Genetic diversity of Barbary lion based on genealogic analysis

Article Details: Received: 2018-09-10 | Accepted: 2018-10-17 | Available online: 2018-09-31https://doi.org/10.15414/afz.2018.21.03.113-118The aim of this study was to evaluate the state of genetic diversity in population of Barbary lion based on the genealogical analysis. Currently, this lion subspecies does not occur in the wild, and its population is considered to be critically endangered. The pedigree file consisted of 545 animals, while the reference population included 445 individuals. Alongside pedigree completeness, the parameters derived from common ancestor were used to analyse the state of genetic diversity in target population. The completeness of pedigree data had significantly decreasing tendency with increasing generations. The pedigree completeness index was the highest in the first generation (68 %). The average value of the inbreeding coefficient was very similar in the reference population and the pedigree file (F = 0.05). Across generations, the trend of inbreeding increase was positive mainly due to the long-term use of specific lines and families for mating. The relative high average relatedness among individuals (AR = 0.06) only reflected the individual increase in inbreeding (3.18 %). As expected the higher level of individual increase in inbreeding was found in the pedigree file (3.41 %). The effective population size at level 26.66 confirmed that the Barbary lion is critically endangered by the loss of diversity. Because of this, the future continuous monitoring of genetic diversity of this subspecies is necessary, especially for long-term conservation purposes.Keywords: Barbary lion, diversity, endangered species, pedigree analysisReferencesALDEN, P. R. et al. (1998) National Audubon Society Field Guide to African Wildlife. New York: Alfred A. Knopf, Inc.BLACK, S. A. (2009) Return of the royal Barbary lion. BBC NEWS [Online]. 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Pedigree Analysis of Slovak Pinzgau Breed

The aim of the study was to assess genetic variability in Slovak Pinzgau breed using pedigree analysis. The whole population consisted of 8311 individuals of that 2399 living animals (2373 cows and 26 sires) in the reference population. Pedigree completeness, parameters based on probability of identity by descent and gene origin was analysed. The mean inbreeding level in the reference population was low 0.57%, mean individual increase in inbreeding 0.25% and average relatedness 1.17%. A total 141 effective founders and 51 effective ancestors were found in the reference, resp. 257 effective founders and 103 effective ancestors in the whole population. The number of 21 effective ancestor explained 50% of diversity in the reference and 51 in the whole population. The results demonstrate need for better monitoring of population and can be implemented in preparation of the strategy for development of breed

Comparison of genetic diversity in dual-purpose and beef Pinzgau populations

The aim of the study was to evaluate the genetic diversity in Slovak dual-purpose (dairy) and beef Pinzgau cattle. Reference population consisted of 3425 living cows (of those 2501 dairy and 924 suckler cows) involved in animal recording. The average number of fully generations traced was 0.99 and 1.17 in dairy and suckler cows, respectively and the average complete generations equivalent was 2.78 in dairy population and 3.19 in beef population. Inbreeding coefficient was computed from three, five, seven and ten generations traced. The results of inbreeding analysis show increasing trend of inbreeding coefficient with increasing number of generations traced taken into account. The average inbreeding coefficient F5 was 0.3599% and 0.1112% in dairy and beef reference populations, respectively. The difference between inbreeding coefficient F3 and F10 was 0.0778% in dairy cows and 0.0537% in suckler cows. The difference between F7 and F10 values was minimal. Overall, inbreeding level in dairy population was higher than in beef population. The average increase in inbreeding was 0.2070% in dairy and 0.0402% in beef population. The effective number of founders, effective number of ancestors and effective number of founder genomes was 210; 82 and 63.49 in dairy population, respectively and 293; 95 and 60.62 in beef population, respectively. These results point out bottleneck effect occurance in given populations. Further population reduction can lead to serious inbreeding problems. Regular monitoring of genetic diversity including inbreeding trends is necessary to use this information in population management

