利用单元内方差分析法估计遗传参数的探讨

在遗传力的估计过程中,需将多种非遗传因素的影响从公畜间方差或者母畜间方差中剔除。在我国常使用的是盛志廉教授提出的单元内同胞相关法。本文对该法从理论上进行了更详细的证明,并将其推广到两层分类方差分析时的情况。同时还给出了当公母畜彼此间有亲缘关系时,利用单元内方差分析估计遗传力的方法。这些方法既可使遗传力的估计简便,又具有多因方差分析的功用。     

利用“全同胞-半同胞”混合家系资料估测性状间的遗传相关

近年来,数量遗传学的理论发展很快,并且广泛应用于动植物的育种实践中,尤其在遗传参数的估计上,提出了不少新的方法。有关利用“全同胞-半同胞”混合家系资料估测性状遗传力的方法,吴常信(1983,会议资料)已做过专门论述。本文旨在推导利用“全同胞-半同胞”混合家系资料估测性状间遗传相关的公式,以充分利用资料所提供的信息。     

利用“全同胞一半同胞”混合家系资料估测性状间的遗传相关

近年来,数量遗传学的理论发展很快,并且 广泛应用于动植物的育种实践中,尤其在遗传 参数的估计上,提出了不少新的方法。有关利 用“全同胞一半同胞”混合家系资料估测性状遗 传力的方法,吴常信（1983,会议资料）已做过 专门论述。本文旨在推导利用“全同胞一半同胞” 混合家系资料估测性状间遗传相关的公式,以 充分利用资料所提供的信息。     

单元内混合家系相关法估算遗传力及遗传相关的探讨

本文取单元内同胞相关法和混合家系亲缘相关法估算畜禽遗传参数之长,推导出单元内混合家系相关法。用这种方法估算遗传参数,既能消除环境单元间的差异,又能充分利用全同胞和半同胞资料,具有扩大信息来源,提高估算准确性和计算方便的优点。     

计算闭锁群体5个混合家系亲缘系数的探讨

亲缘系数（coefficient of relationship）也叫 遗传相关（genetic relationship),是数量遗传中 的重要参数,在计算遗传力、估计育种值、制定 综合选择指数中都有重要的应用意义闺。如果 根据谱系图逐对计算后代亲缘系数然后求平均 数的方法计算混合家系的亲缘系数,工作量大 且容易出错。吴常信闭曾导出计算一个“全同 胞一半同胞刀混合家系亲缘系数的近似公式;张 文灿（动物数量遗传通讯,1982）将吴常信的近 似公式推广到由S个“全同胞一半同胞刀混合家 系组成的群体,导出了计算全群亲缘系数的近 似公式;庞航(31根据全概率公式,导出计算一 个混合家系和S个混合家系亲缘系数的一般公 式。他们的近似或一般计算公式都是在假定雄、 雌亲间或各雄亲间,雄、雌亲间,各雌亲间无亲 缘关系的前提下导出的。对于闭锁群体,在低世 代时,满足或基本满足这些假定,用所导出的公 式计算亲缘系数是较为满意的,但随世代的增 加,各雄亲间,雄、雌亲间,各雌亲间常常存在程 度不同的亲缘关系。若仍采用他们所导出的公 式计算亲缘系数,往往偏低,世代越多,相差越 大。不宜用他们的公式计算闭锁群体S个混合 家系的亲缘系数。然而在闭锁育种中又需要较 准确地计算出闭锁群体混合家系的亲缘系数。 为了解决这个问题,本文首先对混合家系亲缘 系数提出一个较通俗的定义,然后根据这个定 义对计算闭锁群体S个混合家系亲缘系数进行 了探讨。     

