共查询到20条相似文献，搜索用时 15 毫秒
1.
Sara M. Nilson;Joan M. Burke;Brenda M. Murdoch;James L. M. Morgan;Ronald M. Lewis; 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2024,141(3):304-316
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
2.
Yoshinobu Uemoto Keiichi Suzuki Jumpei Yasuda Sanggun Roh Masahiro Satoh 《Animal Science Journal》2021,92(1):e13643
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
3.
W. Drobik E. Martyniuk 《Acta Agriculturae Scandinavica, Section A - Animal Sciences》2014,64(1):36-48
AbstractThe 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
4.
旨在设计利用不同信息来源的模型估计荷斯坦后备牛不同月龄体重性状的遗传参数。本研究于2014—2020年测定并收集了7 122头荷斯坦牛32 338条0～12月龄体重数据,分别利用系谱信息(linear mixed model with pedigree relationship matrix, LM＿A)和系谱-基因组信息构建亲缘关系矩阵(linear mixed model with genotype-pedigree joint relationship matrix, LM＿H),基于母体效应动物模型估计初生重,基于是否考虑初生重作为协变量的单性状动物模型估计2～12月龄各月龄体重遗传力,并利用双性状动物模型估计初生重与其它月龄体重的遗传相关。结果显示,对于初生重,根据赤池信息量准则(Akaike information criterion, AIC),LM＿H方法的拟合程度显著优于LM＿A方法,但两种方法估计的遗传参数相差不大：直接遗传力分别为0.30和0.32,母体遗传力分别为0.08和0.09,个体直接遗传效应和母体遗传效应遗传相关系数分别为-0.65和-0.64;对于2～... 相似文献
5.
Francesca Cecchi Roberta Ciampolini Gianluca Giacalone Gisella Paci 《Animal Science Journal》2014,85(9):868-871
The genealogical data of 471 (whole population: WP) Lizard canaries of an Italian breeder were analyzed to evaluate the genetic variability of the breed. The reference population (RP) comprised 346 living reproductive birds. Average generation interval was 1.61 ± 0.718 for males and 1.72 ± 0.863 for females. The average value of inbreeding (F) and relatedness (AR) in the RP were 15.83% and 22.63%, while the average increase in inbreeding was estimated to be 6.71% per generation (effective population size = 7.49). The results showed the need to reduce the level of inbreeding which would result in significant loss of genetic variation and in significant inbreeding depression. 相似文献
6.
B. K. Baldursdottir T. Kristjansson 《Acta Agriculturae Scandinavica, Section A - Animal Sciences》2013,63(2):53-65
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
7.
牦牛,黑白花牛及其远缘杂种RAPD标记的初步研究 总被引：2，自引：0，他引：2
本文用８０个具有１０个碱基的随机引物对牦牛、黑白花牛及犏牛的基因组ＤＮＡ进行了ＰＣＲ扩增。结果表明有７个引物扩增出清晰且具多态特征的条带,其中,Ｆ１５（ＣＣＡＧＴＡＣＴＣＣ,５６４－１２５ｂｐ）可作为区分牦牛与黑白花牛的重要 的。 试品种相似性指数分析表黑白花牛与犏牛的遗传距离最小（０．５９４２）;黑白花与牦牛的遗传距离最大（０．６４５６）;而犏牛与牦牛的遗传距离居中（０．６４１０）。群体遗传多样 相似文献
8.
