Use of molecular technologies for the advancement of animal breeding: genomic selection in dairy cattle populations in Australia, Ireland and New Zealand
Richard J. Spelman A D , Ben J. Hayes B and Donagh P. Berry CA Livestock Improvement Corporation, Private Bag 3016, Hamilton, New Zealand.
B Department of Primary Industries, GPO Box 4440, Melbourne, Vic. 3001, Australia.
C Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland.
D Corresponding author. Email: rspelman@lic.co.nz
Animal Production Science 53(9) 869-875 https://doi.org/10.1071/AN12304
Submitted: 24 August 2012 Accepted: 2 February 2013 Published: 24 April 2013
Abstract
The New Zealand, Australian and Irish dairy industries have used genomic information to enhance their genetic evaluations over the last 2–4 years. The improvement in the accuracy obtained from including genomic information on thousands of animals in the national evaluation system has revolutionised the dairy breeding programs in the three countries. The genomically enhanced breeding values (GEBV) of young bulls are more reliable than breeding values based on parent average, thus allowing the young bulls to be reliably selected and used in the national herd. Traditionally, the use of young bulls was limited and bulls were not used extensively until they were 5 years old when the more reliable progeny test results became available. Using young sires, as opposed to progeny-tested sires, in the breeding program dramatically reduces the generation interval, thereby facilitating an increase in the rate of genetic gain by 40–50%. Young sires have been marketed on their GEBV in the three countries over the last 2–4 years. Initial results show that the genomic estimates were overestimated in both New Zealand and Ireland. Adjustments have since been introduced into their respective national evaluations to reduce the bias. A bias adjustment has been included in the Australian evaluation since it began; however, official genomic evaluations have not been in place as long as in New Zealand and Ireland, so there has been less opportunity to validate if the correction accounts for all bias. Sequencing of the dairy cattle population has commenced in an effort to further improve the genomic predictions and also to detect causative mutations that underlie traits of economic performance.
References
Berry DP, Kearney JF (2011) Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection. Animal 5, 1162–1169.| Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC38vovV2gtg%3D%3D&md5=d9099a85fe2206a272422a28910b79a1CAS | 22440168PubMed |
Berry DP, Kearney JF, Harris BL (2009) Genomic selection in Ireland. Interbull Bulletin 26–29, 29–34.
Boichard D, Chung H, Dassonneville R, David X, Eggen A, Fritz S, Gietzen KJ, Hayes BJ, Lawley CT, Sonstegard TS, Van Tassell CP, VanRaden PM, Viaud-Martinez KA, Wiggans GR (2012) Bovine LD Consortium. Design of a bovine low-density SNP array optimized for imputation. PLoS ONE 7, e34 130
| Bovine LD Consortium. Design of a bovine low-density SNP array optimized for imputation.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38Xlt12gsL8%3D&md5=57efe32d0f1d0c10a36a2178a48ece55CAS |
Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies using localized haplotype clustering. American Journal of Human Genetics 81, 1084–1097.
| Rapid and accurate haplotype phasing and missing data inference for whole genome association studies using localized haplotype clustering.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXht1KmsL3M&md5=27d443efa1beae518ffdcd981232d323CAS | 17924348PubMed |
Browning BL, Browning SR (2009) A unified approach to genotype imputation and haplotype phase inference for large data sets of trios and unrelated individuals. American Journal of Human Genetics 84, 210–223.
| A unified approach to genotype imputation and haplotype phase inference for large data sets of trios and unrelated individuals.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXisFCrtL8%3D&md5=e29e171b504de9b30094d4e5c8ef783aCAS | 19200528PubMed |
Cole JB, VanRaden PM, O’Connell JR, Van Tassell CP, Sonstegard TS, Schnabel RD, Taylor JF, Wiggans GR (2009) Distribution and location of genetic effects for dairy traits. Journal of Dairy Science 92, 2931–2946.
