Evaluation of genetic variation in the international Brown Swiss population

The international Brown Swiss cattle population pedigree was studied to measure genetic variations and to identify the most influential animals. Twenty-two countries provided pedigree information on 71 497 Brown Swiss bulls used for artificial insemination (AI). The total number of animals with the pedigree is 181 094. The mean inbreeding coefficient for the pedigree population was 0.77%. There was, in most cases, an increase in the mean inbreeding coefficient, with the highest value at 2.89% during the last 5-year period (2000 to 2004). The mean average relatedness for the pedigree population was 1.1%. The effective population size in 2004 was 204. There was notable variation between average generation intervals for the four parental pathways. The longest average generation interval, at 8.73 years, was observed in the sire–son pathway. The average generation interval for the whole population was 6.53 years. Most genetically influential individuals were sires. The highest contributing founder was a sire with a 3.22% contribution, and the highest contributing founder dam made a contribution of 1.75%. The effective number of founders and the effective number of ancestors were 141 and 88, respectively. The study showed that genetic variation within the pedigree population has been decreasing over recent years. Increasing the number of AI bulls with a low individual coefficient of inbreeding could help to maintain a good level of genetic variation in the Brown Swiss population.     

Potential bias in inbreeding depression estimates when using pedigree relationships to assess the degree of homozygosity for loci under selection

A potential bias in estimation of inbreeding depression when using pedigree relationships to assess the degree of homozygosity for loci under selection is indicated. A comparison of inbreeding coefficients based on either pedigree or genotypic frequencies indicated that, as a result of selection, the inbreeding coefficient based on pedigree might not correspond with the random drift of allelic frequencies. Apparent differences in average levels of both inbreeding coefficients were obtained depending on the genetic model (additive versus dominance, initial allelic frequencies, heritability) and the selection system assumed (no versus mass selection). In the absence of selection, allelic frequencies within a small population change over generations due to random drift, and the pedigree-based inbreeding coefficient gives a proper assessment of the accompanying probability of increased homozygosity within a replicate by indicating the variance of allelic frequencies over replicates. With selection, in addition to random drift, directional change in allelic frequencies is not accounted for by the pedigree-based inbreeding coefficient. This result implies that estimation of inbreeding depression for traits under either direct or indirect selection, estimated by a regression of performance on pedigree-based coefficients, should be carefully interpreted.Deceased     

A study of contemporary levels and temporal trends in inbreeding in the Tangier Island, Virginia, population using pedigree data and isonymy

In this study we describe inbreeding in a large pedigree from Tangier Island, Virginia, in which we compare two commonly used methods to estimate inbreeding in humans: pedigree and isonymy (identical surnames of spouses). Genealogical data on 3,512 individuals dating back to 1722 were used. Using the pedigree method, we determined an average inbreeding coefficient (F) of 0.00873 for the community as a whole, and 0.018 for inbred individuals. Analysis of temporal trends showed that inbreeding began around 1800 and peaked at 0.0109 in 1824-1849 and 1875-1899. Thereafter, inbreeding steadily declined to 0.00565 in 1975-1997. Analysis of pedigree structure complexity over time showed that close consanguinity contributes to inbreeding in the earlier cohorts, and remote consanguinity accounts for much of the inbreeding in the later cohorts. The number of common ancestors increases over time, as does the number of paths connecting inbred individuals to these common ancestors. Inbreeding estimates based on the isonymy approach yielded a 2.2-fold higher value of F (0.01945) compared to the pedigree method. Total isonymy estimates over 25-year cohorts overestimated inbreeding values from pedigree data between 1. 5-8-fold. We speculate that the overestimation is probably due to the inability of our data to satisfy the method's assumption of monophyletic origin of each surname. In conclusion, inbreeding in the Tangier Island population is consistent with the isolated nature of its population, and temporal trends reflect patterns in emigration and a breakdown in isolation over time.     