F.J.C. Faria A.E.V. Filho F.E. Madalena & L.A. Josahkian 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2009,126(2):148-153
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
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Aude LALIS Allowen EVIN Marc JANIER Lamine KOIVOGUI Christiane DENYS 《Integrative zoology》2015,10(6):505-514
The commensal rodent Mastomys natalensis is the natural reservoir of Lassa arenavirus (LASV), which causes hemorrhagic fever in West Africa. To study a possible effect of the virus on phenotypic and genotypic variation of its persistently infected host, we compared LASV‐positive and non‐infected wild‐caught M. natalensis. The LASV effects on the phenotypic variation were explored using standard external morphometric measurements, geometric morphometric analyses of the cranial size and shape, and brain case volume. The genetic variability of M. natalensis specimens was assessed using 9 polymorphic microsatellite markers. Independent of sex and age, LASV‐infected animals had smaller external body measurements, reproductive organs, skull size and brain case volume. Cranial shape differences between the 2 groups are represented by a lateral constriction of the entire skull. The genetic variability revealed consanguinity only among the LASV‐positive rodents. We hypothesize that growth impairment may result in a selective disadvantage for LASV‐infected M. natalensis, leading to a preferably commensal lifestyle in areas where the LAVS is endemic and, thereby, increasing the risk of LASV transmission to humans. 相似文献
11.
B. Gredler T.R. Solberg G. Klemetsdal I. Curik J. Sölkner 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2013,130(4):286-293
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
12.
L. Silió C. Barragán A.I. Fernández J. García‐Casco M.C. Rodríguez 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2016,133(2):145-154
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
13.
Danchin-Burge C Leroy G Brochard M Moureaux S Verrier E 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2012,129(3):206-217
A pedigree analysis was performed on eight French dairy cattle breeds to assess their change in genetic variability since a first analysis completed in 1996. The Holstein, Normande and Montbéliarde breeds are selected internationally with over hundreds of thousands cows registered in the performance recording system. Three breeds are internationally selected but with limited numbers of cows in France (Brown Swiss, French Simmental and French Red Pied). The last two remaining breeds (Abondance and Tarentaise) are raised at regional level. The effective numbers of ancestors of cows born between 2004 and 2007 varied between 15 (Abondance and Tarentaise) and 51 (French Red Pied). The effective population sizes (classical approach) varied between 53 (Abondance) and 197 (French Red Pied). This article also compares the genetic variability of the ex situ (collections of the French National Cryobank) and in situ populations. The results were commented in regard to the recent history of gene flows in the different breeds as well as the existence of more or less stringent bottlenecks. Our results showed that whatever the size of the breeds, their genetic diversity impoverished quite rapidly since 1996 and they all could be considered as quite poor from a genetic diversity point of view. It shows the need for setting up cryobanks as gene reservoirs as well as sustainable breeding programmes that include loss of genetic diversity as an integrated control parameter. 相似文献
14.
旨在通过分析娄门鸭保种群体的遗传多样性和群体结构来评估保种效果。本研究在娄门鸭保种群中随机选择同一世代163只90日龄的健康个体(39公,124母),翅静脉采血后提取基因组DNA,利用简化基因组测序技术检测全基因组范围内的单核苷酸多态性(SNPs); 利用R软件计算个体水平的多态信息含量(PIC)、固定指数(Fix-index)、香农信息指数(SHI)、基因多样性指数(Nei)、有效等位基因数(Ne)以及本研究自创的相对多态信息含量(rPIC)等6个遗传多样性指标,并比较分析了不同染色体水平的遗传多样性指标; 同时利用admixture软件分析群体遗传结构,gcta软件分析群体主成分和个体间的亲缘关系,并分析连续性纯合片段(runs of homozygosity,ROH)以及基因组近交系数FROH,评估保种效果。结果显示,163只娄门鸭个体共检测到622 205个SNPs位点,质控过滤后得到374 455个高质量SNPs位点,其中50.70%的位点分布在NC_040046、NC_040047、NC_040048和NC_040049四个染色体中。娄门鸭群体PIC、Nei、Ne、SHI和rPIC指标值分别为0.154 1、0.192 9、1.336、0.296 9和0.410 9,对于SNPs而言,该群体38.80%的SNPs位点属于高度多态性位点,遗传多样性较为丰富; Fix-index值为0.320 8,说明娄门鸭群体出现了分化,这与遗传结构、PCA和亲缘关系分析将娄门鸭群体划分为3个群体的结果一致。PIC、Nei、Ne和SHI四个指标分别在不同染色体上的分布规律均一致,且4个指标两两相关性均达到0.97以上,而Fix-index与其他4个指标的相关性较低,在0.23以下,说明可以选择Fix-index以及PIC等少数指标来评估娄门鸭群体的遗传多样性。163只娄门鸭个体共检测到2 966条ROH,ROH片段长度主要集中在0~2 Mb区间; 基于ROH得到的基因组近交系数FROH在公、母鸭中分别为0.027 5和0.043 3,说明娄门鸭保种群近交程度较低; 具体到染色体水平,NC_040068、NC_040074染色体的FROH值分别达到0.352 4和0.319 3。结果提示,娄门鸭保种群的遗传多样性较丰富,群体基因组近交系数较低,但个别染色体的近交系数较高,且群体出现了部分分化。后续保种中可以将遗传结构分析得到的3个分化的亚群个体之间进行适当的非随机交配,消除目前的群体分化现象,并重点监测染色体近交系数较高的基因组区域,避免个别染色体近交系数上升过快。 相似文献
15.
