动物模型BLUP选择效果的计算机模拟研究

在采用动物模型最佳线性无偏预测(BLUP) 方法对个体育种值进行估计的基础上, 模拟了在一个闭锁群体内连续对单个性状选择10个世代的情形, 并系统地比较了群体规模、公母比例和性状遗传力对选择所获得的遗传进展和群体近交系数变化的影响。结果表明, 扩大育种群规模不仅可以获得更大的持续进展, 同时还可有效缓解近交系数的过快上升; 育种群中公畜比例过低时, 不仅会降低遗传进展, 群体近交系数的上升速度也会加快, 实际中应保证育种群具有一定的规模和适宜的公母比例。对高遗传力性状进行选择时, 可望获得更大的遗传进展, 同时近交系数的上升速度也会快一些。     

母系猪繁殖性状的基因组选择策略

与生长性状相比,猪的繁殖性状具有遗传力低和限性表现的特点,通过传统育种方法很难获得较高的育种值估计准确性,且无法缩短世代间隔。因此,猪的繁殖性状选育策略应与生长性状不同。基因组选择是一种基于全基因组信息的标记辅助选择。与生长性状相比,基因组选择对提高繁殖性状(如产仔数)的预测准确性更具有优势。然而,基因组选择的育种成本较高阻碍了该技术的广泛应用。本文旨在探讨母系猪繁殖性状基因组选择的参考群体构建策略,以节省基因组育种成本和加快遗传进展。     

2020年国内外家兔遗传育种与繁殖研究进展

家兔是中国传统的畜禽品种,同时也是中国畜牧业的重要组成部分。近年来,随着产业升级,生物技术快速发展,国内外家兔遗传育种取得了较大进展。文章分别从传统育种与分子育种2个方面对2020年国内外家兔遗传育种与繁殖研究进展进行了综述,以期为家兔种质资源利用与保护提供参考。国外在传统育种与分子育种上均作了较多研究,在传统育种上主要针对选择和环境因素对家兔生长及繁殖性能的影响进行研究;在分子育种上对生长及肉质相关基因、繁殖性能相关基因及遗传多样性等方面进行研究。国内开展的家兔遗传育种与繁殖研究数量相较国外更多,研究重点集中于分子育种,包括对皮毛性状、肉质性状及繁殖性能相关基因的研究;传统育种主要包括选择和环境效应对家兔生长与繁殖性能的影响。     

Genetic Improvement of Dairy Cow Reproductive Performance

The welfare of cow along with profitability in production are important issues in sustainable animal breeding programmes. Along with an intense/intensive selection for increased milk yield, reproductive performance has declined in many countries, in part due to an unfavourable genetic relationship. The largely unchanged genetic trend in female fertility and calving traits for Scandinavian Red breeds shows that it is possible to avoid deterioration in these traits if they are properly considered in the breeding programme. Today's breeding is international with a global selection and extensive use of the best bulls. The Nordic countries have traditionally recorded and performed genetic evaluation for a broad range of functional traits including reproduction. In recent years many other countries have also implemented genetic evaluation for these traits. Thus, the relative emphasis of dairy cattle breeding objectives has gradually shifted from production to functional traits such as reproduction. Improved ways of recording traits, e.g. physiological measures, early indicator traits, assisted reproductive techniques and increased knowledge of genes and their regulation may improve the genetic selection strategies and have large impact on present and future genetic evaluation programmes. Extensive data bases with phenotypic recordings of traits for individuals and their pedigree are a prerequisite. Quantitative trait loci have been associated to the reproductive complex. Most important traits, including reproduction traits are regulated by a multitude of genes and environmental factors in a complex relationship, however. Genomic selection might therefore be important in future breeding programmes. Information on single nucleotide polymorphism has already been introduced in the selection programmes of some countries.     