ECONOMIC SUSTAINABILITY OF THE LOCAL DUAL-PURPOSE CATTLE

Base economic characteristics (total revenues, total costs, profit and profitability ratio) of the Slovak Pinzgau breed were calculated in this study. Under the actual production and economic conditions of the breed, production system is operated with loss (-457 € per cow and per year) and with negative profitability ratio (-20%). Optimisation of the production parameters on the level defined in the breed standard (5,200 kg milk per cow and year, 92% for conception rate of cows, 404 days of calving interval and 550 g in daily gain of reared heifers) and improved udder health traits (clinical mastitis incidence and somatic cells score) was of positive impact on the total revenues (+34%), on the effective utilisation of costs (+105%) and balanced profit of dairy systems. Next to the positive profitability of the system, higher quality and security of dairy milk products should be mentioned there. Moreover, direct subsidies as an important factor of positive economic result of dairy cattle systems has to be pointed as well. Subsidies should be provided to compensate the real biological limitation of the local breed farmed in marginal areas. However, improvement of the production parameters of the Slovak Pinzgau breed is recommended with the same attention to reach the economic sustainability of dairy production system. To reach economic sustainability of the breed from practical point of view, the farmer activity should be aimed especially to the enhanced herd management

Dedivosť sfarbenia slovenského pinzgauského dobytka

The objective of the work was analysis of chestnut coat colour inheritance of Slovak Pinzgau cattle in accordance to age and farming system. In 304 cows of breeding groups P0,P1,P2 and R3 born between 2000 to 2010 from four breeding herds(4 agricultural cooperatives and JSC: PD Smrečany – farm Veterná Poruba, PD Spišské Bystré – farm Kvetnica, Agria Liptovský Ondrej JSC – farm Liptovská Porúbka, PD LČV Čimhová) was measured intensity of coat colour. For objective measurement of coat colour the handheld Minolta Chromameter CM-2600d was applied using the CIE L*a*b* colour space. The instrument recorded the values L*, a* and b*. The L* value shows the lightness of the colour, a* value indicates the red/green, while the b* value indicates the yellow/blue chromaticity of the colour. The values C* (Chroma/saturation) and h (hue) were derived from the values a* and b*. Average lightness in observed animals was 22.60; average of the red chroma was 8.84 resp. 13.32 for the yellow chroma. Saturation of coat colour was 16.19 resp. 0.97 for hue.Cieľom práce bola analýza dedivosti gaštanovo hnedého plášťového sfarbenia pinzgauských kráv na Slovensku vo vzťahu k veku a systému chovu. Celkovo bolo hodnotených 304 kráv plemenných skupín P0, P1, P2 a R3 narodených v rozpätí rokov 2000 až 2010, pochádzajúcich zo 4 šľachtiteľských chovov (PD Smrečany - farma Veterná Poruba, PD Spišské Bystré - farma Kvetnica, Agria Liptovský Ondrej a.s. - farma Liptovská Porúbka, PD LČV Čimhová), u ktorých bola meraná intenzita hnedého sfarbenia. Pre objektívne meranie intenzity sfarbenia bol použitý prenosný chromameter Minolta CM-2600d so zisťovaním farebného priestoru na škále CIEL*a*b*. Zariadenie zaznamenávalo hodnoty L*, a*, b*. L* zodpovedá jasu sfarbenia a* poukazuje na mieru sfarbenia na škále od červenej k zelenej a b* naopak na škále od žltej k modrej. Taktiež bola meraná saturácia (C) a odtieň (h). Priemerné zistené hodnoty boli (s.d. v zátvorke): 22,60 (4,62) pre jas, 8,84 (2,42) pre intenzitu červenej a 13,32 (3,75) pre intenzitu žltej farby. Saturácia sfarbenia bola 16,19 (3,62). Hodnota odtieňa bola 0,97 (0,17)

