Individual Increase In Inbreeding Research Articles

Pedigree analysis in the mhorr gazelle (Nanger dama mhorr): Genetic variability evolution of the captive population.

Breeding programs have an essential role in the recovery of threatened populations through optimal genetic management and mating strategies. The dama gazelle (Nanger dama) is a North African ungulate listed as critically endangered. The mhorr subspecies is extinct in the wild and currently survives thanks to the creation in 1971 of an ex situ breeding program. The aim of the present study was to assess the evolution of genetic variability in this mhorr gazelle captive population, as well as the mating strategy used in two reference populations studied (Almeria and Europe). The entire pedigree, with 2739 animals, was analyzed to measure demographic characters, pedigree completeness level, probability of gene origin, level of relatedness and genetic structure of the population. The population size has been progressively increasing, with up to 264 individuals alive in Europe at the time of the study. The average number of equivalent complete generations was 5.55. The effective number of founders and ancestors was both 3, and the founder genome equivalent was 1.99. The genetic contributions of the four main ancestors were unbalanced. The average values of inbreeding and average relatedness for the whole pedigree were, respectively, 28.34% and 50.14%. The effective population size was 8.7 by individual increase in inbreeding and 9.8 by individual increase in coancestry. F-statistics evidenced a very small level of population subdivision (F ST = 0.033370). The mating strategy used, based on the minimum coancestry of the individuals, has minimized the losses of genetic variability and helped to balance the genetic contributions between ancestors. The strategy also avoided large subdivisions within the population and the appearance of new bottlenecks. This study shows how pedigree analysis can both be used to determine the genetic variability of the population and to assess the influence of the mating strategy used in the breeding program on such variability.

100 Pedigree Effective Population Size Affects Genomic Prediction Accuracy in Katahdin Sheep

Abstract Katahdin sheep are a composite hair breed of medium-size, relatively prolific, with potential to exhibit resistance to gastrointestinal parasites. Recently, genomic predictions of breeding values were introduced in Katahdins. Prediction accuracy depends on the genetic variation present, and selection using genomically-enhanced breeding values may reduce diversity. We aimed to characterize the current genetic variability in Katahdins utilizing their extensive pedigree. The National Sheep Improvement Program provided the pedigree of 92,030 sheep born from 1984-2019. Two reference populations were defined for animals born between 2017-2019: all Katahdins (n = 23,494), and Katahdins with at least three generations of known Katahdin ancestry (n = 9,327). Using ENDOG and PopReport, effective population sizes (Ne) were estimated. We then considered the effect of Ne on the size of the genomic reference population needed to achieve certain levels of prediction accuracy. Weaning weight, a lowly heritable trait for this breed (h2 = 0.13), was evaluated. Based on individual increase in inbreeding, inbreeding coefficient of animal adjusted for equivalent complete generations, the estimated Ne for the full pedigree, reference 1, and reference 2 were 92, 104, and 87, respectively. When inbreeding coefficients were regressed or log-regressed on birth date and adjusted for generation interval, the Ne estimates were 53 and 49 for reference 1, and 76 and 67 for reference 2, respectively. For our average Ne = 75 with 3,960 effective chromosomal segments, the accuracy of prediction for weaning weight was estimated for genomic reference population sizes (N) of 10k, 15k, 20k, and 25k. Starting at N = 10k, the prediction accuracy was 0.58, and as N increased by 5k increments the accuracy increased to 0.65, 0.70, and 0.74. Conversely, with our smallest Ne = 49 with 2,548 effective chromosomal segments, the prediction accuracy was 0.64, 0.71, 0.75, and 0.78 for N = 10k, 15k, 20k, and 25k, respectively. Estimated Ne varied depending on the method utilized, and tended to be larger for reference 1 than 2. However, this was not the case for Ne based on regression. Inbreeding coefficients were greater in reference 2 than 1, and the generation interval was shorter in reference 2 (2.84 years) than in 1 (2.97 years). These combined differences led to larger Ne estimates for reference 2 than 1, reflecting the impact of different criteria used to obtain this statistic. The generally small, estimated Ne benefitted genomic prediction due to a greater shared number of effective chromosomal segments. Investing in larger genomic reference populations will only marginally increase prediction accuracy even for lowly heritable traits. Selection using genomically-enhanced breeding values will accelerate genetic gains, potentially reducing the Ne of Katahdins and thereby increasing prediction accuracy. Yet, long-term gains may be at risk due to the loss of genetic diversity.

Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs

BackgroundIn spite of the availability of single nucleotide polymorphism (SNP) array data, differentiation between observed homozygosity and that caused by mating between relatives (autozygosity) introduces major difficulties. Homozygosity estimators show large variation due to different causes, namely, Mendelian sampling, population structure, and differences among chromosomes. Therefore, the ascertainment of how inbreeding is reflected in the genome is still an issue. The aim of this research was to study the usefulness of genomic information for the assessment of genetic diversity in the highly endangered Gochu Asturcelta pig breed. Pedigree depth varied from 0 (founders) to 4 equivalent discrete generations (t). Four homozygosity parameters (runs of homozygosity, FROH; heterozygosity-rich regions, FHRR; Li and Horvitz’s, FLH; and Yang and colleague’s FYAN) were computed for each individual, adjusted for the variability in the base population (BP; six individuals) and further jackknifed over autosomes. Individual increases in homozygosity (depending on t) and increases in pairwise homozygosity (i.e., increase in the parents’ mean) were computed for each individual in the pedigree, and effective population size (Ne) was computed for five subpopulations (cohorts). Genealogical parameters (individual inbreeding, individual increase in inbreeding, and Ne) were used for comparisons.ResultsThe mean F was 0.120 ± 0.074 and the mean BP-adjusted homozygosity ranged from 0.099 ± 0.081 (FLH) to 0.152 ± 0.075 (FYAN). After jackknifing, the mean values were slightly lower. The increase in pairwise homozygosity tended to be twofold higher than the corresponding individual increase in homozygosity values. When compared with genealogical estimates, estimates of Ne obtained using FYAN tended to have low root-mean-squared errors. However, Ne estimates based on increases in pairwise homozygosity using both FROH and FHRR estimates of genomic inbreeding had lower root-mean-squared errors.ConclusionsParameters characterizing homozygosity may not accurately depict losses of variability in small populations in which breeding policy prohibits matings between close relatives. After BP adjustment, the performance of FROH and FHRR was highly consistent. Assuming that an increase in homozygosity depends only on pedigree depth can lead to underestimating it in populations with shallow pedigrees. An increase in pairwise homozygosity computed from either FROH or FHRR is a promising approach for characterizing autozygosity.

Assessment of population structure and genetic diversity of German Angora rabbit through pedigree analysis.

The main goals of this investigation were to i) assess the population structure and genetic diversity and ii) determine the efficiency of the ongoing breeding program in a closed flock of Angora rabbits through pedigree analysis. The pedigree records of 6,145 animals, born between 1996 to 2020 at NTRS, ICAR-CSWRI, Garsa were analyzed using ENDOG version 4.8 software package. The genealogical information, genetic conservation index and parameters based on gene origin probabilities were estimated. Analysis revealed that, 99.09% of the kits had both parents recorded in the whole dataset. The completeness levels for the whole pedigree were 99.12%, 97.12%, 90.66%, 82.49%, and 74.11% for the 1st, 2nd, 3rd, 4th, and 5th generations, respectively, reflecting well-maintained pedigree records. The maximum inbreeding, average inbreeding and relatedness were 36.96%, 8.07%, and 15.82%, respectively. The mean maximum, mean equivalent and mean completed generations were 10.28, 7.91, and 5.51 with 0.85%, 1.19%, and 1.85% increase in inbreeding, respectively. The effective population size estimated from maximum, equivalent and complete generations were 58.50, 27.05, and 42.08, respectively. Only 1.51% of total mating was highly inbred. The effective population size computed via the individual increase in inbreeding was 42.83. The effective numbers of founders (fe), ancestors (fa), founder genomes (fg) and non-founder genomes (fng) were 18, 16, 6.22, and 9.50, respectively. The fe/fa ratio was 1.12, indicating occasional bottlenecks had occurred in the population. The six most influential ancestors explained 50% of genes contributed to the gene pool. The average generation interval was 1.51 years and was longer for the sireoffspring pathway. The population lost 8% genetic diversity over time, however, considerable genetic variability still existed in the closed Angora population. This study provides important and practical insights to manage and maintain the genetic variability within the individual flock and the entire population.

