Genomic Selection for Poultry Breeding and its Potential Applications in Developing Countries (Review)

Document Type : Review

Authors

1 Adami Tulu Agricultural Research Center, P. O. Box 35, Batu, Ethiopia

2 Haramaya University, School of Animal and Range Science, P.O. Box 138, Dire Dawa, Ethiopia

Abstract

This review article provides a general overview of advanced molecular techniques and their implementation in the genetic improvement of poultry and presents the potential application of these techniques in developing countries. Advances in molecular genetics have contributed to a significant rate of genetic progress in domestic fowl, especially for traits that are difficult to improve through conventional breeding methods. Compared to developed nations, however, the application of molecular techniques for the genetic improvement of poultry is limited in most developing countries due to a lack of infrastructure, capital, and human resources. This does not mean that it is an impossible task. To implement molecular techniques in developing countries, the potential merit of using these tools for the genetic improvement of poultry should be evaluated in terms of economic costs and benefits of the technology compared with conventional breeding. The existence of conventional genetic evaluation and selection programs is also a prerequisite, along with well-established research institutions and well-trained human resources. More important are the cooperation and partnership with academic and research institutions in developed countries to address challenges in applying molecular tools and associated infrastructures to implement genomic selection in developing countries.

Keywords


Besbes B, Tixier Boichard M, Hoffmann I & Jain GL. 2007. Future trends for poultry genetic resources. International Conference of Poultry in the 21st Century: Avian Influenza and Beyond. Bangkok, Thailand. Pages, 1-25.
Bijma P & Bovenhuis H. 2009. Developments in quantitative genetics and genomics relevant for poultry breeding. In: Hocking PM. (Ed). Biology of Breeding Poultry. Poultry Science Symposium Series. Volume 29. CAB International. Wallingford. Pages, 29-44.
Blasco A & Toro MA. 2014. A short critical history of the application of genomics to animal breeding. Livestock Science, 166: 4-9. DOI: 10.1016/j.livsci. 2014.03.015
Boichard D, Ducrocq V, Croiseau P & Fritz S. 2016. Genomic selection in domestic animals: Principles, applications and perspectives. Comptes Rendus Biologies, 339: 274-277. DOI: 10.1016/j.crvi. 2016.04.007
Bourdon RM. 2014. Understanding Animal Breeding. 2nd Ed. Pearson New International Edition. Pearson Education Limited. Harlow. 513 Pages. 
Calus MPL, Huang H, Vereijken A, Visscher J, ten Napel J & Windig JJ. 2014. Genomic prediction based on data from three layer lines: A comparison between linear methods. Genetics Selection Evolution, 46: 57. DOI: 10.1186/s12711-014-0057-5
Calus MPL. 2010. Genomic breeding value prediction: Methods and procedures. Animal, 4: 157-164. DOI: 10.1017/S1751731109991352
Chen CY, Misztal I, Aguilar I, Tsuruta S, Meuwissen THE, Aggrey SE, Wing T & Muir WM. 2011. Genome-wide marker-assisted selection combining all pedigree phenotypic information with genotypic data in one step: An example using broiler chickens. Journal of Animal Science, 89: 23-28. DOI: 10.2527/jas.2010-3071
Christensen OF & Lund MS. 2010. Genomic prediction when some animals are not genotyped. Genetics Selection Evolution 42: 2. DOI: 10.1186/ 1297-9686-42-2
Dekkers JCM & Hospital F. 2002. The use of molecular genetics in the improvement of agricultural populations. Nature Reviews Genetics, 3: 22-32. DOI: 10.1038/nrg701
