Skip to main content

Animal Genomics—A Current Perspective

  • Chapter
  • First Online:
Advances in Animal Biotechnology
  • 1496 Accesses

Abstract

The livestock sector as an important subsector of agriculture plays an important role in national economy. In current era of molecular genetics, genomics and sequencing technologies applicable to genome, proteome and transriptome sequencing, and access to gigantic sequence data, a number of markers are identified and used to analyze genomic diversity. Molecular markers have emerged as amazing tools for selection of farm animals for beneficial traits, and detecting diseases prior to clinical symptoms. Researchers and scholars as beginners in livestock production and management must be familiar with types, advantages, and prospects of these valuable tools.

Key Points

  • Genetic evaluation of livestock is indispensable for their conservation and utilization

  • Molecular genetic markers have emerged as incredible tools for livestock selection and disease diagnosis.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Ajmone-Marsan P, Negrini R, Milanesi E, Bozzi R, Nijman IJ, Buntjer JB, Valentini A, Lenstra JA (2002) Genetic distances within and across cattle breeds as indicated by biallelic AFLP markers. Anim Genet 33(4):280–286. https://doi.org/10.1046/j.1365-2052.2002.00865.x

    Article  CAS  PubMed  Google Scholar 

  • Anderson S, de Bruijn MH, Coulson AR, Eperon IC, Sanger F, Young IG (1982) Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J Mol Biol 156(4):683–717 (No abstract available)

    Article  CAS  PubMed  Google Scholar 

  • Ashwell MS, Rexroad CE Jr, Miller RH, VanRaden PM (1996) Mapping economic trait loci for somatic cell score in Holstein cattle using microsatellite markers and selective genotyping. Anim Genet 27(4):235–242

    Article  CAS  PubMed  Google Scholar 

  • Ashwell MS, Rexroad CE Jr, Miller RH, VanRaden PM, Da Y (1997) Detection of loci affecting milk production and health traits in an elite US Holstein population using microsatellite markers. Anim Genet 28:216–222

    Article  CAS  Google Scholar 

  • Beckman JS, Weber JL (1992) Survey of human and rat microsatellites. Genomics 12:627–631

    Article  CAS  PubMed  Google Scholar 

  • Badola S, Bhattacharya TK, Biswas TK, Shivakumar BM, Kumar P, Sharma A (2004) A comparison on polymorphism of Beta-lactoglobulin gene in Bos indicus, Bos taurus and Indicine × Taurine crossbred cattle. Asian Aust J Anim Sci 17(6):733–736. https://doi.org/10.5713/ajas.2004.733

    Article  CAS  Google Scholar 

  • Berggren KT, Ellegren H, Hewitt GM, Seddon JM (2005) Understanding the phylogeographic patterns of European hedgehogs, Erinaceus concolor and E. europaeus using the MHC. Heredity (Edinb) 95(1):84–90

    Article  CAS  Google Scholar 

  • Baumung R, Simianer H, Hoffmann I (2004) Genetic diversity studies in farm animals—a survey Studien zur genetischen Diversität landwirtschaftlicher Nutztiere- ein globaler Überblick. J Anim Breed Genet 121(6):361–373

    Article  Google Scholar 

  • Biswas TK, Bhattacharya TK, Narayan AD, Badola S, Kumar P, Sharma A (2003) Growth hormone gene polymorphism and its effect on birth weight in cattle and buffalo. Asian Aust J Anim Sci 16(4):494–497. https://doi.org/10.5713/ajas.2003.494

    Article  CAS  Google Scholar 

  • Bitgood JJ, Shoffner RN (1990) Cytology and cytogenetics. Poultry breeding. Genetics 22:401–427

    Google Scholar 

  • Bjørnstad G, Røed KH (2001) Breed demarcation and potential for breed allocation of horses assessed by microsatellite markers. Anim Genet 32(2):59–65

