Monitoring of genetic diversity in autochthonous Czech poultry breeds assessed by genealogical data

https://doi.org/10.17221/80/2020-CJASCitation:Vostrý L., Vostrá-Vydrová H., Moravčíková N., Hofmanová B., Rychtářová J., Machová K., Brzáková M., Kasarda R. (2020): Monitoring of genetic diversity in autochthonous Czech poultry breeds assessed by genealogical data. Czech J. Anim. Sci., 65: 224-231.
supplementary materialdownload PDF

Czech local poultry breeds face high risks of extinction. Because these populations are closed, they are more likely to lose genetic diversity. The aim of this analysis was to determine the loss of genetic diversity in three Czech autochthonous poultry breeds. Pedigree data from a total of 1 932 Czech Gold Speckled Hens, 325 Czech White Geese and 111 Czech Crested Geese registered in studbooks between 2000 and 2018 were evaluated. Data were analysed to determine the major factors that affect the genetic variability of these breeds. The average numbers of equivalent complete generations ranged from 2.53 to 4.82. The effective numbers of founders were from 29 to 59, representing from 43% to 62% of the total number of founders. The effective number of ancestors was estimated in the range of 21 to 41. The average inbreeding coefficient and relatedness coefficient (in parentheses) for the reference populations were 2.0% (6.5%), 1.9% (4.9%) and 2.1% (9.3%), respectively. The results showed that the effective population size derived from the rate of inbreeding ranged from 46 to 108 and if derived from the rate of coancestry it ranged from 35 to 74. With regard to these results, the analysed breeds showed a high probability of allele loss and consequent loss of genetic diversity.

References:
Boichard D, Maignel L, Verrier E. The value of using probabilities of gene origin to measure genetic variability in a population. Genet Sel Evol. 1997 Jan;29(1):5-23. https://doi.org/10.1186/1297-9686-29-1-5
 
Caballero A, Toro MA. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genet Res. 2000 Jun;75(3):331-43. https://doi.org/10.1017/S0016672399004449
 
Cassell BG, Adamec V, Pearson RE. Effect of incomplete pedigrees on estimates of inbreeding and inbreeding depression for days to first service and summit milk yield in Holsteins and Jerseys. J Dairy Sci. 2003 Sep;86(9):2967-76. https://doi.org/10.3168/jds.S0022-0302(03)73894-6
 
Cervantes I, Goyache F, Molina A, Valera M, Gutierrez JP. Estimation of effective population size from the rate of coancestry in pedigreed populations. J Anim Breed Genet. 2011 Feb;128(1):56-63. https://doi.org/10.1111/j.1439-0388.2010.00881.x
 
Cortes O, Eusebi P, Dunner S, Sevane N, Canon J. Comparison of diversity parameters from SNP, microsatellites and pedigree records in the Lidia cattle breed. Livest Sci. 2019 Jan;219:80-5. https://doi.org/10.1016/j.livsci.2018.11.006
 
Curik I, Ferencakovic M, Solkner J. Genomic dissection of inbreeding depression: A gate to new opportunities. Rev Bras Zootec. 2017 Sep;46(9):773-82. https://doi.org/10.1590/s1806-92902017000900010
 
Doekes HP, Curik I, Nagy I, Farkas J, Kover G, Windig JJ. Revised calculation of Kalinowski’s ancestral and new inbreeding coefficients. Diversity. 2020 Apr;12(4):155.  https://doi.org/10.3390/d12040155
 
Falconer DS, Mackay TFC. Introduction to quantitative genetics. 4th ed. Harlow: Pearson, Prentice Hall; 2009. 464 p.
 
FAO – Food and Agriculture Organization. Secondary guidelines for development of national farm animal genetic resources management plans: Animal recording for medium input production environment. Rome: FAO; 1998.
 
