Evaluation of inbreeding and genetic diversity in Japanese Shorthorn cattle by pedigree analysis

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 (N_ge) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on N_ge 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.     

Analysis of Factors Influencing the Mortality Rates of Xinjiang Brown Cattle and Holstein Cattle Calves

Calves health were related to the quality of entire herd,reducing the mortality rate of calves had important significance to improve the efficiency of pasture. In order to better understand the mortality rate and influencing factors on calves death,the combined methods of field survey and data analysis were adopted to analyze the mortality rate of Xinjiang Brown calves and Holstein calves. Based on the 7 157 calves records of a cattle farm in nearly 16 years, preliminary statistical analysis were taken on these data in Excel. According to the characteristics of Xinjiang climate, the seasons was divided into four parts that from March to May was spring, June to August was summer, September to November was autumn, and December to next year February was winter. Varieties of breeds were the Xinjiang Brown calves and Holstein calves, the years of birth from 1999 to 2014 was divided into 16 levels, the sex of born calves were divided into 2 levels that males and females. The effects of different years, breeds, seasons of birth, sex of calves, and different ages on the mortality rate of Xinjiang Brown calves were analyzed using SAS 8.1 software. The results showed that different breeds, years, seasons of birth, and sex of calves affected the mortality rate of Xinjiang Brown calves with different extent,the mortality rate of Xinjiang Brown calves was higher than Holstein calves (P <0.05);At one month old, the mortality rate of Xinjiang Brown calves was higher than Holstein calves (P <0.05);The mortality rate in 2006, 2009 and 2010 were higher than other years (P <0.05), the calf mortality rate was relatively small from 2011 to 2014;The mortality rate of winter seasons was higher than summer (P <0.05). To reduce the mortality rate of calves was a problem that could not be ignored in the process of cattle breeding. The calves mortality rate was affected by genetic and environmental factors, only by controlling the various environmental factors with reasonable ways, could improve the health level of calves.     

新疆褐牛与荷斯坦牛犊牛死亡率的影响因素分析

犊牛的健康状况关系到整个牛群的质量,降低犊牛的死亡率对提高牧场的效益具有十分重要的意义。为了掌握犊牛死亡率及影响犊牛死亡的因素,试验采取实地调查与资料分析相结合的方法,对新疆褐牛犊牛及荷斯坦牛犊牛死亡率进行了分析,通过Excel对某牛场近16年的7 157条产犊记录进行初步统计,根据新疆的气候特点划分季节,3~5月为春季,6~8月为夏季,9~11月为秋季,12~次年2月为冬季;品种为新疆褐牛犊牛和荷斯坦牛犊牛,年份从1999年到2014年分为16个水平,出生犊牛性别划分为公、母2个水平。利用SAS 8.1软件分析不同年份、品种、出生季节、犊牛性别及不同月龄等因素对新疆褐牛与荷斯坦牛犊牛死亡率的影响,结果表明,品种、年份、产犊季节和犊牛性别对新疆褐牛及荷斯坦牛犊牛死亡率有不同程度的影响,新疆褐牛的犊牛死亡率显著高于荷斯坦牛（P＜0.05）,1月龄时,新疆褐牛的犊牛死亡率显著高于荷斯坦牛（P＜0.05）;2006、2009、2010年的犊牛死亡率显著高于其他年份（P＜0.05）,在2011~2014年,犊牛的死亡率相对较少;冬季的死亡率显著高于夏季（P＜0.05）。降低犊牛的死亡率是牛群繁育过程中一个不可忽略的问题。犊牛的死亡率受到遗传和环境因素的共同影响,只有将各种环境因素给予合理控制,才能提高犊牛的健康水平。     

Investigation of genetic diversity and inbreeding in a Japanese native horse breed for suggestions on its conservation

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.     

Comparison of Estimated Genetic Connectedness among Three Herds of Chinese Holstein Cattle

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.     

Recent breeding history of dog breeds in Sweden: modest rates of inbreeding,extensive loss of genetic diversity and lack of correlation between inbreeding and health

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.     