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
16.
Excessive inbreeding rates and small effective population sizes are an important problem in many populations of dogs. Proper genetic management of these populations can decrease the problem, and several measures are available. However, the effectiveness of these measures is not clear beforehand. Therefore, a simulation model was developed to test measures that aim to decrease the rate of inbreeding. The simulation program was used to evaluate inbreeding restriction measures in the Dutch golden retriever dog population. This population consisted of approximately 600 dams and 150 sires that produce 300 litters each year. The five most popular sires sire approximately 25% of the litters in a year. Simulations show that the small number of popular sires and their high contribution to the next generation are the main determinants of the inbreeding rates. Restricting breeding to animals with a low average relatedness to all other animals in the population was the most effective measure and decreased the rate of inbreeding per generation from 0.41 to 0.12%. Minimizing co‐ancestry of parents was not effective in the long run, but decreased variation in inbreeding rates. Restricting the number of litters per sire generally decreased the generation interval because sires were replaced more quickly, once they met their restriction. In some instances, this lead to an increase in inbreeding rates because the next generations were more related. The simulation tool proved to be a powerful and educational tool for deciding which breeding restrictions to apply, and can be effective in different breeds and species as well. 相似文献
17.
T. Druml R. Baumung & J. Sölkner 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2009,126(5):348-356
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
18.
Estimating genetic connectedness among herds is important for the accuracy of dairy cattle genetic evaluation. When selecting between animals raised in different herds, the accuracy of their genetic evaluations can be influenced by the degree of connectedness among these herds. In this study, two methods were used to measure genetic connectedness, CR （genetic connectedness rating ） and GLt （total number of direct genetic links between group）, among herds from Beijing, Shanghai, and Tianjin. Genetic connectedness between the herds from Beijing and Tianjin was 23.95%, between Beijing and Shanghai was 17. 10%, and between Shanghai and Tianjin it was 14.28%. Genetic connectedness between herds from Beijing and Tianjin was the highest and that between Shanghai and Tianjin was the lowest. The correlation coefficient for the two methods was 0. 808. Some suggestions for improved genetic evaluation of dairy cattle were also discussed. 相似文献
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J. Schäler R. Wellmann J. Bennewitz G. Thaller D. Hinrichs 《Acta Agriculturae Scandinavica, Section A - Animal Sciences》2018,68(2):63-72
Recovering native uniqueness has major importance for breeds with historic introgression. The aim of the study was to estimate population genetic parameters for two local red cattle breeds from Northern Germany and to study possibilities to reverse introgression. Genealogical information consisted of 90,783 individuals for German Angler and 187,255 individuals for Red Dual-Purpose cattle breed, with additional information on sex, born, breed, status, and conventional breeding values. It is concluded that the native genetic contribution could be included as an additional trait in the total merit index in order to recover a part of the native genetic background. Native contributions should be estimated in the long term from marker data in order to account for Mendelian sampling. The maintenance of a sufficient genetic diversity of native alleles can be achieved by an advanced OCS with appropriate constraints. 相似文献