Albrechtsen, A, Nielsen, FC and Nielsen, R
2010. Ascertainment biases in SNP chips affect measures of population divergence. Molecular Biology and Evolution
27, 2534–2547.
Alexander, DH, Novembre, J and Lange, K
2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research
19, 1655–1664.
Bamshad, M and Wooding, SP
2003. Signatures of natural selection in the human genome. Nature Reviews Genetics
4, 99–111.
Barbato, M, Orozco-terWengel, P, Tapio, M and Bruford, MW
2015. SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Frontiers in Genetics
6, 1–12.
Beja-Pereira, A, Alexandrino, P, Bessa, I, Carretero, Y, Dunner, S, Ferrand, N, Jordana, J, Laloe, D, Moazami-Goudarzi, K, Sanchez, A and Canon, J
2003. Genetic characterization of southwestern European bovine breeds: a historical and biogeographical reassessment with a set of 16 microsatellites. Journal of Heredity
94, 243–250.
Blott, SC, Williams, JL and Haley, CS
1998. Genetic relationships among European cattle breeds. Animal Genetics
29, 273–282.
Buckley, F, Lopez-Villalobos, N and Heins, BJ
2014. Crossbreeding: implications for dairy cow fertility and survival. Animal
8, 122–133.
Calus, MP
2010. Genomic breeding value prediction: methods and procedures. Animal
4, 157–164.
Canon, J, Alexandrino, P, Bessa, I, Carleos, C, Carretero, Y, Dunner, S, Ferran, N, Garcia, D, Jordana, J, Laloe, D, Pereira, A, Sanchez, A and Moazami-Goudarzi, K
2001. Genetic diversity measures of local European beef cattle breeds for conservation purposes. Genetic Selection Evolution
33, 311–332.
Chikhi, L, Goossens, B, Treanor, A and Bruford, MW
2004. Population genetic structure of and inbreeding in an insular cattle breed, the Jersey, and its implications for genetic resource management. Heredity
92, 396–401.
Decker, JE, McKay, SD, Rolf, MM, Kim, J, Molina Alcalá, A, Sonstegard, TS, Hanotte, O, Götherström, A, Seabury, CM, Praharani, L, Babar, ME, Correia de Almeida Regitano, L, Yildiz, MA, Heaton, MP, Liu, WS, Lei, CZ, Reecy, JM, Saif-Ur-Rehman, M, Schnabel, RD and Taylor, JF
2014. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genetics
10, e1004254.
De Roos, APW, Hayes, BJ, Spelman, RJ and Goddard, ME
2008. Linkage disequilibrium and persitence of phase in Holsetin-Friesian, Jersey and Anjus cattle. Genetics
179, 1503–1512.
Del Bo, L, Polli, M, Longeri, M, Ceriotti, G, Looft, C, Barre-Dirie, A, Dolf, G and Zanotti, M
2001. Genetic diversity among some cattle breeds in the Alpine area. Journal of Animal Breeding and Genetics
118, 317–325.
Diamond, J
2002. Evolution, consequences and future of plant and animal domestication. Nature
418, 700–707.
Edea, Z, Bhuiyan, MS, Dessie, T, Rothschild, MF, Dadi, H and Kim, KS
2015. Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds. Animal
9, 218–226.
Ehiobu, NG, Goddard, ME and Taylor, JF
1990. Prediction of heterosis in crosses between inbred lines of Drosophila melanogaster
. Theoretical and Applied Genetics
80, 321–325.
Falconer, DS and Mackay, TFC
1996. Introduction to quantitative genetics, 4th edition. Pearson Education LTD, Essex, UK.
Felius, M
2007. Cattle breeds: an encyclopedia. Trafalgar Square Books, North Pomfret, United States.
Gautier, M, Laloë, D and Moazami-Goudarzi, K
2010. Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds. PLoS One
5, e13038.
Gibbs, RA, Taylor, JF, van Tassell, CP, Barendse, W, Eversole, KA, Gill, CA, Green, RD, Hamernik, DL, Kappes, SM, Lien, S, Matukumalli, LK, McEwan, JC, Nazareth, LV, Schnabel, RD, Weinstock, GM, Wheeler, DA, Ajmone-Marsan, P, Boettcher, PJ, Caetano, AR, Garcia, JF, Hanotte, O, Mariani, P, Skow, LC, Sonstegard, TS, Williams, JL, Diallo, B, Hailemariam, L, Martinez, ML, Morris, CA, Silva, LO, Spelman, RJ, Mulatu, W, Zhao, K, Abbey, CA, Agaba, M, Araujo, FR, Bunch, RJ, Burton, J, Gorni, C, Olivier, H, Harrison, BE, Luff, B, Machado, MA, Mwakaya, J, Plastow, G, Sim, W, Smith, T, Thomas, MB, Valentini, A, Williams, P, Womack, J, Woolliams, JA, Liu, Y, Qin, X, Worley, KC, Gao, C, Jiang, H, Moore, SS, Ren, Y, Song, XZ, Bustamante, CD, Hernandez, RD, Muzny, DM, Patil, S, San Lucas, A, Fu, Q, Kent, MP, Vega, R, Matukumalli, A, McWilliam, S, Sclep, G, Bryc, K, Choi, J, Gao, H, Grefenstette, JJ, Murdoch, B, Stella, A, Villa-Angulo, R, Wright, M, Aerts, J, Jann, O, Negrini, R, Goddard, ME, Hayes, BJ, Bradley, DG, Barbosa da Silva, M, Lau, LP, Liu, GE, Lynn, DJ, Panzitta, F and Dodds, KG
2009. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science
324, 528–532.
