Genomic relationships computed from either next-generation sequence or array SNP data

Journal of Animal Breeding and Genetics

Volumn 131, Issue 2, 2014, Pages 85-96

  Perez Enciso M ^a,b,c,d  

^a CENTRE FOR RESEARCH IN AGRICULTURAL GENOMICS CRAG   (Spain)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^c INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

^d WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Coalescence; Genomic selection; Molecular relationship matrix; Next generation sequencing; SNP ascertainment

Indexed keywords

ANIMALIA; BOS; SUIDAE; SUS;

ANIMAL; BIOLOGICAL MODEL; DNA MICROARRAY; DNA SEQUENCE; GENE FREQUENCY; GENETICS; GENOMICS; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; SWINE;

ANIMALS; GENE FREQUENCY; GENOMICS; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SWINE;

EID: 84897606419     PISSN: 09312668     EISSN: 14390388     Source Type: Journal    
DOI: 10.1111/jbg.12074     Document Type: Article

References (24)

1. Chen G.K., Marjoram P., Wall J.D. (2009) Fast and flexible simulation of DNA sequence data. Genome Res., 19, 136-142.
2. Druet T., Macleod I.M., Hayes B.J. (2014) Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions. Heredity, 112, 39-47.
3. Gibbs R.A., Taylor J.F., Van Tassell C.P., Barendse W., Eversole K.A., Gill C.A., Green R.D., Hamernik D.L., Kappes S.M., Lien S., Matukumalli L.K., McEwan J.C., Nazareth L.V., Schnabel R.D., Weinstock G.M., Wheeler D.A., Ajmone-Marsan P., Boettcher P.J., Caetano A.R., Garcia J.F., Hanotte O., Mariani P., Skow L.C., Sonstegard T.S., Williams J.L., Diallo B., Hailemariam L., Martinez M.L., Morris C.A., Silva L.O., Spelman R.J., Mulatu W., Zhao K., Abbey C.A., Agaba M., Araujo F.R., Bunch R.J., Burton J., Gorni C., Olivier H., Harrison B.E., Luff B., Machado M.A., Mwakaya J., Plastow G., Sim W., Smith T., Thomas M.B., Valentini A., Williams P., Womack J., Woolliams J.A., Liu Y., Qin X., Worley K.C., Gao C., Jiang H., Moore S.S., Ren Y., Song X.Z., Bustamante C.D., Hernandez R.D., Muzny D.M., Patil S., San Lucas A., Fu Q., Kent M.P., Vega R., Matukumalli A., McWilliam S., Sclep G., Bryc K., Choi J., Gao H., Grefenstette J.J., Murdoch B., Stella A., Villa-Angulo R., Wright M., Aerts J., Jann O., Negrini R., Goddard M.E., Hayes B.J., Bradley D.G., Barbosa da Silva M., Lau L.P., Liu G.E., Lynn D.J., Panzitta F., Dodds K.G. (2009) Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science, 324, 528-532.
4. Giuffra E., Kijas J.M., Amarger V., Carlborg O., Jeon J.T., Andersson L. (2000) The origin of the domestic pig: independent domestication and subsequent introgression. Genetics, 154, 1785-1791.
5. Groenen M.A., Archibald A.L., Uenishi H., Tuggle C.K., Takeuchi Y., Rothschild M.F., Rogel-Gaillard C., Park C., Milan D., Megens H.J., Li S., Larkin D.M., Kim H., Frantz L.A., Caccamo M., Ahn H., Aken B.L., Anselmo A., Anthon C., Auvil L., Badaoui B., Beattie C.W., Bendixen C., Berman D., Blecha F., Blomberg J., Bolund L., Bosse M., Botti S., Bujie Z., Bystrom M., Capitanu B., Carvalho-Silva D., Chardon P., Chen C., Cheng R., Choi S.H., Chow W., Clark R.C., Clee C., Crooijmans R.P., Dawson H.D., Dehais P., De Sapio F., Dibbits B., Drou N., Du Z.Q., Eversole K., Fadista J., Fairley S., Faraut T., Faulkner G.J., Fowler K.E., Fredholm M., Fritz E., Gilbert J.G., Giuffra E., Gorodkin J., Griffin D.K., Harrow J.L., Hayward A., Howe K., Hu Z.L., Humphray S.J., Hunt T., Hornshøj H., Jeon J.T., Jern P., Jones M., Jurka J., Kanamori H., Kapetanovic R., Kim J., Kim J.H., Kim K.W., Kim T.H., Larson G., Lee K., Lee K.T., Leggett R., Lewin H.A., Li Y., Liu W., Loveland J.E., Lu Y., Lunney J.K., Ma J., Madsen O., Mann K., Matthews