山女鳟(Oncorhynchus masou masou)体重和叉长的遗传力估算

体重和体长作为鱼类的生长性状,是鱼类育种工作中最重要的生产性状之一,而在冷水鱼生产实践中通常利用叉长代替体长。文章采用不平衡巢式设计方法和定向人工授精技术建立了山女鳟(Oncorhynchus masoumasou)29个全同胞家系和14个半同胞家系,并测定全同胞家系和半同胞家系12月龄和24月龄的体重和叉长数据资料,进而利用方差分析法评估了作为引进种的山女鳟第六代群体体重和叉长的遗传力。结果表明:(1)山女鳟整个生长阶段叉长的变异系数明显低于体重变异系数,24月龄时的变异系数明显低于12月龄时的变异系数;(2)山女鳟在12月龄和24月龄雄鱼间和雄鱼内雌鱼间体重和叉长性状差异极显著(P<0.01);(3)山女鳟雌性亲本12月龄和24月龄体重和叉长的方差均大于雄性亲本的方差;(4)山女鳟12月龄体重的遗传力估计值为0.41~0.51,叉长的遗传力的估计值为0.46~0.54;24月龄时体重的遗传力估计值为0.55~0.60,叉长遗传力的估计值为0.53~0.59;(5)山女鳟体重和叉长性状属于中高遗传力,对山女鳟引进群体生长性状进行选择育种潜力巨大,预期能取得较好的遗传进展。研究结果为山女鳟选择育种相关工作提供了必要的参数依据。     

利用家系群体鉴定数量性状多基因的存在

通过重复试验方差分析获得误差方差以探索只利用B、：2和B2：2或F2：3家系世代鉴定多基因存在的方法,混合分布参数的估计采用IECM算法,以油菜株高B1：2和B2：2家系平均数资料和千粒重F2：3家系平均数资料为例阐明该方法。     

单元内混合家系相关法和阈性状法估计遗传力的比较研究

本文提出了一种估计遗传力的方法即单元内混合家系相关法,并用这种方法及阈性状分析法进行了猪肢蹄结实度的遗传力估计,结果表明,对于多阈性状,用单元内混合家系相关法估计的结果准确性好。     

用单元内混合家系相关法计算遗传力时的抽样误差估计

对应用单元内混合家系相关法计算遗传力时的抽样误差估计问题进行了探讨,推导出的抽样误差估计公式可用于遗传力的显著性检验．     

成都白鸡某些性状遗传力的几种估测方法的比较

性状遗传力是进行选种、育种工作不可缺 少的遗传参数。有关鸡的经济行状遗传力,国 外已有许多研究,而国内这方面的报道较少。由 于不同品种同一性状的遗传力不尽相同,因而 国外估测的有关性状遗传力只能供我们参考。 为使成都白鸡今后的选育工作更为科学可靠, 有必要正确估测成都白鸡某些主要经济性状的 遗传力。关于估测性状遗传力的方法,许多学 者作了介绍。这些方法大体可归纳为相关分析 和方差分析两类。相关分析是度量亲缘间的相 似性。方差分析是估测遗传方差在总的表型方 差中所占的比分。度量同胞间的组内相关分析 方法实际上也是一种方差分析。本研究的目的 在于估测成都白鸡某些经济性状的遗传力,比 较使用子亲相关、子亲回归、半同胞相关、全同 胞相关和实际选择反应估测这些性状遗传力的 差别,讨论估测这些性状遗传力的可行方法。     

Estimates of genetic parameters and breeding values from western larch open-pollinated families using marker-based relationship

The availability and affordability of genetic markers made it possible to estimate quantitative genetic parameters without mating designs' structured pedigree. Here, we compared 4-year height's heritability and individuals' breeding values for a western larch common-garden population of 1,418 offspring representing 15 open-pollinated families from a 41-clone seed orchard using (a) classical pedigree models such as half- and full-sib families and (b) a molecular marker-based pedigree-free model using four pair-wise relationship estimation methods using eight informative SSR markers. The results highlighted the commonly observed inflated estimates of genetic parameters often obtained from half-sib analyses, as well as demonstrating some of the full-sib analyses' caveats. The pedigree reconstruction permitted the identification of selfed individuals, thus allowing evaluating the impact of selfing on marker-based genetic parameter estimation. The results demonstrated the utility of marker-based methods as an alternative to the classical pedigree-based approaches. Unlike the pedigree-based methods, the marker-based approach allowed better partitioning the variance components as well as separating the non-additive and additive genetic variance. The theoretical underpinning of the marker-based approach was discussed.     

