近交对狼山鸡繁殖性状影响的研究

利用RAD-seq简化基因组测序鉴定狼山鸡保种群个体基因组SNP标记,计算个体(间)分子近交系数和分子亲缘系数,结合系谱信息组建高、低近交两个试验组。分析后代繁殖性状近交衰退系数,评价近交对繁殖性状的影响。结果显示:利用FROH、FGRM、FHOM和FUNI四种分子近交系数结合亲缘系数kin估算的后代分子近交系数较为一致。低近交组后代的平均分子近交系数小于0.04,高近交组(6个家系)后代的平均分子近交系数介于0.14~0.25。近交对各繁殖性状的效应表现并不一致。高近交组后代母鸡开产日龄、300日龄产蛋数发生显著衰退(P<0.05,P<0.01),且与分子近交系数呈显著相关(P<0.05,P<0.01);开产体重和开产蛋重未发生显著性衰退(P>0.05)。研究结果为进一步探讨狼山鸡繁殖性状近交衰退分子机制提供了基础。     

畜禽群体近交程度分析系统研制

分析群体近交程度是群体遗传学研究的基本内容．对指导动物育种和保种工作具有重要的意义。畜禽群体近交程度分析包括整理系谱资料、计算个体近交系数和群体平均近交系数、个体间亲缘系数和群体平均亲缘系数以及预测后代近交程度等内容．其核心内容是计算近交和亲缘系数、而计算近交和亲缘系数的方法目前主要有通径回路法与亲子协方差表法两种。相比之下以亲子协方差表法更适合一般系谱资料和容易计算机编程。本文围绕亲子协方差表法、在推导出亲子间近交和亲缘系数关系的基础上，采用先进的计算机语言研制了畜禽群体近交程度分析系统。１分…     

大白猪高繁母本新品系系谱结构及近交程度分析

本文通过整理各世代的系谱资料,系统分析了大白猪高繁母本新品系近交程度和世代组成的遗传结构。结果表明:大白猪高繁母本新品系的平均近交系数为1.23%,仍处于较低水平,近交系数年增量为0.239 1%,群体有效含量为209.12头。     

引进台系种猪近交情况分析及其育种策略

宁波福宁种猪有限公司从台湾福昌种猪有限公司引进台系大白原种公猪11头,母猪261头；台系长白公猪10头,母猪275头；杜洛克原种公猪6头,母猪83头.为了更好地利用这些原种猪,笔者采用SAS软件的INBREEO过程,根据引进种猪的个体系谱计算近交系数,结果近交系数范围均在0.0625至0.1250之间,近交个体的比例在3％以下.     

近交对中国荷斯坦牛泌乳性能的影响

为研究近交对中国荷斯坦牛泌乳性能影响，收集2008年5月至2022年2月河南37家奶牛场67 150头中国荷斯坦牛1～5胎次共128 282条泌乳性能记录数据，筛选后用于分析的数据共23 933头奶牛40 737条数据。个体近交系数F_ped是基于系谱信息采用R(v4.1.2)nadiv包计算，将奶牛按照近交系数分为无近交组(F_ped=0)、低近交组(F_ped≤6.25%)和高近交组(F_ped>6.25%)3个组。采用R(v4.1.2)方差分析(aov)函数，分析不同近交系数分组对泌乳性能指标的影响。采用DMU软件(v6)和动物模型按照总数据和分胎次对泌乳性能进行近交衰退评估，在评估模型中近交系数作为协变量，近交系数回归系数即为近交衰退效应值，并进行显著性检验。结果表明：近交对奶牛305 d产奶量、305 d乳脂量和305 d乳蛋白量有极显著影响；近交系数每增加1%,305 d产奶量、305 d乳脂量和305 d乳蛋白量分别减少8.55 kg(P<0.01)、0.22 kg(P<0....     