Optimum contribution selection (OCS) analyses prompted successful conservation actions for Faroese Horse population

The Faroese horse, an endangered indigenous horse breed, is a part of the cultural and societal heritage of the Faroe Islands. Population history describes a severe bottleneck, prompting for quantification of the genetic diversity (level of inbreeding, probability of gene origin, effective population size) and assessment of sustainable conservation potential (Optimum Contribution Selection, OCS) of the Faroese horse population. The pedigree completeness (PCI) of the Faroese horse is adequate for a realistic estimation of the level of inbreeding (PCI5 = 0.96). In concordance with the known population history, the average inbreeding is exceptionally high; in the last cohort, it was equal to 26.8%. An estimate of the effective population size, based on individual increase in inbreeding and coancestry, accounting for the whole population history, was eight. OCS offers a tool to understand and control the increase in the average relationships in the population. Within a fixed number of matings, the repetitive use of stallions resulted in the lowest level of average relationships. Successful follow-up of mating schemes planned together with a holistic assessment of the suitability of an individual as a breeding candidate, will minimize the increase in inbreeding in future generations and maximize the possibility to increase the census size of the Faroese horse population.

Genetic diversity, viability and conservation value of the global captive population of the Moroccan Royal lions.

This study evaluates the diversity of the so-called ‘Moroccan Royal lions’ using genealogical information. Lions are no longer extant in North Africa, but the previous wild population was an important element of the now-recognised northern subspecies (Panthera leo leo) that ranged across West Africa, North Africa and the Middle East into India. The remaining captive population of ‘Moroccan Royal lions’ seems to be significantly endangered by the loss of diversity due to the effective population size decrease. The pedigree file of this captive lion population consisted of 454 individuals, while the reference population included 98 animals (47 males and 51 females). The completeness of the pedigree data significantly decreased with an increasing number of generations. The highest percentage of pedigree completeness (over 70%) was achieved in the first generation of the reference population. Pedigree-based parameters derived from the common ancestor and gene origin were used to estimate the state of diversity. In the reference population, the average inbreeding coefficient was 2.14%, while the individual increase in inbreeding over generations was 2.31%. Overall, the reference population showed lower average inbreeding and average relatedness compared with the pedigree file. The number of founders (47), the effective number of founders (24) and the effective number of ancestors (22) were estimated in the reference population. The effective population size of 14.02 individuals confirms the critically endangered status of the population and rapid loss of diversity in the future. Thus, continuous monitoring of the genetic diversity of the ‘Moroccan Royal lion’ group is required, especially for long-term conservation management purposes, as it would be an important captive group should further DNA studies establish an affinity to P. leo leo.

Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle.

Icelandic Cattle is the only dairy cattle breed native to Iceland. It currently numbers ca. 26000 breeding females. We used 50k genotypes of over 8000 Icelandic Cattle to estimate genomic and pedigree-based inbreeding and to detect selection signatures using the integrated haplotype score. We used 47 Icelandic bulls genotyped with a 770k SNP chip to estimate LD decay for comparison with other Nordic dairy cattle breeds. We detected ROHs on the autosomes and computed ROH-based autosomal inbreeding coefficients. Average inbreeding coefficients according to pedigree and ROHs were 0.0621 and 0.101. Effective population sizes for the years 2009-2017 according to pedigree, ROHs, genomic relationship matrix, excess of homozygosity and individual increase in inbreeding were 81, 65, 60, 58 and 92 respectively. We identified three regions and six candidate genes that showed a signature of selection according to the integrated haplotype score (P<0.05) on chromosomes 1, 16 and 23. The LD structure of Icelandic Cattle is shaped by a long period of isolation and a small founder population. The estimate of LD at distances closer than 0.3Mb is lower in Icelandic Cattle than in Danish Jersey, but is higher than in Danish Holstein and Red Nordic Dairy Cattle breeds. Our findings show that inbreeding rates in Icelandic Cattle currently are sustainable according to FAO guidelines, and our results do not indicate severe historical inbreeding.

Analysis of the Pedigree and Ancestors of the Cutting Population of the Quarter Horse Breed

The aim of this study was to evaluate the genetic diversity and to identify the most influential ancestors in the population of Brazilian Quarter Horses participating in cutting competitions. Data from 1,590 elite horses born between 1970 and 2015, which participated in cutting competitions between 1981 and 2018, were evaluated based on the pedigree file that contained 5,832 animals born since 1834. Evaluation of the quality of the pedigree data showed a mean number of known equivalent generations of 5.4 ± 1.5 and a mean generation interval of 11.7 ± 8.8 years. The inbreeding coefficient (1.98 ± 7.13%), relatedness coefficient (2.18 ± 0.01%), and individual increase in inbreeding (0.43 ± 0.01%) were low. The effective population size (Ne) was 136 animals. The probability of gene origin indicated effective numbers of founders, ancestors, and founder genomes of 255, 37, and 23 animals, respectively. The number of founders and ancestors was 1,852 and 899 animals, respectively, with 10, 50, and 100 ancestors explaining 39.2%, 67.9%, and 91.6%, respectively, of the genetic diversity of the population. The five most influential ancestors were Doc Bar, Peppy San Badger, Freckles Playboy, Poco Lena, and High Brow Cat, accumulating 30.7% of the marginal genetic contributions of the population. Few ancestors were responsible for the genetic diversity, resulting in the narrowing of the initial genetic base. Breeders depend on a small group of ancestors, which could be corrected by increasing the number of breeding animals and by directed mating using ancestors of different origins.

