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1.
    
The complete pedigree of two closed Iberian pig lines (Gamito and Torbiscal), with 798 and 4077 reproducers, has been used to measure the evolution of coancestry (f) and inbreeding (F) for autosomal and X‐linked genes along 16 and 28 respective equivalent discrete generations. At the last generation, the mean values of each line were f = 0.41 and 0.22, F = 0.35 and 0.18, fX = 0.46 and 0.22 and FX = 0.47 and 0.19, respectively. Other calculated parameters were the effective number of founders (final values, 6.8 and 35.2) and non‐founders (1.5 and 2.4), founder genome equivalents (1.2 and 2.3) and effective population size (16.0 and 57.7). Measures of Torbiscal effective size based on rates of coancestry (66.1), inbreeding (65.0) and linkage disequilibrium (71.0) were estimated from whole‐genome SNP genotyping data. Values of new and old inbreeding and their respective rates by generation were computed to detect purging effects of natural selection. The analysis of 6854 Torbiscal litters showed significant negative impacts of new and fast inbreeding on litter size, as expected from the purging hypothesis: ?0.20 born piglets per litter by a 10% of new inbreeding, and ?0.03 and ?0.02 piglets by 1% of total and new inbreeding rates, respectively. The analysis performed on 1274 litters of the Gamito line failed to show purging effects. The only significant results were reductions in ?0.91 and ?0.17 piglets by a 10% of old and X‐linked genes inbreeding, respectively. These results may be useful for some practical issues in conservation programs of farm or captive wild animals.  相似文献   

2.
    
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3.
通过计算畜群内的个体近交系数,可以把握现有畜群的遗传效应,对于畜群的选种选配有着重要的指导意义,能有效地防止近交造成的品种退化等现象。通过Excel函数计算畜群系谱信息中共同祖先出现的次数频率,可简单快速地估算个体间的近交系数,实现近交系数的直观估算,不需要使用者掌握计算机编程知识,可供基层畜牧行业的技术人员参考使用,能快速估算系谱个体的近交情况,使得对群体遗传效应的评估工作极易进行。  相似文献   

4.
    
The accumulation of inbreeding and the loss of genetic diversity is a potential problem in Holstein dairy cattle. The goal of this study was to estimate inbreeding levels and other measures of genetic diversity, using pedigree information from Iranian Holstein cattle. Edited pedigree included 1 048 572 animals. The average number of discrete generation equivalents and pedigree completeness index reached 13.4 and 90%, respectively. The rate of inbreeding was 0.3% per year. Effective number of founders, founder genomes, non‐founders and ancestors of animals born between 2003 and 2011 were 503, 15.6, 16.1 and 25.7, respectively. It was proven that the unequal founder contributions as well as bottlenecks and genetic drift were important reasons for the loss of genetic diversity in the population. The top 10 ancestors with the highest marginal genetic contributions to animals born between 2003 and 2011 and with the highest contributions to inbreeding were 48.20% and 63.94%, respectively. Analyses revealed that the most important cause of genetic diversity loss was genetic drift accumulated over non‐founder generations, which occurred due to small effective population size. Therefore, it seems that managing selection and mating decisions are controlling future co‐ancestry and inbreeding, which would lead to better handling of the effective population size.  相似文献   

5.
    
Using genome‐wide SNP data, we calculated genomic inbreeding coefficients (FROH > 1 Mb, FROH > 2 Mb, FROH > 8 Mb and FROH > 16 Mb) derived from runs of homozygosity (ROH) of different lengths (>1, >2, >8 and > 16 Mb) as well as from levels of homozygosity (FHOM). We compared these values of inbreeding coefficients with those calculated from pedigrees (FPED) of 1422 bulls comprising Brown Swiss (304), Fleckvieh (502), Norwegian Red (499) and Tyrol Grey (117) cattle breeds. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients FROH > 8 Mb and FROH > 16 Mb were similar to the levels estimated from pedigrees. The lowest values were obtained for Fleckvieh (FPED = 0.014, FROH > 8 Mb = 0.019 and FROH > 16 Mb = 0.008); the highest, for Brown Swiss (FPED = 0.048, FROH > 8 Mb = 0.074 and FROH > 16 Mb = 0.037). In contrast, inbreeding estimates based on the genomic coefficients FROH > 1 Mb and FROH > 2 Mb were considerably higher than pedigree‐derived estimates. Standard deviations of genomic inbreeding coefficients were, on average, 1.3–1.7‐fold higher than those obtained from pedigrees. Pearson correlations between genomic and pedigree inbreeding coefficients ranged from 0.50 to 0.62 in Norwegian Red (lowest correlations) and from 0.64 to 0.72 in Tyrol Grey (highest correlations). We conclude that the proportion of the genome present in ROH provides a good indication of inbreeding levels and that analysis based on ROH length can indicate the relative amounts of autozygosity due to recent and remote ancestors.  相似文献   

6.
    