不同来源大白猪总产仔数近交衰退评估

旨在评估两个不同来源大白猪群体经过近8个世代的选育后总产仔数（total number of piglets born，TNB）近交衰退的程度。本研究对1 937头大白猪使用GeneSeek GGP Porcine HD芯片进行分型，其中1 039头来自加系大白猪和898头来自法系大白猪，且两品系均有表型记录和系谱记录，系谱共由3 086头大白猪组成。分别使用系谱、SNP和ROH进行个体近交系数估计，并将近交系数作为协变量利用动物模型对总产仔数进行近交衰退评估。为了精准定位导致总产仔数衰退的基因组片段，又进一步对每条染色体以及显著染色体分段计算近交系数并估计其效应，检测是否能引起总产仔数发生近交衰退现象。对于加系群体，F_ROH、F_GRM和F_PED估计的近交系数均值分别为0.124、0.042和0.013，其中F_ROH和F_PED相关最高，相关系数为0.358；对于法系群体，F_ROH、F_GRM和F_PED均值分别为0.123、0.052和0.007，其中F_ROH和F_GRM相关最高，相关系数为0.371。利用3种不同计算方法所得近交系数用于估计近交衰退时，加系群体的总产仔数均检测到显著的近交衰退，而且当F_ROH、F_GRM和F_PED每增加10%时，总产仔数分别减少0.571、0.341和0.823头；但法系群体仅有F_ROH估计的总产仔数检测到显著近交衰退，F_ROH每增加10%时，总产仔数减少0.690头。为了锁定相关的染色体和基因组区段，首先利用ROH估计每条染色体近交系数并进行近交衰退分析发现，加系群体中检测到第6、7、8和13号染色体产生了显著近的总产仔数交衰退，而法系群体未检测到与近交衰退相关的染色体。然后，又将与加系总产仔数近交衰退显著相关的4条染色体平均分为2、4、6、8个片段进行近交衰退检测，其中平均分成8段后的染色片段的长度范围为15.1~25.8 Mb。在第6、7和8号染色体分别检测到1、2和3个与总产仔数相关的近交衰退染色体片段。这些区域注释到了CUL7、MAPK14和PPARD基因与胎盘发育相关，AREG和EREG基因与卵母细胞成熟有关。本研究利用3种近交系数计算方法对两个不同来源的大白猪总产仔数进行近交衰退评估，在加系大白猪中3种估计方法都能检测到近交衰退的现象，而法系群体中只有F_ROH才能检测到。而且通过ROH方法进一步确定了能引起加系大白猪总产仔数衰退的4条染色体和6个特定的染色体区段，还注释到了与繁殖相关的候选基因。这为揭示近交衰退的遗传机制提供了新的研究手段，也为基因组选种选配提供了参考依据。     

近交系数的算法

<正> 通过计算交系数,可合理地估计近交程度。近交系数的计算则通用莱特的公式:F_x=Σ[(1/2)~(n+1)(1+F_A)],其中F_x为近交系数,n为从近交个体之父通过共同祖先到母的箭头数(通径数)。有几个通路要个别计算后相加,∑即总和的意思。F_A为共同祖先的近交系数,共同祖先不是近交个体时,F_A=0。公式即简化为F_x=∑(1/2)~(n+1)。     

小梅山猪最佳近交区域的研究

将江苏农林职业技术学院小梅山猪育种中心839窝纯种小梅山猪按其近交系数的大小(F=0～39.9%),分成9组,运用数量遗传原理,探讨小梅山猪以产活仔数为主目标性状的繁殖性能近交效应,发现小梅山猪最佳近交区域为近交系数0.1%～14.9%,较佳近交区域近交系数为15%～19.9%;衰退区域近交系数为20%～39.9%。结果表明:小梅山猪具有安全近交区域广、耐近交能力强等优良特性。     

保种猪场系谱记录、管理及群体遗传结构分析——以莱芜猪为例

本研究通过对莱芜猪国家级保种场进行调研,探讨目前我国地方猪保种场在系谱记录、档案管理、系谱应用中存在的共性问题。利用中国地方猪品种登记平台的登记规范对个体进行重新编码并梳理个体系谱信息,在此基础上利用R语言及MEGA软件进行遗传结构分析。通过利用平台及新建电子档案系谱纠正了系谱不完整、不准确等问题。遗传结构分析结果显示:当代群体理论平均近交系数(Ft)为2.15%,实际平均近交系数(Ft。)为3.5%,群体有效含量为92.19头,表明保种群部分个体采用了随机留种方式。所有个体可分为13个家系,但家系中个体数量分布不均衡。调研发现,保种场的系谱仍存在完整性、准确性等影响保种效果评价和影响开发利用的瓶颈问题,故在选种选配时应与时俱进,注重利用平台进行个体信息登记及育种软件利用。此外,本研究仅依靠系谱分析可能并不能反映群体真实的遗传结构,故有必要通过构建分子系谱开展进一步研究。     

畜禽近交系数的快速计算法

在畜禽育种工作中,尤其是在采用家系选择法进行育种时。每一个世代都要计算每个个体的近交系数。为下一个世代选种选配提供依据。在不使用微机的条件下,通常计算个体的近交系数先要画出个体的结构式系谱,然后根据通径计算近交系数。这样较     

