Population Dynamics and Genetic Diversity in Bharat Merino Sheep

Genetic variability of a small captive population of the cobia (Rachycentron canadum) through pedigree analyses

The Martina Franca (MF) donkey, an ancient native breed of Apulia, was mostly famous for mule production. The breed was at serious risk of extinction in the 1980s following the decrease in demand for draft animals because they were increasingly replaced by agricultural machinery. Much has been done in the last few decades to safeguard the existing donkey breeds, but the situation remains critical. Successful implementation of conservation measures includes an evaluation of the present degree of breed endangerment, so the aim of this work was to analyze the demographic and genetic parameters of this breed to suggest effective conservation strategies. With a current breed register counting less than 500 recorded animals, the pedigree data set included 1,658 MF donkeys born between 1929 and 2006. Analyses were carried out on the whole data set as well as on a smaller one consisting of 422 living animals. Demographic and genetic variability parameters were evaluated using the ENDOG (v4.6) software. The pedigree completeness level was evaluated as well as the generation length, which was calculated for each of the 4 gametic pathways. This information was obtained from animal birth date records together with those of their fathers and mothers. The effective number of founders (f(e)), the effective number of ancestors (f(a)), the founder genome (f(g)), individual inbreeding (F), average relatedness (AR), and the rate of inbreeding per generation were analyzed to describe the genetic variability of the population. Because pedigree depth and completeness were appropriate, especially regarding the current population, the parameters defining genetic variability, namely, f(e), f(a), f(g), F, and AR, could be reliably estimated. Analysis of these parameters highlighted the endangerment status of the MF donkey. Our special concern was with the increased percentage of males and females exhibiting increased AR values. Moreover, the effective size of the current population, 48.08, is slightly less than the range of the minimum effective size, and the rates of inbreeding per generation found in the current MF population exceed the maximum recommended level of 1%. Such a scenario heightens concerns over the endangered status of the MF breed and calls for proper conservation measures and breeding strategies, such as selecting individuals for mating when relationships are below 12.5%.

Genetic variability and population structure based on pedigree information for Muzaffarnagari sheep in India

Genomic selection has been applied in dairy cattle breeding over the last decade. Using genomic information may speed up genetic gain as breeding values can be predicted reasonably accurately directly after birth. However, genetic diversity may decrease if the inbreeding rate per generation increases and the effective population size decreases. Despite many positive qualities of the Finnish Ayrshire, for example, high average protein yield and fertility, over time the breed has lost its place as the most common dairy breed in Finland. Thus, maintaining the genetic variability of the breed is becoming more important. The aim of our research was to estimate the impact of genomic selection on inbreeding rate and effective population size using both pedigree and genomic data. The genomic data included 46,914 imputed single nucleotide polymorphism (SNP) variants from 75,038 individuals, and the pedigree data included 2,770,025 individuals. All animals in the data were born between 2000 and 2020. Genomic inbreeding coefficients were estimated as the proportion of SNPs in runs of homozygosity (ROH) out of the total number of SNPs. The inbreeding rate was estimated by regressing the mean genomic inbreeding coefficients on birth years. Effective population size was then estimated based on the inbreeding rate. Additionally, effective population size was estimated from the mean increase in individual inbreeding using pedigree data. Introduction of genomic selection was assumed to have taken place gradually; years 2012-2014 were treated as a transition period from the traditional phenotype-based breeding value estimation to genomic-based estimation. The median length of the identified homozygous segments was 5.5Mbp, and a slight increase in the proportion of segments over 10Mbp was observed after 2010. The inbreeding rate decreased from 2000 to 2011 and subsequently increased slightly. The pedigree- and genomic-based estimates of inbreeding rate were similar to each other. The estimates of effective population size based on the regression method were very sensitive to the number of years considered; thus, the estimates were not very reliable. The effective population size estimated from the mean increase in individual inbreeding reached its highest value of 160 in 2011 and decreased to 150 after that. In addition, the generation interval in the sire path has decreased from 5.5 years to 3.5 years after genomic selection was implemented. Based on our results, after the implementation of genomic selection, the proportion of long ROH stretches has increased, the generation interval in the sire path has decreased, the inbreeding rate has increased and the effective population size has decreased. However, the effective population size is still at a good level, allowing for an efficient selection scheme in the Finnish Ayrshire breed.

