Mapping QTLs with epistatic effects and QTL x environment interactions by mixed linear model approaches

Theoretical and Applied Genetics

Volumn 99, Issue 7-8, 1999, Pages 1255-1264

  Wang, D L ^a,c   Zhu, J ^a   Li, Z K ^b,d   Paterson, A H ^b  

^a ZHEJIANG UNIVERSITY   (China)

^b TEXAS A AND M UNIVERSITY   (United States)

^c ANHUI AGRICULTURAL UNIVERSITY   (China)

^d INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

Epistasis; Mixed linear model; Monte Carlo simulations; QTL mapping method; QTLxenvironment interaction

Indexed keywords

GENE MAPPING; MATHEMATICAL MODEL; QUANTITATIVE TRAIT;

EID: 0032753652     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s001220051331     Document Type: Article

References (50)

1. Allard RW (1988) Future directions in plant population genetics, evolution and breeding. In: Brown AHD, Clegg MT, Kahler AL, Weir BS (eds) Plant population genetics and germplasm resources. Sinauer Associates Inc, Sunderland, Massachusetts, pp 1-19
2. Bradshaw HD, Stettler RF (1995) Molecular genetics of growth and development in Populus. IV. Mapping QTLs with large effects on growth, form, and phenology traits in a forest tree. Genetics 139:963-973
3. Chase K, Adler FR, Lark KG (1997) EPISTAT: a computer program for identifying and testing interactions between pairs of quantitative trait loci. Theor Appl Genet 94:724-730
4. Cockerham CC, Zeng ZB (1996) Design III with marker loci. Genetics 143:1437-1456
5. Doebley J, Stec A, Gustus C (1995) teosinte branched I and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141:333-346
6. nd edn. Longman Press, New York
7. Fernando RL, Grossman M (1989) Marker-assisted selection using best linear unbiased prediction. Genet Selec Evol 21:467-477
8. Fijneman RJA, Devries SS, Jansen RC, Demant P (1996) Complex interactions of new quantitative trait loci, sluc1, sluc2, sluc3 and sluc4, that influence the susceptibility to lung-cancer in the mouse. Nature Genet 14:465-467
9. Fu YB, Ritland K (1996) Marker-based inferences about epistasis for genes influencing inbreeding depression. Genetics 144: 339-348
10. Goddard ME (1992) A mixed model for analyses of data on multiple genetic markers. Theor Appl Genet 83:878-886
11. th EUCARPlA Meeting. Section Biometrics in Plant Breeding. Wageningen, The Netherlands, pp 99-106
12. Haldane JBS (1919) The combination of linkage values and the calculation of distance between the loci of linked factors. J Genet 8:299-309
13. Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315-324
14. Holland JB (1998) EPISTACY: A SAS program for detecting two-locus epistatic interactions using genetic marker information. J Hered 89:374-375
15. Jansen RC (1992) A general mixture model for mapping quantitative trait loci by using molecular markers. Theor Appl Genet 85:252-260
16. Jansen RC (1993) Interval mapping of multiple quantitative trait loci. Genetics 135:205-211
17. Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136:1447-1455
18. Jansen RC, Van Ooijen JW, Stam P, Lister C, Dean C (1995) Genotype by environment interaction in genetic mapping of multiple quantitative trait loci. Theor Appl Genet 91:33-37
19. Jiang CJ, Zeng ZB (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140:1111-1127
20. Jiang CJ, Zeng ZB (1997) Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica 101:47-58
21. Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185-199
22. Lark KG, Chase K, Adler FR, Mansur LM, Orf JJ (1995) Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another. Proc Natl Acad Sci USA 92:4656-4660
23. Li ZK (1997) Molecular analysis of epistasis. In: Paterson AH (ed) Molecular dissection of complex traits. CRC Press, Boca Raton, Florida, pp 119-130
24. Li ZK, Pinson SRM, Park WD, Paterson AH, Stansel JW (1997a) Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics 145:453-465
