新太湖猪选育过程中近交技术的应用及效应分析

利用新太湖猪选育过程中（１９８６～１９９４）６个世代母猪的分娩产仔记录,后备猪生长发育测定资料,分析了近交对繁殖性能和生长发育性状的影响。相关分析表明,近交与产仔数、产活仔数的相关系数分别为－０．１６２５、－０．１５４６。与１８０日龄活重、体高、胸围、及８０ｋｇ时背膘厚度的相关系数分别为－０．１３５,－０．２１１,－０．２１８,－０．２０４。回归分析表明,近交系数每上升１０％,产仔数下降０．３９头,１８０日龄活重下降１．５ｋｇ,背膘厚下降０．０７４８ｃｍ。产仔记录分析表明,母猪近交系数在２０％以下时,产仔数比非近交组下降０．２７头,差异不显著（Ｐ＞０．０５）;近交系数在２０％以上时,下降１．３５头,差异不显著（Ｐ＞０．０５）。生长发育性状表明,近交系数在３０％以上时,１２０日龄活重、１８０日龄活重等性状都显著下降。８０ｋｇ活体背膘厚当个体近交系数上升到２０％以上时,与非近交组相比下降０．１６ｃｍ,差异显著（Ｐ＜０．０５）。     

Influence of imported sport horses on the genetic evaluation of Swedish Warmblood stallions

There is substantial international influence on the Swedish Warmblood (SWB) sport horse population. The SWB Association suspects that imported horses are pre-selected based on their anticipated performance level, which could lead to biased estimated breeding values (EBVs) for stallions. This study examined different strategies to handle records for imported horses in the genetic evaluation. The stallions were evaluated for 10 traits using 3 different EBV estimation methods that were compared based on ranking comparisons of stallions, accuracy, correlations and absolute differences between EBVs. The results showed that the stallions’ EBVs were affected by imported offspring which, as a group, had higher average scores than horses born in Sweden. Sire EBVs differed by up to 0.6 genetic standard deviation of the trait between methods for stallions with >50% imported offspring. Excluding imported offspring lowered the accuracies and caused larger re-ranking compared with including a fixed effect of origin in the model.     

Effects of correcting missing daily feed intake values on the genetic parameters and estimated breeding values for feeding traits in pigs

Daily feed intake (DFI) is an important consideration for improving feed efficiency, but measurements using electronic feeder systems contain many missing and incorrect values. Therefore, we evaluated three methods for correcting missing DFI data (quadratic, orthogonal polynomial, and locally weighted (Loess) regression equations) and assessed the effects of these missing values on the genetic parameters and the estimated breeding values (EBV) for feeding traits. DFI records were obtained from 1622 Duroc pigs, comprising 902 individuals without missing DFI and 720 individuals with missing DFI. The Loess equation was the most suitable method for correcting the missing DFI values in 5–50% randomly deleted datasets among the three equations. Both variance components and heritability for the average DFI (ADFI) did not change because of the missing DFI proportion and Loess correction. In terms of rank correlation and information criteria, Loess correction improved the accuracy of EBV for ADFI compared to randomly deleted cases. These findings indicate that the Loess equation is useful for correcting missing DFI values for individual pigs and that the correction of missing DFI values could be effective for the estimation of breeding values and genetic improvement using EBV for feeding traits.     

Implementation of genetic evaluation and mating designs for the endangered local pig breed ‘Bunte Bentheimer’

