Genetic distances within and across cattle breeds as indicated by biallelic AFLP markers

We tested the use of biallelic Amplified fragment length polymorphism (AFLP) polymorphisms for the estimation of relative genetic distances of cattle individuals within or across breeds. An allele permutation procedure was developed to estimate the stochastic variation of the genetic distance that is inherent to a given dataset. In a panel of 47 Holstein-Friesian cattle analysed with 248 polymorphic markers, the average genetic distance of bulls selected for breeding was slightly lower than the distance of the cows. The observed standard deviation (SD) of the distance indicated genetic subdivision, which for the bulls was explained by variation in the additive relationship derived from herdbook data. Animals from three different breeds, the highly selected Holstein-Friesian, the Italian Brown and the historic Maremmana, were compared on the basis of 106 polymorphic markers. No breed-specific fragments were observed. The mean pair-wise genetic distance within breeds was 85% of the value across breeds, but principal coordinates analysis clustered the animals according to their breed of origin. Calculation of distances between the breeds indicated a relatively divergent position of the Maremmana, relative to the two other breeds. However, biallelic markers indicate that the process of breed formation had only a limited effect on the diversity at marker loci.     

Relationships between the endangered Pustertaler-Sprinzen and three related European cattle breeds as analysed with 20 microsatellite loci

We estimated the genetic relationships between the endangered German Pustertaler-Sprinzen cattle breed and the Pinzgauer, Vosges and Simmental breeds--decided upon after consultation of the available historical literature. Within-breed diversity of the four breeds was also assessed. Twenty microsatellite markers were amplified in 27-50 unrelated individuals from populations of each breed. Within-breed variation was estimated from average heterozygosity values and mean number of alleles. Breed relationships were evaluated by genetic distance and a neighbour-joining tree was calculated from these estimates. Bootstrap resampling of loci tested the robustness of the tree topology obtained. A tree was also constructed from distance matrices using individual animals as operational taxonomic units. From both the average heterozygosity values and mean number of alleles calculated, the Pustertaler breed appears to be no more genetically impoverished than the other breeds analysed. The breed tree showed an 85% support for the Pustertaler-Pinzgauer grouping, and this result is echoed in the genetic distance values and allele-sharing individual tree.     

中国肉牛分子与基因修饰育种研究进展

随着世界肉牛产业科技的快速发展,我国肉牛产业的整体水平得到明显提高并取得丰硕成果。肉牛育种技术实现了由常规杂交育种向分子标记辅助育种、全基因组选择育种和基因组修饰育种的技术跨越,揭示出大量与生长发育、肉质品质、繁殖与疾病等相关的候选基因与分子标记,并逐步应用于肉牛育种实践。与生长发育性状相关的基因或分子标记主要集中在生长激素基因、生肌调节因子家族、肌肉生长抑制因子和胰岛素样生长因子等;参与肉质形成的基因主要集中在脂肪酸运输与沉积相关信号通路、钙蛋白酶信号通路、生肌调节因子家族与肌肉生长抑制因子等;繁殖性状相关基因或分子标记主要集中在GnRH-FSHR-LH、生长分化因子9、催乳素受体和FoxO1等;抗病相关基因主要有MHC基因家族、TOLL样受体4基因等。目前,利用精准基因编辑技术已培育出促生长发育与提高肉品质的肉牛育种新材料。本文总结了近年来我国在肉牛分子与基因组修饰育种领域取得的研究进展,以期为我国肉牛遗传育种技术研究提供参考和借鉴。     

Managing the risk of comparing estimated breeding values across flocks or herds through connectedness: a review and application

Comparing predicted breeding values (BV) among animals in different management units (e.g. flocks, herds) is challenging if units have different genetic means. Unbiased estimates of differences in BV may be obtained by assigning base animals to genetic groups according to their unit of origin, but units must be connected to estimate group effects. If many small groups exist, error of BV prediction may be increased. Alternatively, genetic groups can be excluded from the statistical model, which may bias BV predictions. If adequate genetic connections exist among units, bias is reduced. Several measures of connectedness have been proposed, but their relationships to potential bias in BV predictions are not well defined. This study compares alternative strategies to connect small units and assesses the ability of different connectedness statistics to quantify potential bias in BV prediction. Connections established using common sires across units were most effective in reducing bias. The coefficient of determination of the mean difference in predicted BV was a perfect indicator of potential bias remaining when comparing individuals in separate units. However, this measure is difficult to calculate; correlated measures such as prediction errors of differences in unit means and correlations among prediction errors are suggested as practical alternatives.     