The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (Nge) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on Nge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non-founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.  相似文献   

7.
Abstract

The Icelandic goat breed is a closed population consisting of around 700 animals kept in 45 herds. Several population bottlenecks are known to have occurred and the population has at least twice declined below 100 animals. Here the genetic diversity of the breed was estimated using pedigree information, D-loop sequencing and microsatellite markers. The annual rate of inbreeding was estimated as 3% and the effective population size as 5.1 animals. The effective population size based on molecular markers was estimated in the range of 4.1–8.8 individuals and mtDNA D-loop sequencing identified only three haplotypes. The results presented here show the population to be highly inbred, fragmented and the level of genetic variation among the lowest found in livestock. The results will be an important input into conservation planning for the Icelandic goat.  相似文献   

8.
Zebu breeds play an important role in cattle production systems in Brazil. To assess the genetic variability from animals in the Herd Books of Nelore, Gir and Guzerat breeds, generation intervals, inbreeding, effective population size and parameters of gene origin (effective number of founders, ancestors and founder genomes) were calculated using pedigree records from 1938 to 1998. Breed subdivision was quantified by Wright's F -statistics. Calculations were separately carried out for consecutive 4-year intervals in the period 1979–98. Generation interval was around 8 years for the three breeds. Total inbreeding increased in all the breeds reaching values of 2.13%, 2.28% and 1.75%. Effective population size decreased from 85 to 68 in Nelore, from 70 to 45 in Gir and remained nearly constant around 104 in Guzerat. The quantities assessing the number of contributing ancestors decreased with time in all the breeds, and in the last analysed period the most important ancestor accounted for 14%, 3.1% and 4.1% in Nelore, Gir and Guzerat, respectively. Results indicate that the studied breeds are suffering from a loss of genetic variability which can result in negative effects on breeding and conservation purposes.  相似文献   

9.
在项目搭建的“奶牛精细养殖综合技术平台”上，将对动物个体祖先谱系的跟踪问题转化为满二叉树的数据结构后，选用前序遍历搜索算法，编写了追溯奶牛个体面向4代祖先的自定义“找祖先”函数，利用平台系统设定参数产生的模拟数据，实现了4代以内祖先的谱系跟踪，同时还提供雌性祖先的生产性能数据；以跟踪的谱系数据为基础，将“找祖先”函数和计算近交系数的原理相结合，实现了某个体与指定公牛（或母牛）交配后裔的近交系数监测，以控制近亲繁殖。研究还进一步指出，只要改变寻找祖先的起点，就能实现超过4代的祖先谱系分析。但是，个体谱系高世代（中亲或远亲）追踪必须以超越时空的、完整的奶牛繁殖档案数据库为基础，因此建议尽快建立我国奶牛繁殖科学数据库。  相似文献   

10.
Abstract

The study aimed to identify important factors threatening genetic diversity within small sheep populations, and to propose sustainable management strategies. Demographic evolution, genetic diversity and current genetic management practices were analyzed in a population of Polish Olkuska sheep. Unbalanced contributions of individual rams to the next generation were observed due to differences in the period of their utilization, the number of progeny and the number of daughters used in reproduction. Matings between closely related animals were common. Pedigree completeness was satisfactory and inbreeding coefficient was high, 11.71% for lambs born in 2012. Relatively high values of potential and realized coancestries within flocks showed the importance of keeping more than one ram. The genetic conservation index and average relatedness coefficient, and their comparison between regions was helpful in considering management options. The information on genetic relationships and genetic conservation parameters of rams should be provided to breeders with simple interpretations.  相似文献   

11.
    