Figueredo JS, Cruz JF, Sousa LS, Teixeira NMR, Carneiro PLS, Brito ND, Pinheiro RGS, Lacerda KSO, Mottin VD. Genetic diversity and population structure estimation of Brazilian Somali sheep from pedigree data. Small Rumin Res. 2019 Oct;179:64-9. https://doi.org/10.1016/j.smallrumres.2019.09.010
 
Gholizadeh M. Population structure of Mazandaran native fowls using pedigree analysis. Trop Anim Health Prod. 2017 Mar;49(3):561-7. https://doi.org/10.1007/s11250-017-1228-5
 
Goleman M, Balicki I, Radko A, Jakubczak A, Fornal A. Genetic diversity of the Polish Hunting Dog population based on pedigree analyses and molecular studies. Livest Sci. 2019 Nov;229:114-7. https://doi.org/10.1016/j.livsci.2019.09.017
 
Graczyk M, Andres K, Kapkowska E, Szwaczkowski T. Pedigree analyses of the Zatorska goose population. Czech J Anim Sci. 2015 Nov;60(11):513-20. https://doi.org/10.17221/8560-CJAS
 
Grilz-Seger G, Druml T, Neuditschko M, Dobretsberger M, Horna M, Brem G. High-resolution population structure and runs of homozygosity reveal the genetic architecture of complex traits in the Lipizzan horse. BMC Genomics. 2019 Mar;20:174. https://doi.org/10.1186/s12864-019-5564-x
 
Gutierrez JP, Cervantes I, Molina A, Valera M, Goyache F. Individual increase in inbreeding allows estimating effective sizes from pedigrees. Genet Sel Evol. 2008 Jun;40:359-78. https://doi.org/10.1186/1297-9686-40-4-359
 
Hofmannova M, Pribyl J, Krupa E, Pesek P. Estimation of inbreeding effect on conception in Czech Holstein. Czech J Anim Sci. 2019 Jul;64(7):309-16. https://doi.org/10.17221/154/2018-CJAS
 
Hodges J. Conservation of genes and culture: Historical and contemporary issues. Poult Sci. 2006 Feb;85(2):200-9. https://doi.org/10.1093/ps/85.2.200
 
Kalinowski ST, Hedrick PW, Miller PS. Inbreeding depression in the Speke’s gazelle captive breeding program. Conserv Biol. 2000 Oct;14(5):1375-84. https://doi.org/10.1046/j.1523-1739.2000.98209.x
 
Krupa E, Zakova E, Krupova Z. Evaluation of inbreeding and genetic variability of five pig breeds in Czech Republic. Asian Australas J Anim Sci. 2015 Jan;28(1):25-36. https://doi.org/10.5713/ajas.14.0251
 
Lacy RC. Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivalents. Zoo Biol. 1989 Jan;8(2):111-23. https://doi.org/10.1002/zoo.1430080203
 
Lacy RC. Clarification of genetic terms and their use in the management of captive populations. Zoo Biol. 1995 Nov;14(6):565-77. https://doi.org/10.1002/zoo.1430140609
 
Landi V, Lasagna E, Ceccobelli S, Martinez A, Santos-Silva F, Vega-Pla JL, Panella F, Allain D, Palhiere I, Murawski M, Dunner S, Da Gama LT, Barba C, Delgado JV, Sarti FM. An historical and biogeographical assessment of European Merino sheep breeds by microsatellite markers. Small Rumin Res. 2019 Aug;177:76-81. https://doi.org/10.1016/j.smallrumres.2019.06.018
 
Lutaaya E, Misztal I, Bertrand JK, Mabry JW. Inbreeding in populations with incomplete pedigrees. J Anim Breed Genet. 1999 Dec;116(6):475-80. https://doi.org/10.1046/j.1439-0388.1999.00210.x
 
MacCluer JW, Boyce AJ, Dyke B, Weitkamp LR, Pfennig DW, Parsons CJ. Inbreeding and pedigree structure in standardbred horses. J Hered. 1983 Nov;74(6):394-9. https://doi.org/10.1093/oxfordjournals.jhered.a109824
 
Malecot G. Les mathématiques de l’hérédité [The mathematics of heredity]. Paris: Barnéoud frères; 1948. 63 p. French.
 