A New Algorithm for Explicit Determination of Variance Component Estimations in Mixed Models and Mixed Classifications of Balanced ANOVA

This paper deals with the balanced case of the analysis of variance. The use of a classification function leads to an easy determination of all possible sources of variation of any mixed classification. For mixed models a new method is derived, which allows to represent explicit the ANOVA-estimations of the variance components respectively the estimation of the mean sum of squares of the fixed effects for all sources of variation. Thereby the corresponding F-quotients and the approximate confidence intervals of variance components are received in a simple way.     

Effective Size of Populations under Selection

Equations to approximate the effective size (N(e)) of populations under continued selection are obtained that include the possibility of partial full-sib mating and other systems such as assortative mating. The general equation for the case of equal number of sexes and constant number of breeding individuals (N) is N(e) = 4N/[2(1 - α(I)) + (S(k)(2) + 4Q(2)C(2)) (1 + α(I) + 2α(O))], where S(k)(2) is the variance of family size due to sampling without selection, C(2) is the variance of selective advantages among families (the squared coefficient of variation of the expected number of offspring per family), α(I) is the deviation from Hardy-Weinberg proportions, α(O) is the correlation between genes of male and female parents, and Q(2) is the term accounting for the cumulative effect of selection on an inherited trait. This is obtained as Q = 2/[2 - G(1 + r)], where G is the remaining proportion of genetic variance in selected individuals and r is the correlation of the expected selective values of male and female parents. The method is also extended to the general case of different numbers of male and female parents. The predictive value of the formulae is tested under a model of truncation selection with the infinitesimal model of gene effects, where C(2) and G are a function of the selection intensity, the heritability and the intraclass correlation of sibs. Under random mating r = α(I) = -1/(N - 1) and α(O) = 0. Under partial full-sib mating with an average proportion β of full-sib matings per generation, r & β and α(O) & α(I) & β/ (4 - 3β). The prediction equation is compared to other approximations based on the long-term contributions of ancestors to descendants. Finally, based on the approach followed, a system of mating (compensatory mating) is proposed to reduce rates of inbreeding without loss of response in selection programs in which selected individuals from the largest families are mated to those from the smallest families.     

Heritability estimates and maternal effects on tarsus length in pied flycatchers,Ficedula hypoleuca

Tarsus length has previously been shown to have an additive genetic component in some pied flycatcher populations. In addition to estimation of additive genetic variation by means of repeatability analyses at various ontogenetic stages and degrees of genetic resemblance, we explore in this paper variation among parent-offspring regressions between sexes and years, as well as the influence of hatching date, ectoparasite abundance, egg volume, and male and female condition on the tarsus length of their offspring. Mother-offspring regressions gave heritability estimates consistently higher than father-offspring regressions, although variation among years was large and both types of estimates yielded lower heritability values than those estimated by means of full-sib resemblance. This indicates that common environmental effects were inflating heritability estimates. There existed maternal effects via egg size, larger eggs fledging chicks with larger tarsi. Mean tarsus length of broods decreased with hatching date and, independently, with high loads of ectoparasitic, blood-feeding mites (Acari). The maternal effect via egg size persisted into the adulthood, and confounded the interpretation of differences between heritability slopes. We address the method of examining differences in parent-offspring regressions as a shorthand for estimating extra-pair copulation (EPC) rates. In our population, this method would give an EPC rate of 0–59%, depending on whether the analysis is performed with fledglings recruited to the breeding population or with offspring at the nest.     