Genetic Variability and Population Structure in the Sardinian Anglo-Arab Horse.

Simple SummaryIt is known that animal populations might be affected by bottleneck phenomena, which reduce genetic variability, increase inbreeding and consequentially reduce evolutionary potential. Pedigree completeness, genetic variability and population structure were analyzed in the Sardinian Anglo-Arab horse (SAA) breed, and the analyzed results were compared with three other Italian horse populations: Maremmano, Murgese and Bardigiano (reported in bibliography). In addition, the maternal lineage was analyzed through mitochondrial DNA in order to preserve and improve the breed. The estimated parameters suggest that the SAA breed is well managed, especially when considering the female lineage because it still conserves a high number of founder mares. The role of breeding programs in the conservation of genetic diversity is essential. In fact, a breeding program might lead to fast genetic progress; however, it might also lead to a high level of inbreeding and consequently to a genetic drift. Analyzing both these parameters and the additional use of mitochondrial DNA might be an effective tool not only to verify the success of a breeding program, but also to be helpful for breeders on planning effective mating programs.The Sardinian Anglo Arab (SAA) is a famous horse breed in Italy, with a significant historical background in the island of Sardinia. The aim of the study is to perform an evaluation of genetic variability in SAA using pedigree and mitochondrial data. In the current population, pedigree completeness was observed to be close to 100%, while the inbreeding coefficient and the average relatedness were lower than 3%. The ratio of effective founders/numbers of ancestors was 3.68 for the whole pedigree. The effective population size (Ne) computed by an individual increase in inbreeding (Ne_1) was 456.86, the Ne on equivalent generations (Ne_2) was 184.75, and this value slightly increased to 209.31 when computed by log-regression on equivalent generations (Ne_3). These results suggest the presence of crossbreeding and bottleneck phenomena, and they were compared with other Italian horses (reported in bibliography) to present the SAA among the Italian horse breeds scenario. Furthermore, the noteworthy mitochondrial variability reflects the use of a considerable number of founder mares; the contribution of L lineage was very important, probably because of the re-colonization from the Iberian Peninsula after the Last Glacial Maximum.

Genetic diversity and population structure of Boer and Nubian goats in Mexico

In Mexico, since 2010 the Asociación Mexicana de Criadores de Ganado Caprino de Registro has been undertaking annual national genetic evaluations for the Boer and Nubian goat breeds. Mexican pedigree goat farmers are concerned with maintaining a reasonable high genetic diversity and a low level of inbreeding without loss of genetic gain. This study aimed to assess the genetic diversity and to describe the population structure of the Boer and Nubian goat breeds in Mexico using pedigree analyses to support the development of strategies for breeding programs. Herdbook information collected between 1994–2017 for Boer and from 1991 to 2017 for Nubian were utilized. The information included pedigree records on 18,947 animals for Boer (141 flocks) and 13,744 animals for Nubian (99 flocks). The effective number of founders ( f e ) were 504 and 203, and the effective number of ancestors ( f a ) were 253 and 88, for Boer and Nubian, respectively. The ratio f a / f e was 0.50 for Boer and 0.43 for Nubian, indicating the existence of population bottlenecks. The average inbreeding and relatedness coefficients were 1.02 and 0.28 % for Boer and, 1.39 and 1.04 % for Nubian. The number of most influential ancestors that explained 50 % of the genetic diversity in the population were 109 for Boer and 38 for Nubian. The average generation interval estimated through the four gametic paths was 3.27 ± 0.03 yr for Boer and 4.63 ± 0.06 yr for Nubian. Realized effective population size, computed from the individual increase in inbreeding, was 61.3 ± 24.5 for Boer and 69.3 ± 22.8 for Nubian (kids born from 2013 to 2017 were considered as the reference population for both breeds). The average equivalent completed generations, as a measure of pedigree completeness, were 2.02 for Boer and 2.88 for Nubian. The pedigree completeness index increased over time for both breeds. The results revealed the loss of genetic diversity and the presence of genetic bottlenecks for both populations. The study of the genetic diversity on these populations must continue to prevent the decrease in genetic progress and genetic variability. Additionally, a mating policy that simultaneously allows low levels of inbreeding, high levels of genetic diversity and maximum genetic progress, must be designed.