    Article  PubMed  Google Scholar 

  • Bjørnstad G, Gunby E, Røed KH (2000) Genetic structure of Norwegian horse breeds. J Anim Breed Genet 117:307–317

    Article  Google Scholar 

  • Blears MJ, De Grandis SA, Lee H, Trevors JT (1998) Amplified fragment length polymorphism (AFLP): a review of the procedure and its applications. J Ind Microbiol Biotech 21:99–114. https://doi.org/10.1038/sj.jim.2900537

    Article  CAS  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32(3):314–331 (Review)

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brown JR, Beckenbach AT, Smith MJ (1993) Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon (Acipenser transmontanus). Mol Biol Evol 10(2):326–341

    CAS  PubMed  Google Scholar 

  • Brown WM, George M Jr, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci U S A 76(4):1967–1971

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bruford MW, Bradley DG, Luikart G (2003) DNA markers reveal the complexity of livestock domestication. Nat Rev Genet 4(11):900–910 (Review)

    Article  CAS  PubMed  Google Scholar 

  • Convention on Biological Diversity (CBD) (1992) https://en.wikipedia.org/wiki/Conventionon_Biological_Diversity

  • Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M, Freimer NB (1994) Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci U S A 91:3166–3170. https://doi.org/10.1073/pnas.91.8.3166

    Article  PubMed  PubMed Central  Google Scholar 

  • Dixit SP, Verma NK, Aggarwal RAK, Vyas MK, Rana J, SharmaA Tyagia P, Arya P, Ulmek BR (2010) Genetic diversity and relationship among southern Indian goat breeds based onmicrosatellite markers. Small Rumin Res 91:153–159

    Article  Google Scholar 

  • FAO (2001) The states of the world’s animal genetic resource food and agriculture FAO. Rome, Italy

    Google Scholar 

  • FAO (2007a) In: Rischkowsky B, Pilling D (eds) The state of the world’s animal genetic resources for food and agriculture. Rome. http://www.fao.org/docrep/010/a1250e/a1250e00.htm

  • FAO (2007b) Global plan of action for animal genetic resources and the interlakendeclaration. Rome. http://www.fao.org/docrep/010/a1404e/a1404e00.htm

  • FAO (2007c) In: In: Rischkowsky B, Pilling D (eds) The state of the world’s animal genetic resources for food and agriculture. Rome

    Google Scholar 

  • Fatima S, Bhonga CD, Ranka DN, Joshi CG (2008) Genetic variability and bottleneck studies in Zalawadi, Gohilwadi and Surti goat breeds of Gujarat (India) usingmicrosatellites. Small Rumin Res 77:58–64

    Article  Google Scholar 

  • Gebremedhin B, Flagstad Ø, Bekele A, Chala D, Bakkestuen V, Boessenkool S, Popp M, Gussarova G, Schrøder-Nielsen A, Nemomissa S, Brochmann C, Stenseth NC, Epp LS (2016) DNA metabarcoding reveals diet overlap between the endangered Walia Ibex and domestic goats—implications for conservation. PLoS ONE 11(7):e0159133. https://doi.org/10.1371/journal.pone.0159133 (eCollection 2016)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Georges M, Dietz AB, Mishra A, Nielsen D, Sargeant LS, Sorensen A, Steele MR, Zhao X, Leipold H, Womack JE, Lathrop M (1993) Microsatellite mapping of the gene causing weaver disease in cattle will allow the study of an associated quantitative trait locus. Proc Natl Acad Sci U S A 90(3):1058–1062

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goldstein DB, Schlötterer C (1999) Microsatellites: evolution and applications. Oxford University Press, New York, 368p

    Google Scholar 

  • Hall SJ, Bradley DG (1995) Conserving livestock breed biodiversity. Trends Ecol Evol 10(7):267–270