基于系谱和基因组信息估计荷斯坦青年母牛体重性状遗传参数

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～...     

Pedigree- and marker-based methods in the estimation of genetic diversity in small groups of Holstein cattle

Genetic diversity is often evaluated using pedigree information. Currently, diversity can be evaluated in more detail over the genome based on large numbers of SNP markers. Pedigree- and SNP-based diversity were compared for two small related groups of Holstein animals genotyped with the 50 k SNP chip, genome-wide, per chromosome and for part of the genome examined. Diversity was estimated with coefficient of kinship (pedigree) and expected heterozygosity (SNP). SNP-based diversity at chromosome regions was determined using 5-Mb sliding windows, and significance of difference between groups was determined by bootstrapping. Both pedigree- and SNP-based diversity indicated more diversity in one of the groups; 26 of the 30 chromosomes showed significantly more diversity for the same group, as did 25.9% of the chromosome regions. Even in small populations that are genetically close, differences in diversity can be detected. Pedigree- and SNP-based diversity give comparable differences, but SNP-based diversity shows on which chromosome regions these differences are based. For maintaining diversity in a gene bank, SNP-based diversity gives a more detailed picture than pedigree-based diversity.     

蹄变形奶牛血液流变学的研究

为了更深入探讨奶牛变形蹄的发病机理及对奶牛变形蹄的预防和治疗提供更科学的理论依据。选择长沙地区20头中国荷斯坦牛，系统检测了变形蹄和正常蹄奶牛在夏季（6月份）和冬季（12月份）血液流变学主要指标。夏季时，1S-1、3S-1、5S-1、10S-1、30S-1、60S-1切变率下，变形蹄奶牛全血粘度高于正常蹄奶牛，有显著差异（P〈0．05）。变形蹄奶牛低切全血还原粘度极显著高于正常蹄奶牛（P〈0．01）。变形蹄奶牛红细胞压积高于正常蹄奶牛，差异显著（P〈0．05）。冬季时，5S^-1、10S^-1、30S^-1、200S^-1切变率下，变形蹄奶牛全血粘度高于正常蹄奶牛（P〈0．05）。变形蹄奶牛血浆粘度高于正常蹄奶牛，有显著差异（P〈0．05）。变形蹄奶牛红细胞沉降率较快，也有显著差异（P〈0．05）。变形蹄奶牛与全血粘度增高和红细胞聚集性增强具有相关性。     

牦牛,黑白花牛及其远缘杂种RAPD标记的初步研究

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     

Genetic diversity and genomic inbreeding in Japanese Black cows in the islands of Okinawa Prefecture evaluated using single-nucleotide polymorphism array

Maintaining genetic diversity and inbreeding control are important in Japanese Black cattle production, especially in remote areas such as the islands of Okinawa Prefecture. Using a single-nucleotide polymorphism (SNP) array, we evaluated the genetic diversity and genomic inbreeding in Japanese Black cows from the islands of Okinawa Prefecture and compared them to those from other locations across Japan. Linkage disequilibrium decay was slower in cows in the islands of Okinawa Prefecture. The estimated effective population size declined over time in both populations. The genomic inbreeding coefficient (F_ROH) was estimated using long stretches of consecutive homozygous SNPs (runs of homozygosity; ROH). F_ROH was higher in the cows on the islands of Okinawa Prefecture than on other locations. In total, 818 ROH fragments, including those containing NCAPG and PLAG1, which are major quantitative trait loci for carcass weight in Japanese Black cattle, were present at significantly higher frequencies in cows in the islands of Okinawa Prefecture. This suggests that the ROH fragments are under strong selection and that cows in the islands of Okinawa Prefecture have low genetic diversity and high genomic inbreeding relative to those at other locations. SNP arrays are useful tools for evaluating genetic diversity and genomic inbreeding in cattle.     