Inbreeding, effective population size, and coancestry in the Latxa dairy sheep breed

Traditionally, breeding programs have estimated and managed inbreeding based on pedigree information. The availability of genomic marker panels has made possible new alternatives to achieve more precise estimates, for example in case of missing pedigree. The objective of the present study was to assess and compare, different estimation methods (pedigree-based methodologies, single SNP-based approach (homozygosity) and runs of homozygosity-based method) to analyze the evolution of genetic diversity measured as inbreeding or as coancestry of 3 selected populations of Latxa dairy sheep (Latxa Cara Rubia and Latxa Cara Negra from Euskadi and Navarre). Genomic data came from 972 artificial insemination rams genotyped with the Illumina OvineSNP50 BeadChip (Illumina Inc., San Diego, CA) whose genealogy consisted of 4,484 animals. Inbreeding estimates based on molecular data were more similar between them than compared with those based on pedigree information. However, the SNP-based approach estimations of effective population size differed more, reflecting the sensitivity of effective population size to small changes in the evolution of inbreeding. The 2 Latxa Cara Negra populations showed increases of inbreeding rates with time and effective population sizes between 64 and 103 animals, depending on breed and methodology used. The Latxa Cara Rubia population did not show an increase in inbreeding rate, mainly due to semen importation from the related French population of Manech Tête Rousse. The effective size estimates based on coancestry increase show a higher variability and they are more sensitive to the source of information and the data structure considered. Realized effective population size based on individual increase in inbreeding were in agreement with the previous estimates. Coancestry evolution analysis based on DNA information showed an increase on coancestry during the last 10 yr in all breeds, as a consequence of the selection process. Moreover, the increase on coancestry between Latxa Cara Rubia and Manech Tête Rousse was more noticeable between than within each of those breeds.

Demographic assessment of the Dalmatian dog \u2013 effective population size, linkage disequilibrium and inbreeding coefficients

BackgroundThe calculation of demographic measures is a useful tool for evaluating the genomic architecture of dog breeds and enables ranking dog breeds in terms of genetic diversity. To achieve this for the German Dalmatian dog population, 307 purebred animals of this breed were genotyped on the Illumina Canine high density BeadChip. The analysis of pedigree-based inbreeding was performed based on a pedigree with 25,761 dogs including the genotyped dogs. ResultsThe effective population size derived from squared correlation coefficients between SNP alleles (r2) was 69. The maximum value of r2 was 0.56, resulting in a 50% decay value of 0.28 at a marker distance of 37.5 kb. The effective population size calculated from pedigree data using individual increase in inbreeding over equivalent generations was 116. The pedigree inbreeding coefficient was 0.026. The genomic inbreeding coefficient based on the length of runs of homozygosity (ROH) was calculated for seven length categories of ROHs, and ranged from 0.08 to 0.28. The fixation coefficients FIS_PED and FIS_GENO were at 0.017 and 0.004. PANTHER statistical overrepresentation analysis of genes located in consensus ROHs revealed highly underrepresented biological processes in 50% of the investigated dogs. One of those is the 0.28 fold enriched “immune response”, which might be associated to the high prevalence of allergic dermatitis in the breed. Candidate genes for congenital sensorineural deafness (CCSD, a highly prevalent disease in the Dalmatian) were discovered in consensus ROHs.ConclusionsThe fast decay of r2 and the moderate inbreeding coefficients indicate that the German Dalmatian dog population is rather diverse. Pedigree- and genomic-based inbreeding measures were highly correlated and therefore prove good reliability for the given population. Analyses of consensus ROHs with genes coding for deafness and other breed-defining traits, such as hyperuricosuria, indicate that those ROH became fixed in the Dalmatian population about 500 years ago. In case of the Dalmatian dog, a ROH of 40 SNPs length is enough to investigate signatures of selection (e.g. the ROH with the fixed hyperuricosuria mutation) as far back as the breed formation point approximately 500 years ago.

