Admixture mapping of quantitative traits in Populus hybrid zones: Power and limitations

Heredity

Volumn 111, Issue 6, 2013, Pages 474-485

  Lindtke, D ^a   Gonzalez Martinez S C ^b   Macaya Sanz, D ^b,c   Lexer, C ^a,d  

^a UNIVERSITY OF FRIBOURG   (Switzerland)

^b INIA   (Spain)

^c UNIVERSIDAD POLITÉCNICA DE MADRID   (Spain)

^d JODRELL LABORATORY   (United Kingdom)

Author keywords

Dominance; Leaf morphology; Model selection; Overdominance; Populus alba; Populus tremula

Indexed keywords

DIVERGENCE; DOMINANCE; GENERATION TIME; GENETIC STRUCTURE; HYBRID; LEAF MORPHOLOGY; LOCAL ADAPTATION; MAPPING; PHENOTYPE; REGRESSION ANALYSIS; SIMULATION; TREE;

POPULUS; POPULUS ALBA; POPULUS ALBA X POPULUS TREMULA; POPULUS TREMULA;

MICROSATELLITE DNA;

ARTICLE; CHROMOSOME MAP; CLASSIFICATION; EVALUATION STUDY; GENETIC LINKAGE; GENETICS; GENOTYPE; METHODOLOGY; PLANT CHROMOSOME; POPULUS; QUANTITATIVE TRAIT LOCUS;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENETIC LINKAGE; GENOTYPE; MICROSATELLITE REPEATS; POPULUS; QUANTITATIVE TRAIT LOCI;

EID: 84887621381     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2013.69     Document Type: Article

References (57)