Genomic selection for maternal traits in pigs

The aim of this study was to compare alternative designs for implementation of genomic selection to improve maternal traits in pigs, with a conventional breeding scheme and a progeny testing scheme. The comparison was done through stochastic simulation of a pig population. It was assumed that selection was performed based on a trait that could be measured on females after the first litter, with a heritability of 0.1. Genomic selection increased genetic gain and reduced the rate of inbreeding, compared with conventional selection without progeny testing. Progeny testing could also increase genetic gain and decrease the rate of inbreeding, but because of the increased generation interval, the increase in annual genetic gain was only 7%. When genomic selection was applied, genetic gain was increased by 23 to 91%, depending on which and how many animals were genotyped. Genotyping dams in addition to the male selection candidates gave increased accuracy of the genomic breeding values, increased genetic gain, and decreased rate of inbreeding. To genotype 2 or 3 males from each litter, in order to perform within-litter selection, increased genetic gain 8 to 12%, compared with schemes with the same number of genotyped females but only 1 male candidate per litter. Comparing schemes with the same total number of genotyped animals revealed that genotyping more females caused a greater increase in genetic gain than genotyping more males because greater accuracy of selection was more advantageous than increasing the number of male selection candidates. When more than 1 male per litter was genotyped, and thereby included as selection candidates, rate of inbreeding increased because of coselection of full sibs. The conclusion is that genomic selection can increase genetic gain for traits that are measured on females, which includes several traits with economic importance in maternal pig breeds. Genotyping females is essential to obtain a high accuracy of selection.     

A review on prolificacy genes in sheep

Ovulation rate and litter size are important reproduction traits in sheep and are of high economic value. Reproduction traits typically have low to medium heritabilities and do not exhibit a noticeable response to phenotypic selection. Therefore, inclusion of genetic information of the genes associated with reproductive ability could efficiently enhance the selection response. The most important major genes affecting prolificacy and their genetic diversities in different sheep breeds were reviewed. Different causative mutations with major effects on reproductive traits including ovulation rate and litter size have been found in various sheep breeds around the world. A general overview of the studies on main prolificacy genes showed that some alleles may express different phenotypic effects in different breeds, and thus, further studies on epistatic effects are necessary for more understanding of genetic control of reproductivity in sheep. Regarding the polygenic control of fertility traits, application of new high‐throughput technologies to find new variants is essential for future studies. Moreover, genomewide association studies and genomic best linear unbiased predictions of breeding values are likely to be effective tools for genetic improvement of sheep reproductive performance traits.     

A genealogical survey of Australian registered dog breeds

Breeding practices were analysed for 32 registered dog breeds representing very small registries (120 Central Asian shepherd dogs) through to very large registries (252,521 German shepherd dogs) in Australia. The vast majority (91%) of registered kennels in Australia that were sampled did not regularly employ either close breeding or popular sire usage in their kennels and the weighted mean inbreeding coefficient of Australian pedigree dogs was <5%. Australian breed mean inbreeding coefficients ranged from 0% (Central Asian shepherd dog) to 10.1% (Bichon Frise). Breed effective population sizes ranged from 26 (Ibizan hound) to 1090 (Golden retriever), comparable with other species of domesticated animals. The relatively low levels of inbreeding suggest that pedigree dog disorders are unlikely to arise frequently from the use of popular sires or close breeding in Australian registered dog breeds. It is possible that deleterious allele fixation might be driven by founder effects, genetic drift or adverse selection practices, which were not assessed in this analysis. European popular sire definitions should be revisited for rare breeds.     

2021年国内外家兔遗传育种与繁殖研究进展

兔业是节粮、环保、低耗草食畜牧业中的代表性产业,是中国畜牧业的重要组成部分。家兔遗传育种与繁殖的相关研究是推进兔业发展的重要基础与保障。遗传学、分子生物学、统计学及计算机科学等学科的交叉融合与不断进步,为家兔育种提供了更加先进全面的技术手段。作者从家兔传统育种与分子育种2个方面对国内外2021年家兔遗传育种与繁殖研究进展进行了综述。国外在传统育种与分子育种上均作了一定研究,主要集中在选择与环境效应的影响。国内开展的家兔遗传育种与繁殖研究数量相较国外更多,主要以分子育种为主,包括品种与遗传多样性、皮毛性状功能基因、脂肪和肉质性状相关基因及繁殖性能相关基因的研究;传统育种主要包括选择和环境效应对家兔生长与繁殖性能的影响及生产性能测定等。本综述旨在为家兔育种研究和生产提供参考。     