Genetic Variability and Management in Nero di Parma Swine Breed to Preserve Local Diversity

Simple SummaryThe Nero di Parma is an Italian pig breed with a peculiar breed history. It originates from a native breed called “Nera Parmigiana”, which, in the beginning of the 20th century, was crossed with highly productive breeds, causing the extinction of the original type in the 1970s. During the 1990s a growing interest for organic products and outdoor farming brought the attention back to the local type and a breed recovery project started to reestablish the original breed. The aim of the study was to investigate the genetic diversity of the Nero di Parma breed to provide further insights for breed conservation and to propose breeding strategies.Nero di Parma is an endangered swine breed reared in the North of Italy which nowadays counts 1603 alive pigs. The aims of this study were (i) to explore the genetic diversity of the breed at pedigree level to determine the actual genetic structure, (ii) to evaluate the effectiveness of the breeding recovery project and (iii) to potentially propose breeding strategies for the coming generations. The pedigree dataset contained 14,485 animals and was used to estimate demographic and genetic parameters. The mean equivalent complete generations was equal to 6.47 in the whole population, and it reached a mean value of 7.94 in the live animals, highlighting the quality of the available data. Average inbreeding was 0.28 in the total population, whereas it reached 0.31 in the alive animals and it decreased to 0.27 if only breeding animals were considered. The rate of inbreeding based on the individual increase in inbreeding was equal to 7%. This study showed the effectiveness of the recovery project of the breed. Nevertheless, we found that inbreeding and genetic diversity have reached alarming levels, therefore novel breeding strategies must be applied to ensure long-term survival of this breed.

Analysis of founders and performance test effects on an autochthonous horse population through pedigree analysis: structure, genetic variability and inbreeding

The Maremmano is an autochthonous Italian horse breed, which probably descended from the native horses of the Etruscans (VI century B.C.); the Studbook was acknowledged in 1980, and it includes 12 368 horses born from that year up to 2015. The aim of this study was to evaluate the effect of the selection program on the genetic variability of the Maremmano population; the analysis was performed using both the ‘Endog v 4.8’ program available at http://webs.ucm.es/info/prodanim/html/JP_Web.htm and in-house software on official pedigree data. Four Reference Populations were considered, and the most important one was the population of the 12 368 Maremmano horses officially registered in the National Studbook. The pedigree completeness of this population was very good because it was more than 90% at the third parental generation and more than 70% at the fifth generation; the pedigree traced back to a maximum of 10.50 generations with an average of 3.30 complete generations and 5.70 equivalent complete generations. The average generation interval was 10.65±4.72 years, with stallions used for longer periods than mares. The intervals ranged from 10.15±4.45 (mother–daughter) to 10.99±4.93 (father–daughter). The effective number of founders (fe) was 74 and the effective number of ancestors (fa) was 30 so that the ratio fe/fa was 2.47. The founder genome equivalents (fg) was 13.72 with a ratio fg/fe equal to 0.18. The mean of the genetic conservation index was 5.55±3.37, and it ranged from 0.81 to 21.32. The average inbreeding coefficient was 2.94%, with an increase of 0.1%/year, and the average relatedness coefficient was 5.52%. The effective population size (Ne) computed by an individual increase in inbreeding was 68.1±13.00; the Ne on equivalent generations was 42.00, and this value slightly increased to 42.20 when computed by Log regression on equivalent generations. The analysis confirmed the presence of seven traditional male lines. The percentage of Thoroughbred blood in the foals born in 2015 was 20.30% and has increased 0.21%/year since 1980; in particular, it increased more than twice (0.51%/year) until 1993 and afterwards slightly fluctuated. The pedigree analysis confirmed the completeness of genealogical information and the traditional importance that breeders gave to the male lines; although the genetic diversity of Maremmano seemed to be not endangered by the selection program, some effects on the population structure were found and a more scientific approach to genetic conservation should be incorporated in the selection plans.

Pedigree structure of American bison (Bison bison) population

An effective realization of breeding programs in zoos is strongly determined by completeness of animal pedigree information. The knowledge of pedigree structure allows to maintain optimal genetic variability of a given population. The aim of this study was to estimate the parameters describing the pedigree structure of American bison housed in zoos in the context of further management of the population. Finally, 4269 American bison were analysed (1883 males, 2217 females, and 169 with unknown sex). The registered animals were born between years 1874 and 2013. The following pedigree parameters were estimated: number of fully traced generations, number of complete generations equivalent, index of pedigree completeness, individual inbreeding coefficients, increase of inbreeding for each individual, effective population size, and genetic diversity. The maximum number of fully traced generations was 3 (the mean value is 0.693). The mean inbreeding coefficient for the population studied was 3.26%, whereas individual increase in inbreeding ranged from 0 to 25.12%. Although the pedigree parameters (including the inbreeding level) in the American bison obtained in the present study seem to be acceptable (from the perspective of other wild animal populations), they can be over/underestimated due to incomplete pedigree.