Community genomics: a community-wide perspective on within-species genetic diversity.

Rates of inbreeding and genetic diversity in Canadian Holstein and Jersey cattle

The present study aimed to elucidate the population structure and genetic diversity along with the estimation of genealogical parameters in Vrindavani cattle using pedigree data. The study was based on pedigree data on 12,718 animals, spread across multiple generations during a 52-year period (between 1971 and 2023). The pedigree data was used to estimate different population genealogical parameters including the generation interval; pedigree completeness; rate and level of inbreeding; effective population size; and parameters characterizing the probabilities of gene origin. The ENDOG program was used for estimation of different parameters while using population after 2010as reference cohort. The results revealed the maximum number of generations (MG) to be 13, while the numbers of completed (CG) and equivalent generations (EqG) were 3.23 and 1.95, respectively. The mean generation interval for the population was 6.9years. The average inbreeding coefficient of animals in the whole and reference population was 1.11 and 3.44%, respectively; with 0.68% rate of inbreeding per generation. The average additive relationship among all the animals and those in the reference population was 1.16 and 5.49%, respectively. The average effective population sizes for the maximum, equivalent, and complete generations were 115.56, 56.42, and 46.02, respectively. The effective population size on the basis of regression and log-regression on birth date was 77.40 and 71.24, respectively. The probabilities of gene origin were estimated by the effective number of founders (fe) and ancestors (fa), which was 115 and 78, respectively. The fe/fa ratio in the reference population was 1.20, indicating that occasional bottlenecks may have occurred in the population. The analysis revealed a loss of 5.3% of total heterozygosity as compared to base population, though significant variability exists in the latest generations. The results revealed that considerable genetic variability exists within the population that may be exploited through appropriate breed improvement programs targeting various economic traits.

Simple SummaryThe main aim of modern breeding programs in dairy cows is to improve productivity, functional and health traits. The use of only a few top sires leads to more efficient milk production, but also it could lead to a decline in the gene pool, smaller effective population size and an increase of inbreeding. Deleterious effects of inbreeding in dairy cattle may reduce the benefits of the genetic gains. Due to this fact, it is important to monitor the genetic diversity in dairy cattle breeds. In this study, pedigree data were used to show the losses of genetic variability and its association with the heavy use of imported US Brown Swiss bulls and semen in the German Brown population. Strategies to decrease rate of inbreeding through sires with less relationships to the most important ancestors should be considered in future breeding strategies.Increase of inbreeding and loss of genetic diversity have large impact on farm animal genetic resources. Therefore, the aims of the present study were to analyse measures of genetic diversity as well as recent and ancestral inbreeding using pedigree data of the German Brown population, and to identify causes for loss of genetic diversity. The reference population included 922,333 German Brown animals born from 1990 to 2014. Pedigree depth and completeness reached an average number of complete equivalent generations of 6.24. Estimated effective population size for the German Brown reference population was about 112 with a declining trend from 141 to 95 for the birth years. Individual inbreeding coefficients increased from 0.013 to 0.036. Effective number of founders, ancestors and founder genomes of 63.6, 36.23 and 20.34 indicated unequal contributions to the reference population. Thirteen ancestors explained 50% of the genetic diversity. Higher breed proportions of US Brown Swiss were associated with higher levels of individual inbreeding. Ancestral inbreeding coefficients, which are indicative for exposure of ancestors to identical-by-descent alleles, increased with birth years but recent individual inbreeding was higher than ancestral inbreeding. Given the increase of inbreeding and decline of effective population size, measures to decrease rate of inbreeding and increase effective population size through employment of a larger number of sires are advisable.

