC Press.
13. Müllner D. 2013. fastcluster: Fast hierarchical, agglomerative clustering routines for R and Python. J Statistical Software. 53:1-18.
14. Narula SC, Desu MM. 1981. Algorithm 170: Computation of probability and non-centrality parameter of a non-central chi-squared distribution. J R Stat Soc Series C Appl Stat. 30:349-352.
15. Preedy KF, Hackett CA. 2016. A rapid marker ordering approach for highdensity genetic linkage maps in experimental autotetraploid populations using multidimensional scaling. Theor Appl Genet. 129:2117-2132.
16. R Core Team. 2014. R: A language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing. Available from: Http://www.R-project.org
17. Schwarz GE. 1978. Estimating the dimension of a model. Ann Stat. 6:461-464.
18. Serang O, Mollinari M, Garcia AA. 2012. Efficient exact maximum a posteriori computation for bayesian SNP genotyping in polyploids. PLoS One. 7:e30906.
19. Van Ooijen JW. 2006. JoinMap ® 4; Software for the calculation of genetic linkage maps in experimental populations. Wageningen (Netherlands): Kyazma B.V.
20. Vogogias A, Kennedy J, Archambault D, Smith VA, Currant H. 2016. MLCut: Exploring multi-level cuts in dendrograms for biological data. In: Cagatay Turkay and Tao Ruan Wan, editors. EG UK computer graphics and visual computing. Bournemouth (UK): The Eurographics Association, p. 1-8.
21. Voorrips RE, Gort G, Vosman B. 2011. Genotype calling in tetraploid species from bi-allelic marker data using mixture models. BMC Bioinformatics. 12:172.