The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 from the National Sheep Improvement Program, our objectives were to (i) estimate the completeness and quality of the pedigree, (ii) calculate diversity statistics for the whole pedigree and relevant reference subpopulations and (iii) assess the impact of current diversity on genomic selection. Reference 1 was Katahdins born from 2017 to 2019 (n = 23,494), while reference 2 was a subset with at least three generations of Katahdin ancestry (n = 9327). The completeness of the whole pedigree, and the pedigrees of reference 1 and reference 2, were above 50% through the fourth, fifth and seventh generation of ancestors, respectively. Effective population size (Ne) averaged 111 animals with a range from 42.2 to 451.0. The average generation interval was 2.9 years for the whole pedigree and reference 1, and 2.8 years for reference 2. The mean individual inbreeding and average relatedness coefficients were 1.62% and 0.91%, 1.74% and 0.90% and 2.94% and 1.46% for the whole pedigree, reference 1, and reference 2, respectively. There were over 300 effective founders in the whole pedigree and reference 1, with 169 in reference 2. Effective number of ancestors were over 150 for the whole pedigree and reference 1, while there were 67 for reference 2. Prediction accuracies increased as the reference population grew from 1k to 7.5k and plateaued at 15k animals. Given the large number of founders and ancestors contributing to the base genetic variation in the breed, the Ne is sufficient to maintain diversity while achieving progress with selection. Stable low rates of inbreeding and relatedness suggest that incorporating genetic conservation in breeding decisions is currently not of high priority. Current Ne suggests that with limited genotyping, high levels of accuracy for genomic prediction can be achieved. However, intense selection on GEBV may cause loss of genetic diversity long term.  相似文献   

12.
    
The pedigree of the current Austrian Noriker draught horse population comprising 2808 horses was traced back to the animals considered as founders of this breed. In total, the number of founders was 1991, the maximum pedigree length was 31 generations, with an average of 12.3 complete generations. Population structure in this autochthonous Austrian draught horse breed is defined by seven breeding regions (Carinthia, Lower Austria, Salzburg, Styria, Tyrol, Upper Austria and Vorarlberg) or through six coat colour groups (Bay, Black, Chestnut, Roan, Leopard, Tobiano). Average inbreeding coefficients within the breeding regions ranged from 4.5% to 5.5%; for the colour groups, the coefficients varied from 3.5% to 5.9%. Other measures of genetic variability like the effective number of founders, ancestors and founder genomes revealed a slightly different genetic background of the subpopulations. Average coancestries between and within breeding areas showed that the Salzburg population may be considered as the nucleus or original stock whereas all other subpopulations showed high relationship to horses from Salzburg. The target of draught horse breeding in the 21st century does not meet the breeding concept of maximizing genetic gains any more. Stabilizing selection takes place. In this study, we show that demographic factors as well as structure given by different coat colours helped to maintain genetic diversity in this endangered horse breed.  相似文献   

13.
    
Multilocus homozygosity, measured as the proportion of the autosomal genome in homozygous genotypes or in runs of homozygosity, was compared with the respective pedigree inbreeding coefficients in 64 Iberian pigs genotyped using the Porcine SNP60 Beadchip. Pigs were sampled from a set of experimental animals with a large inbreeding variation born in a closed strain with a completely recorded multi‐generation genealogy. Individual inbreeding coefficients calculated from pedigree were strongly correlated with the different SNP‐derived metrics of homozygosity (r = 0.814–0.919). However, unequal correlations between molecular and pedigree inbreeding were observed at chromosomal level being mainly dependent on the number of SNPs and on the correlation between heterozygosities measured across different loci. A panel of 192 SNPs of intermediate frequencies was selected for genotyping 322 piglets to test inbreeding depression on postweaning growth performance (daily gain and weight at 90 days). The negative effects on these traits of homozygosities calculated from the genotypes of 168 quality‐checked SNPs were similar to those of inbreeding coefficients. The results support that few hundreds of SNPs may be useful for measuring inbreeding and inbreeding depression, when the population structure or the mating system causes a large variance of inbreeding.  相似文献   

14.
    