The amount of genetic diversity in a finite biological population mostly depends on the interactions among evolutionary forces and the effective population size (Ne) as well as the time since population establishment. Because the Ne estimation helps to explore population demographic history, and allows one to predict the behavior of genetic diversity through time, Ne is a key parameter for the genetic management of small and isolated populations. Here, we explored an Ne-based approach using a bighorn sheep population on Tiburon Island, Mexico (TI) as a model. We estimated the current (Ncrnt) and ancestral stable (Nstbl) inbreeding effective population sizes as well as summary statistics to assess genetic diversity and the demographic scenarios that could explain such diversity. Then, we evaluated the feasibility of using TI as a source population for reintroduction programs. We also included data from other bighorn sheep and artiodactyl populations in the analysis to compare their inbreeding effective size estimates. The TI population showed high levels of genetic diversity with respect to other managed populations. However, our analysis suggested that TI has been under a genetic bottleneck, indicating that using individuals from this population as the only source for reintroduction could lead to a severe genetic diversity reduction. Analyses of the published data did not show a strict correlation between HE and Ncrnt estimates. Moreover, we detected that ancient anthropogenic and climatic pressures affected all studied populations. We conclude that the estimation of Ncrnt and Nstbl are informative genetic diversity estimators and should be used in addition to summary statistics for conservation and population management planning.

The present study conducted on an organised herd of Sahiwal cattle to elucidate the population structure parameter based on seven decades of genealogical information. The genealogical data (N = 4164) spanning 1949 to 2023 maintained at ICAR-National Dairy Research Institute, Karnal, India was considered with the aim to evaluate depth and accuracy of pedigree, population parameter and genetic diversity in different breeding schemes for whole population and pertinent reference cohort. The animal born from 1979 to 2009 grouped as reference 1 and from 2010 to 2023 as reference 2 cohort. The comprehensiveness of the whole population, reference 1 and reference 2 was over 50% up to the fourth, third and sixth generations respectively. The average relatedness and inbreeding coefficient were 5.92% and 2.69% for whole population, 5.44% and 1.96% for reference 1 and 6.98% and 3.85% for reference 2 respectively. The effective population size varied from 32.31 to 145.51 in the study. The average generation interval varies from 9.2 years in reference 1 to 8.2 years in whole pedigree and 6.6 years in reference 2 under study. The ratio (fe/fa) of effective number of founders (fe) and ancestors (fa) were 1.67, 1.59 and 1.90 for the whole, reference 1 and reference 2 respectively. The estimate for fg/fa ratio indicated that 54% of ancestral genetic diversity is retained in the current generation. Thus, present study provides critical insights to maintain effective population size, rate and level of inbreeding with contribution of founders in current population for optimum genetic diversity and improving breeding efficiency in planning future breeding programs.

Inbreeding is a critical issue in both conservation and animal breeding, as it can severely impact survival, reproductive success and genetic diversity (GD) in domestic species. The Brown Swiss cattle were introduced in South America around a century ago; however, the breeding scheme–derived consequences have been neglected by breeders for numerous generations. The present research aimed to elucidate the population evolution, inbreeding and GD in introduced South American Brown Swiss cattle using genealogical databases. The study was based on official registered records from 8686 animals across multiple generations (until 2023). Different estimates related to population structure, including pedigree completeness, inbreeding rate (F), effective population size (Ne) and generation interval (GI), among others, were evaluated. Moreover, the characterisation of the probabilities of gene origin (effective number of founders [fe] and ancestors [fa]) and the GD loss were assessed. The results revealed that in the last period, GMax was 12.33, while the GCom and GEqu were 2.37 and 5.43, respectively. The mean GI was 7.11 years, and the mean F of 1.27% in the historical and the most recent populations was 5.60 and 2.78, respectively. The F increased between 0.10% and 0.50% per chronological period, showing an increasing tendency of the inbreeding values throughout time. The average Ne‐census, Ne‐ ΔFp and Ne‐GEqu were 339.50, 143.80 and 95.40, respectively. Thus, a declining tendency of the effective population size was observed over time. The probabilities of gene‐origin–derived traits were 55 and 32 for fe and fa, respectively. The fe/fa ratio in the population was 1.72, indicating that occasional bottlenecks may have occurred in this breed. The GD analysis revealed a loss of 3.35% of total heterozygosity over time, though significant variability exists among chronological periods. In conclusion, this study revealed that considerable GD loss exists within the Brown Swiss cattle population, which needs better management mainly due to the relatively low founder effect and the low number of animals for maintaining a moderate reservoir of population diversity. Finally, these results emphasise the significance of overseeing GD and reducing inbreeding impacts. Successful breeding programmes are vital to improve conservation strategies and long‐term sustainable practices in South American Brown Swiss cattle.