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     

基于基因组和系谱信息的不同选配方案效果模拟研究

基因组选配（genomic mating,GM）是利用基因组信息进行优化的选种选配,可以有效控制群体近交水平的同时实现最大化的遗传进展。但基因组选配是对群体中所有个体进行选配,这与实际的育种工作有点相悖。本研究模拟了遗传力为0.5的9 000头个体的基础群数据,每个世代根据GEBV选择30头公畜、900头母畜作为种用个体,而后使用基因组选配、同质选配、异质选配、随机交配4种不同的选配方案。其中基因组选配中分别选取遗传进展最大的解、家系间方差最大的解、近交最小的解所对应的交配方案进行选育。每种方案选育5个世代,比较其后代群体的平均GEBV、每世代的遗传进展、近交系数、遗传方差,并重复5次取平均值。结果表明,3种基因组选配方案的ΔG均显著高于随机交配和异质选配（P<0.01）,而且,选取遗传进展最大的基因组选配方案的ΔG比同质选配还高出4.3%。3种基因组选配的方案的ΔF比同质选配低22.2%~94.1%,而且选取近交最小的基因组选配方案ΔF比异质选配低11.8%。同质选配的遗传方差迅速降低,在第5世代显著低于除基因组选配中选择遗传进展最大的方案以外的所有方案（P<0.05）,3种基因组选配方案的遗传方差比同质选配高10.8%~32.2%。这表明基因组选配不仅可以获得比同质选配更高的遗传进展,同时有效的降低了近交水平,并且减缓了遗传方差降低速度,保证了一定的遗传变异。基因组选配作为一种有效的可持续育种方法,在畜禽育种中开展十分有必要。     

Genomic selection strategies to improve maternal traits in Norwegian White Sheep

This study tested and compared different implementation strategies for genomic selection for Norwegian White Sheep, aiming to increase genetic gain for maternal traits. These strategies were evaluated for their genetic gain ingrowth, carcass and maternal traits, total genetic gain, a weighted sum of the gain in each trait and rates of inbreeding through a full-scale stochastic simulation. Results showed genomic selection schemes to increase genetic gain for maternal traits but reduced genetic gain for other traits. This could also be obtained by selecting rams for artificial selection at a higher age. Implementation of genomic selection in the current breeding structure increased genetic gain for maternal traits up to 57%, outcompeted by reducing the generation interval for artificial insemination rams from current 3 to 2 years. Then, total genetic gain for maternal traits increased by 65%–77% and total genetic gain by18%–20%, but at increased rates of inbreeding.     

Genetic-statistical analysis of environmental and genetic influences on the outcome of the juvenile and breeding performance tests for behaviour traits in Hovawart dogs

The objective of the present study was to evaluate the importance of genetic and environmental sources of variation for results of behaviour tests recorded at juvenile and breeding performance tests in the Hovawart dog. For these analyses behaviour test results of 1882 (juvenile evaluation), respectively 929 dogs (breeding performance test) born in 1995 to 2000 had been used. Variance component estimation was performed for the traits appearance, play instinct, hunting affinity, group of people, shoot, acoustical and optical influences and temperament using multivariate linear animal models and Residual Maximum Likelihood (REML). The models included test-year-season, sex, litter size, age and inbreeding coefficient of the animal as fixed effects. Additive genetic effects of the animal, permanent environmental effect of the litter and the effect of the kennel were considered as random factors.The sex of the dog was significant for appearance, play instinct, hunting affinity, acoustical and optical influences of juvenile evaluation and for the traits temperament, play instinct, hunting affinity, acoustical and one of the optical influences of breeding performance test.The age of the dog at test significantly influenced the traits play instinct, hunting affinity and acoustical influences of juvenile evaluation and optical influences and hunting affinity of breeding performance test. All traits with exception of hunting affinity and group of people were significantly affected by the test-year-season. The inbreeding coefficient was significant for appearance of juvenile evaluation and play affinity of breeding performance test. The effect litter size did not influence any of the traits significantly.The estimated heritabilities for the behaviour traits of juvenile and breeding performance test ranged from h2 = 0.01 to h2 = 0.13, respectively h2 = 0.01 to h2 = 0.14, with standard errors of up to 0.03. The additive genetic correlations between most of the traits were moderately to highly positive (r(g) = 0.20 to r(g) = 1.0, respectively r(g) = 0.29 to r(g) = 1.0). Negative additive genetic correlations were only found for a few traits of juvenile (r(g) = -0.02 to r(g) = -0.58) and breeding performance test (r(g) = -0.28 to r(g) = -0.83). Progress in breeding for the behaviour traits investigated here may only be meaningful when information from all relatives is used in an animal model instead of selection based on the phenotype of the single animal.     