    Article  CAS  PubMed  Google Scholar 

  • Hebert PD, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc Biol Sci 270(1512):313–321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hebsgaard MB, Wiuf C, Gilbert MT, Glenner H, Willerslev E (2007) Evaluating Neanderthal genetics and phylogeny. J Mol Evol 64(1):50–60 (Epub 2006 Dec 1)

    Article  CAS  PubMed  Google Scholar 

  • Jarne P, Lagoda PJ (1996) Microsatellites, from molecules to populations and back. Trends Ecol Evol 11(10):424–429

    Article  CAS  PubMed  Google Scholar 

  • Jonker M, Van Meurs G, 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. https://doi.org/10.1111/j.1399-0039.1982.tb01417.x

    Article  CAS  PubMed  Google Scholar 

  • Jordana J, Folch P, Aranguren JA (2001) Microsatellite analysis of genetic diversity in the Catalonian donkey breed. J Anim Breed Genet 118:57–63

    Article  CAS  Google Scholar 

  • Kantanen J, Olsaker I, Holm LE, Lien S, Vilkki J, Brusgaard K, Eythorsdottir E, Danell B, Adalsteinsson S (2000) Genetic diversity and population structure of 20 North European cattle breeds. J Hered 91(6):446–457

    Article  CAS  PubMed  Google Scholar 

  • Kimura M, Crow JF (1964) The number of alleles that can be maintained in a finite population. Genetics 49:725–738 (No abstract available. PMID: 14156929)

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kimura M, Ohta T (1978) Stepwise mutation model and distribution of allelic frequencies in a finite population. ProcNatlAcadSci U S A 75(6):2868–2872

    Article  CAS  Google Scholar 

  • Köhler-Rollefson I (1997) Indigenous practices of animal genetic resource management and their relevance for the conservation of domestic animal diversity in developing countries. J. Anim Breed Genet 114:231–238. https://doi.org/10.1111/j.1439-0388.1997.tb00509.x

    Article  PubMed  Google Scholar 

  • Kumar KG, Ponsuksili S, Schellander K, Wimmers K (2004) Molecular cloning and sequencing of porcine C5 gene and its association with immunological traits. Immunogenetics 55(12):811–817 (Epub 2004 Feb 10)

    Article  CAS  PubMed  Google Scholar 

  • Koringa PG, Joshi CG, Solanki JV, Rank DN (2008) Genetic characterization and bottleneck studies in Kathiawari horse breed of India. Haryana Vet 47:77–83

    Google Scholar 

  • Li S, Wang Q, Lin X, Jin X, Liu L, Wang C, Chen Q, Liu J, Liu H (2017) The use of “omics” in lactation research in dairy cows. Int J Mol Sci 18(5). pii: E983. https://doi.org/10.3390/ijms18050983 (Review)

    Article  PubMed Central  CAS  Google Scholar 

  • Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44(3):397–401

    CAS  PubMed  PubMed Central  Google Scholar 

  • Luikart G, Allendorf FW, Cornuet JM, Sherwin WB (1998a) Distortion of allele frequency distributions provides a test for recent population bottlenecks. J Hered 89(3):238–247

    Article  CAS  PubMed  Google Scholar 

  • Luikart G, Sherwin WB, Steele BM, Allendorf FW (1998b) Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change. Mol Ecol. 7(8):963–974

    Article  CAS  PubMed  Google Scholar 

  • MacHugh DE, Bradley DG (2001) Livestock genetic origins: goats buck the trend. Proc Natl Acad Sci U S A 98(10):5382–5384 (No abstract available)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maji S, Krithika S, Vasulu TS (2009) Phylogeographic distribution of mitochondrial DNA macrohaplogroup M in India. J Genet 88(1):127–139

    Article  PubMed  Google Scholar 

  • Mallott EK, Garber PA, Malhi RS (2017) Integrating feeding behavior, ecological data, and DNA barcoding to identify developmental differences in invertebrate foraging strategies in wild white-faced capuchins (Cebus capucinus). Am J Phys Anthropol 162(2):241–254. https://doi.org/10.1002/ajpa.23113 (Epub 2016 Oct 5)