Genetic relationships among European cattle breeds

Genetic relationships among 37 European cattle breeds were investigated using blood group and serum protein polymorphisms. The 18 859 animals included in the study represented a random sample from pedigree populations in the UK. Within-breed variation was estimated by average heterozygosity and number of alleles observed, and breed relationships were evaluated by genetic distance. Standard errors of the heterozygosity, number of alleles and genetic distance were obtained by bootstrapping. The significance of breed differences was tested using an exact test of differentiation. French, Italian and Channel Island breeds were found to have generally higher heterozygosities and a greater number of alleles than breeds from mainland Britain and North Europe. Genetic distances ranged between 0·011 (±0·005) and 0·309 (±0·071). Two major breed groups were identified; a group of French, Italian and Channel Island breeds together with the Simmental and Gelbvieh, and a second group consisting of the mainland British and North European breeds. The exact test of breed differentiation showed all breeds to be significantly different from one another ( P < 0·0001). Overall relationships among breeds reflected their geographical origin and common ancestry rather than the agricultural use for which the breeds have been selected.     

Genomic reaction norm models exploiting genotype × environment interaction on sexual precocity indicator traits in Nellore cattle

Brazilian beef cattle are raised predominantly on pasture in a wide range of environments. In this scenario, genotype by environment (G×E) interaction is an important source of phenotypic variation in the reproductive traits. Hence, the evaluation of G×E interactions for heifer’s early pregnancy (HP) and scrotal circumference (SC) traits in Nellore cattle, belonging to three breeding programs, was carried out to determine the animal’s sensitivity to the environmental conditions (EC). The dataset consisted of 85 874 records for HP and 151 553 records for SC, from which 1800 heifers and 3343 young bulls were genotyped with the BovineHD BeadChip. Genotypic information for 826 sires was also used in the analyses. EC levels were based on the contemporary group solutions for yearling body weight. Linear reaction norm models (RNM), using pedigree information (RNM_A) or pedigree and genomic information (RNM_H), were used to infer G×E interactions. Two validation schemes were used to assess the predictive ability, with the following training populations: (a) forward scheme—dataset was split based on year of birth from 2008 for HP and from 2011 for SC; and (b) environment-specific scheme—low EC (−3.0 and −1.5) and high EC (1.5 and 3.0). The inclusion of the H matrix in RNM increased the genetic variance of the intercept and slope by 18.55 and 23.00% on average respectively, and provided genetic parameter estimates that were more accurate than those considering pedigree only. The same trend was observed for heritability estimates, which were 0.28–0.56 for SC and 0.26–0.49 for HP, using RNM_H, and 0.26–0.52 for SC and 0.22–0.45 for HP, using RNM_A. The lowest correlation observed between unfavorable (−3.0) and favorable (3.0) EC levels were 0.30 for HP and −0.12 for SC, indicating the presence of G×E interaction. The G×E interaction effect implied differences in animals’ genetic merit and re-ranking of animals on different environmental conditions. SNP marker–environment interaction was detected for Nellore sexual precocity indicator traits with changes in effect and variance across EC levels. The RNM_H captured G×E interaction effects better than RNM_A and improved the predictive ability by around 14.04% for SC and 21.31% for HP. Using the forward scheme increased the overall predictive ability for SC (20.55%) and HP (11.06%) compared with the environment-specific scheme. The results suggest that the inclusion of genomic information combined with the pedigree to assess the G×E interaction leads to more accurate variance components and genetic parameter estimates.     

Random amplified polymorphic DNA in cattle and sheep: application for detecting genetic variation

The present study investigated the use of the random amplified polymorphic DNA (RAPD) method to detect genetic variation in cattle and sheep. The animals studied consisted of samples from five Finnish cattle breeds: native Eastern (18 animals), Northern (24), Western Finncattle (24), Finnish Ayrshire (24), and Finnish Friesian (18); as well as a white (6 animals) and a grey (9) colour type of Finnsheep. The cattle and sheep populations were analysed with 11 and 13 RAPD primers demonstrating the most repeatable amplification pattern. Two out of ten RAPD fragments tested by cross hybridization showed homology between the two species. The RAPD method did not prove efficient for finding new polymorphisms in either species, because we found only three polymorphic RAPD markers for cattle and seven markers for sheep with different allele frequencies between the breeds. Although there is a greater presence of polymorphic RAPD markers in sheep, according to the similarity indices the sheep populations showed a higher degree of homogeneity than the cattle breeds. However, the interbreed and intrabreed similarity indices for cattle did not suggest any significant differentiation of the Finnish breeds, contrary to earlier results based on blood group and protein polymorphism.     

Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size

In times of rapid global and unforeseeable environmental changes, there is an urgent need for a sustainable cattle breeding policy, based on a global view. Most of the indigenous breeds are specialized in a particular habitat or production system but are rapidly disappearing. Thus, they represent an important resource to meet present and future breeding objectives. Based on 105 microsatellites, we obtained thorough information on genetic diversity and population structure of 16 cattle breeds that cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the North-West of Europe. Breeds under strict artificial selection and indigenous breeds under traditional breeding schemes were included. The overall results showed that the genetic diversity is widespread in Buša breeds in the Anatolian and Balkan areas, when compared with the alpine and north-western European breeds. Our results reflect long-term evolutionary and short-term breeding events very well. The regular pattern of allele frequency distribution in the entire cattle population studied clearly suggests conservation of rare alleles by conservation of preferably unselected traditional breeds with large effective population sizes. From a global and long-term conservation genetics point of view, the native and highly variable breeds closer to the domestication centre could serve as valuable sources of genes for future needs, not only for cattle but also for other farm animals.     

Breed differences in frequency of BoLA specificities*

A total of 675 cattle of five purebred and one crossbred group were tested for lymphocyte antigens. The purebred animals represented progeny of 107 sires. Lymphocytotoxicity sera obtained from parous cows were used to detect six antigens which are controlled by codominant alleles at the BoLA-TxA locus. Gene frequencies for the six alleles varied within breeds and large differences were observed between breeds for a given allele.     

Should genetic groups be fitted in BLUP evaluation? Practical answer for the French AI beef sire evaluation

Some analytical and simulated criteria were used to determine whether a priori genetic differences among groups, which are not accounted for by the relationship matrix, ought to be fitted in models for genetic evaluation, depending on the data structure and the accuracy of the evaluation. These criteria were the mean square error of some extreme contrasts between animals, the true genetic superiority of animals selected across groups, i.e. the selection response, and the magnitude of selection bias (difference between true and predicted selection responses). The different statistical models studied considered either fixed or random genetic groups (based on six different years of birth) versus ignoring the genetic group effects in a sire model. Including fixed genetic groups led to an overestimation of selection response under BLUP selection across groups despite the unbiasedness of the estimation, i.e. despite the correct estimation of differences between genetic groups. This overestimation was extremely important in numerical applications which considered two kinds of within-station progeny test designs for French purebred beef cattle AI sire evaluation across years: the reference sire design and the repeater sire design. When assuming a priori genetic differences due to the existence of a genetic trend of around 20% of genetic standard deviation for a trait with h² = 0.4, in a repeater sire design, the overestimation of the genetic superiority of bulls selected across groups varied from about 10% for an across-year selection rate p = 1/6 and an accurate selection index (100 progeny records per sire) to 75% for p = 1/2 and a less accurate selection index (20 progeny records per sire). This overestimation decreased when the genetic trend, the heritability of the trait, the accuracy of the evaluation or the connectedness of the design increased. Whatever the data design, a model of genetic evaluation without groups was preferred to a model with genetic groups when the genetic trend was in the range of likely values in cattle breeding programs (0 to 20% of genetic standard deviation). In such a case, including random groups was pointless and including fixed groups led to a large overestimation of selection response, smaller true selection response across groups and larger variance of estimation of the differences between groups. Although the genetic trend was correctly predicted by a model fitting fixed genetic groups, important errors in predicting individual breeding values led to incorrect ranking of animals across groups and, consequently, led to lower selection response.     

牛肌肉生长抑制素基因突变的遗传效应与育种应用

肌肉生长抑制素（myostatin,MSTN）基因主要在骨骼肌中表达,参与调控骨骼肌的生长发育。MSTN基因在不同物种中具有极强的进化保守性,同时还具有较多的突变多态性。在牛的不同品种中,存在不同位点的有义突变,突变型牛均表现为骨骼肌发达,呈现双肌表型,生长速度与产肉率显著提高。同时,该基因突变也引起显著的生理性遗传效应。对国内外肉牛的MSTN基因突变类型、突变后遗传效应及在肉牛育种应用等方面作了重点阐述,以期为我国地方品种肉牛改良和选育研究提供参考。