Marital and migration structure and inbreeding in the Adyg population]

Endogamy and gametic indices for both Russian and Adyg populations living in the Adyg autonomous region of Krasnodar district were determined on different levels of territorial units: village, rural, community (a group of villagers) and rural region. Inbreeding coefficient was estimated for Adyg population and its structure analysed: a random component contributes mostly to the inbreeding coefficient (Fst = 0.00991), non-random component of the inbreeding coefficient being Fis = 0.010009, which testifies to negative marital assortativity among Adygs. Local inbreeding "a" and decline in the inbreeding "phi" coefficient at a distance from 0 to 500 km were calculated using the Malecot's formula: the coefficient "a" was found to be 0.00397, which is in good accordance with the Fst.     

Pedigree analysis and inbreeding effects over morphological traits in Campolina horse population

Genetic improvement, without control of inbreeding, can go to loss of genetic variability, reducing the potential for genetic gains in the domestic populations. The aim of this study was to analyze the population structure and the inbreeding depression in Campolina horses. Phenotype information from 43 465 individuals was analyzed, data provided by the Campolina Breeders Association. A pedigree file containing 107 951 horses was used to connected the phenotyped individuals. The inbreeding coefficient was performed by use of the diagonal of the relationship matrix and the genealogical parameters were computed using proper softwares. The effective population size was estimated based on the rate of inbreeding and census information, and the stratification of the population was verified by the average relationship coefficient between animals born in different regions of Brazil. The effects of inbreeding on morphological traits were made by the use of inbreeding coefficient as a covariate in the model of random regression. The inbreeding coefficient increased from 1990 on, impacting effective population size and, consequently, shrinking genetic variability. The paternal inbreeding was greater than maternal, which may be attributed to the preference for inbred animals in reproduction. The average genetic relationship coefficient of animals born in different states was lower than individuals born within the same state. The increase in the inbreeding coefficient was negatively associated with all studied traits, showing the importance to avoid genetic losses in the long term. Although results do not indicate a severe narrowing of the population until the present date, the average relationship coefficient shows signs of increase, which could cause a drastic reduction in genetic variability if inbred mating is not successfully controlled in the Campolina horse population.     

利用高密度SNP标记分析中国荷斯坦牛基因组近交

畜禽育种中传统上利用系谱信息评估群体近交程度?近年来随着高通量单核苷酸多态(single nucleotide polymorphism, SNP)检测成本降低,使利用基因组信息分析真实的基因组近交程度成为可能?本研究利用牛54 K SNP 芯片数据统计了北京地区2107头荷斯坦牛基因组上的长纯合片段(runs of homozygosity, ROH)的频率和分布,计算了2种基因组近交系数,即染色体上ROH的长度占基因组总长度的比例(Froh)及个体所有标记基因型中纯合子所占比例,即基因组纯合度(Fhom),进而分析了两种基因组近交系数之间的相关性以及基因组近交与系谱近交系数之间的相关性?结果表明,共检测到44 676个ROH片段,其长度主要分布在1~10 Mb之间?不同长度的ROH散布于个体基因组内,短ROH较长ROH更为常见?ROH在染色体上并非均匀分布,ROH频率最高的区域为10号染色体中部?两种基因组近交系数之间相关性很高(91%以上),但基因组近交与系谱近交之间的相关性较低(低于50%)?系谱完整性是影响基因组近交与系谱近交结果一致的重要因素,基因组近交系数能够反映个体真实的近交,本研究为评估群体近交水平提供了有力工具?     