    Article  PubMed  Google Scholar 

  • Martín-Burriel I, García-Muro E, Zaragoza P (1999) Genetic diversity analysis of six Spanish native cattle breeds using microsatellites. Anim Genet 30(3):177–182

    Article  PubMed  Google Scholar 

  • 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, Moore SS (2008) An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC Genet 20(9):37. https://doi.org/10.1186/1471-2156-9-37

    Article  CAS  Google Scholar 

  • Mishra BP, Kataria RS, Bulandi SS, Prakash B, Kathiravan P, Mukesh M, Sadana DK (2009a) Riverine status and genetic structure of Chilika buffalo of eastern India as inferred from cytogenetic and molecular marker-based analysis. J Anim Breed Genet 126(1):69–79. https://doi.org/10.1111/j.1439-0388.2008.00759.x

    Article  CAS  PubMed  Google Scholar 

  • Mishra BP, Kataria RS, Kathiravan P, Bulandi SS, Singh KP, Sadana DK (2009b) Evaluation of genetic variability and mutation drift equilibrium of Banni buffalo using multi locus microsatellite markers. Trop Anim Health Prod 41(7):1203–1211. https://doi.org/10.1007/s11250-008-9301-8 (Epub 2009 Jan 9)

    Article  CAS  PubMed  Google Scholar 

  • Mishra BP, Kataria RS, Kathiravan P, Singh KP, Sadana DK, Joshi BK (2010) Microsatellite based genetic structuring reveals unique identity of Banni among river buffaloes of Western India. Livestock Sci 127:257–261

    Article  Google Scholar 

  • Moxon ER, Wills C (1999) DNA microsatellites: agents of evolution? Sci Am 280(1):94–99 (No abstract available)

    Article  CAS  PubMed  Google Scholar 

  • Mukesh M, Sodhi M, Kataria RS, Mishra BP (2009) Use of microsatellite multilocus genotypic data for individual assignment assay in six native cattle breeds from North West Region of India. Livestock Sci 121:72–77

    Article  Google Scholar 

  • Negrini R, Nijman IJ, Milanesi E, Moazami-Goudarzi K, Williams JL, Erhardt G, Dunner S, Rodellar C, Valentini A, Bradley DG, Olsaker I, Kantanen J, Ajmone-Marsan P, Lenstra JA (2007) European cattle genetic diversity consortium. Differentiation of European cattle by AFLP fingerprinting. Anim Genet 38(1):60–66

    Article  CAS  PubMed  Google Scholar 

  • O’Brien SJ (1994) A role for molecular genetics in biological conservation. Proc Natl Acad Sci U S A 91(13):5748–5755 (Review)

    Article  PubMed  PubMed Central  Google Scholar 

  • Ostrander EA, Jong PM, Rine J, Duyk G (1992) Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proc Natl Acad Sci U S A 89(8):3419–3423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pal A, Chakravarty AK, Bhattacharya TK, Joshi BK, Sharma A (2004) Detection of polymorphism of growth hormone gene for the analysis of relationship between allele type and growth traits in Karan Fries cattle. Asian Aust J Anim Sci 17:1334–1337

    Article  CAS  Google Scholar 

  • Pandey AK, Tantia MS, Kumar D, Mishra B, Chaudhury P, Vijh RK (2002) Microsatellite analysis of three poultry breeds of India. Asian Aus J Anim Sci 15(11):1536–1542. https://doi.org/10.5713/ajas.2002.1536 (Published online January 1, 2002)

    Article  CAS  Google Scholar 

  • Popescu NC, Evans CH, DiPaolo JA (1976) Chromosome patterns (G and C bands) of in vitro chemical carcinogen-transformed guinea pig cells. Cancer Res 36(4):1404–1413

