Breed Characterization: Tools and Their Applications

Addisu Hailu¹, Addis Getu²

¹Department of Life Science, University of Gondar, Gondar, Ethiopia.
²Department of Animal Production and Extension, University of Gondar, Gondar, Ethiopia.

DOI: 10.4236/oalib.1101438                

Abstract

During the subsequent history of livestock, the main evolutionary forces of mutation, selective breeding, adaptation, isolation and genetic drift have created an enormous diversity of local populations. Organizing and documentation of basic tools for breed characterization are the major aims of the review with the scope of available markers. This farm animal genetic diversity has a primary requirement to meet current production needs in various environments. In addition, farm animal genetic diversity has a great application of allowing sustained genetic improvement, and to facilitate rapid adaptation to changing breeding objectives. Furthermore, animal genetic diversity provides wider range opportunity for selection and improving. The nondescript breed could be Identified and characterizing by morphological or/and molecular markers to know their potential, to know their special adaptive trait and their status for further actions (improvement, conservation). Markers are conspicuous object used to distinguish or to show variation in population or individual level. Morphological markers normally refer to external animal characteristics which can be obtained by direct visual observation and measurement and used in the identification, classification, and characterization of genetic evolution of different species or populations. Since the measurement and identification of animal morphological traits usually take a long time and limited application in evaluation of qualitative traits, molecular markers have developed quickly, and they are becoming more and more informed. Whatever data type (morphological and molecular data) needs appropriate statistical application. In general, diversity, markers and statistical application are the preliminary tools of breed characterization and breed improvements.