Pedigree and marker information requirements to monitor genetic variability

There are several measures available to describe the genetic variability of populations. The average inbreeding coefficient of a population based on pedigree information is a frequently chosen option. Due to the developments in molecular genetics it is also possible to calculate inbreeding coefficients based on genetic marker information. A simulation study was carried out involving ten sires and 50 dams. The animals were mated over a period of 20 discrete generations. The population size was kept constant. Different situations with regard to the level of polymorphism and initial allele frequencies and mating scheme (random mating, avoidance of full sib mating, avoidance of full sib and half sib mating) were considered. Pedigree inbreeding coefficients of the last generation using full pedigree or 10, 5 and 2 generations of the pedigree were calculated. Marker inbreeding coefficients based on different sets of microsatellite loci were also investigated. Under random mating, pedigree-inbreeding coefficients are clearly more closely related to true autozygosity (i.e., the actual proportion of loci with alleles identical by descent) than marker-inbreeding coefficients. If mating is not random, the demands on the quality and quantity of pedigree records increase. Greater attention must be paid to the correct parentage of the animals.     

Inbreeding as measured by isonymy, pedigrees, and population size in Törbel, Switzerland.

Törbel provides an interesting test case for the study of the relationship between inbreeding measured by pedigrees and inbreeding measured by isonymy. At the start of this investigation, we were aware that isonymy could introduce biases into the calculation of the inbreeding coefficient in either direction. However, it was expected that in Switzerland, inbreeding from isonymy would be an overestimate due to patrilocal residence and polyphyletic names. One way of dealing with this problem [13] was not to be concerned with the absolute value of inbreeding but only in the difference between estimates. Any bias introduced in the estimate itself disappears in such comparisons, so that a trend of inbreeding can be ascertained correctly. However, it was considered equally important to subject several populations to both a complete pedigree analysis and an isonymic analysis to determine the relationship between estimates of inbreeding. Despite the fact that several authors (Swedlund [18], for example) warned users of isonymy to exercise caution, the careless application of isonymy still persists. In the present study, estimates of inbreeding from isonymy were brought into line with other methods based on pedigree analysis and population size. However, it was possible to do this only in Törbel where pedigree depth was extensive and relatively complete. Similar corrections are possible only when the distribution of mono- and polyphyletic names is known and when migration data are reliable. If the trouble is taken to make these corrections, the same time and effort might as well be spent in pedigree analysis (when fairly complete ascertainment is possible) to achieve the same end result.     

Inbreeding and genetic structure in the endangered Sorraia horse breed: implications for its conservation and management

The Sorraia horse is a closed breed with reduced effective population size and considered in critical maintained risk status. The breed exists in 2 main breeding populations, one in Portugal and one in Germany, with a smaller population size. A set of 22 microsatellite loci was used to examine genetic diversity and structure of the Sorraia horse breed and to compare individual inbreeding coefficient F, estimated from pedigree data, with individual heterozygosity and mean d(2). The Sorraia horse shows lower levels of microsatellite diversity when compared with other horse breeds. Due to management strategies, there are clear differences in the genetic structure of the 2 main Sorraia horse populations. Individual heterozygosity was shown to be a good estimator, used together with or as an alternative to inbreeding coefficient, in predicting fitness and evaluating the inbreeding level of the Sorraia horse. The information gathered in this study, combined with information available from previous studies, offers an important and wide information base for the future development of an effective breeding management of the Sorraia horse in order to preserve this endangered breed.     

Pedigrees and microsatellites among endangered ungulates: what do they tell us?

Relationships between pedigree coefficients of inbreeding and molecular metrics are generally weak, suggesting that measures of heterozygosity estimated using microsatellites may be poor surrogates of genome-wide inbreeding. We compare three endangered species of gazelles ( Gazella ) with different degrees of threat in their natural habitats, for which captive breeding programmes exist. For G. dorcas, the species with the largest founding population, the highest and most recent number of founding events, the correlation between pedigree coefficient of inbreeding and molecular metrics was higher than for outbred populations of mammals, probably because it has both higher mean f and variance. For the two species with smaller founding populations, conventional assumptions about founders, i.e. outbred and unrelated, are unrealistic. When realistic assumptions about the founders were made, clear relationships between pedigree coefficients of inbreeding and molecular metrics were revealed for G. cuvieri. This population had a small founding population, but it did experience admixture years later; thus, the relationship between inbreeding and molecular metrics in G. cuvieri is very similar to the expected values but lower than in G. dorcas . In contrast, no relationship was found for G. dama mhorr which had a much smaller founding population than had been previously assumed, which probably had high levels of inbreeding and low levels of genetic variability, and no admixture. In conclusion, the strength of the association between pedigree coefficient of inbreeding and molecular metrics among endangered species depends on the level of inbreeding and genetic variability present in the founding population, its size and its history.     