近交与贴现对优化群体规模的影响

小群体的闭锁选育不可避免产生近交及遗传方差下降，导致近期与远期选择效果的矛盾。本文通过考察猪核心群育种方案中群体规模及公母比例对近交增量（％）及累积育种产出（元）的作用，分析遗传方差下降以及育种产出的贴现等因素对选择方案评估效果的影响。群体有效规模主要受每世代选择公猪头数的影响，为了控制群体近交增量必须维持一定的公猪头数。在所模拟的１６种方案中，１５代的贴现累积选择进展以每代选择８头公猪为最高；而母猪规模越大，累积选择进展越高。不考虑近交引起遗传方差的下降，或不进行选择进展的贴现，都造成过高估计选择方案的效果，且导致选择不适当的方案；对各世代选择进展进行贴现时，需要考虑较大的世代数，否则也会影响各选择方案的比较结果。     

Genetic analysis of markers of the performance test for herding dogs. 1. Performance traits

The objective of the present study was to analyse data based on records of sheep dog trials in order to evaluate the importance of genetic and environmental sources of variation and to draw conclusions for breeding purposes. The data analysed consisted of 2745 test results recorded at 48 sheep dog trials carried out in Germany from 1994 to 1998, on which a total of 337 sheep dogs had attended. Tested dogs descended from 147 sires and 201 dams, with a mean inbreeding coefficient of about 2.8%. Variance components of working traits were estimated applying Restricted Maximum Likelihood methods. Additive genetic effects, permanent environmental effects of the animal and the effect of the handler were treated as random factors using multivariate linear models. Additionally, the model included the fixed effects of the age of the dogs at the sheep dog trial, sex, the level of difficulty of the exercises as well as the event itself, the starting number of the dog, the number of the dogs' tests at the particular event and the number of dogs presented on sheep dog trials by their handlers. The inbreeding coefficient was regarded as a linear covariate. Sex of the dog and starting number did not explain a significant proportion of variance for traits analysed, whereas the event of the sheep dog trial and the starting class usually were of significant importance. The analyses were performed using all sheep dog trial classes and for each of the three classes separately. Repeatabilities of herding traits within the same event of sheep dog trial estimated from animal effect mostly varied within a range from w = 0.1 to w = 0.5 whereas repeatabilities estimated over all events of sheep dog trials mostly gave estimates from w = 0.1 to w = 0.3. The estimated heritabilities for the herding performance traits ranged from h2 < or = 0.001 to h2 = 0.13 with standard errors in the range between 0.001 and 0.08. The selection possibilities appear to be rather limited given the heritability estimates and the low number of progeny of parents.     

There is room for selection in a small local pig breed when using optimum contribution selection: a simulation study

Selection progress must be carefully balanced against the conservation of genetic variation in small populations of local breeds. Well-defined breeding programs?with specified selection traits are rare in local pig breeds. Given the small population size,?the focus is often on the management of genetic diversity. However, in local breeds, optimum contribution selection can be applied to control the rate of inbreeding and to avoid reduced performance in traits with high market value. The aim of this study was to assess the extent to which a breeding program aiming for improved product quality in a small local breed would be feasible. We used stochastic simulations to compare 25 scenarios. The scenarios differed in?size of population, selection intensity of boars, type of selection (random selection, truncation selection based on BLUP breeding values, or optimum contribution selection based on BLUP breeding values), and heritability of?the selection trait. It was assumed that the local breed is used in an extensive system for a high-meat-quality market.?The?simulations showed that in the smallest population (300 female reproducers), inbreeding increased by 0.8% when selection was performed at random. With optimum contribution selection, genetic progress can be achieved that is almost as great as that with truncation selection based on BLUP breeding values (0.2 to 0.5 vs. 0.3 to 0.5 genetic SD, P < 0.05), but at a considerably decreased rate of inbreeding (0.7 to 1.2 vs. 2.3 to 5.7%, P < 0.01). This confirmation of the potential utilization of OCS even in small populations is important in the context of sustainable management and the use of animal genetic resources.     