Keywords

Animal Breeding, Animal Genetic Resource Diversity, Markers, Statistics

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Köhler-Rollefson, I. (2000) Management of Animal Genetic Diversity at Community Level. Eschborn, Hesse.
[2]	FAO (Food and Agriculture Organization of the United Nations) (1999) Statistical Database. Food and Agriculture Organization of the United Nations. Rome. www.fao.org
[3]	Weigend, S., Groeneveld, L.F., Lenstra, J.A., Eding, H., Toro, M.A., Scherf, B., Pilling, D., Negrini, R., Finlay, E.K., Jianlin, H. and Groeneveld, E., The GLOBALDIV Consortium (2009) Genetic Diversity in Farm Animals—A Review. International Society for Animal Genetics, Animal Genetics, 41, 6-31.
[4]	Notter D.R. (1999) The Importance of Genetic Diversity in Livestock Populations of the Future. Journal of Animal Science, 77, 61-69.
[5]	FAO (Food and Agriculture Organization of the United Nations) (2011) Draft Guidelines on Phenotypic Characterization. Intergovernmental Technical Working Group on Animal Genetic Resources for Food and Agriculture and Commission on Genetic Resources for Food and Agriculture, Rome, 24-26 November 2011, 87 p.
[6]	Van Wezel, I.L. and Rodgers, R.J. (1996) Morphological Characterization of Bovine Primordial Follicles and Their Environment in Vivo. Biology of Reproduction, 55, 1003-1011. http://dx.doi.org/10.1095/biolreprod55.5.1003
[7]	Gizaw, S., Van Arendonk, J.A.M., Komen, H., Windig, J.J. and Hanotte, O. (2007) Population Structure, Genetic Variation and Morphological Diversity in Indigenous Sheep of Ethiopia. Animal Genetics, 38, 621-628. http://dx.doi.org/10.1111/j.1365-2052.2007.01659.x
[8]	Zewdu, W. (2004) Indigenous Cattle Genetic Resources, Their Husbandry Practices, and Breeding Objectives in Northwestern Ethiopia. M.Sc. Thesis, Alemaya University, Alemaya, 143 p.
[9]	Yang, W.J., Kang, X.L., Yang, Q.F., Lin, Y. and Fang, M.Y. (2013) Review on the Development of Genotyping Methods for Assessing Farm Animal Diversity. Journal of Animal Science and Biotechnology, 4, 2. http://dx.doi.org/10.1186/2049-1891-4-2
[10]	Nadler, C.F., Hoffmann, R.S. and Woolf, A. (1973) G-Band Patterns as Chromosomal Markers, and the Interpretation of Chromosomal Evolution in Wild Sheep (Ovis). Cellular and Molecular Life Sciences, 29, 117-119. http://dx.doi.org/10.1186/2049-1891-4-2
[11]	Popescu, N.C., Evans, C.H. and Di Paolo, J.A. (1976) Chromosome Patterns (G and C Bands) of in Vitro Chemical Carcinogen-Transformed Guinea Pig Cells. Cancer Research, 36, 1404-1413.
[12]	Bitgood, J.J. and Shoffner, R.N. (1990) Cytology and Cytogenetics. Poultry Breeding Genetics, 22, 401-427.
[13]	Becak, M.L., Becak, W. and Roberts, F.L. (1973) Fish, Amphibians, Reptiles and Birds. Springer-Verlag, Berlin, Heidelberg and New York.
[14]	Buvanendran, V. and Finney, D.J. (1967) Linkage Relationships of Egg Albumen Loci in the Domestic Fowl. British Poultry Science, 8, 9-13. http://dx.doi.org/10.1080/00071666708415644
[15]	Drinkwater, R.D. and Hetzel, D.J.S. (1991) Application of Molecular Biology to Understanding Genotype-Environment Interactions in Livestock Production. Proceedings of an International Symposium on Nuclear Techniques in Animal Production and Health, Vienna, 15-19 April 1991, 437-452.
[16]	Jonker, J., Meurs, G. and Balner, H. (1982) Typing for RhLA-D in Rhesus Monkeys: II. Genetics of the D Antigens and Their Association with DR Antigens in a Population of Unrelated Animals. Tissue Antigens, 19, 69-78. http://dx.doi.org/10.1111/j.1399-0039.1982.tb01417.x
[17]	Koh, M.C., Lim, C.H., Chua, S.B., Chew, S.T. and Phang, S.T.W. (1998) Random Amplified Polymorphic DNA (RAPD) Fingerprints for Identification of Red Meat Animal Species. Meat Science, 48, 275-285. http://dx.doi.org/10.1016/S0309-1740(97)00104-6