Inbreeding depression in closed populations impairs animal fitness, health, and productivity. However, not all inbreeding is expected to be equally damaging. Recent inbreeding is thought to be more harmful than ancient inbreeding because selection decreases the frequency of unfavourable alleles with time. Accordingly, selection efficiency is improved by inbreeding in a process called purging. This research aimed to quantify inbreeding depression on growth and prolificacy traits in two lines of rabbits selected for just one growth (Caldes line) or prolificacy (Prat line) trait, and also to find some evidence of purging of deleterious alleles by selection. Caldes line comprised 51 generations and 124,371 animals in the pedigree. Prat line comprised 34 generations and 161,039 animals in the pedigree. The effects of old, intermediate, and new inbreeding (Fold, Fint, and Fnew), as well as total cumulated classical inbreeding (F) and 3 measurements of ancestral inbreeding (AHC, Fa.K, and Fa.B) were estimated for average daily gain (ADG), slaughter weight (SW), weaning weight (WW), born alive (BA), the total number of kits (NT), and the number of weaned kits (NW). There was a clear inbreeding depression for all growth and prolificacy traits in the Caldes line (−7.19 g/d, −0.45 kg, −0.25 kg, −6 kits, −4 kits, and −4 kits per unit of increase in F for ADG, SW, WW, BA, NT, and NW, respectively) and also in Prat line (−7.48 g/d, −0.31 kg, −0.11 kg, −4 kits, −5 kits, and −4 kits per unit of increase in F for ADG, SW, WW, BA, NT, and NW, respectively). The inbreeding partition appears to be a reliable alternative for assessing inbreeding depression and purging. Thus, for example, in the Caldes line and for ADG the regression coefficients were −7.61, −5.41, and 7.76 g/d per unit of increase in Fnew, Fint, and Fold, respectively. In addition, AHC and Fa.B may provide more accurate evidence of purging than Fa.K. This study confirms the existence of inbreeding depression for growth and prolificacy traits in both lines of rabbits and shows evidence of purging of deleterious recessive alleles involved both in growth and prolificacy, independently of the selection criteria established in the line.  相似文献   

15.
蜥蜴和蟾蜍延脑听觉核团传入投射的比较研究   总被引：2，自引：0，他引：2  
本文采用ＨＲＰ示踪技术对两栖类蟾蜍和爬行类蜥蜴外周听感受器向延脑的传入投射进行了比较研究。结果表明：蟾蜍的背侧第八神经核接受外周听神经的传入投射,且背侧第八神经核趋于分化为两个亚核：蜥蜴耳蜗发出的听神经上行投射到延脑的角状核和巨细胞核。  相似文献   

16.
    
Twenty‐five subpopulations (i.e. populations of prefectures) of more than 2000 Japanese Black cows younger than or equal to 10 years of age were analyzed to evaluate the genetic relationships in the current population. The total number of cows analyzed was 392 346 and their pedigrees were traced back to 1944 or before. Using the pedigree records, the genetic relationships among the subpopulations were estimated by the two different measurements: (i) the average additive relationship coefficients and (ii) Nei's standard genetic distances. Principal component analysis (PCA) was performed to the matrix of the average additive relationship coefficients, and the factor loadings of subpopulations were plotted on the plane to visualize the genetic configuration of subpopulations. To understand the grouping process of the subpopulations, cluster analysis was applied to the matrix of the Nei's genetic distances, and a dendrogram was constructed. There was a high consistency between the results from PCA and cluster analysis. Eight subpopulations with relatively low migration rates showed their unique genetic compositions, and the other 17 subpopulations with high migration rates formed a single cluster. The major cause of the genetic similarity among the 17 subpopulations was inferred to be the strong genetic influence from one subpopulation (Hyogo prefecture) with prominent characteristics for meat quality.  相似文献   

17.
    
In this study, the effect of different measurements of ancestral inbreeding on birthweight, calving ease and stillbirth were analysed. Three models were used to estimate the effect of ancestral inbreeding, and the estimated regression coefficient of phenotypic data on different measurements of ancestral inbreeding was used to quantify the effect of ancestral inbreeding. The first model included only one measurement of inbreeding, whereas the second model included the classical inbreeding coefficients and one alternative inbreeding coefficient. The third model included the classical inbreeding coefficients, the interaction between classical inbreeding and ancestral inbreeding, and the classical inbreeding coefficients of the dam. Phenotypic data for this study were collected from February 1998 to December 2008 on three large commercial milk farms. During this time, 36 477 calving events were recorded. All calves were weighed after birth, and 8.08% of the calves died within 48 h after calving. Calving ease was recorded on a scale between 1 and 4 (1 = easy birth, 4 = surgery), and 69.95, 20.91, 8.92 and 0.21% of the calvings were scored with 1, 2, 3 and 4, respectively. The average inbreeding coefficient of inbred animals was 0.03, and average ancestral inbreeding coefficients were 0.08 and 0.01, depending on how ancestral inbreeding was calculated. Approximately 26% of classically non‐inbred animals showed ancestral inbreeding. Correlations between different inbreeding coefficients ranged between 0.46 and 0.99. No significant effect of ancestral inbreeding was found for calving ease, because the number of animals with reasonable high level of ancestral inbreeding was too low. Significant effects of ancestral inbreeding were estimated for birthweight and stillbirth. Unfavourable effects of ancestral inbreeding were observed for birthweight. However, favourable purging effects were estimated for stillbirth, indicating that purging could be partly beneficial for genetic improvement of stillbirth.  相似文献   

18.
    
