Genome-Wide Effects of Long-Term Divergent Selection
To understand the genetic mechanisms leading to phenotypic differentiation, it is important to identify genomic regions under selection. We scanned the genome of two chicken lines from a single trait selection experiment, where 50 generations of selection have resulted in a 9-fold difference in body weight. Analyses of nearly 60,000 SNP markers showed that the effects of selection on the genome are dramatic. The lines were fixed for alternative alleles in more than 50 regions as a result of selection. Another 10 regions displayed strong evidence for ongoing differentiation during the last 10 generations. Many more regions across the genome showed large differences in allele frequency between the lines, indicating that the phenotypic evolution in the lines in 50 generations is the result of an exploitation of standing genetic variation at 100s of loci across the genome.
Vyšlo v časopise:
Genome-Wide Effects of Long-Term Divergent Selection. PLoS Genet 6(11): e32767. doi:10.1371/journal.pgen.1001188
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1001188
Souhrn
To understand the genetic mechanisms leading to phenotypic differentiation, it is important to identify genomic regions under selection. We scanned the genome of two chicken lines from a single trait selection experiment, where 50 generations of selection have resulted in a 9-fold difference in body weight. Analyses of nearly 60,000 SNP markers showed that the effects of selection on the genome are dramatic. The lines were fixed for alternative alleles in more than 50 regions as a result of selection. Another 10 regions displayed strong evidence for ongoing differentiation during the last 10 generations. Many more regions across the genome showed large differences in allele frequency between the lines, indicating that the phenotypic evolution in the lines in 50 generations is the result of an exploitation of standing genetic variation at 100s of loci across the genome.
Zdroje
1. Maynard SmithJ
HaighJ
1974 The hitch-hiking effect of a favourable gene. Genet Res 23 23 35
2. BerryAJ
AjiokaJW
KreitmanM
1991 Lack of polymorphism on the Drosophila fourth chromosome resulting from selection. Genetics 129 1111 1117
3. OrrHA
BetancourtAJ
2001 Haldane's sieve and adaptation from the standing genetic variation. Genetics 157 875 884
4. PrzeworskiM
CoopG
WallJD
2005 The signature of positive selection on standing genetic variation. Evolution 59 2312 2323
5. HermissonJ
PenningsPS
2005 Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169 2335 2352
6. PenningsPS
HermissonJ
2006a Soft sweeps II – molecular population genetics of adaptation from recurrent mutation or migration. Mol Biol Evol 23 1076 1084
7. JacobssonL
ParkHB
WahlbergP
FredrikssonR
Perez-EncisoM
2005 Many QTLs with minor additive effects are associated with a large difference in growth between two selection lines in chickens. Genet Res 86 115 125
8. HillWG
2005 A century of corn selection. Science 307 683 684
9. HillWG
BungerL
2004 Inferences on the genetics of quantative traits from long-term selection in laboratory and domestic animals. Plant Breeding Rev 24 169 210
10. DunningtonEA
SiegelPB
1996 Long-term divergent selection for eight-week body weight in White Plymouth Rock chickens. Poult Sci 75 1168 1179
11. SabetiPC
VarillyP
FryB
LohmuellerJ
HostetterE
2007 Genome-wide detection and characterization of positive selection in human populations. Nature 449 913 918
12. PenningsPS
HermissonJ
2006b Soft sweeps III: the signature of positive selection from recurrent mutation. PLoS Genetics 2 e186 doi:10.1371/journal.pgen.0020186
13. TeotónioH
CheloIM
BradićM
RoseMR
LongAD
2009 Experimental evolution reveals natural selection on standing genetic variation. Nat Genet 41 251 257
14. RaquinA-L
BrabantP
RhonéB
BalfourierF
LeroyP
2008 Soft selective sweep near a gene that increases plant height in wheat. Mol Ecol 17 741 756
15. PurcellS
NealeB
Todd-BrownK
ThomasL
FerreiraMAR
2007 PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81 559 575
16. CarlborgÖ
JacobssonL
ÅhgrenP
SiegelP
AnderssonL
2006 Epistasis and the release of genetic variation during long-term selection. Nat Genet 38 418 420
17. WahlbergP
CarlborgÖ
FoglioM
TordirX
SyvänenA-C
2009 Genetic analysis of an F2 intercross between two chicken lines divergently selected for body-weight. BMC Genomics 10 248
18. FalconerDS
MackayTFC
1996 Introduction to Quantitative Genetics. 4th ed. Essex, UK Longmans Green, Harlow
19. KimuraM
CrowJF
1978 Effect of overall phenotypic selection on genetic change at individual loci. Proc Natl Acad Sci USA 75 6168 6171
20. MarquezGL
LewisRM
WieglandEN
SiegelPB
2009 Inbreeding and population structure in lines of chickens divergently selected for high and low 8-week body weight. Poultry Science 88 E-suppl. 1 161 2009 Poultry Science Association Annual Meeting Abstracts
21. GillespieJH
1998 Population Genetics: A Concise Guide. Baltimore John Hopkins University Press 174
22. CastleWE
1921 An improved method of estimating the number of genetic factors concerned in cases of blending inheritance. Proc Natl Acad Sci USA 81 6904 6907
23. WrightS
1968 Evolution and the Genetics of Populations: Volume 1, Genetic and biometric foundations. Chicago University of Chicago Press 469
24. ZengZB
1992 Correcting the bias of Wright estimates of the number of genes affecting a quantitative character—a further improved method. Genetics 131 987 1001
25. OttoSP
JonesCD
2000 Detecting the undetected: Estimating the total number of loci underlying a quantitative trait. Genetics 156 2093 2107
26. BucklerES
HollandJB
BradburyPJ
AcharyaCB
BrownPJ
2009 The genetic architecture of maize flowering time. Science 325 714 718
27. LaurieCC
ChasalowSD
LeDeauxJR
McCarrollR
BushD
2004 The genetic architecture of response to long-term artificial selection for oil concentration in the maize kernel. Genetics 168 2141 2155
28. WeedonMN
LangoH
LindgrenCM
WallaceC
EvansDM
2008 Genome-wide association analysis identifies 20 loci that influence adult height. Nat Genet 40 575 583
29. ParkH-B
JacobssonL
WahlbergP
SiegelPB
AnderssonL
2006 QTL analysis of body composition and metabolic traits in an intercross between chicken lines divergently selected for growth. Physiol Genomics 25 216 223
30. RubinCJ
ZodyMC
ErikssonJ
MeadowsJR
SherwoodE
2010 Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464 587 591
31. R Development Core Team 2007 R: A language and environment for statistical computing. Vienna R Foundation for Statistical Computing
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Genetika Reprodukčná medicínaČlánok vyšiel v časopise
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