Molecular and pedigree analysis applied to conservation of animal genetic resources: the case of Brazilian Somali hair sheep

The first registers of Somali sheep in Brazil are from the beginning of the 1900s. This breed, adapted to the dry climate and scarce food supply, is restricted in the northeast region of the country. Molecular marker technologies, especially those based on genotyping microsatellite and mtDNA loci, can be used in conjunction with breeding (pedigree analysis) and consequently the maintenance of genetic variation in herds. Animals from the Brazilian Somali Conservation Nuclei from Embrapa Sheep and Goats in Ceará State were used to validate genetic monitoring by traditional pedigree methods and molecular markers. Nineteen microsatellite markers and 404 base pairs from the control region of mtDNA were used. For total herd diversity, an average 5.32 alleles were found, with expected heterozygosity of 0.5896, observed heterozygosity of 0.6451, 0.4126 for molecular coancestrality, and coefficient of inbreeding (F _IS) was −0.095. Comparing molecular coancestrality means over the years, there was a consistent increase in this parameter within the herd, increasing from 0.4157 to 0.4769 in 2 years (approx. 12% variation). Sixteen mtDNA haplotypes were identified. Inbreeding and other estimates from genealogical analyses confirm the results from molecular markers. From these results, it is possible to state that microsatellites are useful tools in genetic management of herds, especially when routine herd recording is not carried out, or there were gaps in recent generations. As well as pedigree control, genetic diversity can be optimized. Based on the results, and despite herd recording in the herd of Brazilian Somali of Embrapa Sheep and Goats, additional management measures need to be carried out in this herd to reduce inbreeding and optimize genetic variation.     

Pedigree analysis and inbreeding depression on growth traits in Brazilian Marchigiana and Bonsmara breeds

The study of population structure by pedigree analysis is useful to identify important circumstances that affect the genetic history of populations. The intensive use of a small number of superior individuals may reduce the genetic diversity of populations. This situation is very common for the beef cattle breeds. Therefore, the objectives of the present study were to analyze the pedigree and possible inbreeding depression on traits of economic interest in the Marchigiana and Bonsmara breeds and to test the inclusion of the individual inbreeding coefficient (F(i)) or individual increases in inbreeding coefficient (ΔF(i)) in the genetic evaluation model for the quantification of inbreeding depression. The complete pedigree file of the Marchigiana breed included 29,411 animals born between 1950 and 2003. For the Bonsmara breed, the pedigree file included 18,695 animals born between 1988 and 2006. Only animals with at least 2 equivalent generations of known pedigree were kept in the analyses of inbreeding effect on birth weight, weaning weight measured at about 205 d, and BW at 14 mo in the Marchigiana breed, and on birth weight, weaning weight, and scrotal circumference measured at 12 mo in the Bonsmara breed. The degree of pedigree knowledge was greater for Marchigiana than for Bonsmara animals. The average generation interval was 7.02 and 3.19 for the Marchigiana and Bonsmara breed, respectively. The average inbreeding coefficient was 1.33% for Marchigiana and 0.26% for Bonsmara. The number of ancestors explaining 50% of the gene pool and effective population size computed via individual increase in coancestry were 13 and 97.79 for Marchigiana and 41 and 54.57 for Bonsmara, respectively. These estimates indicate reduction in genetic variability in both breeds. Inbreeding depression was observed for most of the growth traits. The model including ΔF(i) can be considered more adequate to quantify inbreeding depression. The inclusion of F(i) or ΔF(i) in the genetic evaluation model may not result in better fit to the data. A genetic evaluation with simultaneous estimation of inbreeding depression can be performed in Marchigiana and Bonsmara breeds, providing additional information to producers and breeders.     

Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis

The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability in the Murrah dairy breed of water buffalo (Bubalus bubalis) in Brazil. Pedigree analysis was performed on 5,061 animals born between 1972 and 2002. The effective number of founders (fe) was 60, representing 6.32?% of the potential number of founders. The effective number of ancestors (fa) was 36 and the genetic contribution of the 17 most influent ancestors explained 50?% of the genetic variability in the population. The ratio fe/fa (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.66. Completeness level for the whole pedigree was 76.8, 49.2, 27.7, and 12.8?% for, respectively, the first, second, third, and fourth known parental generations. The average inbreeding values for the whole analyzed pedigree and for inbreed animals were, respectively, 1.28 and 7.64?%. The average relatedness coefficient between individuals of the population was estimated to be 2.05?%??the highest individual coefficient was 10.31?%. The actual inbreeding and average relatedness coefficient are probably higher than estimated due to low levels of pedigree completeness. Moreover, the inbreeding coefficient increased with the addition of each generation to the pedigree, indicating that incomplete pedigrees tend to underestimate the level of inbreeding. Introduction of new sires with the lowest possible average relatedness coefficient and the use of appropriate mating strategies are recommended to keep inbreeding at acceptable levels and increase the genetic variability in this economically important species, which has relatively low numbers compared to other commercial cattle breeds. The inclusion of additional parameters, such as effective number of founders, effective number of ancestors, and fe/fa ratio, provides better resolution as compared to the inclusion of inbreeding coefficient and may help breeders and farmers adopt better precautionary measures against inbreeding depression and other deleterious genetic effects.     