[18]	Demeke, T., Adams, R.P. and Chibbar, R. (1992) Potential Taxonomic Use of Random Amplified Polymorphic DNA (RAPD): A Case Study in Brassica. Theoretical and Applied Genetics, 84, 990-994. http://dx.doi.org/10.1007/BF00227415
[19]	Koller, B., Lehmann, A. and McDermott, J.M. (1993) Identification of Apple Cultivars Using RAPD Markers. Theoretical and Applied Genetics, 85, 901-904. http://dx.doi.org/10.1007/BF00225036
[20]	Meunier, J.R. and Grimont, P.A.D. (1993) Factors Affecting Reproducibility of Random Amplified Polymorphic DNA Fingerprinting. Research in Microbiology, 144, 373-379. http://dx.doi.org/10.1016/0923-2508(93)90194-7
[21]	Blears, M.J., De Grandis, S.A., Lee, H. and Trevors, J.T. (1998) Amplified Fragment Length Polymorphism (AFLP): A Review of the Procedure and Its Applications. Journal of Industrial Microbiology and Biotechnology, 21, 99-114. http://dx.doi.org/10.1038/sj.jim.2900537
[22]	Vos, P., Hogers, R., Bleeker, M., Reijans, M., Lee, T.V.D., Hornes, M., Friters, A., Pot, J., Paleman, J., Kuiper, M. and Zabeau, M. (1995) AFLP: A New Technique for DNA Fingerprinting. Nucleic Acids Research, 23, 4407-4414. http://dx.doi.org/10.1093/nar/23.21.4407
[23]	Vos, P. and Kuiper, M. (1997) AFLP Analysis. In: Caetano-Anollés, G. and Gresshoff, P.M., Eds., DNA Markers: Protocols, Applications, and Overviews, Wiley, New York, 115-131.
[24]	Paglia, G. and Morgante, M. (1998) PCR-Based Multiplex DNA Fingerprinting Technique for the Analysis of Conifer genome. Molecular Breeding, 4, 173-177. http://dx.doi.org/10.1023/A:1009637608702
[25]	Ajmone-Marsan, P., Negrini, R., Milanesi, E., Bozzi, R., Nijman, I.J., Buntjer, J.B., Valentini, A. and Lenstra, J.A. (2002) Genetic Distances within and across Cattle Breeds as Indicated by Biallelic AFLP Markers. Animal Genetics, 33, 280-286. http://dx.doi.org/10.1046/j.1365-2052.2002.00865.x
[26]	Negrini, R., Nijmanl, I.J., Milanesi, E., Moazami-Goudarzi, K., Williams, J.L., Erhardt, G., Dunner, S., Rodellar, C., Valentini, A., Bradley, D.G., Olsaker, I., Kantanen, J., Ajmone-Marsan, P. and Lenstra, J.A. (2007) The European Cattle Genetic Diversity Consortium: Differentiation of European cattle by AFLP Fingerprinting. Animal Genetics, 38, 60-66. http://dx.doi.org/10.1111/j.1365-2052.2007.01554.x
[27]	Litt, M. and Luty, J.A. (1989) A Hyper Variable Microsatellite Revealed by in Vitro Amplification of a Dinucleotide Repeat within the Cardiac Muscle Actin Gene. The American Journal of Human Genetics, 44, 397-401.
[28]	Tautz, D. (1898) Hypervariability of Simple Sequences as a General Source for Polymorphic DNA Markers. Nucleic Acids Research, 17, 6463-6471.
[29]	Tautz, D., Arctander, P., Minelli, A. and Thomas, R.H. (2002) DNA Points the Way Ahead in Taxonomy. Nature, 418, 479. http://dx.doi.org/10.1038/418479a
[30]	Fang, M., Braunschweig, M., Hu, X., Hu, L., Feng, J., Li, N. and Wu, C. (2005) Genetic Variation of Exon 2 of SLA-DQB Gene in Chinese Pigs. Biochemical Genetics, 43, 119-125. http://dx.doi.org/10.1007/s10528-005-1504-3
[31]	Fang, M., Larson, G., Soares Ribeiro, H., Li, N. and Andersson, L. (2009) Contrasting Mode of Evolution at a Coat Color Locus in Wild and Domestic Pigs. PLoS Genetics, 5, e1000341. http://dx.doi.org/10.1371/journal.pgen.1000341
[32]	Hiendleder, S., Hiendleder, S., Thomsen, H., Reinsch, N., Bennewitz, J., Leyhe-Horn, B., Looft, C., Xu, N., Medjugorac, I., Russ, I., Kühn, C., Brockmann, G.A., Blümel, J., Brenig, B., Reinhardt, F., Reents, R., Averdunk, G., Schwerin, M., Förster, M., Kalm, E. and Erhardt, G. (2003) Mapping of QTL for Body Conformation and Behavior in Cattle. Journal of Heredity, 94, 496-506. http://dx.doi.org/10.1093/jhered/esg090