Genetic diversity and effect of inbreeding on litter size of the Romanov sheep

The objective of the present study was to describe the population structure and quantify the effect of inbreeding on litter size in Romanov sheep in the Czech Republic. The analysis was based on the pedigree information of 26,447 animals. The numbers of generations were 19, with average equivalent known generations of 6.41. The effective numbers of founders and ancestors contributing to the current genetic pool were, respectively, 92.96 and 47.41 respectively. The average inbreeding coefficients were 5.5% and the average inbreeding rate was 1%. The corresponding estimates of effective population size were 48.28 and 45.64, based on an individual increase in inbreeding or coancestry, respectively. Classical inbreeding coefficient and two kinds of new inbreeding coefficient were used to quantify the effect of inbreeding. The effect of all tested kind of inbreeding on litter size was statistically significant, but very small (around −0.05 lambs per change of 1% in inbreeding). Statistical difference measured by ΔAICc was not-significant. These statistics suggest that the genetic variability has decreased and inbreeding depression is occurred, and without changes in breeding strategy the genetic variability might continue to decline.

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

The genealogical information of a small captive population of the cobia fish was evaluated to assess the genetic variability and the status of inbreeding through pedigree analyses. Pedigree data (n = 238) for 6 years (2010–2016) were analyzed and offspring born from 2015 to 2016 were considered as reference population to compute the population genetic parameters based on the gene origin probabilities using the program ENDOG (version 4.8). Molecular marker based FAP (Family Assignment Program, version 3.6) was used for parentage assignment. The pedigree completeness was 68% for the parent, 29% for the grandparents and 7% for the great-grandparents generations with a mean equivalent to complete generations of 2.66. Mean generation interval, computed from four pathways, was 2.38 years. Considering the reference population into account the coefficients of average inbreeding and average relatedness were computed as 9.6% and 9.9%, respectively. The mean values of individual increase in inbreeding (rate of inbreeding) were 6.5% and 2.5% for the reference population and for the whole pedigree, respectively. Realized effective population size was computed from the individual increase in inbreeding and from the individual increase in coancestry as 7.7 and 10.6, respectively. The effective numbers of founders (fe), ancestors (fa), founder genomes (fg) and non-founder genomes (nfe) for the reference population were computed as 6, 6, 3.8 and 11.1, respectively. About 85% of total genetic variation was explained by 7 most influential ancestors, with a maximum individual contribution of 33.5%. Though the genetic bottleneck, as expressed by the fe/fa ratio as 1.0, was not evident, the loss of genetic variability caused by genetic drift was evident by fg/fe ratio which was 0.64 for the reference population. The analysis revealed the evidences on loss of genetic diversity with a very critical effective population size. Recommendations were made to improve the genetic variability in the herd. The present study signifies the importance of maintaining the pedigree and can help in carrying out similar studies on captive-bred fish species where small populations are inevitable.

Genetic structure of a small closed population of the New Zealand white rabbit through pedigree analyses

The genetic structure of a small population of New Zealand White rabbits maintained at the Sheep Breeding and Research Station, Sandynallah, The Nilgiris, India, was evaluated through pedigree analyses. Data on pedigree information (n=2503) for 18 yr (1995-2012) were used for the study. Pedigree analysis and the estimates of population genetic parameters based on the gene origin probabilities were performed. The analysis revealed that the mean values of generation interval, coefficients of inbreeding and equivalent inbreeding were 1.49 yr, 13.23 and 17.59%, respectively. The proportion of population inbred was 100%. The estimated mean values of average relatedness and individual increase in inbreeding were 22.73 and 3.00%, respectively. The percentage increase in inbreeding over generations was 1.94, 3.06 and 3.98 estimated through maximum generations, equivalent generations and complete generations, respectively. The number of ancestors contributing the majority of 50% genes (f&lt;sub&gt;a50&lt;/sub&gt;) to the gene pool of reference population was only 4, which might have led to reduction in genetic variability and increased the amount of inbreeding. The extent of genetic bottleneck assessed by calculating the effective number of founders (f&lt;sub&gt;e&lt;/sub&gt;) and the effective number of ancestors (f&lt;sub&gt;a&lt;/sub&gt;), as expressed by the f&lt;sub&gt;e&lt;/sub&gt;/f&lt;sub&gt;a&lt;/sub&gt; ratio was 1.1, which is indicative of the absence of stringent bottlenecks. Up to 5th generation, 71.29% pedigree was complete, reflecting the well maintained pedigree records. The maximum known generations were 15, with an average of 7.9, and the average equivalent generations traced were 5.6, indicating a fairly good depth in pedigree. The realized effective population size was 14.93, which is very critical, and with the increasing trend of inbreeding the situation has been assessed as likely to become worse in future. The proportion of animals with the genetic conservation index (GCI) greater than 9 was 39.10%, which can be used as a scale to use such animals with higher GCI to maintain balanced contribution from the founders. From the study, it was evident that the herd was completely inbred, with a very high inbreeding coefficient, and the effective population size was critical. Recommendations were made to reduce the probability of deleterious effects of inbreeding and to improve genetic variability in the herd. The present study can help in carrying out similar studies to meet the demand for animal protein in developing countries.