Received: 2016-02-23  |  Accepted: 2016-04-21  |  Available online: 2016-05-30 dx.doi.org/10.15414/afz.2016.19.02.59-63 The 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 diversity References 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/10.1186/1297-9686-29-1-5 Cabalero, 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/S0016672399004449 Gutiérrez, 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.14.0251 Lacy, 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.1430080203 Lacy, 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.1430140609 Melka, 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.12050 McParland, 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.2006-367 Maignel, 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/10.1186/1297-9686-24-4-305 Pavlík.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.2014.17.04.122-126 Stachowic, 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.2010-3308 ŠIDLOVÁ, 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.2012.12645 Trakovická, 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.35

Submitted 2020-06-26 | Accepted 2020-08-18 | Available 2020-12-01 https://doi.org/10.15414/afz.2020.23.mi-fpap.52-57 In this study, inbreeding and effective population size of the Latvian gene conservation cattle breeds Latvian Brown (LB) and Latvian Blue (LZ) were analysed. The study was based on the pedigree data of 319 LB and 712 LZ cows that were alive at the time of data selection. The inbreeding level in LB and LZ has been increasing during the last decade and at the end of the year 2019, it was 2.61% and 5.20% for LB and LZ, respectively. The average increase of inbreeding from 2010 to 2019 was 1.80% for LB and 2.26% for LZ. The proportions of inbred animals with an inbreeding level greater than 10% were 0.60% and 2.14% in LB and LZ, respectively. Effective population size based on the rate of inbreeding decreased and was close or within the minimum range of recommended effective population size. The current study demonstrates that the inbreeding has increased, and the effective population size decreased in both populations. Therefore, the breeding organizations have to monitor and control the rate of inbreeding in LB and LZ populations over time. Keywords: inbreeding, Latvian Brown, Latvian Blue, native breed References Addo, S., Schäler, J., Hinrichs, D. and Thaller, G. E. (2017). Genetic diversity and ancestral history of the German Angler and the Red-and-White dual-purpose cattle breeds assessed through pedigree analysis. Agricultural Sciences, 8, 1033-1047. https://doi.org/10.4236/as.2017.89075 Doekes, H. P., Veerkamp, R. F., Bijma, P., de Jong, G., Hiemstra, S. J. and Windig, J. J. (2019). Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle. Genetics Selection Evolution, 51(1), 54. https://doi.org/10.1186/s12711-019-0497-z FAO. ©2019. Domestic Animal Diversity Information System (DAD-IS). Retrieved May 2, 2020 from http://www.fao.org/dad-is. GrÄ«slis, Z. (2006). Blue cows in Vidzeme. Jelgava. BÅ SA “Zilā govs”, 1–36. In Latvian. GrÄ«slis, Z. and Å imkevica, D. (2018). Latvian Blue selection. BÅ SA “Zilā govs”, Jelgava, 1–43. In Latvian. GrÄ«slis, Z., Markey, L. and Zutere, R. (2005). The inbreeding analysis in Latvian Blue cow population. Proceedings of the 11th Baltic animal breeding and genetics conference, Lithuania, 65–69. Groeneveld, E., Westhuizen, B.v.d., Maiwashe, A., Voordewind, F. and Ferraz, J. B. S. (2009). POPREP: a generic report for population management. Genetics and Molecular Research, 8(3), 1158–1178. https://doi.org/10.4238/vol8-3gmr648 Jonkus, D., Paura, L. and Cielava, L. (2020). Longevity