A pedigree including 1538 individuals of the endangered pig breed ‘Bunte Bentheimer’ and 3008 records of the fertility traits ‘number of piglets born alive’ (NBA) and ‘number of piglets weaned’ (NW) were used to i) characterize the population structure, ii) to estimate genetic (co)variance components and estimated breeding values (EBVs) and iii) to use EBVs for the application of the concept of optimal genetic contributions. The average coefficient of inbreeding increased from F = 0.103 to F = 0.121 within the two recent cohorts. Average rate of inbreeding amounted to 1.66%, which resulted in an effective population size of N_e = 30 animals in the recent cohort. Average generation interval was 3.07 years considering the whole pedigree, and in total, only 612 sows and boars generated offspring. Estimated heritabilities for both traits NBA and NW were 0.12, and the estimated genetic correlation between both traits was 0.96. The variance component due to the service sire was higher than in commercial pig breeds, presumably due to the widespread use of natural service boars. The EBVs for NBA from 333 selection candidates (63 boars and 270 sows) were used to determine optimal genetic contributions. Based on selected animals and their optimal genetic contributions, specific mating designs were evaluated to minimize inbreeding in the next generation. Best results were achieved when using a simulated annealing algorithm and allowing artificial insemination.     

Accuracies of estimated breeding values from ordinary genetic evaluations do not reflect the correlation between true and estimated breeding values in selected populations

The accuracy of estimated breeding values (EBVs) is an important parameter in livestock genetic improvement. It is used to calculate response to selection and to express the credibility of individual EBVs. Although it is well-known that selection reduces accuracy, this effect is not well-studied and accuracies from genetic evaluations are not adjusted for selection. This work investigates the effect of selection on accuracy of EBVs estimated using best linear unbiased predictors. Results show that accuracies in a selected population may be considerably smaller than the ordinary accuracy from genetic evaluation. Accuracy of the parent average is dramatically reduced by selection, up to a factor of three. Expressions for equilibrium accuracies in selected populations are presented and depend only on the unselected accuracy and the intensity of selection. Thus, schemes with the same unselected accuracy and intensity of selection also have the same equilibrium accuracy and response to selection. At the same unselected accuracy, therefore, schemes based on between-family information do not show greater reduction in response and accuracy because of the Bulmer effect. An example shows that benefit of genomic selection may be underestimated when the effect of selection on accuracy is ignored. Finally, this work argues that the SE of an EBV and the correlation between true and EBVs are different things, and that accuracies should not be adjusted for selection when they primarily serve to indicate the SEs of EBVs.     

Genetic management of Dutch golden retriever dogs with a simulation tool

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.     

全基因组选择模型研究进展及展望

全基因组选择是一种利用覆盖全基因组的高密度标记进行选择育种的新方法,可通过早期选择缩短世代间隔,提高育种值估计准确性等加快遗传进展,尤其对低遗传力、难测定的复杂性状具有较好的预测效果,真正实现了基因组技术指导育种实践。随着芯片和测序技术日趋成熟,高密度标记芯片检测成本不断降低,全基因组选择模型的不断升级和优化,预测准确性不断提高,全基因组选择已成为动物遗传改良的重要手段和研究热点。目前,全基因组选择已经成为奶牛遗传评估的标准方法,并取得重要进展,在其它物种中的应用正在逐步开展。本文主要对全基因组选择的统计模型发展进行综述,总结全基因组选择在动物遗传育种中的应用现状,讨论当前存在的问题,并对全基因组选择模型的发展方向和应用前景进行展望。     

智慧养猪与智能猪场的应用现状与分析

在智能信息化时代,传统的人工养殖已经越发彰显其劣势.智慧养猪开启的智能装备和大数据模式正走进养猪人的视野.文章综述了在智慧养猪背景下,智能饲喂系统、环控系统、监控系统、AI和大数据在猪场的应用现状,并进行了简要分析,以期为农牧公司智能猪场的建设提供参考.     

苏氨酸在养猪生产中的应用研究

苏氨酸是猪营养需要的必需氨基酸,尤其是添加合成赖氨酸配制低蛋白日粮时,猪日粮中的苏氨酸就成为第一限制性氨基酸,可进一步改善饲料的氨基酸平衡和降低饲料的配方成本。本文综述了苏氨酸在养猪生产中的生理作用、免疫功能、缺乏症、营养需要量和应用效果。     