L., McLaren S., Morozumi T., Murtaugh M.P., Narayan J., Nguyen D.T., Ni P., Oh S.J., Onteru S., Panitz F., Park E.W., Park H.S., Pascal G., Paudel Y., Perez-Enciso M., Ramirez-Gonzalez R., Reecy J.M., Rodriguez-Zas S., Rohrer G.A., Rund L., Sang Y., Schachtschneider K., Schraiber J.G., Schwartz J., Scobie L., Scott C., Searle S., Servin B., Southey B.R., Sperber G., Stadler P., Sweedler J.V., Tafer H., Thomsen B., Wali R., Wang J., Wang J., White S., Xu X., Yerle M., Zhang G., Zhang J., Zhang J., Zhao S., Rogers J., Churcher C., Schook L.B. (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491, 393-398.
6. Hayes B.J., Lewin H.A., Goddard M.E. (2013) The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation. Trends Genet., 29, 206-214.
7. Hickey J.M. (2013) Sequencing millions of animals for genomic selection 2.0. J. Anim. Breed. Genet., 130, 331-332.
8. Huang W., Li L., Myers J.R., Marth G.T. (2012) ART: a next-generation sequencing read simulator. Bioinformatics, 28, 593-594.
9. Hudson R.R. (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics, 18, 337-338.
10. Lachance J., Tishkoff S.A. (2013) SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it. BioEssays, 35, 780-786.
11. Larkin D.M., Daetwyler H.D., Hernandez A.G., Wright C.L., Hetrick L.A., Boucek L., Bachman S.L., Band M.R., Akraiko T.V., Cohen-Zinder M., Thimmapuram J., Macleod I.M., Harkins T.T., McCague J.E., Goddard M.E., Hayes B.J., Lewin H.A. (2012) Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. Proc. Natl Acad. Sci., 109, 7693-7698.
12. Li H., Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
13. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
14. Matukumalli L.K., Schroeder S., DeNise S.K., Sonstegard T., Lawley C.T., Georges M., Coppieters W., Gietzen K., Medrano J.F., Rincon G., Lince A., Eggen A., Glaser L., Cam G., Van Tassell C. (2011) Analyzing LD blocks and CNV segments in cattle: Novel genomic features identified using the BovineHD BeadChip. (ed. by Pub. No. 370-2011-002 II, San Diego, CA).
15. Meuwissen T., Goddard M. (2010) Accurate prediction of genetic values for complex traits by whole-genome resequencing. Genetics, 185, 623-631.
16. Nielsen R., Slatkin M. (2013) An Introduction to Population Genetics. Sinauer, Sunderland, MA.
17. Nielsen R., Hubisz M.J., Clark A.G. (2004) Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data. Genetics, 168, 2373-2382.
18. Nielsen R., Paul J.S., Albrechtsen A., Song Y.S. (2011) Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet., 12, 443-451.
19. Nordborg M., Tavare S. (2002) Linkage disequilibrium: what history has to tell us. Trends Genet., 18, 83-90.
20. Ojeda A., Ramos-Onsins S.E., Marletta D., Huang L.S., Folch J.M., Perez-Enciso M. (2011) Evolutionary study of a potential selection target region in the pig. Heredity (Edinb), 106, 330-338.
21. Raineri E., Ferretti L., Esteve-Codina A., Nevado B., Heath S., Perez-Enciso M. (2012) SNP calling by sequencing pooled samples. BMC Bioinformatics, 13, 239.
22. Toro M.A., Garcia-Cortes L.A., Legarra A. (2011) A note on the rationale for estimating genealogical coancestry from molecular markers. Genet. Sel. Evol., 43, 1-10.
23. VanRaden P.M. (2008) Efficient methods to compute genomic predictions. J. Dairy Sci., 91, 4414-4423.
24. Yang J., Manolio T.A., Pasquale L.R., Boerwinkle E., Caporaso N., Cunningham J.M., de Andrade M., Feenstra B., Feingold E., Hayes M.G., Hill W.G., Landi M.T., Alonso A., Lettre G., Lin P., Ling H., Lowe W., Mathias R.A., Melbye M., Pugh E., Cornelis M.C., Weir B.S., Goddard M.E., Visscher P.M. (2011) Genome partitioning of genetic variation for complex traits using common SNPs. Nat. Genet., 43, 519-525.