Comparative Studies on the Estimation of Genetic Variances by Several Variance Components Estimation Method

Using a quantitative genetic model, this paper compares four different methods for estimating genetic variance components. Given various genetic parameters, data were generated and estimates computed. The number of negative estimates, the sample mean, the sample variance, and the sample mean squared error were computed for each method. It is shown that, if the genetic values are not very small, the traditional MATHER -JINKS method is at least as good as any other method. The ML method might be preferable only if the genetic values are very small and the number of loci large.     

Estimation of Design and Genetic Components of Variance in Double Cross Mating Designs

The present paper deals with the estimation of design and genetic components of variance based on full double crosses and partial tetra-allel crosses. We have presented the explicit experissions for the symmetric sums estimators of design components of variance based on Hinkelmann's model. Consequently we have also presented explicitly the genetic components of variance based on full double crosses and partial tetra-allel crosses. The procedure is also illustrated with the help of a hypothetical data.     

The Loss of Genetic Diversity in Sichuan Taimen as Revealed by DNA Fingerprinting

Species endangerment often derives from the “endangerment” of genetic diversity, thus loss of genetic diversity is an important cause of species extinction. Since historical specimens were unavailable, previous studies mainly described the genetic diversity status in the current population rather than the loss of genetic variation over time. In this study, we collected samples during1998–1999 and obtained historical specimens from 1957 to 1958. Based on the two sets of fish, we determined the changes in genetic diversity of Sichuan taimen using DNA fingerprinting. The differences in genetic parameters between the present samples and historical taimens revealed their loss of genetic variation. As a result, the existing populations have lower viability, and proper management has to be implemented to preserve genetic diversity.     

(GTG)5探针产生的DNA指纹图在近交系小鼠遗传检测中的应用

目的探讨用非放射性标记的寡聚核苷酸探针(GTG)5进行近交系小鼠的DNA指纹分析。方法用非放射性标记的寡聚核苷酸探针(GTG)5制作BALB/c、C57BL/6J、DBA/2、C3H近交系小鼠的DNA指纹图,对这四个品系的小鼠进行遗传检测,分析各品系内和品系间的遗传变异性。结果(GTG)5探针可产生具有良好多态性的DNA指纹图,平均图带数为8~12条。各品系内的DNA指纹图平均相似系数(-x)在0.96~1.00的范围内,具有相同指纹图的概率(P)均在3.1×10-1以上,极显著地高于品系间的相似系数(0.22~0.39)和相同指纹图的概率(P<1.07×10-4)。结论(GTG)5可用于制作近交系小鼠的DNA指纹图以对其进行遗传检测。     

Genetically Distinct Populations in an Asian Soldier-Producing Aphid, Pseudoregma bambucicola (Homoptera: Aphididae), Identified by DNA Fingerprinting and Molecular Phylogenetic Analysis

To estimate genetic structure of a soldier-producing aphid, Pseudoregma bambucicola, samples from natural populations throughout southeastern Asia were analyzed by a DNA fingerprinting technique. We unexpectedly found that P. bambucicola comprises two geographic groups, the northern group and the southern group, which are genetically distinct from each other but morphologically almost indistinguishable. Molecular phylogenetic and statistical analyses based on mitochondrial ribosomal DNA sequences demonstrated that the northern and southern groups of P. bambucicola are not closely related but constitute distinct lineages in the genus Pseudoregma. Detailed morphological reexamination revealed that the two groups could be distinguished by the number of setae on the 8th abdominal tergite of 1st instar nymphs and soldiers. From these results, it was suggested that P. bambucicola should be divided into two species. The northern group from Japan, Taiwan, Hong Kong, and northern Vietnam retains the name P. bambucicola, whereas we suggest that the name P. carolinensis (R. Takahashi, 1941, Tenthredo 3, 208–220) should be used for the southern group from Thailand, Malay Peninsula, Java, Irian Jaya, and Micronesia. The morphological resemblance between P. bambucicola and P. carolinensis might be due to shared ancestral characters of the genus Pseudoregma.     