Relationships between Longevity and Linear Type Traits in Holstein Cattle Population of Southern Africa

Relationships between longevity and linear type traits were estimated using data on 34,201 cows with lifetime information and linear type scores. The longevity trait considered was the number of lactations initiated and the linear type traits were rump height, body depth, angularity, rear udder height, fore udder attachment, udder depth, fore teat placement and fore teat length. Fixed effects included in the models were herd year, season of calving and herd-date of classification-classifier and days in milk. Age at first calving and age at classification were included as linear and quadratic covariates. Heritability estimates were low for longevity and moderate for most type traits except rump height and fore teat length. All the phenotypic correlations between longevity and the linear type traits were slightly positive (0.01 to 0.09) except the relationships with rump height and fore teat length which were -0.01 and -0.02, respectively. Genetic correlations between longevity and udder traits as well as angularity were moderate to high and positive (0.22 to 0.48). The only notable negative genetic correlations were longevity with body depth and fore teat length (-0.15 and -0.07, respectively). The genetic correlations suggest that selection for udder traits and angularity should improve longevity in the Holstein cattle population.     

Selection on multiple QTL with control of gene diversity and inbreeding for long-term benefit

The purpose of this study was to develop and investigate selection strategies that aim at maximizing long-term genetic response while conserving gene diversity and controlling inbreeding in populations of limited effective size, assuming complete knowledge of all genes affecting a quantitative trait. Three selection strategies were proposed to select on 100 quantitative trait loci (QTL) and compared with truncation selection on breeding value. Alternative selection strategies aimed at maximizing the average breeding value of parents with a penalty on (1) the number of unfavourable QTL genotypes among parents (OS-I), (2) the negative of the logarithm of the frequency of the favourable allele at each QTL among parents (OS-II), and (3) the average pedigree relationship among parents (OS-III). When all QTL and their effects were known, the strategies examined were able to obtain extra long-term responses, conserve QTL diversity and reduce inbreeding, compared with truncation selection. Strategy OS-II was the most effective in conserving QTL diversity and OS-III in reducing inbreeding. By changing the magnitude of the penalties applied, the impact on long-term response, inbreeding and diversity can be controlled. Extra long-term responses over truncation selection of OS-I and OS-II were even greater when effects of QTL were estimated rather than assumed known, indicating the applicability of results to practical strategies for marker-assisted selection. Extra responses are expected to be reduced for larger population sizes.     

Estimation of ancestral inbreeding effects on stillbirth,calving ease and birthweight in German Holstein dairy cattle

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.     

闭锁群体BLUP选择下遗传方差和近交系数的变化

采用计算机随机模拟方法模拟了在一个闭锁群体内连续对单个性状进行 1 5个世代选择的情况。选择过程中世代不重叠 ,每个世代的种畜根据动物模型最佳线性无偏预测 (BLUP)法估计的育种值进行选留 ,并在此基础上系统地比较了不同群体规模、公母比例和性状遗传力对群体遗传方差和近交系数变化的影响。结果表明 ,扩大育种群规模、增加公畜比例以及对低遗传力性状进行选择时 ,群体遗传方差降低的速度和近交系数上升的速度会更慢 ,在长期选择时可望获得更大的持续进展和适宜的近交增量     

遗传标记在苜蓿遗传多样性研究中的应用

介绍了当前广泛应用的苜蓿遗传多样性研究技术及其研究现状,包括苜蓿Medicago形态学和等位酶分析、种质资源和种内杂合性、进化与亲缘关系、抗逆性以及遗传连锁作图等几个方面的研究概况,同时提出了今后苜蓿遗传多样性分子标记研究的重点发展方向.     