Population structure of Mazandaran native fowls using pedigree analysis

The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability of the Mazandaran native fowls in Iran by quantifying the pedigree completeness index, effective population size, genetic diversity, inbreeding level, and individual increase in inbreeding. The pedigree completeness analysis showed 3.31 full, 10.19 maximum, and 6.30 equivalent generations. The effective number of founders (f _e) was 131, representing 5% of the potential number of founders. The effective number of ancestors (f _a) was 81, and the genetic contribution of the 37 most influent ancestors explained 50% of the genetic variability in the population. The ratio f _e/f _a (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.62. The inbreeding coefficient increased over generations and the average was 1.93%. The average relatedness coefficient between individuals of the population was estimated to be 2.59%. The effective population size, based on the number of full generations, was 56. Family size analysis showed that fewer males than females were used, resulting in the observed levels of inbreeding. Average inbreeding coefficient in the Mazandaran native fowls can be regarded to be below critical levels. However, considering the relationship coefficients of individuals is recommended to aid maintaining genetic diversity of Mazandaran native fowls.     

Variance of actual inbreeding derived from the number and variance of chromosome segment

The inbreeding coefficient (F) is used as a central parameter inferring a proportion of alleles identical by descent within an individual and by genetic variability within a population. The actual inbreeding coefficient varies around a central value, the inbreeding coefficient. C ockerham and W eir (1983) derived the method for computing the variance of inbreeding while reviewing several other methods. The variance of inbreeding in their report was considered to be of two components: one within population and the other between population of varied pedigrees. If pedigree is fixed, F is easily computed for an individual by the standard method (F alconer 1989). For domestic animals, pedigree information is usually available because it is requisite for a programme of genetic improvement. In this study, the variance of inbreeding coefficient was derived for an individual with a pedigree having a single path to a foundation animal.     

On individual‐specific prediction of hidden inbreeding depression load

Inbreeding depression is caused by increased homozygosity in the genome and merges two genetic mechanisms, a higher impact from recessive mutations and the waste of overdominance contributions. It is of major concern for the conservation of endangered populations of plants and animals, as major abnormalities are more frequent in inbred families than in outcrosses. Nevertheless, we lack appropriate analytical methods to estimate the hidden inbreeding depression load (IDL) in the genome of each individual. Here, a new mixed linear model approach has been developed to account for the inbreeding depression‐related background of each individual in the pedigree. Within this context, inbred descendants contributed relevant information to predict the IDL contained in the genome of a given ancestor; moreover, known relationships spread these predictions to the remaining individuals in the pedigree, even if not contributing inbred offspring. Results obtained from the analysis of weaning weight in the MARET rabbit population demonstrated that the genetic background of inbreeding depression distributed heterogeneously across individuals and inherited generation by generation. Moreover, this approach was clearly preferred in terms of model fit and complexity when compared with classical approaches to inbreeding depression. This methodology must be viewed as a new tool for a better understanding of inbreeding in domestic and wild populations.     

Pedigree information reveals moderate to high levels of inbreeding and a weak population structure in the endangered Catalonian donkey breed

The Catalonian donkey is one of the most endangered donkey breeds in the world. At present, five main subpopulations exist: AFRAC, which consists of many genetically connected Catalonian localities; Berga, which consists of a single herd located also in Catalunya but under private management; and three minor non‐Catalonian subpopulations (Huesca, Sevilla and Toledo). In this study, we analysed the pedigree information of the Catalonian donkey herdbook to assess the genetic diversity and population structure of the breed. We found that the Catalonian donkey has suffered an important loss of genetic diversity and moderate to high increases of inbreeding because of the abuse of a few individuals in matings. This scenario is mainly characterized by the fact that both the effective number of founders and ancestors for the whole population was 70.6 and 27, respectively, while the equivalent number of founders was 146.5 and the number of ancestors explaining overall genetic variability was 93. In addition, only 14% of animals born between the 1960s and 1970s were significantly represented in the pedigree. Our results also show that subpopulations where breeders exchanged reproductive individuals had low levels of inbreeding and average relatedness. One subpopulation, Berga, was reproductively isolated and showed high levels of inbreeding (F = 7.22%), with average relatedness (AR = 6.61%) playing an important role in increasing the values of these coefficients in the whole pedigree. Using genealogical F‐statistics we have found little evidence of population structuring (F_ST = 0.0083) with major genetic differences among non‐Catalonian subpopulations.     