[33]	Montaldo, H.H. and Meza-Herrera, C.A. (1998) Use of Molecular Markers and Major Genes in the Genetic Improvement of Livestock. Electronic Journal of Biotechnology, 1, 83-89. http://dx.doi.org/10.2225/vol1-issue2-fulltext-4
[34]	Lander, E.S. (1996) The New Genomics: Global Views of Biology. Science, 274, 536-539. http://dx.doi.org/10.1126/science.274.5287.536
[35]	Kruglyak, L. (1997) The Use of a Genetic Map of Biallelic Markers in Linkage Studies. Nature Genetics, 17, 21-24. http://dx.doi.org/10.1038/ng0997-21
[36]	Vignal, A., Milan, D. and SanCristobal, M. (2002) A Review on SNP and Other Types of Molecular Markers and Their Use in Animal Genetics. Genetics Selection Evolution, 34, 275-305. http://dx.doi.org/10.1186/1297-9686-34-3-275
[37]	Syvänen, A.C. (2001) Accessing Genetic Variation: Genotyping Single Nucleotide Polymorphisms. Nature Reviews Genetics, 2, 930-942. http://dx.doi.org/10.1038/35103535
[38]	Primmer, C.R., Borge, T. and Lindell, J. (2002) Single-Nucleotide Polymorphism Characterization in Species with Limited Available Sequence Information: High Nucleotide Diversity Revealed in the Avian Genome. Molecular Ecology, 11, 603-612. http://dx.doi.org/10.1046/j.0962-1083.2001.01452.x
[39]	Tsuchihashi, Z. and Dracopoli, N.C. (2002) Progress in High-Throughput SNP Genotyping Methods. The Pharmacogenomics Journal, 2, 103-110. http://dx.doi.org/10.1038/sj.tpj.6500094
[40]	Werner, M., Sych, M., Herbon, N., Illig, T., Konig, I.R. and Wjst, M. (2002) Large-Scale Determination of SNP Allele Frequencies in DNA Pools Using MALDI-TOF Mass Spectrometry. Human Mutation, 20, 57-64. http://dx.doi.org/10.1002/humu.10094
[41]	Welsh, J. and McClelland, M. (1990) Fingerprinting Genomes Using PCR with Arbitrary Primers. Nucleic Acids Research, 18, 7213-7218. http://dx.doi.org/10.1093/nar/18.24.7213
[42]	Hebert, P.D.N., Cywinska, A., Ball, S.L. and de Waard, J.R. (2003) Biological Identifications through DNA Barcodes. Proceedings of the Royal Society B: Biological Sciences, 270, 313-321. http://dx.doi.org/10.1098/rspb.2002.2218
[43]	Stoecklem, M. (2003) Taxonomy, DNA, and the Bar Code of Life. BioScience, 53, 796-797. http://dx.doi.org/10.1641/0006-3568(2003)053[0796:TDATBC]2.0.CO;2
[44]	Hebert, P.D.N., Penton, E.H. and Burns, J.M. (2004) Ten Species in One: DNA Barcoding Reveals Cryptic Species in the Neotropical Skipper Butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences of the United States of America, 101, 14812-14817. http://dx.doi.org/10.1073/pnas.0406166101
[45]	Hajibabaei, M., Janzen, D.H. and Burns, J.M. (2006) DNA Barcodes Distinguish Species of Tropical Lepidoptera. Proceedings of the National Academy of Sciences of the United States of America, 103, 968-971. http://dx.doi.org/10.1073/pnas.0510466103
[46]	Meyer, C.P. and Paulay, G. (2005) DNA Barcoding: Error Rates Based on Comprehensive Sampling. PLoS Biology, 3, 2229-2238. http://dx.doi.org/10.1371/journal.pbio.0030422
[47]	Meier, R., Shiyang, K. and Vaidya, G. (2006) DNA Barcoding and Taxonomy in Diptera: A Tale of High Intraspecific Variability and Low Identification Success. Systematic Biology, 55, 715-728. http://dx.doi.org/10.1080/10635150600969864
[48]	Gianola, D. (2013) Statistics in Animal Breeding. Journal of the American Statistical Association, 95, 296-299.
[49]	Williams, J.G.K., Kubeilik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. (1990) DNA Polymorphisms Amplified by Arbitrary Primers Are Useful as Genetic Markers. Nucleic Acids Research, 18, 6531-6535. http://dx.doi.org/10.1093/nar/18.22.6531