西安荷斯坦奶牛群5个基因座位遗传多态性的PCR-RFLP分析

应用PCR-RFLP方法对西安荷斯坦牛的κ-en、β-lg、β-lg5′侧翼区、CSN1S2、IGFBP-3共5个基因座位进行了多态性分析。结果表明，在西安荷斯坦牛群中，没有发现携带CSN1S2^P等位基因的个体，其多态信息含量为0。κ-en基因座位呈现低度多态(PIC=0．2366)，β-lg、β-lg5′侧翼区、IGFBP-3基因座位的多态信息含量分别为0．3168、0．3689、0．4439，均呈现中度多态。κ-en、β-lg、β-lg5′侧翼区、IGFBP-3、CSNIS2基因座位的杂合度和DNA多态度分别为0．2742、0．3947、0．4879、0．4891、0和0．0255、0．0116、0．0333、0．0112、0。而且，在西安荷斯坦牛群中，κ-en、β-lg、β-lg5′侧翼区、IGFBP-3共4个基因座位均处于Hardy-Weinberg平衡状态，CSN1S2基因座位处于纯合状态。     

荷斯坦泌乳牛4种炎性细胞因子随胎次变化规律的研究

本试验选择北京地区5个牛场不同胎次(1胎、3胎、5胎及以上)、无临床疾病记录的150头荷斯坦泌乳牛,于2017年7月至8月测定促炎细胞因子肿瘤坏死因子-α(TNF-α)、白细胞介素-6(IL-6)和抑炎细胞因子白细胞介素-10(IL-10)、转化生长因子-β(TGF-β)4种血液炎性细胞因子浓度,利用SAS 9.4软件GLM过程分析血液炎性细胞因子浓度随胎次变化的规律,所用固定模型考虑了牛场、胎次、泌乳阶段等因素影响,同时进行各细胞因子间Pearson相关性分析;利用GLM过程分析炎性细胞因子对产奶性能的影响,产奶性能指标包括日产奶量、校正日产奶量、乳蛋白率、乳脂率、乳糖率,所用固定模型考虑了牛场、胎次、泌乳阶段、炎性细胞因子水平等因素的影响。结果显示:荷斯坦牛血液IL-6和TGF-β浓度随胎次升高显著降低;整体来说,IL-6和TGF-β显著正相关,IL-10和TGF-β显著负相关;5胎及以上胎次奶牛各细胞因子间相关关系均不显著;5胎及以上胎次奶牛日产奶量、校正日产奶量和乳糖率显著降低;高TNF-α组的奶牛日产奶量显著低于低TNF-α组,高IL-10组奶牛乳脂率和校正日产奶量显著高于低IL-10组。综上,高胎次奶牛生产性能的降低可能与炎性细胞因子的变化有关。     

克隆荷斯坦牛的生长、繁育和生产性能

本文报道了12头加系荷斯坦克隆母牛的生长发育、配种繁殖和生产性能状况．比较了克隆牛和非克隆牛的部分生产指标。结果表明,在良好的饲养管理条件下,克隆牛的平均初生重、6月龄、18月龄和1产后体重分别达41．6、191．8、520．8和651．1kg;第1次配种月龄为16．7个月。受孕月龄为19．2个月,产犊月龄为28．6个月;第1泌乳期305d产奶量为7029．7kg,乳脂率3．73％,乳蛋白率3．27％．符合加系荷斯坦牛的生产性能指标。克隆牛生长发育和产奶量指标均略高于非克隆牛,但产间距比非克隆牛长。克隆牛疾病发生情况、类别、治疗效果和非克隆牛相似：有2头克隆牛死于心脏病．其原因有待作深入研究。     

中国荷斯坦牛GlyCAM1基因遗传多态性的研究

以273头中国荷斯坦牛为研究对象,利用CRS—PCR、PCR—SSCP及DNA测序技术检测了GlyCAM1基因外显子3、内含子3的遗传多态性。结果表明：GlyCAM1基因分别在外显子3和内含子3的第2081（A／C）、2417（C／T）位存在突变,2个位点的等位基因频率A／B分别为0．7525,0．2475和0．9046,0．0954;经菇。适合性检验,中国荷斯坦牛内含子3的突变达到Hardy—Weinberg平衡状态（P〉0．05）,但其外显子3的突变未达到Hardy—Weinberg平衡状态（P〈0．05）。