Model selection for quantitative trait loci mapping in a full-sib family

Genetics and Molecular Biology

Volumn 35, Issue 3, 2012, Pages 622-631

  Tong, Chunfa ^a   Zhang, Bo ^a   Li, Huogen ^a   Shi, Jisen ^a  

^a NANJING FORESTRY UNIVERSITY   (China)

Author keywords

Full sib family; Interval mapping; Model selection; Quantitative trait locus

Indexed keywords

ACCURACY; AKAIKE INFORMATION CRITERION; ARTICLE; BAYESIAN INFORMATION CRITERION; COMPUTER PROGRAM; CROSS BREEDING; FAMILY; GENE SEGREGATION; GENETIC LINKAGE; LAPLACE EMPIRICAL CRITERION; QUANTITATIVE TRAIT LOCUS MAPPING; SIMULATION; STATISTICAL MODEL; TREE;

EID: 84865364655     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/S1415-47572012005000044     Document Type: Article

References (38)

1. Akaike H (1974) A new look at the statistical model identification. IEEE Trans Automat Contr 19:716-723.
2. Andersson L, Haley CS, Ellegren H, Knott SA, Johansson M, Andersson K, Andersson-Eklund L, Edfors-Lilja I, Fredholm M, Hansson I, et al. (1994) Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science 263:1771-1774.
3. Churchill GA and Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963-971.
4. Dempster AP, Laird NM and Rubin DB (1977) Maximum likelihood from incomplete data via EM algorithm. J R Stat Soc Ser B (Methodological) 39:1-38.
5. Doerge RW (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet 3:43-52.
6. Doerge RW and Churchill GA (1996) Permutation tests for multiple loci affecting a quantitative character. Genetics 142:285-294.
7. Gan S, Shi J, Li M, Wu K, Wu J and Bai J (2003) Moderate-density molecular maps of Eucalyptus urophylla S. T. Blake and E. tereticornis Smith genomes based on RAPD markers. Genetica 118:59-67.
8. Grattapaglia D and Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: Mapping strategy and RAPD markers. Genetics 137:1121-1137.
9. Haley CS, Knott SA and Elsen JM (1994) Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics 136:1195-1207.
10. Han K, Bradshaw HD, Gordon MP and Han KH (1994) Adventitious root and shoot regeneration in vitro is under major gene control in an F2 family of hybrid poplar (Populus trichocarpa ttP. deltoides). Forest Genet 1:139-146.
11. Jansen RC and Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136:1447-1455.
12. Kao C-H, Zeng Z-B and Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152:1203-1216.
13. Kullback S and Leibler RA (1951) On information and sufficiency. Ann Math Statist 22:79-86.
14. Lander ES and Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185-199.
15. Lin M, Lou XY, ChangMand Wu RL (2003) A general statistical framework for mapping quantitative trait loci in nonmodel systems: Issue for characterizing linkage phases. Genetics 165:901-913.
16. Lincoln SE and Lander ES (1990) Mapping Genes Controlling Quantitative Traits Using MAPMAKER/QTL. Technical Report. Whitehead Institute for Biomedical Research, Cambridge, 46 pp.
17. Lu Q, Cui YH and Wu RL (2004) A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family. BMC Genetics 5:e20.
18. Maliepaard C, Jansen J and Van Ooijen JW (1997) Linkage analysis in a full-sib family of an outbreeding plant species: Overview and consequences for applications. Genet Res 70:237-250.
19. Martinez O and Curnow RN (1992) Estimating the locations and the size of the effects of quantitative trait loci using flanking markers. Theor Appl Genet 85:480-488.
20. McLachlan G and Pell D (2000) Finite Mixture Models. John Wiley & Sons, New York, 419 pp.
21. Plomion CD, Malley MO and Durel CE (1995) Genomic analysis in maritime pine (Pinus pinaster). Comparison of two RAPD maps using selfed and open-pollinated seeds of the same individual. Theor Appl Genet 90:1028-1034.
22. Roberts SJ, Husmeier D, Rezek I and Penny W (1998) Bayesian approaches to Gaussian modeling. IEEE Trans Pattern Anal Mach Intell 20:1133-1142.
23. Schwarz G (1978) Estimating the dimension of a model. Ann Stat 6:461-464.
24. Shepherd M, Cross M, Dieters MJ and Herry R (2003) Genetic maps for Pinus elliottii var. elliottii and P. caribaea var. hondurensis using AFLP and microsatellite markers. Theor Appl Genet 106:1409-1419.
25. Tong CF, Zhang B and Shi JS (2010) A hidden Markov model approach to multilocus linkage analysis in a full-sib family. Tree Genet Genomes 6:651-662.
26. Van Ooijen JW (2006) JoinMap 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen, Netherlands.
27. Van Ooijen JW (2009) MapQTL 6, Software for the mapping of quantitative trait loci in experimental populations of diploid species. Kyazma BV, Wageningen, Netherlands.
28. Wang S, Basten CJ and Zeng Z-B (2010) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC.
29. WuRL, Han YF, Hu JJ, Fang JJ, Li L, LiLMand Zeng Z-B (2000) An integrated genetic map of Populus deltoids based on amplified fragment length polymorphisms. Theor Appl Genet 100:1249-1256.
30. Wu RL, Ma CX, Painter I and Zeng Z-B (2002) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theor Popul Biol 61:349-363.
31. Wu RL, Ma CX and Casella G (2007) Statistical Genetics of Quantitative Traits: Linkage, Maps and QTL. Springer, New York, 365 pp.
32. Xu S and Atchley WR (1996) Mapping quantitative trait loci for complex binary diseases using line crosses. Genetics 143:1417-1424.
33. Xu C, Li Z and Xu S (2005) Joint mapping of quantitative trait loci for multiple binary characters. Genetics 169:1045-1059.
34. Yi N and Xu S (2000) Bayesian mapping of quantitative trait loci for complex binary traits. Genetics 155:1391-1403.
35. Yin TM, Zhang XY, Huang MR, Wang MX, Zhuge Q, Tu SM, Zhu LH and Wu RL (2002) Molecular linkage maps of the Populus genome. Genome 45:541-555.
36. Zeng Z-B (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci USA 90:10972-10976.
37. Zeng Z-B (1994) Precision mapping of quantitative trait loci. Genetics 136:1457-1468.
38. Zeng Z-B, Kao C-H and Basten CJ (1999) Estimating the genetics architecture of quantitative traits. Genet Res 74:279-289.