Development of Genome-Wide Scan for Selection Signature in Farm Animals
ZHANG Wen-guang
1.College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R.China
2.Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, P.R.China
3.Institute of ATCG, Nei Mongol Bio-Information, Hohhot 010020, P.R.China
摘要 Identifying targets of positive selection in farm animals has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of selection. This review described important recent results derived from the application of genome-wide scan to the study of genetic changes in farm animals. These included findings of regions of the genome that showed breed differentiation, evidence of selective sweeps within individual genomes and signatures of demographic events. Particular attention is focused on the study of the implications for domestication. To date, sixteen genome-wide scans for recent or ongoing positive selection have been performed in farm animals. A key challenge is to begin synthesizing these newly constructed maps of selection into a coherent narrative of animal breed evolutionary history and derive a deeper mechanistic understanding of how animal populations improve or evolve. The major insights from the surveyed studies are highlighted and directions for future study are suggested.
Abstract Identifying targets of positive selection in farm animals has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of selection. This review described important recent results derived from the application of genome-wide scan to the study of genetic changes in farm animals. These included findings of regions of the genome that showed breed differentiation, evidence of selective sweeps within individual genomes and signatures of demographic events. Particular attention is focused on the study of the implications for domestication. To date, sixteen genome-wide scans for recent or ongoing positive selection have been performed in farm animals. A key challenge is to begin synthesizing these newly constructed maps of selection into a coherent narrative of animal breed evolutionary history and derive a deeper mechanistic understanding of how animal populations improve or evolve. The major insights from the surveyed studies are highlighted and directions for future study are suggested.
The authors thank Wang Wen, Kunming Institute of Zoology, CAS, for valuable suggestions on manuscript preparation, and thank Dr. He Yanghua, China Agricultural University, for providing references. Support for this work was provided by the Inner Mongolia Autonomous Region (2010ZD11), the National Natural Science Foundation of China (30960246, 31260538) and the Key Projects in the National Science & Technology Pillar Program (30960242011BAD28B05).
ZHANG Wen-guang.
2013.
Development of Genome-Wide Scan for Selection Signature in Farm Animals. Journal of Integrative Agriculture, 12(8): 1461-1470.
[1]Akey J M. 2009. Constructing genomic maps of positiveselection in humans: Where do we go from here?Genome Research, 19, 711-722
[2]Akey J M, Ruhe A L, Akey D T, Wong A K, Connelly C F,Madeoy J, Nicholas T J, Neff M W. 2010. Trackingfootprints of artificial selection in the dog genome.Proceedings of the National Academy of Sciences ofthe United States of America, 107, 31160-31165
[3]Akey J M, Zhang G, Zhang K, Jin L, Shriver M D. 2002.Interrogating a high-density SNP map for signatures ofnatural selection. Genome Research, 12, 1805-1814
[4]Amaral A J, Ferretti L, Megens H J, Crooijmans R P M A,Nie H, Ramos-Onsins S E, Perez-Enciso M, Schook L B,Groenen M A M. 2011. Genome-wide footprints of pigdomestication and selection revealed through massiveparallel sequencing of pooled DNA. PLoS ONE, 6,e14782. doi: 10.1371/journal.pone.0014782
[5]Barendse W, Harrison B E, Bunch R J, Thomas M B, TurnerL B. 2009. Genome wide signatures of positive selection:The comparison of independent samples and theidentification of regions associated to traits. BMCGenomics, 10, 178.
[6]Dekkers J. 2004. Commercial application of marker- andgene-assisted selection in livestock: strategies andlessons. Journal of Animal Science, 82(E-Suppl.), E313-E328.Excoffier L, Hofer T, Foll M. 2009. Detecting loci underselection in a hierarchically structured population.Heredity, 103, 285-298
[7]Flori L, Fritz S, Jaffrézic F, Boussaha M, Gut I, Heath S,Foulley J L, Gautier M. 2009. The genome response toartificial selection: a case study in dairy cattle. PLoSOne, 4, e6595.
[8]Gautier M, Flori L, Riebler A, Jaffrézic F, Laloé D, Gut I,Moazami-Goudarzi K, Foulley J L. 2009. A whole genomeBayesian scan for adaptive genetic divergence in WestAfrican cattle. BMC Genomics, 21, 10:550. doi: 10.1186/1471-2164-10-550
[9]Gu J, Orr N, Park S D, Katz L M, Sulimova G, MacHugh D E,Hill E W 2009 A genome scan for positive selection inthoroughbred horses. PLoS ONE, 4, e5767. doi: 10.1371/journal.pone.0005767
[10]Harr B, Kauer M, Schlötterer C. 2002. Hitchhiking mapping- a population based fine scale mapping strategy foradaptive mutations in Drosophila melanogaster.Proceedings of the National Academy of Sciences ofthe United States of America, 99, 12949-12954
[11]Hurst L D. 2009. Fundamental concepts in genetics: geneticsand the understanding of selection. Nature ReviewsGenetic, 10, 83-93
[12]Jessica L P, James R M, Molly E M. 2011. The identificationof signatures of selection in modern horse breeds usinggenome-wide SNP data. In: Proceedings of Plant &Animal Genomes XIX Conference. Town & Country Convention Center, San Diego, CA.