天津长白猪简化综合育种值的研究

研究了天津长白猪各种简化综合育种值中目标性状的经济权重及其与完全综合育种值的相关。结果表明，简化综合育种值中只包含一人目标性状时，最好的性状避料转化效率，与完全综合育种值的相关系数（ｒ）等于０．８７；包含２个目标性状时，最佳的性状组合是饲料转化效率与瘦肉率；包括３个目标性状时，最好的目标性状组合是窝活仔数、日增竽圾瘦肉主，它已经达到很高的精确度，与完全综合育种值的相关为１．００。     

Comparing deregression methods for genomic prediction of test‐day traits in dairy cattle

We aimed to investigate the performance of three deregression methods (VanRaden, VR; Wiggans, WG; and Garrick, GR) of cows’ and bulls’ breeding values to be used as pseudophenotypes in the genomic evaluation of test‐day dairy production traits. Three scenarios were considered within each deregression method: (i) including only animals with reliability of estimated breeding value (REL_EBV ) higher than the average of parent reliability (REL_PA ) in the training and validation populations; (ii) including only animals with REL_EBV higher than 0.50 in the training and REL_EBV higher than REL_PA in the validation population; and (iii) including only animals with REL_EBV higher than 0.50 in both training and validation populations. Individual random regression coefficients of lactation curves were predicted using the genomic best linear unbiased prediction (GBLUP), considering either unweighted or weighted residual variances based on effective records contributions. In summary, VR and WG deregression methods seemed more appropriate for genomic prediction of test‐day traits without need for weighting in the genomic analysis, unless large differences in REL_EBV between training population animals exist.     

Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations

Using genome‐wide SNP data, we calculated genomic inbreeding coefficients (F_ROH > _1 Mb, F_{ROH > 2 Mb}, F_{ROH > 8 Mb} and F_{ROH > 16 Mb}) derived from runs of homozygosity (ROH) of different lengths (>1, >2, >8 and > 16 Mb) as well as from levels of homozygosity (F_HOM). We compared these values of inbreeding coefficients with those calculated from pedigrees (F_PED) 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 F_{ROH > 8 Mb} and F_{ROH > 16 Mb} were similar to the levels estimated from pedigrees. The lowest values were obtained for Fleckvieh (F_PED = 0.014, F_{ROH > 8 Mb} = 0.019 and F_{ROH > 16 Mb} = 0.008); the highest, for Brown Swiss (F_PED = 0.048, F_{ROH > 8 Mb} = 0.074 and F_{ROH > 16 Mb} = 0.037). In contrast, inbreeding estimates based on the genomic coefficients F_{ROH > 1 Mb} and F_{ROH > 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.     

MIM: an indirect method to assess inbreeding and coancestry in large incomplete pedigrees of selected dairy cattle

In real data, inbreeding is usually underestimated because of missing pedigree information. A method adapted to the dairy cattle situation is presented to approximate inbreeding when the stored population pedigree is incomplete. Missing parents in incomplete pedigrees were given a dummy identification and assigned to groups (up to nine for a given birth date of progeny). These groups were linked to contemporary reference groups with known parents. An explicit model considered that polygenic breeding values in a censored group were centred on a function of the average breeding value in the corresponding reference group and deviated independently. Inbreeding coefficients were obtained progressively over birth dates starting from founders. For each date considered, the parameters pertaining to its groups were computed using the parameters already obtained from groups belonging to the previous dates. The updating algorithms were given in detail. An indirect method was implemented to expedite mass computations of the relationship coefficients involved (MIM). MIM was compared to Van Raden's (VR) method using simulated populations with 20 overlapping generations and different rates of missing sires and dams. In the situation of random matings, the average inbreeding coefficients by date obtained by MIM were close to true values, whereas they were strongly underestimated by VR. In the situation of assortative matings, MIM gave average inbreeding coefficients moderately underestimated, whereas those of VR's method were still strongly underestimated. The main conclusion of this study adapted to the situation of dairy cattle with incomplete pedigrees was that corrections for inbreeding and coancestry coefficients are more efficient with an explicit appropriate genetic model than without.     