1. Adler W, Oswald K, Fischer R (1994). Exkursionsflora von Oesterreich. Verlag Eugen Ulmer: Stuttgart and Vienna, Germany and Austria
2. Akaike H (1973). Information theory as an extension of the maximum likelihood principle. In: Petrov BN, Csaki F (eds) Second International Symposium on Information Theory. Akademiai Kiado: Budapest, pp 267-281
3. Barrett RDH, Schluter D (2008). Adaptation from standing genetic variation. Trends Ecol Evol 23: 38-44
4. Barton NH, Keightley PD (2002). Understanding quantitative genetic variation. Nat Rev Genet 3: 11-21 (Pubitemid 34506600)
5. Beavis WD (1998). QTL analyses: power, precision and accuracy. In: Paterson AH (ed) Molecular Dissection of Complex Traits. CRC Press: New York, NY, USA, pp 145-162
6. Bradshaw HD, Otto KG, Frewen BE, Mckay JK, Schemske DW (1998). Quantitative trait loci affecting differences in floral morphology between two species of monkeyflower (Mimulus). Genetics 149: 367-382 (Pubitemid 28246811)
7. Briscoe D, Stephens JC, Obrien SJ (1994). Linkage disequilibrium in admixed populations-Applications in gene-mapping. J Hered 85: 59-63 (Pubitemid 24057427)
8. Broman KW, Speed TR (2002). A model selection approach for the identification of quantitative trait loci in experimental crosses. J R Stat Soc B 64: 641-656
9. Buerkle CA, Lexer C (2008). Admixture as the basis for genetic mapping. Trends Ecol Evol 23: 686-694
10. Chakraborty R, Weiss KM (1988). Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc Natl Acad Sci USA 85: 9119-9123 (Pubitemid 19001851)
11. Charlesworth D, Willis JH (2009). The genetics of inbreeding depression. Nat Rev Genet 10: 783-796
12. Churchill GA, Doerge RW (1994). Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971 (Pubitemid 24337818)
13. Coyne JA, Orr HA (2004). Speciation. Sinauer Associates: Sunderland, MA.
14. de Carvalho D, Ingvarsson PK, Joseph J, Suter L, Sedivy C, Macaya-Sanz D et al. (2010). Admixture facilitates adaptation from standing variation in the European aspen (Populus tremula L.), a widespread forest tree. Mol Ecol 19: 1638-1650
15. Erickson DL, Fenster CB, Stenoien HK, Price D (2004). Quantitative trait locus analyses and the study of evolutionary process. Mol Ecol 13: 2505-2522 (Pubitemid 39151611)
16. Falush D, Stephens M, Pritchard JK (2003). Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587 (Pubitemid 37102217)
17. Falush D, Stephens M, Pritchard JK (2007). Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7: 574-578 (Pubitemid 47035522)
18. Funk DJ, Nosil P, Etges WJ (2006). Ecological divergence exhibits consistently positive associations with reproductive isolation across disparate taxa. Proc Natl Acad Sci USA 103: 3209-3213 (Pubitemid 43346449)
19. Gompert Z, Lucas LK, Nice CC, Buerkle CA (2013). Genome divergence and the genetic architecture of barriers to gene flow between Lycaeides idas and L melissa. Evolution; doi:10.1111/evo.12021
20. Grandillo S, Ku HM, Tanksley SD (1999). Identifying the loci responsible for natural variation in fruit size and shape in tomato. Theor Appl Genet 99: 978-987 (Pubitemid 29527046)
21. Grueber CE, Nakagawa S, Laws RJ, Jamieson IG (2011). Multimodel inference in ecology and evolution: challenges and solutions. J Evol Biol 24: 699-711
22. Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, Clayton DG et al. (2003). Control of confounding of genetic associations in stratified populations. Am J Hum Genet 72: 1492-1504 (Pubitemid 36628388)
23. Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM (2004). Design and analysis of admixture mapping studies. Am J Hum Genet 74: 965-978 (Pubitemid 38568969)
24. Kearsey MJ, Farquhar AGL (1998). QTL analysis in plants; where are we now? Heredity 80: 137-142 (Pubitemid 28102285)
25. Lexer C, Buerkle CA, Joseph JA, Heinze B, Fay MF (2007). Admixture in European Populus hybrid zones makes feasible the mapping of loci that contribute to reproductive isolation and trait differences. Heredity 98: 74-84 (Pubitemid 46173896)
26. Lexer C, Fay MF, Joseph JA, Nica MS, Heinze B (2005a). Barrier to gene flow between two ecologically divergent Populus species, P. alba (White poplar) and P. Tremula (European aspen): the role of ecology and life history in gene introgression. Mol Ecol 14: 1045-1057 (Pubitemid 40466234)
27. Lexer C, Joseph J, Van Loo M, Prenner G, Heinze B, Chase MW et al. (2009). The use of digital image-based morphometrics to study the phenotypic mosaic in taxa with porous genomes. Taxon 58: 349-364
