Analysis of population structure and genetic variability in Iranian buffaloes (Bubalus bubalis) using pedigree information
Navid Ghavi Hossein-Zadeh
+ Author Affiliations
- Author Affiliations
Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran. Email: nhosseinzadeh@guilan.ac.ir; navid.hosseinzadeh@gmail.com
Animal Production Science 56(7) 1130-1135 https://doi.org/10.1071/AN14738
Submitted: 4 August 2014 Accepted: 5 December 2014 Published: 25 March 2015
Abstract
The objective of this study was to use pedigree analysis to evaluate the population structure, genetic variability and inbreeding in Iranian buffaloes. The analysis was based on the pedigree information of 42 285 buffaloes born from 549 sires and 6376 dams within 1697 herds. Pedigree information used in this study was collected during 1976 to 2012 by the Animal Breeding Centre of Iran. The CFC program was applied to calculate pedigree statistics and genetic structure analysis of the Iranian buffaloes. Also, the INBUPGF90 program was used for calculating regular inbreeding coefficients for individuals in the pedigree. The analysis of pedigree indicated that inbreeding coefficient ranged from 0% to 31% with an average of 3.42% and the trend of inbreeding was significantly positive over the years (P < 0.0001). Average coancestry was increased in recent years and overall generation interval was 6.62 years in Iranian buffaloes. Founder genome equivalent, founder equivalent, effective number of founders and effective number of non-founders were increased from 1976 to 2002, but their values decreased from 2002 onwards. A designed mating system to avoid inbreeding may be applied to this population of buffalo to maintain genetic diversity.
Additional keywords: generation interval, inbreeding, mating system, pedigree analysis, population size.
References
Aguilar I, Misztal I (2008) Technical note: recursive algorithm for inbreeding coefficients assuming nonzero inbreeding of unknown parents. Journal of Dairy Science 91, 1669–1672.| Technical note: recursive algorithm for inbreeding coefficients assuming nonzero inbreeding of unknown parents.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXktVelt7c%3D&md5=9c02e9cdab57073ec06e93d1173b9f72CAS | 18349260PubMed |
Alvarez I, Royo LJ, Fernandez I, Gutierrez JP, Gomez E, Goyache F (2004) Genetic relationships and admixture among sheep breeds from Northern Spain assessed using microsatellites. Journal of Animal Science 82, 2246–2252.
Animal Science Research Institute of Iran (2004) ‘Iran’s country report on farm animal genetic resources, July 2004.’ (Ministry of Jihad-e-Agriculture, Agricultural Research and Education Organization, Animal Science Research Institute of Iran: Tehran, Iran)
Barczak E, Wolc A, Wójtowski J, Slósarz P, Szwaczkowski T (2009) Inbreeding and inbreeding depression on body weight in sheep. Journal of Animal and Feed Sciences 18, 42–50.
Boichard D, Maignel L, Verrier É (1997) The value of using probabilities of gene origin to measure genetic variability in a population. Genetics, Selection, Evolution. 29, 5–23.
| The value of using probabilities of gene origin to measure genetic variability in a population.Crossref | GoogleScholarGoogle Scholar |
Borghese A (2005) ‘Buffalo production and research.’ (FAO Regional Office for Europe Inter-Regional Cooperative Research Network on Buffalo (ESCORENA: Rome, Italy): Available at http://www.fao.org/docrep/010/ah847e/ah847e00.htm [Verified 28 November 2014]
Caballero A, Toro MA (2000) Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genetical Research 75, 331–343.
| Interrelations between effective population size and other pedigree tools for the management of conserved populations.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD3cvgsVSltg%3D%3D&md5=1fe3b83f75e4e091391457bd22ac20d7CAS | 10893869PubMed |
Colleau JJ (2002) An indirect approach to the extensive calculation of relationship coefficients. Genetics, Selection, Evolution. 34, 409–421.
| An indirect approach to the extensive calculation of relationship coefficients.Crossref | GoogleScholarGoogle Scholar | 12270102PubMed |
Eteqadi B, Ghavi Hossein-Zadeh N, Shadparvar AA (2014) Population structure and inbreeding effects on body weight traits of Guilan sheep in Iran. Small Ruminant Research 119, 45–51.
| Population structure and inbreeding effects on body weight traits of Guilan sheep in Iran.Crossref | GoogleScholarGoogle Scholar |
Falconer DS, MacKay TFC (1996) ‘Introduction to quantitative genetics.’ 4th edn. (Longman Group: Harlow, Essex, UK)
FAO (2007) ‘The state of the world’s animal genetic resources for food and agriculture.’ (Eds B Rischkowsky, D Pilling) (FAO: Rome, Italy)
Frankham R, Ballou JD, Briscoe DA (2002) ‘Introduction to conservation genetics.’ (Cambridge University Press: Cambridge, UK)
Ghavi Hossein-Zadeh N (2012a) Bayesian estimates of genetic changes for body weight traits of Moghani sheep using Gibbs sampling. Tropical Animal Health and Production 44, 531–536.
| Bayesian estimates of genetic changes for body weight traits of Moghani sheep using Gibbs sampling.Crossref | GoogleScholarGoogle Scholar | 21789547PubMed |
Ghavi Hossein-Zadeh N (2012b) Inbreeding effects on body weight traits of Iranian Moghani sheep. Archiv fur Tierzucht 55, 171–178.
