A whole-genome association study for pig reproductive traits

Animal Genetics

Volumn 43, Issue 1, 2012, Pages 18-26

  Onteru, S K ^a   Fan, B ^a,b   Du, Z Q ^a   Garrick, D J ^a   Stalder, K J ^a   Rothschild, M F ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

biological pathways; parity; reproductive traits; whole genome association

Indexed keywords

ANIMAL; ARTICLE; FEMALE; GENETIC ASSOCIATION; GENETICS; PARITY; PHYSIOLOGY; QUANTITATIVE TRAIT LOCUS; REPRODUCTION; SWINE;

ANIMALS; FEMALE; GENOME-WIDE ASSOCIATION STUDY; PARITY; QUANTITATIVE TRAIT LOCI; REPRODUCTION; SUS SCROFA;

SUIDAE;

EID: 84855704572     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2011.02213.x     Document Type: Article

References (33)

1. Becker D., Tetens J., Brunner A., Bürstel D., Ganter M., Kijas J., International Sheep Genomics Consortium &, Drögemüller C., (2010) Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3) gene. PLoS ONE 13, e8689.
2. Bi W., Drake C.J., &, Schwarz J.J., (1999) The transcription factor MEF2C-null mouse exhibits complex vascular malformations and reduced cardiac expression of angiopoietin 1 and VEGF. Developmental Biology 211, 255-67. (Pubitemid 29343280)
3. Cassady J.P., Johnson R.K., Pomp D., Rohrer G.A., Van Vleck L.D., Spiegel E.K., &, Rohrer G.A., (2001) Identification of quantitative trait loci affecting reproduction in pigs. Journal of Animal Science 79, 623-33. (Pubitemid 33616425)
4. Cecchinato A., de los Campos G., Gianola D., Gallo L., &, Carnier P., (2010) The relevance of purebred information for predicting genetic merit of survival at birth of crossbred piglets. Journal of Animal Science 88, 481-90.
5. Chen Y., Zhu J., Lum P.Y., et al. (2008) Variations in DNA elucidate molecular networks that cause disease. Nature 452, 429-35. (Pubitemid 351450844)
6. Duijvesteijn N., Knol E.F., Merks J.W., Crooijmans R.P., Groenen M.A., Bovenhuis H., &, Harlizius B., (2010) A genome-wide association study on androsterone levels in pigs reveals a cluster of candidate genes on chromosome 6. BMC Genetics 11, 42.
7. Fan B., Onteru S.K., Mote B.E., Serenius T., Stalder K.J., &, Rothschild M.F., (2009) Large-scale association study for structural soundness and leg locomotion traits in the pig. Genetics Selection and Evolution 41, 14.
8. Fan B., Onteru S.K., Du Z.-Q., Garrick D.J., Stalder K.J., &, Rothschild M.F., (2011) Genome-wide association study identifies loci for body composition and structural soundness traits in pigs. PLoS ONE 6, e14726.
9. Fernando R.L., &, Garrick D.J., (2008) GenSel-User Manual for a Portfolio of Genomic Selection Related Analyses. Animal Breeding and Genetics, Iowa State University, Ames.
10. Fernando R.L., Nettleton D., Southey B.R., Dekkers J.C.M., Rothschild M.F., &, Soller M., (2004) Controlling the proportion of false positives in multiple dependent tests. Genetics 166, 611-9. (Pubitemid 38364744)
11. Feugang J.M., Kaya A., Page G.P., Chen L., Mehta T., Hirani K., Nazareth L., Topper E., Gibbs R., &, Memili E., (2009) Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility. BMC Genomics 10, 176.
12. Haneberg E.H.A.T., Knol E.F., &, Merks J.W.M., (2001) Estimates of genetic parameters for reproduction traits at different parities in Dutch Landrace pigs. Livestock Production Science 69, 179-86. (Pubitemid 32442425)
13. King A.H., Jiang Z., Gibson J.P., Haley C.S., &, Archibald A.L., (2003) Mapping quantitative trait loci affecting female reproductive traits on porcine chromosome 8. Biology of Reproduction 68, 2172-9. (Pubitemid 36687010)
14. Kizilkaya K., Fernando R.L., &, Garrick D.J., (2010) Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes. Journal of Animal Science 88, 544-51.
15. Meuwissen T.H.E., Hayes B.J., &, Goddard M.E., (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157, 1819-29. (Pubitemid 32298846)
16. Nikitin A., Egorov S., Daraselia N., &, Mazo M., (2003) Pathway studio-the analysis and navigation of molecular networks. Bioinformatics 19, 2155-7. (Pubitemid 37408171)
