Detecting inbreeding depression for reproductive traits in Iberian pigs using genome-wide data

Genetics Selection Evolution

Volumn 47, Issue 1, 2015, Pages

  Saura, María ^a   Fernández, Almudena ^a   Varona, Luis ^b   Fernández, Ana I ^a   De Cara, Maria Ángeles R ^c   Barragán, Carmen ^a   Villanueva, Beatriz ^a  

^a INIA   (Spain)

^b UNIVERSIDAD DE ZARAGOZA   (Spain)

^c UNIVERSITÉ PARIS DESCARTES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME; DATA SET; DETECTION METHOD; DOMESTIC SPECIES; ECOLOGICAL MODELING; EXTINCTION; GENOME; GENOTYPE; INBREEDING DEPRESSION; INHIBITOR; PHENOTYPE; PIG; POLYMORPHISM; REPRODUCTIVE STRATEGY;

IBERIAN PENINSULA;

ANIMALIA; SUIDAE;

ANIMAL; FEMALE; GENETIC ASSOCIATION; GENETICS; HOMOZYGOTE; INBREEDING; MALE; PIG; QUANTITATIVE TRAIT LOCUS; REPRODUCTION; REPRODUCTIVE FITNESS; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; FEMALE; GENETIC FITNESS; GENOME-WIDE ASSOCIATION STUDY; HOMOZYGOTE; INBREEDING; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; REPRODUCTION; SUS SCROFA; SWINE;

EID: 84938863331     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1186/s12711-014-0081-5     Document Type: Article

References (28)