Because native breeds can serve as genetic resources for adapting to environment changes, their conservation is important for future agroecosystems. Using pedigree analysis, we investigated genetic diversity and inbreeding in Japanese Hokkaido native horses, which have adapted to a cold climate and roughage diet. Genetic diversity was measured as the number of founders and the effective number of founders, ancestors and genomes. All metrics imply a decrease in genetic diversity. A comparison of these metrics suggested that pedigree bottlenecks contributed more than did random gene losses to the reduction of genetic diversity. Estimates of marginal contributions of ancestors suggest that the bottlenecks arose mainly because related stallions had been used for breeding. A tendency for an increase in inbreeding coefficients was observed. F‐statistics revealed that a small effective population size majorly contributed to this increase, although non‐random mating in particular regions also contributed. Because the bottlenecks are thought to have reduced the effective population size, our results imply that mitigation of bottlenecks is important for conservation. To this end, breeding should involve genetically diverse stallions. In addition, to prevent non‐random mating observed in particular regions, efforts should be made to plan mating with consideration of kinships.  相似文献   

19.
    
Pedigree information was traditionally used to assess inbreeding. The availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) has emerged as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify the chromosomal contribution to genome-wide inbreeding. Unfortunately, the identification of ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify an ROH segment has major effects on the estimation of inbreeding and inbreeding depression, yet it is arbitrarily set. To overcome this limitation, a search algorithm to approximate mutation enrichment was developed to determine the minimum length of ROH segments. It consists of finding genome segments with significant effect differences in trait means between animals with high and low burdens of autozygous intervals with a specific length. The minimum length could be determined heuristically as the smallest interval at which a significant signal is detected. The proposed method was tested in an inbred Hereford cattle population genotyped for 30,220 SNPs. Phenotypes recorded for six traits were used for the approximation of mutation loads. The estimated minimum length was around 1 Mb for yearling weight (YW) and average daily gain (ADG) and 4 Mb for birth weight and weaning weight. These trait-specific thresholds estimated using the proposed method could be attributed to a trait-dependent effect of homozygosity. The detection of significant inbreeding effects was well aligned with the estimated thresholds, especially for YW and ADG. Although highly deleterious alleles are expected to be more frequent in recent inbreeding (long ROH), short ROH segments (<5 Mb) could contain a large number of less deleterious mutations with substantial joint effects on some traits (YW and ADG). Our results highlight the importance of accurate estimation of the ROH-based inbreeding and the necessity to consider a trait-specific minimum length threshold for the identification of ROH segments in inbreeding depression analyses. These thresholds could be determined using the proposed method provided the availability of phenotypic information.  相似文献   

20.
    
One problem in modern dogs is a high occurrence of physical diseases, defects and disorders. Many breeds exhibit physical problems that affect individual dogs throughout life. A potential cause of these problems is inbreeding that is known to reduce the viability of individuals. We investigated the possible correlation between recent inbreeding and health problems in dogs and used studbook data from 26 breeds provided by the Swedish Kennel Club for this purpose. The pedigrees date back to the mid‐20th century and comprise 5–10 generations and 1 000–50 000 individuals per pedigree over our study period of 1980–2010. We compared levels of inbreeding and loss of genetic variation measured in relation to the number of founding animals during this period in the investigated dog breeds that we classified as ‘healthy’ (11 breeds) or ‘unhealthy’ (15) based on statistics on the extent of veterinary care obtained from Sweden's four largest insurance companies for pets. We found extensive loss of genetic variation and moderate levels of recent inbreeding in all breeds examined, but no strong indication of a difference in these parameters between healthy versus unhealthy breeds over this period. Thus, recent breeding history with respect to rate of inbreeding does not appear to be a main cause of poor health in the investigated dog breeds in Sweden. We identified both strengths and weaknesses of the dog pedigree data important to consider in future work of monitoring and conserving genetic diversity of dog breeds.  相似文献   

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