28. Lexer C, Joseph JA, Van Loo M, Barbara T, Heinze B, Bartha D et al. (2010). Genomic admixture analysis in European Populus spp. reveals unexpected patterns of reproductive isolation and mating. Genetics 186: 699-U391
29. Lexer C, Rosenthal DM, Raymond O, Donovan LA, Rieseberg LH (2005b). Genetics of species differences in the wild annual sunflowers, Helianthus annuus and H. petiolaris. Genetics 169: 2225-2239 (Pubitemid 40695632)
30. Lexer C, Widmer A (2008). The genic view of plant speciation: Recent progress and emerging questions. Philos Trans R Soc Ser B 363: 3023-3036
31. Lindtke D, Buerkle CA, Barbara T, Heinze B, Castiglione S, Bartha D et al. (2012). Recombinant hybrids retain heterozygosity at many loci: new insights into the genomics of reproductive isolation in Populus. Mol Ecol 21: 5042-5058
32. Lynch M, Walsh B (1998). Genetics and Analysis of Quantitative Traits. Sinauer: Sunderland, MA, USA.
33. Mackay TFC (2001). The genetic architecture of quantitative traits. Annu Rev Genet 35: 303-339
34. Malek TB, Boughman JW, Dworkin I, Peichel CL (2012). Admixture mapping of male nuptial colour and body shape in a recently formed hybrid population of threespine stickleback. Mol Ecol 21: 5265-5279
35. McKeigue PM (1998). Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture. Am J Hum Genet 63: 241-251 (Pubitemid 30428340)
36. McKeigue PM (2005). Prospects for admixture mapping of complex traits. Am J Hum Genet 76: 1-7 (Pubitemid 40023761)
37. Neuenschwander S, Hospital F, Guillaume F, Goudet J (2008). quantiNemo: an individualbased program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation. BioInformatics 24: 1552-1553 (Pubitemid 351911714)
38. Nolte AW, Tautz D (2010). Understanding the onset of hybrid speciation. Trends Genet 26: 54-58
39. Orr HA (1998). Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data. Genetics 149: 2099-2104 (Pubitemid 28375975)
40. Orr HA (2001). The genetics of species differences. Trends Ecol Evol 16: 343-350
41. Pakull B, Groppe K, Meyer M, Markussen T, Fladung M (2009). Genetic linkage mapping in aspen (Populus tremula L. and Populus tremuloides Michx.). Tree Genet Genom 5: 505-515
42. Petit RJ, Hampe A (2006). Some evolutionary consequences of being a tree. Annu Rev Ecol Evol Syst 37: 187-214 (Pubitemid 44907617)
43. Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945-959 (Pubitemid 30397141)
44. R Development Core Team (2011). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing: Vienna, Austria, http://www. r-project.org/.
45. Rae AM, Ferris R, Tallis MJ, Taylor G (2006). Elucidating genomic regions determining enhanced leaf growth and delayed senescence in elevated CO2 Plant Cell Environ 29: 1730-1741 (Pubitemid 44141729)
46. Rieseberg LH, Archer MA, Wayne RK (1999a). Transgressive segregation, adaptation and speciation. Heredity 83: 363-372 (Pubitemid 29511313)
47. Rieseberg LH, Buerkle CA (2002). Genetic mapping in hybrid zones. Am Nat 159: S36-S50 (Pubitemid 34172093)
48. Rieseberg LH, Whitton J, Gardner K (1999b). Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species. Genetics 152: 713-727 (Pubitemid 29272722)
49. Schwarz G (1978). Estimating dimension of a model. Ann Stat 6: 461-464
50. Stölting KN, Nipper R, Lindtke D, Caseys C, Waeber S, Castiglione S et al (2013). Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species. Mol Ecol 22 842-855
51. Tanksley SD (1993). Mapping polygenes. Annu Rev Genet 27: 205-233 (Pubitemid 24011353)
52. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U et al. (2006). The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604 (Pubitemid 44414027)
53. Wang YX, Zhang B, Sun XY, Tan BY, Xu LA, Huang MR et al. (2011). Comparative genome mapping among Populus adenopoda, P. alba, P. deltoides, P. euramericana and P. Trichocarpa. Genes Genet Syst 86: 257-268
54. Whittingham MJ, Stephens PA, Bradbury RB, Freckleton RP (2006). Why do we still use stepwise modelling in ecology and behaviour? J Anim Ecol 75: 1182-1189 (Pubitemid 44175184)
55. Winkler CA, Nelson GW, Smith MW (2010). Admixture mapping comes of age. Annu Rev Genom Hum Genom 11: 65-89
56. Zeng ZB, Liu JJ, Stam LF, Kao CH, Mercer JM, Laurie CC (2000). Genetic architecture of a morphological shape difference between two Drosophila species. Genetics 154: 299-310 (Pubitemid 30045921)
57. Zhu XF, Luke A, Cooper RS, Quertermous T, Hanis C, Mosley T et al. (2005). Admixture mapping for hypertension loci with genome-scan markers. Nat Genet 37: 177-181.