具有亲缘关系矩阵的混合模型的方差组分迭代估计——应用于计算BLUP的方差比值和遗传参数

论述的是来自非均街资料的混合模型中具有亲缘关系矩阵时利用迭代法估计方差组分问题。这篇文章表明计算程序是可行的,只要能够按照混合模型中固定效应的结构矩阵和Henderson方法3的固定效应的假设条件正确地计算二次型约化平方和,就可获得较为精确的方差组分估计值;而且表明方差初始比值k偏高或偏低,不影响迭代求解的最后结果,这是因为在迭代过程中可以通过结构矩阵x'x和x'x的控制而自行调整。这些方差组分不仅可应用于选种种畜用的BLUP计算,还可用来估计遗传参数。     

A general maximum likelihood analysis of variance components in generalized linear models

This paper describes an EM algorithm for nonparametric maximum likelihood (ML) estimation in generalized linear models with variance component structure. The algorithm provides an alternative analysis to approximate MQL and PQL analyses (McGilchrist and Aisbett, 1991, Biometrical Journal 33, 131-141; Breslow and Clayton, 1993; Journal of the American Statistical Association 88, 9-25; McGilchrist, 1994, Journal of the Royal Statistical Society, Series B 56, 61-69; Goldstein, 1995, Multilevel Statistical Models) and to GEE analyses (Liang and Zeger, 1986, Biometrika 73, 13-22). The algorithm, first given by Hinde and Wood (1987, in Longitudinal Data Analysis, 110-126), is a generalization of that for random effect models for overdispersion in generalized linear models, described in Aitkin (1996, Statistics and Computing 6, 251-262). The algorithm is initially derived as a form of Gaussian quadrature assuming a normal mixing distribution, but with only slight variation it can be used for a completely unknown mixing distribution, giving a straightforward method for the fully nonparametric ML estimation of this distribution. This is of value because the ML estimates of the GLM parameters can be sensitive to the specification of a parametric form for the mixing distribution. The nonparametric analysis can be extended straightforwardly to general random parameter models, with full NPML estimation of the joint distribution of the random parameters. This can produce substantial computational saving compared with full numerical integration over a specified parametric distribution for the random parameters. A simple method is described for obtaining correct standard errors for parameter estimates when using the EM algorithm. Several examples are discussed involving simple variance component and longitudinal models, and small-area estimation.     

Relationships Between Kendall's Coefficient of Concordance and a Nonparametric Measure of Phenotypic Stability with Implications for the Consistency in Rankings as Affected by Variance Components

For a two-way classification with rows (= genotypes) and columns (= environments) relationships between Kendall's coefficient of concordance W and a nonparametric measure of phenotypic stability S (= variance among the ranks over the environments) are presented. This provides an analogy between Wricke's ecovalence and the sum of squares of genotype-environment interactions on the parametric side and S and Kendall's W on the nonparametric side: S is a genotype's contribution to the discordance (1 — W) in the data set, while Wricke's ecovalence is a genotype's contribution to the genotype-environment interaction sum of squares. Genotype x environment interactions may lead, but must not necessarily lead to non-identical rank orders of the genotypes in different environments (crossover versus noncrossover interactions). When does interaction become rank interaction? The similarity of the rank orders (measured by W) can be approximately expressed by the ratio of the genotypic variance and sum of genotypic variance plus residual variance. For the consistency of rankings this relation leads to an approximate test of significance which is based on variance components. Finally, a numerical example is given using grain yield data of 20 genotypes (varieties) of winter wheat in 10 environments (locations) from German registration trials.     