Inbreeding and genetic diversity loss of four cattle beef breeds in Slovakia

Received: 2016-02-23   |   Accepted: 2016-04-21   |   Available online: 2016-05-30dx.doi.org/10.15414/afz.2016.19.02.59-63The aim of the paper was to evaluate trends in inbreeding and loss of genetic diversity in four beef cattle breeds (Blonde d´Aquitaine-BA, Charolais-CH, Limousine-LI, Simmental-SM). The highest ratio of inbred animals was found in the SM breed (63.6 %) and the lowest in the LI (14.1 %). The highest average inbreeding intensity we found in the SM, the lowest in the BA. The amount of genetic diversity in the reference population accounting for diversity loss due to genetic drift and unequal founder contributions was the highest in the SM (6.2 %), following the BA (3.5 %), LI (1.1 %) and CH (0.9 %). The proportion of genetic diversity lost due to genetic drift was higher in BA, CH, LI than the loss of genetic diversity due to unequal founder contribution.Keywords: beef cattle, pedigree analysis, inbreeding, genetic diversityReferences Boichard, D., Maignel,L. and Verrier. E. (1997) The value of using probabilities of gene origin to measure genetic variability in a population. Genet. Sel. Evol., vol.29, no. 5, pp.5-23. doi:http://dx.doi.org/10.1186/1297-9686-29-1-5Cabalero, A. and Toro, M.A. (2000) Interrelations between effective population size and other tools for management of conserved populations. Genet. Res., vol. 75, no. 3, pp.331-343. doi:http://dx.doi.org/10.1017/S0016672399004449Gutiérrez, J.P. and Goyache, F. ( 2005)  Note on ENDOG: a computer program for analysis pedigree information. J. Anim.Breed. Genet., vol.122. pp.172-176.Gutiérrez, J.P., Goyache, F. and Cervantes, F. ( 2009) Endog v 4.6. A computer program for monitoring genetic variability of populations using pedigree information. User guide. Madrid: Universidad Complutense de Madrid. 45 p..Kadlečík, O. and Pavlík,I. (2012) Genealogical analysis in small populations: The case of four Slovak beef cattle breeds. Slovak J. Anim. Sci., vol.  45, no. 4. pp. 111-117.Kasarda. R. and Kadlečík. O. (2007) An economic impact of inbreeding in the purebred population of Pinzgau cattle in Slovakia on milk production traits. Czech J. Anim. Sci., vol. 52, no. 1, pp. 7-11.Krupa, E., Žáková, E. and Krupová, Z. (2015) Evaluation of inbreeding and genetic variability of five pig breeds in Czech Republic. Asian Australas. J.Anim. Sci.. vol. 28, no. 1, pp. 25-36. doi: http://dx.doi.org/10.5713/ajas.14.0251Lacy, R.C. (1989) Analysis of founder representation in pedigree: Founder equivalents and founder genome equivalents. Zool.Biol., vol. 8, no. 2, pp. 111-123. doi:http://dx.doi.org/10.1002/zoo.1430080203Lacy, R.C. (1995) Classification of genetic terms and their use in the management of captive populations. Zoo. Biol., vol. 14, no. 6, pp. 565-577. doi:http://dx.doi.org/10.1002/zoo.1430140609Melka, M.G. et al. (2013) Analyses of genetic diversity in five Canadian dairy breeds using pedigree data. J. Anim. Breed. Genet., vol. 130, pp. 476–486. doi:http://dx.doi.org/10.1111/jbg.12050McParland, S. et al. (2007) Inbreeding trends and pedigree analysis of Irish dairy and beef cattle populations. Journal of Animal Science, vol. 85, no. 2, pp.322-331. doi:http://dx.doi.org/10.2527/jas.2006-367Maignel, L., Boichard, D. and Verrier.E. (1996) Genetic variability of French dairy breeds estimated from pedigree information. Interbul Bulletin, vol. 14, pp.49-54.Meuwissen, T.H.E. and Luo,Z. (1992) Computing in breeding coefficients in large populations. Genet. Sel. Evol., vol. 24. pp. 305-313. doi:http://dx.doi.org/10.1186/1297-9686-24-4-305Pavlík.I, et al. (2014) Pedigree analysis of Thoroughbred horses in Slovakia. Acta fytotechnica et zootechnica, vol. 17, no. 4, pp. 122-126. doi:http://dx.doi.org/10.15414/afz.2014.17.04.122-126Stachowic, K. et al. (2011) Schenkel Rates of inbreeding and genetic diversity in Canadian Holstein and Jersey cattle. J. Dairy Sci., vol. 94, no.  10, pp. 5160–5175. doi: http://dx.doi.org/10.3168/jds.2010-3308ŠIDLOVÁ, V. et al. (2015) Genomic variability among cattle populations based on runs of homozygosity. Poljoprivreda, vol. 21. no. 1 (Supplement), pp. 44-47.Tang, G. Q. et al. (2013) Inbreeding and genetic Ddversity in three imported swine breeds in China using pedigree data Asian Australas. J. Anim.Sci., vol.26, no. 6, pp.755-765.  doi:http://dx.doi.org/10.5713/ajas.2012.12645Trakovická, A. et al.(2015) Impact of SNPs in candidate genes on economically important traits in Pinzgau cattle. Poljoprivreda. vol. 21, no. 1(Supplement), pp. 150-154. doi:http://dx.doi.org/10.18047/poljo.21.1.sup.3