| Distribution and location of genetic effects for dairy traits.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXmsFemsLc%3D&md5=92a73a5d0f96b3b52fb18ef97cca1720CAS | 19448026PubMed |
Cromie AR, Berry DP, Wickham B, Kearney JF, Pena J, van Kaam JBCH, Gengler N, Szyda J, Schnyder U, Coffey M, Moster B, Hagiya K, Weller JI, Abernethy D, Spelman R (2010) International genomic co-operation; who, what, when, where, why and how? InterBull Bulletin 42, 1–8.
de Haas Y, Calus MP, Veerkamp RF, Wall E, Coffey MP, Daetwyler HD, Hayes BJ, Pryce JE (2012) Improved accuracy of genomic prediction for dry matter intake of dairy cattle from combined European and Australian data sets. Journal of Dairy Science
| Improved accuracy of genomic prediction for dry matter intake of dairy cattle from combined European and Australian data sets.Crossref | GoogleScholarGoogle Scholar | 22863091PubMed | Aug 2. [Epub ahead of print]
de Roos AP, Schrooten C, Veerkamp RF, van Arendonk JA (2011) Effects of genomic selection on genetic improvement, inbreeding, and merit of young versus proven bulls. Journal of Dairy Science 94, 1559–1567.
| Effects of genomic selection on genetic improvement, inbreeding, and merit of young versus proven bulls.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXmvFeit7k%3D&md5=8b9511d30a675e17a8507a4d06dc8dbdCAS | 21338821PubMed |
Fisher PJ, Hyndman DL, Bixley MJ, Oback FC, Popovic L, McGowan LT, Berg BC, Wells DN (2012) Potential for genomic selection of bovine embryos. Proceedings of the New Zealand Society of Animal Production 72, 156–158.
Harris BL, Johnson DL (2010) Genomic predictions for New Zealand dairy bulls and integration with national genetic evaluation. Journal of Dairy Science 93, 1243–1252.
| Genomic predictions for New Zealand dairy bulls and integration with national genetic evaluation.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXitlOis78%3D&md5=556cfb60c02e085c8bc0915ae9464bbdCAS | 20172244PubMed |
Hayden EC (2011) Fetal screening comes to market. Nature 478, 440
| Fetal screening comes to market.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhtlOnu77L&md5=9d3ce6653743c7a9d9a36f8b61aafcf8CAS | 22031414PubMed |
Hayes BJ, Pryce J, Chamberlain AJ, Bowman PJ, Goddard ME (2010) Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits. PLOS Genetics 6, e1001 139
| Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits.Crossref | GoogleScholarGoogle Scholar |
Humblot P, Le Bourhis D, Fritz S, Colleau JJ, Gonzalez C, Joly CG, Malafosse A, Heyman Y, Amigues Y, Tissier M, Ponsart C (2010) Reproductive technologies and genomic selection in cattle. Veterinary Medicine International 2010, 192 787
Kearney JF, Cromie AR, Berry DP (2010) Implementation and update of genomic selection in Irish Holstein-Friesian dairy cattle. In ‘9th world congress on genetics applied to livestock production, Leipzig, Germany’. Available at http://www.kongressband.de/wcgalp2010/assets/pdf/0889.pdf [verified 4 April 2013]
McHugh N, Meuwissen THE, Cromie AR, Sonesson AK (2011) Use of female information in dairy cattle genomic breeding programs. Journal of Dairy Science 94, 4109–4118.
| Use of female information in dairy cattle genomic breeding programs.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXpsVylurY%3D&md5=57080796ac17d30701efc2aed62e78d0CAS |
Nieuwhof GJ, Beard KT, Konstantinov KV, Reich CM, Mason B, Hayes BJ (2012) Validation of genomic evaluations in Australian Jersey cattle using a reference set that includes cows. In ‘Proceedings for the 5th Australasian Dairy Science symposium’. pp. 31–33.