1. Charlesworth B, Charlesworth D: The genetic basis of inbreeding depression. Genet Res 1999, 74:329-340.
2. DeRose MA, Roff DA: A comparison of inbreeding depression in life-history and morphological traits in animals. Evolution 1999, 53:1288-1292.
3. Saura M, Fernández A, Rodríguez MC, Toro MA, Barragán C, Fernández AI, Villanueva B: Genome-wide estimates of coancestry and inbreeding in a closed herd of Iberian pigs. PLoS ONE 2013, 8:e78314.
4. Keller MC, Visscher PM, Goddard ME: Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics 2011, 189:237-249.
5. McQuillan R, Eklund N, Pirastu N, Kuningas M, McEvoy B, Esko T, Corre T, Davies G, Kaakinen M, Lyytikäinen LP, Kristiansson K, Havulinna AS, Gögele M, Vitart V, Tenesa A, Aulchenko Y, Hayward C, Johansson A, Boban M, Ulivi S, Robino A, Boraska V, Igl W, Wild SH, Zgaga L, Amin N, Theodoratou E, Polašek O, Girotto G, Lopez LM: Evidence of inbreeding depression in human height. PLoS Genet 2012, 8:e1002655.
6. Bjelland DW, Weigel KA, Vukasinovic N, Nkrumah JD: Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. J Dairy Sci 2013, 96:1-10.
7. Broman KW, Weber JL: Long homozygous chromosomal segments in reference families from the centre d'Etude du polymorphisme humain. Am J Hum Genet 1999, 65:1493-1500.
8. Keller MC, Simonson MA, Ripke S, Neale BM, Gejman PV, Howrigan DP, Lee SH, Lencz T, Levinson DF, Sullivan PF, Schizophrenia Psychiatric Genome-Wide Association Study Consortium: Runs of homozygosity implicate autozygosity as a schizophrenia risk factor. PLoS Genet 2012, 8:e1002656.
9. Pemberton TJ, Absher D, Feldman MW, Myers RM, Rosenberg NA, Li JZ: Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet 2012, 91:275-292.
10. McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, Macleod AK, Farrington SM, Rudan P, Hayward C, Vitart V, Rudan I, Wild SH, Dunlop MG, Wright AF, Campbell H, Wilson JF: Runs of homozygosity in European populations. Am J Hum Genet 2008, 83:359-372.
11. Toro MA, Rodrigáñez J, Silió L, Rodríguez MC: Genealogical analysis of a closed herd of black hairless Iberian Pigs. Conserv Biol 2000, 14:1843-1851.
12. Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV, Kane JM, Raju Kucherlapati R, Malhotra AK: Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci USA 2007, 104:19942-19947.
13. de Cara MAR, Villanueva B, Toro MA, Fernández J: Using genomic tools to maintain diversity and fitness in conservation programmes. Mol Ecol 2013, 22:6091-6099.
14. Groeneveld E, Kovac M, Mielenz N: VCE Users' Guide and Reference Manual Version 6.0. Mariensee, Germany: Institute of Farm Animal Genetics; 2008.
15. Groeneveld E, Kovac M, Wang T: PEST, a General Purpose BLUP Package for Multivariate Prediction and Estimation. In Proceedings of the 4th World Congress on Genetics Applied to Livestock Production: 23-27 July 1990. Edinburgh. Edited by W. G. Hill, R. Thompson and J. A. Wooliams; 1990:488-491.
16. Muñoz M, Alves E, Ramayo-Caldas Y, Casellas J, Rodríguez C, Folch JM, Silió L, Fernández AI: Recombination rates across porcine autosomes inferred from high-density linkage maps. Anim Genet 2011, 43:620-623.
17. Fisher RA: A fuller theory of "junctions" in inbreeding. Heredity 1954, 8:187-197.
18. Fernández A, Rodrigáñez J, Zuzúarregui J, Rodríguez MC, Silió L: Genetic parameters for litter size and weight at different parities in Iberian pigs. Span J Agric Res 2008, 6:98-106.
19. Noguera JL, Rodríguez C, Varona L, Tomàs A, Muñoz G, Ramírez O, Barragán C, Arqué M, Bidanel JP, Amills M, Ovilo C, Sánchez A: A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL. BMC Genomics 2009, 10:636.
20. Geisert RD, Ashworth MD, Malayer JR: Expression of inter-alpha-trypsin inhibitor heavy chains in endometrium of cyclic and pregnant gilts. Reproduction 2003, 126:621-627.
21. Balcells I, Castelló A, Noguera JL, Fernández-Rodríguez A, Sánchez A, Tomás A: Sequencing and gene expression of the porcine ITIH SSC13 cluster and its effect on litter size in an Iberian∈×∈Meishan F2 population. Anim Reprod Sci 2011, 128:85-92.
22. Onteru SK, Fan B, Du Z-Q, Garrick DJ, Stalder KJ, Rothschild MF: A whole-genome association study for pig reproductive traits. Anim Genet 2011, 43:18-26.
23. Ferencakovic M, Hamzic E, Gredler B, Solberg TR, Klemetsdal G, Curik I, Sölkner J: Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations. J Anim Breed Genet 2012, 130:286-293.
24. Walling CA, Nussey D, Morris A, Clutton-Brock TH, Kruuk LEB, Pemberton JM: Inbreeding depression in red deer calves. BMC Evol Biol 2011, 11:318.
25. Silió L, Rodríguez MC, Fernández A, Barragán C, Benítez R, Óvilo C, Fernández AI: Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics. J Anim Breed Genet 2013, 130:349-360.
26. Ku CS, Naidoo N, Teo SM, Pawitan Y: Regions of homozygosity and their impact on complex diseases and traits. Hum Genet 2011, 129:1-15.
27. Simón-Sánchez J, Kilarski LL, Nalls MA, Martínez M, Schulte C, Holmans P, International Parkinson's Disease Genomics Consortium, Wellcome Trust Case Control Consortium, Gasser T, Hardy J, Singleton AB, Wood NW, Brice A, Heutink P, Williams N, Morris HR: Cooperative genome-wide analysis shows increased homozygosity in early onset Parkinson's disease. PLoS ONE 2012, 7:e28787.
28. Pryce JE, Haile-Mariam M, Goddard ME, Hayes BJ: Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle. Genet Sel Evol 2014, 46:71.