Genetic diversity of Barbary lion based on genealogic analysis

Genetic diversity of Barbary lion based on genealogic analysis

The most important sires in Pinzgau population

Received: 2016-05-24 | Accepted: 2016-08-02 | Available online: 2017-06-20 http://dx.doi.org/10.15414/afz.2017.20.01.28-30 The aim of this study was to calculate the inbreeding coefficients of the most used sires in population of Slovak Pinzgau and summarize milk production of theirs daughters as main criterion in present in selection of sires besides pedigree based level of inbreeding of future progeny. The runs of homozygosity (ROH) greater than 4 Mb cover on average 1.9 % of genome, ROH ˃ 8 Mb cover 1.3 % and ROH ˃ 16 Mb cover 0.4. Obtained results were compared to genealogical pedigree analysis; the observed inbreeding was higher than that expected based on pedigree data (0.16 %), despite the fact that ROH > 16 Mb representing recent inbreeding approximately three generations ago. The average milk performance of evaluated Slovak Pinzgau cows has been 5259 kg of milk, 3.6 % of protein and 3.85 % of fat. These results are important for the management of the Pinzgau population in Slovakia due to more precise values of inbreeding obtained as well as knowledge about the ancient inbreeding which was not possible to estimate from the pedigree data. Keywords: inbreeding, milk performance, runs of homozygosity, Slovak Pinzgau cattle References ALBRECHTSEN A., NIELSEN F.C. and NIELSEN R. (2010) Ascertainment biases in SNP chips affect measures of population divergence. Molecular Biology and Evolution , vol. 27, pp. 2534-2547. doi: http://dx.doi.org/10.1093/molbev/msq148 BJELLAND, D.W. et al. (2013) Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. Journal of Dairy Science , vol. 96, pp. 4697-4706. doi: http://dx.doi.org/10.3168/jds.2012-6435 CHARLESWORTH, D. and WILLIS, J. (2009) The genetics of inbreeding depression. Nature Reviews Genetics , vol. 10, pp. 783-796. doi: http://dx.doi.org/10.1038/nrg2664 FERENCAKOVIC, M. et al. (2011) Runs of Homozygosity Reveal Genomewide Autozygosity in the Austrian Fleckvieh Cattle. Agriculturae Conspectus Scientificus , vol. 76, no. 4, pp. 325-328. GURGUL, A., et al. (2016) The use of runs of homozygosity for estimation of recent inbreeding in Holstein cattle. Journal of Applied Genetics , vol. 57, pp. 1-4. doi: http://dx.doi.org/10.1007/s13353-016-0337-6 GUTIERREZ, J.P. et al. (2008) Individual increase in inbreeding allows estimating realised effective sizes from pedigrees. Genetics Selection Evolution , vol. 40, pp. 359-378. doi: http://dx.doi.org/10.1186/1297-9686-40-4-359 MARRAS, G. et al. (2015) Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Animal Genetics , vol. 46, no. 2, pp. 110-121. doi: http://dx.doi.org/10.1111/age.12259 PAVLIK, I. et al. (2014) Joint genealogical analysis as a tool for diversity evaluation in Pinzgau cattle populations. Archive Tierz ucht, vol. 57, no. 14, pp. 1-12. doi: http://dx.doi.org/10.7482/0003-9438-57-014 PURCELL, S. et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. The American Journal of Human Genetics , vol. 81, pp. 559-575. doi: http://dx.doi.org/10.1086/519795 SAS Institute Inc: SAS/STAT Software. (2011) Cary NC: SAS Institute Inc: Version 9.3. THE BREEDING SERVICES OF THE SLOVAK REPUBLIC. (2014) Results of dairy herd milk recording in Slovak Republic for control year 2013-2014. [Online]. Available at http://pssr.sk/org/publ/2014/hd/rocenka/ml_13_14/rocenka/Mliekova_rocenka_2014.pdf . [Accessed: 1st March 2017].