The influence of selection and epistasis on inbreeding depression estimates

Inbreeding depression estimates obtained by regression of the individual performance on the inbreeding were studied by stochastic simulation under various genetic models (solely additive, partial dominance, overdominance and epistasis), and mating strategies (random mating versus selection). In all models, inbreeding depression estimates based on the individual pedigree inbreeding coefficients were compared with estimates based on the true level of autozygosity. For the model with partial dominance and selection, the estimates of inbreeding depression from pedigree information were more negative (lower) than those based on true inbreeding coefficients whereas, in contrast, they were less negative (higher) for the models with overdominance and selection. The difference in the variation of true and pedigree individual inbreeding coefficient indicated that biased estimates might occur even in random mating populations. The estimation of inbreeding depression was further complicated when epistatic effects were present. The sign and the magnitude of the inbreeding effect (depression) estimates might be rather heterogeneous if additive by dominance effects are present because they are strongly dependent on the gene frequency. It was also shown that inbreeding depression is possible in models with negative additive by dominance effects. In models with dominance by dominance inheritance it was difficult to assess the non-linear relationship between performance and inbreeding, while at the same time, non-linear estimates based on pedigree information were extremely biased. The results obtained indicate that new or additional methodologies are required if reliable conclusions about consequences of inbreeding depression are needed.     

Estimation of inbreeding and effective population size of full‐blood wagyu cattle registered with the American Wagyu Cattle Association

The objective of this research was to examine the population structure of full‐blood (100%) Wagyu cattle registered in the United States with the American Wagyu Association, with the aim of estimating and comparing the levels of inbreeding from both pedigree and genotypic data. A total of 4132 full‐blood Wagyu cattle pedigrees were assessed and used to compute the inbreeding coefficients (F_IT and F_ST) and the effective population size (N_e) from pedigree data for the period 1994 to 2011. In addition to pedigree analysis, 47 full‐blood Wagyu cattle representing eight prominent sire lines in the American Wagyu cattle population were genotyped using the Illumina BovineSNP50 BeadChip. Genotypic data were then used to estimate genomic inbreeding coefficients (F_ROH) by calculating runs of homozygosity. The mean inbreeding coefficient based on the pedigree data was estimated at 4.80%. The effective population size averaged 17 between the years 1994 and 2011 with an increase of 42.9 in 2000 and a drop of 1.8 in 2011. Examination of the runs of homozygosity revealed that the 47 Wagyu cattle from the eight prominent sire lines had a mean genomic inbreeding coefficient (F_ROH) estimated at 9.08% compared to a mean inbreeding coefficient based on pedigree data of 4.8%. These data suggest that the mean genotype inbreeding coefficient of full‐blood Wagyu cattle exceeds the inbreeding coefficient identified by pedigree. Inbreeding has increased slowly at a rate of 0.03% per year over the past 17 years. Wagyu breeders should continue to utilize many sires from divergent lines and consider outcrossing to other breeds to enhance genetic diversity and minimize the adverse effects of inbreeding in Wagyu.     

Rates of inbreeding and genetic adaptation for populations managed as herds in zoos with a rotational mating system or with optimized contribution of parents

This study compares two genetic management scenarios for species kept in herds, such as deer. The simulations were designed so that their results can be extended to a wide range of zoo populations. In the first scenario, the simulated populations of size 3 × 20, 6 × 40 or 20 × 60 (herds × animals in herd) were managed with a rotational mating (RM) scheme in which 10%, 20% or 50% of males were selected for breeding and moved between herds in a circular fashion. The second scenario was based on optimal contribution theory (OC). OC requires an accurate pedigree to calculate kinship; males were selected and assigned numbers of offspring to minimize kinship in the next generation. RM was efficient in restriction of inbreeding and produced results comparable with OC. However, RM can result in genetic adaptation of the population to the zoo environment, in particular when 20% or less males are selected for rotation and selection of animals is not random. Lowest rates of inbreeding were obtained by combining OC with rotation of males as in the RM scheme. RM is easy to implement in practice and does not require pedigree data. When full pedigree is available, OC management is preferable.