Genome-Wide Estimates of Coancestry,Inbreeding and Effective Population Size in the Spanish Holstein Population

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.     

Analysis of genealogical structure of populations. II. The use od numerical pedigrees for calculation of inbreeding coefficient

A method for calculation of inbreeding coefficient F in a numerical pedigree with no reference to its graphic representation is suggested. For calculation of F, a formula that does not take into account inbreeding coefficients of common ancestors and admits intersections in a loop is used. An advantage of this method is that it automatically finds all loops formed by paths to common ancestors. Detecting these loops via their tracing in a graphic pedigree with intersecting lines of descent creates a possibility of errors. A criterion of existence of at least one common link for two numerical paths is presented. It enables one to exclude pairs of paths to common ancestors that do not form loops. The methods considered for computing F in a given pedigree give exact values of the inbreeding coefficient for autosomal and sex-linked loci and generalize the known approximate approaches. The methods are illustrated by examples.     

Medicogenetic study of isolates in Uzbekistan. I. Statement of the problem and characteristics of the groups studied]

The paper comprises results of studying some demographic and populaton characteristics of the inhabitans of the Samarkand region as a whole and two villages, Karakent and Ishan, inhabited with Uzbeks-Khoja, a special religious-social caste in the past. It is shown that 87.4% of marriages in the Samarkand region are of international character (the information has been obtained on 7995 married couples). The frequency of consanguineous marriages is 11.6%, and among them 40.5% are first-cousin marriages and 39.1% are marriages of remote relatives. The coefficients of inbreeding are rather high among the Jewish, Tajik and Uzbek communities. The coefficient of inbreeding as a whole is F=0.0042 in this region and approaches to the maximal level, characterizing a panmix population. The average size of a family in the villages of Karakent and Ishan is approximately 4.0 persons. The values of reproductive performance, the nature of termination of pregnancies do not differ from those of panmix population. The percentage of intravillage and consanguineous marriages are 56% and 12.5% for the first village, and 25% and 2% for the second one respectively. The coefficient of inbreeding for karakent is F=0.0064, for Ishan--F=0.0014. Taking into consideration the historical development of the two villages and the cumulative data, the conclusion is drawn that Karakent is an isolate on a religious ground whereas Ishan is a disintegrated isolate.     

Understanding and predicting the fitness decline of shrunk populations: inbreeding, purging, mutation, and standard selection

The joint consequences of inbreeding, natural selection, and deleterious mutation on mean fitness after population shrinkage are of great importance in evolution and can be critical to the conservation of endangered populations. I present simple analytical equations that predict these consequences, improving and extending a previous heuristic treatment. Purge is defined as the "extra" selection induced by inbreeding, due to the "extra" fitness disadvantage (2d) of homozygotes for (partially) recessive deleterious alleles. Its effect is accounted for by using, instead of the classical inbreeding coefficient f, a purged inbreeding coefficient g that is weighed by the reduction of the frequency of deleterious alleles caused by purging. When the effective size of a large population is reduced to a smaller stable value N (with Nd ≥ 1), the purged inbreeding coefficient after t generations can be predicted as g(t) ≈ [(1 - 1/2N) g(t)(-1) + 1/2N](1 - 2d f(t)(-1)), showing how purging acts upon previously accumulated inbreeding and how its efficiency increases with N. This implies an early fitness decay, followed by some recovery. During this process, the inbreeding depression rate shifts from its ancestral value (δ) to that of the mutation-selection-drift balance corresponding to N (δ*), and standard selection cancels out the inbreeding depression ascribed to δ*. Therefore, purge and inbreeding operate only upon the remaining δ - δ*. The method is applied to the conservation strategy in which family contributions to the breeding pool are equal and is extended to make use of genealogical information. All these predictions are checked using computer simulation.     