Harris, BL and Kolver, ES
2001. Review of Holsteinization of intensive pastoral dairy farming in New Zealand. Journal of Dairy Science
84 (suppl.), E56–E61.
Harris, BL, Winkelman, AM and Johnson, DE
2014. Across-breed genomic prediction in dairy cattle. Proceedings of the 10th World Congress of Genetics Applied to Livestock Production. Livestock Improvement Corporation, Hamilton, New Zealand.
Hawksworth, DL
1995. Biodiversity: measurement and estimation. Chapman and Hall, London, UK.
Hayes, BJ, Bowman, PJ, Chamberlain, AJ and Goddard, ME
2009. Invited review: genomic selection in dairy cattle: progress and challenges. Journal of Dairy Science
92, 433–443.
Hayes, BJ, Visscher, PM, McPartlan, HC and Goddard, ME
2003. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research
13, 635–643.
Horan, B, Dillon, P, Faverdin, P, Delaby, L, Buckley, F and Rath, M
2005. The interaction of strain of Holstein-Friesian cows and pasture-based feed systems on milk yield, body weight and body condition score. Journal of Diary Science
88, 1231–1243.
Jolliffe, IT
2002. Principal component analysis Springer. Springer-Verlag, New York.
Kahn, L and Cottle, D
2014. Beef cattle production and trade. CSIRO Publishing, Victoria, Australia.
Kantanen, J, Olsaker, I, Holm, L-E, Lien, S, Vilkki, J, Brusgaard, K, Eythorsdottir, E, Danell, B and Adalsteinsson, S
2000. Genetic diversity and population structure of 20 north European cattle breeds. Journal of Heredity
91, 446–457.
Kijas, JW, Lenstra, JA, Hayes, B, Boitard, S, Porto Neto, LR, San Cristobal, M, Servin, B, McCulloch, R, Whan, V, Gietzen, K, Paiva, S, Barendse, W, Ciani, E, Raadsma, H, McEwan, J and Dalrymple, B, other members of the International Sheep Genomics C
2012. Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology
10, e1001258.
Kim, E and Rothschild, MF
2014. Genomic adaptation of admixed dairy cattle in East Africa. Frontiers in Genetics
5, 443–453.
Kristensen, TN, Hoffmann, AA, Pertoldi, C and Stronen, AV
2015. What can livestock breeders learn from conservation genetics and vice versa?
Frontiers in Genetics
6, 1–12.
Kuehn, LA, Keele, JW, Bennett, GL, McDaneld, TG, Smith, TP, Snelling, WM, Sonstegard, TS and Thallman, RM
2011. Predicting breed composition using breed frequencies of 50 000 markers from the US Meat Animal Research Center 2000 Bull Project. Journal of Animal Science
89, 1742–1750.
LIC
2015. Livestock Improvement Corporation. Retrieved on 17 April 2015 from www.lic.co.nz
Lewis, J, Abas, Z, Dadousis, C, Lykidis, D, Paschou, P and Drineas, P
2011. Tracing cattle breeds with principal components analysis ancestry informative SNPs. PLoS One
6, e18007.
MacHugh, DE, Loftus, RT, Bradley, DG, Sharp, PM and Cunningham, P
1994. Microsatellite DNA variation within and among European cattle breeds. Proceedings of the Royal Society: Biological Sciences
256, 25–31.
MacHugh, DE, Loftus, RT, Cunningham, P and Bradley, DG
1998. Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers. Animal Genetics
29, 333–340.
MacHugh, DE, Shriver, MD, Loftus, RT, Cunningham, P and Bradley, DG
1997. Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics
146, 1071–1086.
Matukumalli, LK, Lawley, CT, Schnabel, RD, Taylor, JF, Allan, MF, Heaton, MP, O’Connell, J, Moore, SS, Smith, TPL, Sonstegard, TS and Van Tassell, CP
2009. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One
4, e5350.
McKay, SD, Schnabel, RD, Murdoch, BM, Matukumalli, LK, Aerts, J, Coppieters, W, Crews, D, Dias Neto, E, Gill, CA, Gao, C, Mannen, H, Wang, Z, Van Tassell, CP, Williams, JL, Taylor, JF and Moore, SS
2008. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC Genetics
9, 37.