Dekkers JCM & van der Werf JHJ. 2007. Strategies, limitations and opportunities for marker-assisted selection in livestock. In: Guimarães EP, Ruane J, Scherf BD, Sonnino A & Dargie JD. (Eds). Marker-Assisted Selection: Current Status and Future Perspectives in Crops, Livestock, Forestry and Fish. Food and Agriculture Organization of the United Nations (FAO). Rome. Pages, 167-184.
Dekkers JCM. 2012. Application of genomics tools to animal breeding. Current Genomics, 13: 207-212. DOI: 10.2174/138920212800543057
Eggen A. 2012. The development and application of genomic selection as a new breeding paradigm. Animal Frontiers, 2: 10-15. DOI: 10.2527/af.2011-0027
Eisen EJ. 2007. Animal breeding: What does the future hold? Asian-Australasian Journal of Animal Sciences, 20: 453-460. DOI: 10.5713/ajas.2007.453
Fan B, Du ZQ, Gorbach DM & Rothschild MF. 2010. Development and application of high-density SNP arrays in genomic studies of domestic animals. Asian-Australasian Journal of Animal Sciences, 23: 833-847. DOI: 10.5713/ajas.2010.r.03
FAO. 2011. Biotechnologies for Agricultural Development. Proceedings of the FAO International Technical Conference on "Agricultural Biotechnologies in Developing Countries: Options and Opportunities in Crops, Forestry, Livestock, Fisheries and Agro-industry to face the Challenges of Food Insecurity and Climate Change". Food and Agriculture Organization of the United Nations (FAO). Rome. 569 Pages.
FAO. 2018. World Livestock: Transforming the Livestock Sector through the Sustainable Development Goals. Food and Agriculture Organization of the United Nations (FAO). Rome. 222 Pages. 
Fleming DS, Koltes JE, Markey AD, Schmidt CJ, Ashwell CM, Rothschild MF, Persia ME, Reecy JM & Lamont SJ. 2016. Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600k genotyping array. BMC Genomics, 17: 407. DOI: 10.1186/s12864-016-2711-5
Fleming DS, Weigend S, Simianer H, Weigend A, Rothschild M, Schmidt C, Ashwell C, Persia M, Reecy J & Lamont SJ. 2017. Genomic comparison of indigenous African and Northern European chickens reveals putative mechanisms of stress tolerance related to environmental selection pressure. G3-Genes Genomes Genetics, 7: 1525-1537. DOI: 10.1534/g3.117.041228
Flint APF & Woolliams JA. 2008. Precision animal breeding. Philosophical Transactions of the Royal Society B, 363: 573–590. DOI: 10.1098/rstb. 2007.2171
Fulton JE. 2008. Molecular genetics in a modern poultry breeding organization. World's Poultry Science Journal, 64: 171-176. DOI: 10.1017/ S0043933907001778
Fulton JE. 2012. Genomic selection for poultry breeding. Animal Frontiers, 2: 30-36. DOI: 10.2527/af.2011-0028
Goddard ME & Hayes BJ. 2007. Genomic selection. Journal of Animal Breeding and Genetics, 124: 323-330. DOI: 10.1111/j.1439-0388.2007.00702.x
Habimana R, Okeno TO, Ngeno K, Mboumba S, Assami P, Gbotto AA, Keambou CT, Nishimwe K, Mahoro J & Yao N. 2020. Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers. PLOS ONE, 15(4): e0225084. DOI: 10.1371/journal.pone. 0225084
Hayes BJ, Lewin HA & Goddard ME. 2013. The future of livestock breeding: Genomic selection for efficiency, reduced emissions intensity, and adaptation. Trends in Genetics, 29: 206-214. DOI: 10.1016/j.tig.2012.11.009
Heidaritabar M, Vereijken A, Muir WM, Meuwissen T, Cheng H, Megens HJ, Groenen MAM & Bastiaansen JWM. 2014. Systematic differences in the response of genetic variation to pedigree and genome-based selection methods. Heredity, 113: 503-513. DOI: 10.1038/hdy.2014.55
Heidaritabar M. 2016. Genomic selection in egg-laying chickens. PhD Dissertation. Wageningen University, Wageningen, the Netherlands. 220 Pages.
Hoffmann I. 2005. Research and investment in poultry genetic resources – challenges and options for sustainable use. World's Poultry Science Journal, 61: 57-70. DOI: 10.1079/WPS200449
International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432: 695-716. DOI: 10.1038/nature03154