On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs

In recent years there has been a dramatic increase in the availability of high density genetic marker data for both model and non‐model organisms. A potential application of these data is to infer relatedness in the absence of a complete pedigree. Using a marker panel of 771 SNPs genotyped in three generations of an extensive zebra finch pedigree, correlations between pedigree relatedness and seven marker‐based estimates of relatedness were examined, as was the relationship between heterozygosity and inbreeding. Although marker‐based and pedigree relatedness were highly correlated, the variance in estimated relatedness was high. Further, the correlation between heterozygosity and inbreeding was weak, even though mean inbreeding coefficient is typical of that seen in wild vertebrate pedigrees; the weak relationship was in part due to the small variance in inbreeding in the pedigree. Our data suggest that using marker information to reconstruct the pedigree, and then calculating relatedness from the pedigree, is likely to give more accurate relatedness estimates than using marker‐based estimators directly.     

Quantifying realized inbreeding in wild and captive animal populations

Most molecular measures of inbreeding do not measure inbreeding at the scale that is most relevant for understanding inbreeding depression—namely the proportion of the genome that is identical-by-descent (IBD). The inbreeding coefficient F_Ped obtained from pedigrees is a valuable estimator of IBD, but pedigrees are not always available, and cannot capture inbreeding loops that reach back in time further than the pedigree. We here propose a molecular approach to quantify the realized proportion of the genome that is IBD (propIBD), and we apply this method to a wild and a captive population of zebra finches (Taeniopygia guttata). In each of 948 wild and 1057 captive individuals we analyzed available single-nucleotide polymorphism (SNP) data (260 SNPs) spread over four different genomic regions in each population. This allowed us to determine whether any of these four regions was completely homozygous within an individual, which indicates IBD with high confidence. In the highly nomadic wild population, we did not find a single case of IBD, implying that inbreeding must be extremely rare (propIBD=0–0.00094, 95% CI). In the captive population, a five-generation pedigree strongly underestimated the average amount of realized inbreeding (F_Ped=0.013<propIBD=0.064), as expected given that pedigree founders were already related. We suggest that this SNP-based technique is generally useful for quantifying inbreeding at the individual or population level, and we show analytically that it can capture inbreeding loops that reach back up to a few hundred generations.     

Integrating microsatellite and pedigree analyses to facilitate the captive management of the endangered Mississippi sandhill crane (Grus canadensis pulla)

The minimization of kinship in captive populations is usually achieved through the use of pedigree information. However, pedigree knowledge alone is not sufficient if pedigree information is missing, questionable, or when the founders of the captive population are related to one another. If this is the case, higher levels of inbreeding and lower levels of genetic diversity may be present in a captive population than those calculated by pedigree analyses alone. In this study, the genetic status of the critically endangered Mississippi sandhill crane (MSC) (Grus canadensis pulla) was analyzed using studbook data from the U.S. Fish and Wildlife Service managed captive breeding program as well as microsatellite DNA data. These analyses provided information on shared founder genotypes, allowing for refined analysis of genetic variation in the population, and the development of a new DNA-based studbook pedigree that will assist in the genetic management of the MSC population.     