Ghavi Hossein-Zadeh N (2014) Linear and threshold analysis of direct and maternal genetic effects for secondary sex ratio in Iranian buffaloes. Journal of Applied Genetics 55, 365–372.
| Linear and threshold analysis of direct and maternal genetic effects for secondary sex ratio in Iranian buffaloes.Crossref | GoogleScholarGoogle Scholar | 24648274PubMed |
Ghavi Hossein-Zadeh N, Madad M, Shadparvar AA, Kianzad D (2012) An observational analysis of secondary sex ratio, stillbirth and birth weight in Iranian buffaloes (Bubalus bubalis). Journal of Agricultural Science and Technology 14, 1477–1484.
Głażewska I, Jezierski T (2004) Pedigree analysis of Polish Arabian horses based on founder contributions. Livestock Production Science 90, 293–298.
| Pedigree analysis of Polish Arabian horses based on founder contributions.Crossref | GoogleScholarGoogle Scholar |
González-Recio O, López de Maturana E, Gutiérrez JPJ (2007) Inbreeding depression on female fertility and calving ease in Spanish dairy cattle. Journal of Dairy Science 90, 5744–5752.
| Inbreeding depression on female fertility and calving ease in Spanish dairy cattle.Crossref | GoogleScholarGoogle Scholar | 18024768PubMed |
Goyache F, Gutierrez JP, Fernandez I, Gomes E, Alvarez I, Díez J, Royo LJ (2003) Using pedigree information to monitor genetic variability of endangered population: the Xalda sheep breed of Asturias as an example. Journal of Animal Breeding and Genetics 120, 95–105.
| Using pedigree information to monitor genetic variability of endangered population: the Xalda sheep breed of Asturias as an example.Crossref | GoogleScholarGoogle Scholar |
Gutiérrez JP, Cervantes I, Molina A, Valera M, Goyache F (2008) Individual increase in inbreeding allows estimating realised effective sizes from pedigrees. Genetics Selection Evolution 40, 359–378.
| Individual increase in inbreeding allows estimating realised effective sizes from pedigrees.Crossref | GoogleScholarGoogle Scholar |
Harder B, Bennewitz J, Reinsch N, Mayer M, Kalm E (2005) Effect of missing sire information on genetic evaluation. Archiv fur Tierzucht 48, 219–232.
Hill WG (1979) A note on effective population size with overlapping generations. Genetics 92, 317–322.
Lacy RC (1989) Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalents. Zoo Biology 8, 111–123.
| Analysis of founder representation in pedigrees: founder equivalents and founder genome equivalents.Crossref | GoogleScholarGoogle Scholar |
Lacy RC (1995) Clarification of genetic terms and their use in the management of captive populations. Zoo Biology 14, 565–577.
| Clarification of genetic terms and their use in the management of captive populations.Crossref | GoogleScholarGoogle Scholar |
MacKinnon KM (2003) Analysis of inbreeding in a closed population of crossbred sheep. MSc Thesis, Virginia Polytechnic Institute and State University Blacksburg, Virginia, USA.
Maignel L, Boichard D, Verrier E (1996) Genetic variability of French dairy breeds estimated from pedigree information. Interbull Bulletin 14, 49–54.
Malécot G (1969) ‘The mathematics of heredity.’ (Freeman: San Francisco, CA)
Malhado CHM, Ramos AA, Carneiro PLS, Azevedo DMMR, Martins Filho R, Souza JC (2008) Improvement and population structure of Mediterranean water buffaloes raised in Brazil. Pesquisa Agropecuária Brasileira 215–220.