家犬基因组及表型特征的遗传研究进展

犬具有丰富的遗传多样性,犬、人和鼠3种生物的基因组分析发现,犬与人、鼠的保守性非常高。犬的特殊群体结构使其成为研究形态、行为等多样性、哺乳动物进化遗传基础和疾病的良好模型。本文就家犬起源进化、基因组结构、犬表型特征的遗传变异、基因定位等研究进展做一综述,以期为犬遗传育种研究提供理论基础,并为人类疾病的预防、诊断和治疗提供新的思路与方法。     

Gametic gene flow method accounts for genomic imprinting

Findings within the last 15 years emphasize the possible role of genomic imprinting for trait expression in livestock species. In genetic evaluation, genomically imprinted traits can be treated by models with two different breeding values per animal; one accounts for the paternal and the other for the maternal expression pattern. Relative weighting factors for these breeding values were derived by a generalized version of the discounted gene flow method, which was extended to a gametic level to account for parent‐of‐origin effects. The gametic approach proved also useful for calculating the expected increase in inbreeding induced by one round of selection and its dynamics over time. The gametic gene flow method was applied to a hypothetical pig breeding programme. Relative weighting factors were higher for the paternally inherited genetic effect even in female selection paths, but depend on the breeding scheme heavily. The maximum medium‐term increase in inbreeding due to selection exceeded the long‐term increase in a range of 20–100%.     

国外生猪育种体系简析及对我国生猪育种的几点思考

选择是生猪育种的核心,而准确地选择和选种依赖于完善和成熟的育种体系。国际养猪发达国家(国际育种企业)对育种体系不断完善,长期进行生长、繁殖和肉品质等各类性状的表型测定,运用多场联合评估和基因组选择等方法不断提高遗传评估的准确性,不断挖掘新的育种性状,并进行测定、评估和选育,实现了种猪群体持续的遗传改良和综合性能的不断提升。本文对欧美发达国家(国际育种企业)的生猪育种技术体系进行了综述,以期为我国的生猪育种工作提供参考,并促进我国生猪种业的创新发展。     

2019年国内外家兔遗传育种与繁殖研究进展

家兔是节粮型草食小动物,其养殖投资少、见效快,已成为中国促进农民增收、助力脱贫攻坚的优势产业。近年来,随着生命科学的发展,国内外家兔遗传育种取得了较大进展。文章分别从家兔传统育种、分子育种和繁殖等方面对国内外2019年家兔遗传育种与繁殖研究进展进行了综述。国外在传统育种、分子育种和家兔繁殖方面均作了较多的研究,传统育种主要是针对选择和环境及添加物对家兔生产性能影响的研究;分子育种方面主要是对繁殖性状相关基因的研究,其中产仔数及精液蛋白方面的研究较多,其次是生长、肉质、毛色等性状相关基因的研究;而繁殖方面的研究主要针对公兔精液的保存方法及添加物对家兔精液品质、产仔数和受胎率的影响。国内家兔遗传育种与繁殖研究也主要包括传统育种、分子育种和家兔繁殖,但国内的研究重点在分子育种研究,其中品种与遗传多样性及皮毛性状功能基因的研究较多,主要采用高通量测序、常规基因克隆和基因编辑的方法筛选对研究性状具有重要调控功能的基因及调控网络;而传统育种性状评定和家兔繁殖方面的研究相对较少。该综述可为家兔的育种和生产研究提供参考。     

Research Progress on Genetic Breeding and Reproduction of Domestic and International Rabbits in 2019

The rabbit is a kind of grain-saving and small herbivore animal.Rabbit breeding which is low investment and obvious efficiency has become an advantageous industry of increasing income of rural farmers and poverty alleviation.In recent years,with the development of life science,great progress has been made in rabbit genetic breeding at home and abroad.In this paper,the research progress in genetic breeding and reproduction of rabbits in 2019 are reviewed from the traditional breeding,molecular breeding and reproduction of rabbits.For abroad,lots of researches involved in traditional breeding,molecular breeding and reproduction were done.Effects of selection,environment and additives on productive performance had been analyzed in traditional breeding.Molecular breeding mainly focused on reproductive performance among which there were more studies on litter size and spermatine.Secondly,the related genes of growth,meat quality and hair color were studied.The research on reproduction mainly focuses on the preservation method of male rabbit semen and the effects of additives on rabbit semen quality,litter size and conception rate.In China,genetic breeding and reproduction research on rabbit also mainly included traditional breeding,molecular breeding and reproduction,but the focus of domestic research was molecular breeding,among which breed and genetic diversity and functional genes of fur trait were mainly researched using high-throughput sequencing,gene cloning and gene editing to screen the important functional genes and regulatory networks related to research traits.However,compared with molecular breeding,there are fewer studies on the traits evaluation of traditional breeding and rabbit reproduction.This review can provide references for rabbit breeding and production.