Challenges in inbreeding estimation of large populations based on Polish Holstein-Friesian cattle pedigree

The aim of this study was to evaluate observed and future inbreeding level in Polish Holstein-Friesian cattle population. In total, over 9.8 mln animals were used in the analysis coming from the pedigree of Polish Federation of Cattle Breeders and Dairy Farmers. Inbreeding level, as an average per birth year, was estimated with the method accounting for missing parent information with the assumption of year 1950 as the base year of the population. If an animal had no ancestral records, an average inbreeding level from its birth year was assigned. Twice the average inbreeding level served as relatedness of the animal to the population, which enabled estimation of inbreeding in its offspring. The future inbreeding of potential offspring was estimated as an average of animals (bulls and cows) available for mating in a certain year. It was observed that 30–50% of animals born between 1985 and 2015 had no relevant ancestral information, which is caused by a high number of new animals and/or entire farms entering the national milk recordings. For the year 2015, the observed inbreeding level was 3.30%, which was more than twice the inbreeding with the classical approach (without missing parent information) and higher by 0.4% than the future inbreeding. The average increase of inbreeding in years 2010–2015 was 0.10%, which is similar to other countries monitored by World Holstein-Friesian Federation. However, the values might be underestimated due to low pedigree completeness. The estimates of future inbreeding suggested that observed inbreeding could be even lower and also increase slower, which indicates a constant need to monitor rate of increase in inbreeding over time. The most important aspect of presented results is the necessity to advise individual farmers to keep precise recordings of the matings on their farm in order to improve the pedigree completeness of Polish Holstein-Friesian and to use suitable mating programs to avoid too rapid growth of inbreeding.     

Analysis of genealogical structure of populations. I. A method of collecting genealogical data in numerical form

A method for collecting genealogical data with respect to an individual, a family, and members of the whole population is suggested. The essence of vertical pedigree construction consists of the same type of steps for filling in data (in the fixed order which excludes skips in the enumeration of lines of descent) about the father and the mother of the next ancestor. Each number in the received ordered list of ancestors uniquely determines a path (line of descent) to the given pedigree member. The path is explicitly described by a sequence of digits 0 and 1 (that corresponds to the sequence of fathers and mothers in the line of descent) at binary notation of this number. As a result, a pedigree is presented as a set of numbered rows that contain information, which uniquely identifies direct ancestors as individual persons. Results of joining separate pedigrees are recorded as a family list that contains lists of children for each parental pair. A pair of parents (more exactly, pointers of their families in the previous generation and numbers of pair members in their families) plays the role of the family "heading." Such a family list permits one to trace lines of descent and relationships for any population members presented in the list. It contains all genealogical information within the bounds of the study in a compact form. Here the process of collection requires considerably less time than traditional graphic representation of pedigrees. In addition, due to repeated checks of data during accumulation of material, error is minimized. Using pedigrees that have been collected, it is possible to calculate the coefficient of inbreeding manually. In connection with the wide prevalence of personal computers at present, it is also important that the data received are in fact ready to direct input to a computer for further automated data processing.     

Medico-genetic study of the population of Turkmenia. V. A population and demographic description of the Nokhur isolate

The paper deals with demographic, genealogical and genetic characterization of one Turkmenian isolate--"Nochur". The data on its load of hereditary diseases were published previously. The Turkmenian "Nochurly" tribe consists of 19 large and small clanes. 600 nuclear families live in a small mountain valley of the same name. The share of prereproductive age class is 60%, of reproductive class--29%, this value for postreproductive class being 11%. The average number of children per family, when the families have completed their reproductive period, is 6.84. The average duration of generation (the mean parental age to the birth time of a mean newborn) is 37.7 and 31 years for a man and woman, respectively. Immigration into Nochur is practically absent, there is a flow of emigrants to the capital of the Republic, Ashkhabad. A very high level of assortative mating has been noted, the minimal estimation of inbreeding coefficient being 0.033 (the pedigree) and the maximal--0.0529 (isonimy). Diminishing of the number of lethal equivalents between 1940-1965 and 1966-1980 was discovered. This can be explained by a decrease in natural selection pressure. The data on distribution of genetic markers of the ABO, MN, Rh, Hp and Pp systems within this isolated population are presented.