17. Noguera J.L., Varona L., Babot D., &, Estany J., (2002) Multivariate analysis of litter size for multiple parities with production traits in pigs: II. Response to selection for litter size and correlated response to production traits. Journal of Animal Science 80, 2548-55. (Pubitemid 41138373)
18. Onteru S.K., Fan B., Nikkila M.T., Garrick D.J., Stalder K.J., &, Rothschild M.F., (2011) Whole-genome association analyses for lifetime reproductive traits in the pig. Journal of Animal Science 89, 988-95.
19. Phillippe M., Bradley D.F., Ji H., Oppenheimer K.H., &, Chien E.K., (2006) Phospholipid scramblase isoform expression in pregnant rat uterus. Journal of the Society for Gynecologic Investigation 13, 497-501. (Pubitemid 44528296)
20. Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A.R., Bender D., Maller J., Bakker P.I.W., Daly M.J., &, Sham P.C., (2007) PLINK: a toolset for 9 whole-genome association and population-based linkage analysis. American Journal of Human Genetics 81, 559-75. (Pubitemid 47330214)
21. Ramos A.M., Crooijmans R.P.M.A., Affara N.A., et al. (2009) Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS ONE 4, e6524.
22. Rempel L.A., Nonneman D.J., Wise T.H., Erkens T., Peelman L.J., &, Rohrer G.A., (2010) Association analyses of candidate single nucleotide polymorphisms on reproductive traits in swine. Journal of Animal Science 88, 1-15.
23. Rothschild M.F., Jacobson C., Vaske D., et al. (1996) The estrogen receptor locus is associated with a major gene influencing litter size in pigs. Proceedings of the National Academy of Sciences of the United States of America 93, 201-5. (Pubitemid 26038127)
24. Sarrazin S., Mossadegh-Keller N., Fukao T., et al. (2009) MafB restricts M-CSF-dependent myeloid commitment divisions of hematopoietic stem cells. Cell 138, 300-13.
25. Serenius T., Stalder K.J., &, Fernando R.L., (2008) Genetic associations of sow longevity with age at first farrowing, number of piglets weaned, and wean to insemination interval in the Finnish Landrace swine population. Journal of Animal Science 86, 3324-9.
26. Siewerdt F., Cardellino R.A., &, Rosa V.C.D., (1995) Genetic parameters of litter traits in three pig breeds in southern Brazil. Brazilian Journal of Genetics 18, 199-205.
27. Spotter A., Muller S., Hamann H., &, Distl O., (2009) Effect of polymorphisms in the genes for LIF and RBP4 on litter size in two German pig lines. Reproduction in Domestic Animals 44, 100-5.
28. Stalder K.J., Knauer M., Bass T.J., Rothschild M.F., &, Mabry J.W., (2004) Sow longevity. Pig News and Information 25, 53N-74N.
29. Sun X., Habier D., Fernando R.L., Garrick D.J., &, Dekkers J.C.M., (2010) Genomic breeding value prediction and QTL mapping of QTLMAS2010 data using Bayesian methods. BMC Proceedings In press.
30. Tribout T., Lannuccelli N., Druet T., Gilbert H., Riquet J., Gueblez R., Mercat M.J., Bidanel J.P., Milan D., &, Le Roy P., (2008) Detection of quantitative trait loci for reproduction and production traits in Large White and French Landrace pig populations. Genetics Selection and Evolution 40, 61-78. (Pubitemid 350308262)
31. Vallet J.L., Freking B.A., Leymaster K.A., &, Christenson R.K., (2005) Allelic variation in the erythropoietin receptor gene is associated with uterine capacity and litter size in swine. Animal Genetics 36, 97-103. (Pubitemid 40518691)
32. Yallampalli C., Chauhan M., Thota C.S., Kondapaka S., &, Wimalawansa S.J., (2002) Calcitonin gene-related peptide in pregnancy and its merging receptor heterogeneity. Trends in Endocrinology and Metabolism 13, 263-9. (Pubitemid 36733972)
33. Zhou Y., Bellingard V., Feng K.-T., McMaster M., &, Fisher S.J., (2003) Human cytotrophoblasts promote endothelial survival and vascular remodeling through secretion of Ang2, PlGF, and VEGF-C. Developmental Biology 263, 114-25. (Pubitemid 37268007)