Pryce JE, Hayes BJ (2012) A review of how dairy farmers can use and profit from genomic technologies. Animal Production Science 52, 180–184.
| A review of how dairy farmers can use and profit from genomic technologies.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XjtlSjtbg%3D&md5=3b611d0d4d2995404e046dce28ca03d4CAS |
Pryce JE, Goddard ME, Raadsma HW, Hayes BJ (2010) Deterministic models of breeding scheme designs that incorporate genomic selection. Journal of Dairy Science 93, 5455–5466.
| Deterministic models of breeding scheme designs that incorporate genomic selection.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXnvVSjtQ%3D%3D&md5=d7d3ed494d409c7b223a82ccb383f876CAS | 20965361PubMed |
Pryce JE, Arias J, Bowman PJ, Davis SR, Macdonald KA, Waghorn GC, Wales WJ, Williams YJ, Spelman RJ, Hayes BJ (2012a) Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625 000 single nucleotide polymorphism markers. Journal of Dairy Science 95, 2108–2119.
| Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625 000 single nucleotide polymorphism markers.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XkslejtLg%3D&md5=2dd0a6d745b1ac544d77eb1d5d41b36cCAS | 22459856PubMed |
Pryce JE, Hayes BJ, Goddard ME (2012b) Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information. Journal of Dairy Science 95, 377–388.
| Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhs1OlsrnL&md5=73a8897692e84886decee00dcb0b7759CAS | 22192217PubMed |
Robinson JL, Dombrowski DB, Harpestad GW, Shanks RD (1984) Detection and prevalence of UMP synthase deficiency among dairy cattle. The Journal of Heredity 75, 277–280.
Shuster DE, Kehrli ME, Ackermann MR, Gilbert RO (1992) Identification and prevalence of a genetic defect that causes leukocyte adhesion deficiency in Holstein cattle. Proceedings of the National Academy of Sciences of the United States of America 89, 9225–9229.
| Identification and prevalence of a genetic defect that causes leukocyte adhesion deficiency in Holstein cattle.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK3sXkslSitLc%3D&md5=c97cc14172c91ac5b3b9e96e034d28a9CAS | 1384046PubMed |
Thomsen B, Horn P, Panitz F, Bendixen E, Petersen AH, Holm LE, Nielsen VH, Agerholm JS, Arnbjerg J, Bendixen C (2006) A missense mutation in the bovine SLC35A3 gene, encoding a UDP-N-acetylglucosamine transporter, causes complex vertebral malformation. Genome Research 16, 97–105.
| A missense mutation in the bovine SLC35A3 gene, encoding a UDP-N-acetylglucosamine transporter, causes complex vertebral malformation.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XhslChtLY%3D&md5=05a5b212ffc2ce1700a8f0fb6e4929d0CAS | 16344554PubMed |
Veerkamp RF, Coffey M, Berry D, de Haas Y, Strandberg E, Bovenhuis H, Calus M, Wall E (2012) Genome-wide associations for feed utilisation complex in primiparous Holstein-Friesian dairy cows from experimental research herds in four European countries. Animal 6, 1738–1749.
| Genome-wide associations for feed utilisation complex in primiparous Holstein-Friesian dairy cows from experimental research herds in four European countries.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhsVKltLzO&md5=22de856a508c94d0ae44aa441c3a89ebCAS | 23031337PubMed |
Wiggans GR, VanRaden PM, Cooper TA (2011) The genomic evaluation system in the United States: past, present, future. Journal of Dairy Science 94, 3202–3211.
| The genomic evaluation system in the United States: past, present, future.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXnvFCns7w%3D&md5=b84384478196fc4197ea3c215ebb9f75CAS | 21605789PubMed |
Winkelman AM, Spelman RJ (2010) Response using genome-wide selection in dairy cattle breeding schemes. In ‘World congress for genetics applied to livestock production, Leipzig, Germany’. Available at http://www.kongressband.de/wcgalp2010/assets/pdf/0290.pdf [verified 4 April 2013]