25. Li ZK, Pinson SRM, Paterson AH, Park WD, Stansel JW (1997b) Genetics of hybrid sterility and hybrid breakdown in an intersubspecific rice (Oryza sativa L.) population. Genetics 145: 1139-1148
26. Mather K, Jinks JL (1982) Biometrical genetics, 3rd edn. Chapman and Hall, London
27. Meuwissen THE, Goddard ME (1997) Estimation of effects of quantitative trait loci in large complex pedigrees. Genetics 146:409-416
28. Moreno-Gonzalez J (1992) Genetic models to estimate additive and non-additive effects of marker-associated QTLs using multiple regression techniques. Theor Appl Genet 85:435-444
29. Neale DB, Sederoff RR (1996) Genome mapping in gymnosperms: a case study in loblolly pine (Pinus taeda L.). In: Paterson AH, Landes RG (eds) Genome mapping in plants. Academic Press, Georgetown, Texas, pp 308-319
30. Paterson AH, Damon S, Hewitt JD, Zamir D, Rabinowitch HD, Lincoln SE et al. (1988) Resolution of quantitative traits into Mendelian factors by using a complete map of restriction fragment length polymorphisms. Nature 335:721-726
31. Paterson AH, Deverna JW, Lanini B, Tanksley SD (1991) Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics 127:181-197
32. Patterson HD, Thompson R (1971) Recovery of inter-block information when block sizes are unequal. Biometrika 58:545-554
33. th Int Biometric Conf. Biometric Society, Washington, D.C
34. Pooni HS, Coombs DJ, Jinks PS (1987) Detection of epistatsis and linkage of interacting genes in the presence of reciprocal differences. Heredity 58:257-266
35. Routman EJ, Cheverud JM (1997) Gene effects on a quantitative trait: two-locus epistatic effect measured at microsatellite markers and at estimated QTLs. Evolution 51:1654-1662
36. Sari-Gorla M, Calinski T, Kaczmarek Z, Krajewski P (1997) Detection of QTLxenvironment interaction in maize by a least squares interval mapping method. Heredity 78:146-157
37. Spickett SG, Thoday JM (1966) Regular response to selection. 3. Interaction between located polygenes. Genet Res 7:96-121
38. Stuber CW, Edwards MD, Wendel JF (1987) Molecular marker-facilitated investigations of quantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action. Genetics 116:113-248
39. Tanksley SD, Hewitt JD (1996) Use of molecular markers in breeding for soluble solids in tomato - a re-examination. Theor Appl Genet 75:811-823
40. Tinker NA, Mather DE (1995) Methods for QTL analysis with progeny replicated in multiple environments. JQTL (http://probe.gig.usda.gov:8000/otherdocs/jqtl/) 1 (1)
41. Utz HF, Melchinger AE (1996) PLABQTL: a program for composite interval mapping of QTLs. JQTL (http://probe.gig.usda.gov:8000/otherdocs/jqtl/) 2 (1)
42. Weller JI (1986) Maximum-likelihood techniques for the mapping and analysis of quantitative trait loci with the aid of genetic markers. Biometrics 42:627-640
43. 2 population of an indicaljaponica cross in rice. Theor Appl Genet 91:825-829
44. Xiao J, Li J, Yuan L, Tanksley SD (1995) Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers. Genetics 140:745-754
45. Yan JQ, Zhu J, He CX, Benmoussa M, Wu P (1998). Molecular dissection of developmental behavior of plant height in rice (Oryza sativa L.). Genetics 150:1257-1265
46. Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, Li XH, et al. (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 94:9226-9231
47. Zeng ZB (1993) Theoretical basis of separation of multiple linked gene effects on mapping quantitative trait loci. Proc Natl Acad Sci USA 90:10972-10976
48. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457-1468
49. Zhu J (1998) Mixed-model approaches of mapping genes for complex quantitative traits. In: Wang LZ, Dai JR (eds) Proc Genet and Crop Breed of China. Chinese Agricultural Science and Technology Publication House, Beijing, pp 19-20
50. Zhu J, Weir BS (1998) Mixed-model approaches for genetic analysis of quantitative traits. In: Chen LS, Ruan SG, and Zhu J (eds) Advanced topics in biomathematics. Proc Inter Conf on Mathematical Biol. World Scientific Publishing Co., Singa-pore, pp 321-330