Malhado CHM, Malhado ACM, Carneiro PLS, Ramos AA, Ambrosini DP, Pala A (2012) Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis. Tropical Animal Health and Production 44, 1891–1897.
| Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis.Crossref | GoogleScholarGoogle Scholar |
Marcondes CR, Vozzi PA, Cunha BRN, Lobo RB, Araujo CV, Marques JRF (2010) Genetic variability in water buffalo from nucleus herd by pedigree analysis. Arquivo Brasileiro de Medicina Veterinária e Zootecnia 62, 706–711.
| Genetic variability in water buffalo from nucleus herd by pedigree analysis.Crossref | GoogleScholarGoogle Scholar |
Martínez RA, García D, Gallego JL, Onofre G, Pérez J, Cañón J (2008) Genetic variability in Colombian Creole cattle populations estimated by pedigree information. Journal of Animal Science 86, 545–552.
| Genetic variability in Colombian Creole cattle populations estimated by pedigree information.Crossref | GoogleScholarGoogle Scholar | 18073285PubMed |
Mc Parland S, Kearney JF, Rath M, Berry DP (2007) Inbreeding effects on milk production, calving performance, fertility, and conformation in Irish Holstein-Friesians. Journal of Dairy Science 90, 4411–4419.
| Inbreeding effects on milk production, calving performance, fertility, and conformation in Irish Holstein-Friesians.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXpslCjs7g%3D&md5=fc0d9104efd271084c90de6ef495a6baCAS | 17699061PubMed |
Miglior F, Burnside EB, Dekkers JC (1995) Nonadditive genetic effects and inbreeding depression for somatic cell counts of Holstein cattle. Journal of Dairy Science 78, 1168–1173.
| Nonadditive genetic effects and inbreeding depression for somatic cell counts of Holstein cattle.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK2MXmtVGru70%3D&md5=44c23b0c473c3c16d3b159b0d3437babCAS | 7622727PubMed |
Norberg E, Sorenson AC (2007) Inbreeding trend and inbreeding depression in the Danish populations of Texel, Shropshire and Oxford Down. Journal of Animal Science 85, 299–304.
| Inbreeding trend and inbreeding depression in the Danish populations of Texel, Shropshire and Oxford Down.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXht1emu7Y%3D&md5=af136943fbbcc476e7cc50a58005818fCAS | 17235016PubMed |
Rendo F, Iriondo M, Jugo BM, Mazon LI, Aguirre A, Vicario A, Estonba A (2004) Tracking diversity and differentiation in six sheep breeds from the North Iberian Peninsula through DNA variation. Small Ruminant Research 52, 195–202.
| Tracking diversity and differentiation in six sheep breeds from the North Iberian Peninsula through DNA variation.Crossref | GoogleScholarGoogle Scholar |
Sanders K, Bennewitz J, Kalm E (2006) Wrong and missing sire information affects genetic gain in the Angeln dairy cattle population. Journal of Dairy Science 89, 315–321.
| Wrong and missing sire information affects genetic gain in the Angeln dairy cattle population.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XisVSrug%3D%3D&md5=14115bc1cc4e2d37943b902a0e0128a9CAS | 16357295PubMed |
Santana ML, Aspilcueta-Borquis RR, Bignardi AB, Albuquerque LG, Tonhati H (2011) Population structure and effects of inbreeding on milk yield and quality of Murrah buffaloes. Journal of Dairy Science 94, 5204–5211.
| Population structure and effects of inbreeding on milk yield and quality of Murrah buffaloes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXht1eisb3K&md5=cce1506aadbd976ed65fa5173a7d1f41CAS | 21943770PubMed |
Sargolzaei M, Iwaisaki H, Colleau JJ (2006) CFC: A tool for monitoring genetic diversity. Proceedings of the 8th world congress on genetics applied to livestock production, CD-ROM Communication 27–28. Belo Horizonte, Brazil, 13–18 August 2006. (WCGALP)
Tavakolian J (2000) ‘An introduction to genetic resources of native farm animals.’ (Animal Science Research Institute: Karaj, Iran)
Valera M, Molina A, Gutierréz JP, Gómez J, Goyache F (2005) Pedigree analysis in the Andalusian horse: population structure, genetic variability and influence of the Carthusian strain. Livestock Production Science 95, 57–66.
| Pedigree analysis in the Andalusian horse: population structure, genetic variability and influence of the Carthusian strain.Crossref | GoogleScholarGoogle Scholar |
Vasconcellos BF, Tonhati H (1998) Inbreeding and its effects on some productive and reproductive traits in a Murrah buffalo herd. Journal of Animal Breeding and Genetics 115, 299–306.
Wall E, Brotherstone S, Kearney JF, Woolliams JA, 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.
| Impact of nonadditive genetic effects in the estimation of breeding values for fertility and correlated traits.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXmslWg&md5=c9b899516f66b1fbaae34ad80e24222fCAS | 15591402PubMed |
Woolliams JA, Mäntysaari EA (1995) Genetic contributions of Finnish Ayshire bulls over four generations. Animal Science 61, 177–187.
| Genetic contributions of Finnish Ayshire bulls over four generations.Crossref | GoogleScholarGoogle Scholar |