Simultaneous Discovery,Estimation and Prediction Analysis of Complex Traits Using a Bayesian Mixture Model

Gene discovery, estimation of heritability captured by SNP arrays, inference on genetic architecture and prediction analyses of complex traits are usually performed using different statistical models and methods, leading to inefficiency and loss of power. Here we use a Bayesian mixture model that simultaneously allows variant discovery, estimation of genetic variance explained by all variants and prediction of unobserved phenotypes in new samples. We apply the method to simulated data of quantitative traits and Welcome Trust Case Control Consortium (WTCCC) data on disease and show that it provides accurate estimates of SNP-based heritability, produces unbiased estimators of risk in new samples, and that it can estimate genetic architecture by partitioning variation across hundreds to thousands of SNPs. We estimated that, depending on the trait, 2,633 to 9,411 SNPs explain all of the SNP-based heritability in the WTCCC diseases. The majority of those SNPs (>96%) had small effects, confirming a substantial polygenic component to common diseases. The proportion of the SNP-based variance explained by large effects (each SNP explaining 1% of the variance) varied markedly between diseases, ranging from almost zero for bipolar disorder to 72% for type 1 diabetes. Prediction analyses demonstrate that for diseases with major loci, such as type 1 diabetes and rheumatoid arthritis, Bayesian methods outperform profile scoring or mixed model approaches.     

Modified full-sib selection and estimation of genetic parameters

Summary A cycle of full-sib selection is completed in three seasons while that of a modified method is completed in two seasons. In modified full-sib selection, selected families can be recombined and new families generated following a partial-diallel cross. The components of genetic variance can be estimated from the partial-diallel analysis of such families. Thus, in addition to performing selection, genetic parameters can be estimated.     

A QTL study of cattle behavioral traits in embryo transfer families.

Two behavioral traits, temperament and habituation, were measured in 130 calves from 17 full-sib families which comprise the Canadian Beef Cattle Reference Herd. Using variance components, heritability was calculated as 0.36 for temperament and 0.46 for habituation. Genotyping of 162 microsatellites at approximately 20 cM intervals allowed the detection of six quantitative trait loci (QTL) for behavior traits on cattle chromosomes 1, 5, 9, 11, 14, 15.     

Breeding Value and Variance Component Estimation from Data Containing Inbred Individuals: Application to Gynogenetic Families in Common Carp (Cyprinus Carpio L.)

Under gynogenetic reproduction, offspring receive genes only from their dams and completely homozygous offspring are produced within one generation. When gynogenetic reproduction is applied to fully inbred individuals, homozygous clone lines are produced. A mixed model method was developed for breeding value and variance component estimation in gynogenetic families, which requires the inverse of the numerator relationship matrix. A general method for creating the inverse for a population with unusual relationships between animals is presented, which reduces to simple rules as is illustrated for gynogenetic populations. The presence of clones in gynogenetic populations causes singularity of the numerator relationship matrix. However, clones can be regarded as repeated observations of the same genotype, which can be accommodated by modifying the incidence matrix, and by considering only unique genotypes in the estimation procedure. Optimum gynogenetic sib family sizes for estimating heritabilities and estimates of their accuracy were derived and compared to those for conventional full-sib designs. This was done by means of a deterministic derivation and by stochastic simulation using Gibbs sampling. Optimum family sizes were smallest for gynogenetic families. Only for low heritabilities, there was a small advantage in accuracy under the gynogenetic design.     

Estimation of quantitative genetic parameters using marker-inferred relatedness in Japanese flounder: a case study of upward bias

Marker-based methods for estimating heritability have been proposed as an effective means to study quantitative traits in long-lived organisms and natural populations. However, practical examinations to evaluate the usefulness and robustness of a regression method are limited. Using several quantitative traits of Japanese flounder Paralichthys olivaceus, the present study examined the influence of relatedness estimator and population structure on the estimation of heritability and genetic correlation under a regression method with 7 microsatellite loci. Significant heritability and genetic correlation were detected for several quantitative traits in 2 laboratory populations but not in a natural population. In the laboratory populations, upward bias in heritability appeared depending on the relatedness estimators and the populations. Upward bias in heritability increased with decreasing the actual variance of relatedness, suggesting that the estimates of heritability under the regression method tend to be overestimated due to the underestimation of the actual variance of relatedness. Therefore, relationship structure and precise estimation of relatedness are critical for applying this method.