[13]Joanna L K, Willie J S. 2008. Positive selection in the humangenome: from genome scans to biological significance.Annual Review of Genomics and Human Genetics, 9,143-160
[14]Kijas J W, Johannes A L, Ben H, Simon B, Laercio R P N,Magali S C, Bertrand S, Russell M, Vicki W, Kimberly G,et al. 2012. Genome-wide analysis of the world’s sheepbreeds reveals high levels of historic mixture and strongrecent selection. PLoS Biology, 10, e1001258. doi: 10.1371/journal.pbio.1001258
[15]Kim Y, Stephan W. 2002. Detecting a local signature ofgenetic hitchhiking along a recombining chromosome.Genetics, 160, 765-777
[16]Kimura R, Fujimoto A, Tokunaga K, Ohashi J. 2007. Apractical genome scan for population-specific strongselective sweeps that have reached fixation. PLoS ONE,2, e286. doi: 10.1371/journal.pone.0000286
[17]Kuhn C, Leveziel H, Renand G, Goldammer T, Schwerin M,Williams J L. 2005. Genetic markers for beef quality. In:Hocquette J F, Gigli S, eds., Indicators of Milk andBeef Quality. EAAP Publication, No. 112.Lewontin R, Krakauer J. 1973. Distribution of genefrequency as a test of theory of selective neutrality of polymorphisms. Genetics, 74, 175-195
[18]Lu D, Miller S, Sargolzaei M, Voort G V, Caldwell T, Abo-Ismail M K, Wang Z, Mah J, Plastow G, Moore S. 2010.Genome wide scan for signals of recent selection inAngus beef cattle. In: The 9th World Congress onGenetics Applied to Livestock Production. Leipzig,Germany.Matthieu F, Oscar G. 2008. A genome-scan method toidentify selected loci appropriate for both dominant andcodominant markers: A Bayesian perspective. Genetics,180, 977-993
[19]McCue M E, Bannasch D L, Petersen J L, Gurr J, Bailey E,Binns M M, Distl O, Guérin G, Hasegawa T, Hill E W, etal. 2012. A high density SNP array for the domestichorse and extant perissodactyla: utility for associationmapping, genetic diversity, and phylogeny studies.PLoS Genetics, 8, e1002451. doi: 10.1371/journal.pgen.1002
[20]Nielsen R, Bustamante C, Clark A G, Glanowski S, SacktonT B, Hubisz M J, Fledel-Alon A, Tanenbaum D M,Civello D, White T J, et al. 2005. A scan for positivelyselected genes in the genomes of humans andchimpanzees. PLoS Biology, 3, 976-985
[21]Qanbari S, Pimentel E C, Tetens J, Thaller G, Lichtner P,Sharifi A R, Simianer H. 2010. A genome-wide scan forsignatures of recent selection in Holstein cattle. AnimalGenetics, 41, 377-389
[22]Quilez J, Short A D, Martínez V, Kennedy L J, Ollier W,Sanchez A, Altet L, Francino O. 2011. A selective sweepof >8 Mb on chromosome 26 in the Boxer genome. BMCGenomics, 1;12:339. doi:10.1186/1471-2164-12-339
[23]Rubin C J, Zody M C, Eriksson J, Meadows J R, SherwoodE, Webster M T, Jiang L, Ingman M, Sharpe T, Ka S, etal. 2010. Whole-genome resequencing reveals lociunder selection during chicken domestication. Nature,464, 587-591
[24]Sabeti P C, Reich D E, Higgins J M, Levine H Z, Richter D J,Schaffner S F, Gabriel S B, Platko J V, Patterson N J,McDonald G J, et al. 2002. Detecting recent positiveselection in the human genome from haplotypestructure. Nature, 419, 832-837
[25]Sabeti P C, Schaffner S F, Fry B, Lohmueller J, Varilly P,Shamovsky O, Palma A, Mikkelsen T S, Altshuler D,Lander E S. 2006. Positive natural selection in the humanlineage. Science, 312, 1614-1620
[26]Stella A, Ajmone-Marsan P, Lazzari B and Boettcher P. 2010.Identification of selection signatures in cattle breedsselected for dairy production. Genetics, 185, 1451-1461
[27]The Bovine HapMap Consortium. 2009. Genome-widesurvey of SNP variation uncovers the genetic structureof cattle breeds. Science, 324, 528-532
[28]Thorisson G A, Stein L D. 2003. The SNP Consortiumwebsite: Past, present and future. Nucleic AcidsResearch, 31, 124-127
[29]Vaysse A, Ratnakumar A, Derrien T, Axelsson E, RosengrenPielberg G, Sigurdsson S, Fall T, Seppälä E H, HansenM S T, Lawley C T, et al. 2011. Identification of genomicregions associated with phenotypic variation betweendog breeds using selection mapping. PLoS Genetics,7,e1002316. doi: 10.1371/journal.pgen.1002316.Weir B S, Cardon L R, Anderson A D, Nielsen D M, Hill WG. 2005. Measures of human population structure showheterogeneity among genomic regions. GenomeResearch, 15, 1468-1476
[30]Williams J L. 2005. The use of marker-assisted selection inanimal breeding and biotechnology. Scientific andTechnical Review, 24, 379-391
[31]Wright S. 1951. The genetic structure of populations.Annals of Eugenics, 15, 323-354.