Ledur MC, Peixoto JO, Nones K & Coutinho LL. 2012. Applied genomics: The Brazilian experience. XXIV World's Poultry Congress. Salvador, Bahia, Brazil. Pages, 1-8.
Legarra A, Christensen OF, Aguilar I & Misztal I. 2014. Single Step, a general approach for genomic selection. Livestock Science, 166: 54–65. DOI: 10.1016/j.livsci.2014.04.029
Liu T, Luo C, Wang J, Ma J, Shu D, Lund MS, Su G & Qu H. 2017. Assessment of the genomic prediction accuracy for feed efficiency traits in meat-type chickens. PLOS ONE, 12(3): e0173620. DOI: 10.1371/journal.pone.0173620
Lyimo CM, Weigend A, Msoffe PL, Eding H, Simianer H & Weigend S. 2014. Global diversity and genetic contributions of chicken populations from African, Asian and European regions. Immunogenetics, Molecular Genetics and Functional Genomics, 45: 836–848. DOI: 10.1111/ age.12230
Meuwissen T, Hayes B & Goddard M. 2016. Genomic selection: A paradigm shift in animal breeding. Animal Frontiers, 6: 6-14. DOI: 10.2527/af.2016-0002
Meuwissen THE, Hayes BJ & Goddard ME. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157: 1819-1829. DOI: 10.1093/genetics/157.4.1819
Misztal I & Legarra A. 2017. Invited review: Efficient computation strategies in genomic selection. Animal, 11: 731-736. DOI: 10.1017/S175173111 6002366
Moniruzzaman M, Khatun R & Mintoo AA. 2014. Application of marker assisted selection for livestock improvement in Bangladesh. Bangladesh Veterinarian, 31: 1-11. DOI: 10.3329/bvet. v31i1. 22837
Mrode R, Tarekegn GM, Mwacharo JM & Djikeng A. 2018. Invited review: Genomic selection for small ruminants in developed countries: how applicable for the rest of the world? Animal, 12: 1333-1340. DOI: 10.1017/S1751731117003688
Muchadeyi FC & Dzomba EF. 2017. Genomics tools for the characterization of genetic adaptation of low input extensively raised chickens. In: Manafi M. (Ed). Poultry Science, 11: 211-229. DIO: 10.5772/ 65679.
Muir WM. 2003. Incorporating molecular information in breeding programs: Applications and limitations. In: Muir WM & Aggrey SE. (Eds). Poultry Genetics, Breeding and Biotechnology. CABI Publishing. Wallingford. Pages, 549-562.
Ngeno K, van der Waaij EH, Megens HJ, Kahi AK, van Arendonk JAM & Crooijmans RPMA. 2015. Genetic diversity of different indigenous chicken ecotypes using highly polymorphic MHC‐linked and non‐MHC microsatellite markers. Animal Genetic Resources, 56: 1-7. DOI: 10.1017/S207863 3614000484
Okumu ON, Ngeranwa JJN, Binepal YS, Kahi AK, Bramwel WW, Ateya LO & Wekesa FC. 2017. Genetic diversity of indigenous chickens from selected areas in Kenya using microsatellite markers. Journal of Genetic Engineering and Biotechnology, 15: 489–495. DOI: 10.1016/j.jgeb. 2017.04.007
Park W, Srikanth K, Lim D, Park M, Hur T, Kemp S, Dessie T, Kim MS, Lee S-R, te Pas MFW, Kim J-M & Park J-E. 2018. Comparative transcriptome analysis of Ethiopian indigenous chickens from low and high altitudes under heat stress condition reveals differential immune response. Immunogenetics, Molecular Genetics and Functional Genomics, 50, 42–53. DOI: 10.1111/ age.12740
Preisinger R. 2012. Genome-wide selection in poultry. Animal Production Science, 52: 121-125. DOI: 10.1071/AN11071
Psifidi A, Banos G, Matika O, Desta TT, Bettridge J, Hume DA, Dessie T, Christley R, Wigley P, Hanotte O, & Kaiser P. 2016. Genome‑wide association studies of immune, disease and production traits in indigenous chicken ecotypes. Genetics Selection Evolution, 48: 74. DOI: 10.1186/s12711-016-0252-7
Psifidi A, Banos G, Matika O, Tadelle D, Christley R, Wigley P, Bettridge J, Hanotte O, Desta T & Kaiser P. 2014. Identification of SNP markers for resistance to Salmonella and IBDV in indigenous Ethiopian chickens. 10th World Congress of Genetics Applied to Livestock Production. Vancouver, Canada.
Rothschild MF & Plastow GS. 2014. Applications of genomics to improve livestock in the developing world. Livestock Science, 166: 76–83. DOI: 10.1016/j.livsci.2014.03.020