McParland, S, Kearney, JF, Rath, M and Berry, DP
2007a. Inbreeding effects on milk production, calving performance, fertility, and conformation in Irish Holstein-Friesians. Journal of Dairy Science
90, 4411–4419.
McParland, S, Kearney, JF, Rath, M and Berry, DP
2007b. Inbreeding trends and pedigree analysis of Irish dairy and beef cattle populations. Journal of Animal Science
85, 322–331.
Melka, MG and Schenkel, FS
2012. Analysis of genetic diversity in Brown Swiss, Jersey and Holstein populations using genome-wide single nucleotide polymorphism markers. BMC Research Notes
5, 161.
Meuwissen, THE and Luo, Z
1992. Computing inbreeding coefficients in large populations. Genetic Selection Evolution
24, 305–313.
Miglior, F, Muir, BL and Van Doormaal, BJ
2005. Selection indices in Holstein cattle of various countries. Journal of Dairy Science
88, 1255–1263.
Nei, M
1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics
89, 583–590.
Ohta, T and Kimura, M
1971. Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population. Genetics
68, 571–580.
Paradis, E, Claude, J and Strimmer, K
2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics
20, 289–290.
Patterson, N, Price, AL and Reich, D
2006. Population structure and eigenanalysis. PLoS Genetics
2, 2074–2093.
Penasa, M, López-Villalobos, N, Evans, RD, Cromie, AR, Dal Zotto, R and Cassandro, M
2010. Crossbreeding effects on milk yield traits and calving interval in spring-calving dairy cows. Journal of Animal Breeding and Genetics
127, 300–307.
Porter, V
1991. Cattle – a handbook to the breeds of the world. Facts on File Inc, New York, USA.
Price, AL, Patterson, NJ, Plenge, RM, Weinblatt, ME, Shadick, NA and Reich, D
2006. Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics
38, 904–909.
Pruett, CL and Winker, K
2008. The effects of sample size on population genetic diversity estimates in song sparrows Melospiza melodia
. Journal of Avian Biology
39, 252–256.
Purcell, S, Neale, B, Todd-Brown, K, Thomas, L, Ferreira, MA, Bender, D, Maller, J, Sklar, P, de Bakker, PI, Daly, MJ and Sham, PC
2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics
81, 559–575.
Pryce, JE, Haile-Mariam, M, Goddard, ME and Hayes, BJ
2014. Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle. Genetics Selection Evolution
46, 71.
Purfield, DC, Berry, DP, McParland, S and Bradley, DG
2012. Runs of homozygosity and population history in cattle. BMC Genetics
13, 70–80.
Sørensen, MK, Norberg, E, Pedersen, J and Christensen, LG
2008. Invited review: crossbreeding in dairy cattle: a Danish perspective. Journal of Dairy Science
91, 4116–4128.
Stachowicz, K, Sargolzaei, M, Miglior, F and Schenkel, FS
2011. Rates of inbreeding and genetic diversity in Canadian Holstein and Jersey cattle. Journal of Dairy Science
94, 5160–5175.
Thompson, JR, Everett, RW and Hammerschmidt, NL
2000. Effects of inbreeding on production and survival in Holsteins. Journal of Dairy Science
83, 1856–1864.
Tracy, CA and Widom, H
2009. The distributions of random matrix theory and their applications. In New trends in mathematical physics (ed. V Sidoravicius), pp. 753–765. Springer, The Netherlands.
Wall, E, Brotherstone, S, Kearney, JF, Woolliams, JA and Coffey, MP
2005. Impact of nonadditive genetic effects in the estimation of breeding values for fertility and correlated traits. Journal of Dairy Science
88, 376–385.
Weigel, KA
2001. Controlling inbreeding in modern breeding programs. Journal of Dairy Science
84, E177–E184.
Weir, BS and Cockerham, CC
1984. Esti mating F-statistics for the analysis of population structure. Evolution
38, 1358–1370.
Weir, BS and Hill, WG
2002. Estimating F-statistics. Annual Review of Genetics
36, 721–750.
Williams, JL, Aguilar, I, Rekaya, R and Bertrand, JK
2010. Estimation of breed and heterosis effects for growth and carcass traits in cattle using published crossbreeding studies. Journal of Animal Science
88, 460–466.
Xu, L, Bickhart, DM, Cole, JB, Schroeder, SG, Song, J, Tassell, CPV, Sonstegard, TS and Liu, GE
2015. Genomic signatures reveal new evidences for selection of important traits in domestic cattle. Molecular Biology and Evolution
32, 711–725.
Zhao, F, McParland, S, Kearney, JF, Du, L and Berry, DP
2015. Detection of selection signatures in dairy and beef cattle using high-density genomic information. Genetics Selection Evolution
47, 49.