Porcine endogenous retrovirus copy number in different pig breeds is not related to genetic diversity

The risk of zoonoses is a major obstacle to xenotransplantation. Porcine endogenous retrovirus (PERV) poses a potential risk of zoonotic infection, and its control is a prerequisite for the development of clinical xenotransplantation. The copy number of PERV varies among different breeds, and it has been suggested that the PERV integrations number is increased by inbreeding. The purpose of this study was (i) to examine the copy number of PERV in different Spanish pig breeds, Spanish wild boar and commercial cross-bred pigs from five different farms and genetic background (CCP1-CCP5) and (ii) to investigate the correlation between PERV copy number and the genetic background of the pigs in order to improve the selection of pigs for xenotransplantation. PERV copy number was determined by quantitative, real-time polymerase chain reactions. Thirty-four microsatellite markers were genotyped to describe the genetic diversity within populations (observed and expected heterozygosities, Ho and He, respectively) and the inbreeding coefficient (F). Pearson's correlation coefficient was used to determine the relationship between PERV copy number and Ho, He and F. The copy number of PERV among different pig breeds was estimated to range between three (CCP1) and 43 copies (Iberian Pig). Statistical differences were found among the studied populations concerning PERV copy number. No correlation was found between the PERV copy number and the heterozygosity (calculated at an individual level or at a population level) or the inbreeding coefficient of each population. Our data suggest that pigs inbreeding does not increase PERV copy number and support the idea that careful selection of pigs for organ donation with reduced PERV copy number will minimize the risk of retrovirus transmission to the human receptor.     

Population genetic structure and diversity of the East Balkan Swine (Sus scrofa) in Bulgaria,revealed by mitochondrial DNA and microsatellite analyses

The East Balkan Swine (EBS) is the only indigenous pig breed in Bulgaria. We analyzed the mitochondrial DNA (mtDNA) control region and 21 microsatellite loci for 198 individuals from 11 farms in Bulgaria. Obtained 11 mtDNA haplotypes including three novel ones were grouped to two major clades, European clade E1 (146/198 individuals, 73.7%) and Asian clade A (52/198, 26.3%). The mixture of the two clades may have resulted from historical crossbreeding between the European and Asian pig breeds. Clade A was frequent in southeastern Bulgaria (Burgas Province), but less frequent or absent in northeastern Bulgaria (Varna and Shumen Provinces). The distribution of Europe- and Asia-specific haplotypes relative to EBS farm locations could be attributed to regional differences of breeding systems (e.g., crossbreeding with imported commercial pigs). A microsatellite analysis showed high heterozygosities for all the EBS farms, and negative inbreeding coefficients presumably due to crossing with commercial pigs or wild boars and/or efforts to reduce inbreeding by farmers. Bayesian clustering analyses showed that all farm populations are genetically well distinguishable from one another. Although diversity has been maintained by the efforts of farmers and a breeding association, the effective population size remains small, and conservation efforts should be continued.     

里岔黑猪哺乳仔猪饲养管理技术

哺乳仔猪是指从出生到断奶阶段的仔猪,是生猪养殖各环节的关键和基础.哺乳仔猪成活率高低关系到猪场养猪生产水平的高低,是影响养殖场经济效益的重要因素.因此,提高哺乳仔猪成活率一直是猪场所关心的.文章主要综述了里岔黑猪哺乳仔猪培育在环境、营养、管理和保健等方面技术要点,以期为猪场提供参考.     

Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers in 236 samples. All estimated loci were very polymorphic indicated by high values of polymorphism information content (from 0.76 in S0225 to 0.92 in Sw2410). Indigenous populations had very high level of genetic diversity (mean He = 0.75); of all indigenous breeds, Lung Pu showed highest mean number of alleles (MNA = 10.1), gene diversity (He = 0.82), allele richness (5.33) and number of private alleles (10). Thirteen percentage of the total genetic variation observed was due to differences among populations. The neighbour‐joining dendrogram obtained from Nei's standard genetic distance differentiated eight populations into four groups including Yorkshire, two wild populations, Mong Cai population and a group of four other indigenous populations. The Bayesian clustering with the admixture model implemented in Structure 2.1 indicated seven possible homogenous clusters among eight populations. From 79% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations.     