Ruane J & Sonnino A. 2007. Marker-assisted selection as a tool for genetic improvement of crops, livestock, forestry and fish in developing countries: An overview of the issues. In: Guimarães EP, Ruane J, Scherf BD, Sonnino A & Dargie JD. (Eds). Marker-Assisted Selection: Current Status and Future Perspectives in Crops, Livestock, Forestry and Fish. Food and Agriculture Organization of the United Nations (FAO). Rome. Pages, 3-13.
Sitzenstock F, Ytournel F, Sharifi AR, Cavero D, Täubert H, Preisinger R & Simianer H. 2013. Efficiency of genomic selection in an established commercial layer breeding program. Genetics Selection Evolution, 45: 29. DOI: 10.1186/1297-9686-45-29
Sonnino A, Carena MJ, Guimarães EP, Baumung R, Pilling D & Rischkowsky B. 2007. An assessment of the use of molecular markers in developing countries. In: Guimarães EP, Ruane J, Scherf BD, Sonnino A & Dargie JD. (Eds). Marker-Assisted Selection: Current Status and Future Perspectives in Crops, Livestock, Forestry and Fish. Food and Agriculture Organization of the United Nations (FAO). Rome. Pages, 15-26.
Stock KF & Reents R. 2013. Genomic selection: status in different species and challenges for breeding. Reproduction in Domestic Animals, 48 (Suppl. 1): 2-10. DOI: 10.1111/rda.12201
Tixier-Boichard M, Leenstra F, Flock DK, Hocking PM & Weigend S. 2012. A century of poultry genetics. World's Poultry Science Journal, 68: 307-321. DOI: 10.1017/S0043933912000360
Toro MA. 2011. Future trends in animal breeding due to new genetic technologies. Advances in Animal Biosciences, 1: 546-557. DOI: 10.1017/S2040 470010005431
van Arendonk JAM & Bovenhuis H. 2003. Designs and methods to detect QTL for production traits based on mapped genetic markers. In: Muir WM & Aggrey SE. (Eds). Poultry Genetics, Breeding and Biotechnology. CABI Publishing. Wallingford. Pages, 439-464.
Vitezica ZG, Aguilar I, Misztal I & Legarra A. 2011. Bias in genomic predictions for populations under selection. Genetic Research Cambridge, 1-10. DOI: 10.1017/S001667231100022X
Wang C, Habier D, Peiris BL, Wolc A, Kranis A, Watson KA, Avendano S, Garrick DJ, Fernando RL, Lamont SJ & Dekkers JCM. 2013. Accuracy of genomic prediction using an evenly spaced, low-density single nucleotide polymorphism panel in broiler chickens. Poultry Science, 92: 1712-1723. DOI: 10.3382/ps.2012- 02941
Weller JI. 2016. Genomic Selection in Animals. 1st Ed. John Wiley and Sons, Inc. Hoboken, New Jersey. 175 Pages.
Wolc A, Kranis A, Arango J, Settar P, Fulton JE, O'Sullivan N, Avendaño S, Watson KA, Preisinger R, Habier D, Lamont SJ, Fernando R, Garrick DJ & Dekkers JCM. 2014. Applications of genomic selection in poultry. 10th World Congress of Genetics Applied to Livestock Production. Vancouver, Canada.
Wolc A, Kranis A. Arango J, Settar P, Fulton JE, O'Sullivan NP, Avendano A, Watson KA, Hickey JM, de los Campos G, Fernando RL, Garrick DJ & Dekkers JCM. 2016. Implementation of genomic selection in the poultry industry. Animal Frontiers, 6: 23-31. DOI: 10.2527/af.2016-0004
Wolc A, Stricker C, Arango J, Settar P, Fulton JE, O'Sullivan NP, Preisinger R, Habier D, Fernando R, Garrick DJ, Lamont SJ & Dekkers JCM. 2011. Breeding value prediction for production traits in layer chickens using pedigree or genomic relationships in a reduced animal model. Genetics Selection Evolution, 43:5. DOI: 10.1186/1297-9686-43-5
Wolc A, Zhao HH, Arango J, Settar P, Fulton JE, O'Sullivan NP, Preisinger R, Stricker C, Habier D, Fernando RL, Garrick DJ, Lamont SJ & Dekkers JCM. 2015. Response and inbreeding from a genomic selection experiment in layer chickens. Genetics Selection Evolution, 47: 59. DOI: 10.1186/s12711-015-0133-5
Wolc A. 2014. Understanding genomic selection in poultry breeding. World's Poultry Science Journal, 70: 309-314. DOI: 10.1017/S004393391400032