    CAS  PubMed  Google Scholar 

  • Ron M, Band M, Yanai A, Weller JI (1994) Mapping quantitative trait loci with DNA microsatellites in a commercial dairy cattle population. Anim Genet 25(4):259–264

    Article  CAS  PubMed  Google Scholar 

  • Ruane J (1999) A critical review of the value of genetic distance studies in conservation of animal genetic resources. J Anim Breed Genet 116:317–323. https://doi.org/10.1046/j.1439-0388.1999.00205.x

    Article  Google Scholar 

  • Saitbekova N, Gaillard C, Obexer-Ruff G, Dolf G (1999) Genetic diversity in Swiss goat breeds based on microsatellite analysis. Anim Genet 30(1):36–41

    Article  CAS  PubMed  Google Scholar 

  • Saitbekova N, Schlapfer J, Dolf G, Gaillard C (2001) Geneticrelationships in Swiss sheep breeds based on microsatellite analysis. J Anim Breed Genet 118:379–387

    Article  Google Scholar 

  • Singh (2018). https://www.vetextension.com/current-livestock-animal-husbandry-statistics-india/ (June 15, 2019)

  • Sodhi M, Mukesh M, Mishra BP, Ahlawat SP, Prakash B, Sobti RC (2011a) Microsatellite analysis of genetic population structure of zebu cattle (Bos indicus) breeds from north-western region of India. Anim Biotechnol 22(1):16–29. https://doi.org/10.1080/10495398.2011.536091

    Article  PubMed  Google Scholar 

  • Sodhi M, Mukesh M, Mishra BP, Parvesh K, Joshi BK (2011b) Analysis of genetic variation at the prolactin-RsaI (PRL-RsaI) locus in Indian native cattle breeds (Bos indicus). Biochem Genet 49(1–2):39–45. https://doi.org/10.1007/s10528-010-9383-7

    Article  CAS  PubMed  Google Scholar 

  • Spencer CC, Neigel JE, Leberg PL (2000) Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks. Mol Ecol 9(10):1517–1528

    Article  CAS  PubMed  Google Scholar 

  • Strand M, Prolla TA, Liskay RM, Petes TD (1993) Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature. 365(6443):274–276 (Erratum in: Nature 1994 Apr 7; 368(6471):569)

    Article  CAS  PubMed  Google Scholar 

  • Takezaki N, Nei M (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144(1):389–399

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tarnita CE, Antal T, Ohtsuki H, Nowak MA (2009) Evolutionary dynamics in set structured populations. Proc Natl Acad Sci U S A 106(21):8601–8604. https://doi.org/10.1073/pnas.0903019106 (Epub 2009 May 11)

    Article  PubMed  PubMed Central  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23(21):4407–4414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44(3):388–396

    CAS  PubMed  PubMed Central  Google Scholar 

  • Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18(24):7213–7218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18(22):6531–6535

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang W, Kang X, Yang Q, Lin Y, Fang MY (2013) Review on the development of genotyping methods for assessing farm animal diversity. J Anim Sci Biotechnol 4:2. https://doi.org/10.1186/2049-1891-4-2

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang R, Zhao A, Wang X, Zhang Z (2017) Diversity of tick species on domestic animals in Shandong Province, China, using DNA barcoding. Exp Appl Acarol 73(1):79–89. https://doi.org/10.1007/s10493-017-0161-7

    Article  CAS  PubMed  Google Scholar 

  • Zhu Y, Strassmann JE, Queller DC (2000) Insertions, substitutions, and the origin of microsatellites. Genet Res 76(3):227–236

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Birbal Singh .

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Singh, B., Mal, G., Gautam, S.K., Mukesh, M. (2019). Animal Genomics—A Current Perspective. In: Advances in Animal Biotechnology. Springer, Cham. https://doi.org/10.1007/978-3-030-21309-1_28

Download citation

Publish with us

Policies and ethics