Relationship between genealogical and microsatellite information characterizing losses of genetic variability: Empirical evidence from the rare Xalda sheep breed

Preservation of rare genetic stocks requires continual monitoring of populations to avoid losses of genetic variability. Genetic variability can be described using genealogical and molecular parameters characterizing variation in allelic frequencies over time and providing interesting information on differentiation that occurred after the foundation of a conservation program. Here we analyze the pedigree of the rare Xalda sheep breed (1851 individuals) and the polymorphism of 14 microsatellites in 239 Xalda individuals. Individuals were assigned to a base population (BP) or 4 different cohorts (from C1 to C4) according to their pedigree information. Genetic parameters were computed at a genealogical and molecular level, namely inbreeding (F), observed (H_o) and expected (H_e) heterozygosity, individual coancestry coefficients (f and f_m), average relatedness (AR), mean molecular kinship (Mk), average number of allele per locus (A), effective number of ancestors (f_a), effective population size (N_e and N_e(m)) and founder genome equivalents (N_g and N_g(m)). In general, the computed parameters increased with pedigree depth from BP to C4, especially for the genealogical information and molecular coancestry-based parameters (f_m, Mk and N_g(m)). However, H_o and H_e showed the highest values for C1 and the molecular heterozygote deficiency within population (F_IS(m)) showed the lowest value for C1, thus indicating that loss of genetic variability occurs very soon after the implementation of conservation strategies. Although no genealogical or molecular parameters are sufficient by themselves for monitoring populations at the beginning of a conservation program, our data suggests that coancestry-based parameters may be better criteria than those of inbreeding or homozygosity because of the rapid and strong correlation established between f and f_(m). However, the obtaining of molecular information in well-established conservation programs could not be justified, at least in economic terms.     

Evaluation of smallholder pig production systems in North Vietnam: Pig production management and pig performances

This study investigated the productive adaptability of pig breeds under different smallholder production conditions in Vietnam, comparing an indigenous with a Vietnamese improved breed. Fieldwork was conducted in four villages with different remoteness in North Vietnam from 2001 to 2002, in 64 households keeping the improved Mong Cai or indigenous Ban as sow breeds and progeny for fattening. Four visits per farm yielded 234 structured interviews. Reproductive performances were derived from 135 litters. Individual weights of pigs (n = 755) were obtained. Data were analysed by regression, linear and generalised linear, especially loglinear models.

Two distinct pig production systems were identified, that differed in remoteness, market access, resource availability, distribution of pig breeds and pig production intensity. Higher performances of 1.4 and 1.5 litters year^− 1, 8.4 and 8.4 piglets weaned litter^− 1, 66.6 and 93.0 kg piglets weaned sow^− 1 year^− 1, and 136 and 177 g day^− 1 ADG were found in two villages near town with semi-intensive production conditions and a high rate of improved Mong Cai sows and MC and LW × MC offspring in the observed population. Lower performances of 1.1 and 1.1 litters year^− 1, 4.6 and 5.5 piglets weaned litter^− 1, 20.5 and 30.9 kg piglets weaned sow^− 1 year^− 1, and 66 and 85 g day^− 1 ADG were observed in parallel to higher incidences of indigenous Ban pigs away from town under extensive conditions. Total live weight offtake per household per year was higher near town and in one village distant to town. MC and LW × MC remained even under demand-driven conditions below the performance potential reported for improved genotypes. Under resource-driven conditions with a saving-oriented production pattern, the higher-yielding but more demanding Mong Cai might not be an efficient production alternative as a further performance reduction can be assumed. A considerable live weight output was observed under resource-driven conditions and with a higher percentage of crossbred LW × Ban offspring in the population, possibly representing a promising production alternative. Factors influencing the performance expression of pigs, and the suitability of different methods for the assessment of performance parameters on-farm are discussed.     

规模化养猪场的科学用水管理

本文就猪场用水的来源、用途、水的质量安全标准和猪场用水质量控制及科学用水管理措施作一综述.