Influence of Maximum Inbreeding Avoidance under BLUP EBV Selection on Pinzgau Population Diversity

Evaluated was effect of mating (random vs. maximum avoidance of inbreeding) under BLUP EBV selection strategy.  Existing population structure was under Monte Carlo stochastic simulation analyzed from the point to minimize increase of inbreeding. Maximum avoidance of inbreeding under BLUP selection resulted into comparable increase of inbreeding then random mating in average of 10 generation development. After 10 generations of simulation of mating strategy was observed ΔF= 6,51 % (2 sires), 5,20 % (3 sires), 3,22 % (4 sires) resp. 2,94 % (5 sires). With increased number of sires selected, decrease of inbreeding was observed. With use of 4, resp. 5 sires increase of inbreeding was comparable to random mating with phenotypic selection. For saving of genetic diversity and prevention of population loss is important to minimize increase of inbreeding in small populations. Classical approach was based on balancing ratio of sires and dams in mating program. Contrariwise in the most of commercial populations small number of sires was used with high mating ratio

SPATIAL STRUCTURE OF THE LIPIZZAN HORSE GENE POOL BASED ON MICROSATELLITE VARIATIONS ANALYSIS

The aim of this study was to determine the current state of genetic diversityand to assess the substructure and spatial structure at individual level based onanalysis of microsatellite variations within Lipizzan horse population. The genomicDNA samples were obtained from totally 418 horses, originating from Slovenian(357) and Slovak (61) studs. A set of 13 microsatellite markers (AHT4, AHT5,ASB2, HMS1, HMS2, HMS3, HMS6, HMS7, HTG10, HTG4, HTG6, HTG7, andVHL20) have been used for analysis of genetic variability. Across all microsatelliteloci the average number of alleles 6.65 and effective allele number at level 3.37were found. The obtained Shannon's information index (I=1.37) indicated highdegree within population genetic diversity. The prevalence of heterozygousgenotype in sample confirmed also the average value of observed heterozygosity(Ho=0.67) and FIS index (-0.026). The most of the genetic variation in sample wasconserved within individuals (95%) and the subdivision of horse populationsexplained only 4%. Similarly, the obtained pairwise values of FST index (0.02) andNei's genetic identity (0.90) reflected mainly common ancestors used in breedinghistory of both population. But the principal coordinate analysis showed thedivision of individuals into the two separate clusters according to the studs wherethey come from. The membership probability resulted from spatial structureanalysis suggested that the frequencies of alleles varied across the two regions thatindicated the evidence of strong distinction in relation to the current breeding statusof analysed populations and strategy of studs