and milk production efficiency of Latvian local breeds during last decades. Agronomy Research, 18(S2), 1316–1322. https://doi.org/10.15159/ar.20.064 LDC. (2019). Latvian brown cow conservation program from 2019 and nearest future. Retrieved May 26, 2020 from https://www.ldc.gov.lv/upload/doc/doc20.pdf. In Latvian Mäki-Tanila, A., Fernandez, J., Toro, M. and Meuwissen, T. (2010) Assessment and management or genetic variation. In Mäki-Tanila, A. et al. (eds.) Local cattle breeds in Europe. Development of policies and strategies for self-sustaining breeds. The Netherlands: Wageningen Academic Publishers (pp. 98–119) Mc Parland, S., Kearney, F. and Berry, D. P. (2009). Purging of inbreeding depression within the Irish Holstein-Friesian population. Genetics Selection Evolution, 41, 16. https://doi.org/10.1186/1297-9686-41-16 Mc Parland, S., Kearney, J. F., Rath, M. and Berry, D. P. (2007). Inbreeding effects on milk production, calving performance, fertility, and conformation in Irish Holstein-Friesians. Journal of Dairy Science, 90(9), 4411–4419. https://doi.org/10.3168/jds.2007-0227 Oldenbroek, K. and Van der Waaij, L. (2015). Animal Breeding and Genetics for BSc students. Centre for Genetic Resources and Animal Breeding and Genomics Group, Wageningen University and Research Centre, the Netherlands. Retrieved May 26, 2020 from https://wiki.groenkennisnet.nl/display/TAB/ Sørensen, A. C., Sørensen, M. K. and Berg, P. (2005). Inbreeding in Danish dairy cattle breeds. Journal of Dairy Science, 88(5), 1865–1872. https://doi.org/10.3168/jds.S0022-0302(05)72861-7 Zutere, R., GrÄ«slis, Z. and Sjakste, T. 2006. Breeding programs in Latvian livestock. Proceedings of the 12th Baltic animal breeding conference. Jurmala, Latvia, 6–13.   Â

The amount of genetic variability at neutral marker loci is expected to decrease, and the degree of genetic differentiation among populations to increase, as a negative function of effective population size. We assessed the patterns of genetic variability and differentiation at seven microsatellite loci in the common frog (Rana temporaria) in a hierarchical sampling scheme involving three regions (208-885 km apart), three subregions within regions and nine populations (5-20 km apart) within subregions, and related the variability and differentiation estimates to variation in local population size estimates. Genetic variability within local populations decreased significantly with increasing latitude, as well as with decreasing population size and regional site occupancy (proportion of censured localities occupied). The positive relationship between population size and genetic variability estimates was evident also when the effect of latitude (cf. colonization history) was accounted for. Significant genetic differentiation was found at all hierarchical levels, and the degree of population differentiation tended to increase with increasing latitude. Isolation by distance was evident especially at the regional sampling level, and its strength increased significantly towards the north in concordance with decreasing census and marker-based neighbourhood size estimates. These results are in line with the conjecture that the influence of current demographic factors can override the influence of historical factors on species population genetic structure. Further, the observed reductions in genetic variability and increased degree of population differentiation towards the north are in line with theoretical and empirical treatments suggesting that effective population sizes decline towards the periphery of a species' range.

Genetic diversity of Barbary lion based on genealogic analysis