Marquez GC, Siegel PB, Lewis RM. Genetic diversity and population structure in lines of chickens divergently selected for high and low 8-week body weight. Poult Sci. 2010 Dec;89(12):2580-8. https://doi.org/10.3382/ps.2010-01034
 
Moravcikova N, Kasarda R, Vosty L, Krupova Z, Krupa E, Lehocká K, Olsanska B, Trakovicka A, Nadasky R, Zidek R, Belej L, Golian J. Analysis of selection signatures in the beef cattle genome. Czech J Anim Sci. 2019 Dec;64(12):491-503. https://doi.org/10.17221/226/2019-CJAS
 
Nandolo W, Meszaros G, Banda LJ, Gondwe TN, Lamuno D, Mulindwa HA, Nakimbugwe HN, Wurzinger M, Utsunomiya YT, Woodward-Greene MJ, Liu M, Liu G, Van Tassell CP, Curik I, Rosen BD, Solkner J. Timing and Extent of Inbreeding in African Goats. Front Genet. 2019 Jun;10:537. https://doi.org/10.3389/fgene.2019.00537
 
Nei M. Molecular evolutionary genetic. New York: Columbia University Press; 1987. 512 p.
 
Pham MH, Tran XH, Berthouly-Salazar C, Tixier-Boichard M, Chen CF, Lee YP. Monitoring of genetic diversity in Taiwan conserved chickens assessed by pedigree and molecular data. Livest Sci Feb. 2016;184:85-91. https://doi.org/10.1016/j.livsci.2015.12.013
 
Vostra-Vydrova H, Vostry L, Hofmanova B, Krupa E, Vesela Z, Schmidova J. Genetic diversity within and gene flow between three draught horse breeds using genealogical information. Czech J Anim Sci. 2016a Oct;61(10):462-72. https://doi.org/10.17221/91/2015-CJAS
 
Vostra-Vydrova H, Vostry L, Hofmanova B, Krupa E, Zavadilova L. Pedigree analysis of the endangered Old Kladruber horse population. Lives Sci. 2016b Mar;185:17-23. https://doi.org/10.1016/j.livsci.2016.01.001
 
Vostra-Vydrova H, Vostry L, Hofmanova B, Moravcikova N, Vesela Z, Vrtkova I, Novotna A, Kasarda R. Genetic diversity and admixture in three native draught horse breeds assessed using microsatellite markers. Czech J Anim Sci. 2018 Mar;63(3):85-93. https://doi.org/10.17221/51/2017-CJAS
 
Vostry L, Milerski M, Schmidova J, Vostra-Vydrova H. Genetic diversity and effect of inbreeding on litter size of the Romanov sheep. Small Rumin Res. 2018 Nov;168:25-31. https://doi.org/10.1016/j.smallrumres.2018.09.004
 
Woelders H, Zuidberg CA, Hiemstra SJ. Animal genetic resources conservation in the Netherlands and Europe: Poultry perspective. Poult Sci. 2006 Feb;85(2):216-22. https://doi.org/10.1093/ps/85.2.216
 
Wright S. Coefficients of inbreeding and relationship. Am Nat. 1922;56:330-8. https://doi.org/10.1086/279872
 
Wright S. The genetical structure of populations. Ann Eugen. 1949;15:323-54. https://doi.org/10.1111/j.1469-1809.1949.tb02451.x
 
Zanetti E, De Marchi M, Dalvit C, Cassandro M. Genetic characterization of local Italian breeds of chickens undergoing in situ conservation. Poult Sci. 2010 Mar;89(3):420-7. https://doi.org/10.3382/ps.2009-00324
 
supplementary materialdownload PDF

© 2020 Czech Academy of Agricultural Sciences