Genetic evaluation of the mating system in the blue-and-yellow macaw (Ara ararauna, Aves, Psittacidae) by DNA fingerprinting

More than 90% of birds are socially monogamous, although genetic studies indicate that many are often not sexually monogamous. In the present study, DNA fingerprinting was used to estimate the genetic relationships between nestlings belonging to the same broods to evaluate the mating system in the socially monogamous macaw, Ara ararauna. We found that in 10 of 11 broods investigated, the nestlings showed genetic similarity levels congruent with values expected among full-sibs, suggesting that they shared the same parents. However, in one brood, the low genetic similarity observed between nestlings could be a result of intraspecific brood parasitism, intraspecific nest competition or extra-pair paternity. These results, along with available behavioral and life-history data, imply that the blue-and-yellow macaw is not only socially, but also genetically monogamous. However, the occurrence of eventual cases of extra-pair paternity cannot be excluded.     

Distribution of Mating Types and Genetic Diversity of Ascochyta rabiei Populations in Tunisia Revealed by Mating-type-specific PCR and Random Amplified Polymorphic DNA Markers

The distribution of mating types of Ascochyta rabiei (teleomorph: Didymella rabiei) was determined in Tunisia using a MAT‐specific PCR assay. Among 123 isolates tested, 80% were MAT1‐1 and 20%MAT1‐2. Only MAT1‐1 isolates were present in the Beja and Bizerte regions of Tunisia, whereas both mating types were present in Nabeul, Kef and Jendouba. In the latter three regions, the hypothesis of random mating could not be rejected based on chi‐squared tests of mating‐type ratios (P > 0.05). The lower frequency of the MAT1‐2 coupled with the restricted distribution of this mating type in Tunisia may indicate a recent introduction of MAT1‐2 in Tunisia. This speculation is consistent with the recent (2001) observation of D. rabiei pseudothecia on chickpea debris in Tunisia. Forty isolates representative of the five regions were genetically analysed using 10 random amplified polymorphic DNA (RAPD) primers to provide a preliminary estimate of genetic diversity of the pathogen in Tunisia. Among 129 putative RAPD loci amplified, 81% were polymorphic and 32 unique RAPD fingerprints were detected. A high level of genetic differentiation was detected among subpopulations (G_ST = 0.33). Cluster analyses revealed that isolates from Bizerte, Beja and Jendouba were genetically similar and distinct from isolates sampled in Nabeul and Kef. MAT1‐1 isolates were clustered separately from MAT1‐2 isolates in Jendouba and Nabeul suggesting that recombination may not yet be occurring in these regions despite the occurrence of both mating types in equal frequency in these regions. This lack of recombination between MAT1‐1 and MAT1‐2 also supports the hypothesis of a recent introduction of MAT1‐2 into Tunisia.     

The evolution and functional divergence of the beta-carotene oxygenase gene family in teleost fish—Exemplified by Atlantic salmon

In mammals, two carotenoid cleaving oxygenases are known; beta-carotene 15,15′-monooxygenase (BCMO1) and beta-carotene 9′,10′-oxygenase (BCO2). BCMO1 is a key enzyme in vitamin A synthesis by symmetrically cleaving beta-carotene into 2 molecules of all-trans-retinal, while BCO2 is responsible for asymmetric cleavage of a broader range of carotenoids. Here, we show that the Atlantic salmon beta-carotene oxygenase (bco) gene family contains 5 members, three bco2 and two bcmo1 paralogs. Using public sequence databases, multiple bco genes were also found in several additional teleost species. Phylogenetic analysis indicates that bco2a and bco2b originate from the teleost fish specific genome duplication (FSGD or 3R), while the third and more distant paralog, bco2 like, might stem from a prior duplication event in the teleost lineage. The two bcmo1 paralogs (bcmo1 and bcmo1 like) appear to be the result of an ancient duplication event that took place before the divergence of ray-finned (Actinopterygii) and lobe-finned fish (Sarcopterygii), with subsequent nonfunctionalization and loss of one Sarcopterygii paralog. Gene expression analysis of the bcmo1 and bco2 paralogs in Atlantic salmon reveals regulatory divergence with tissue specific expression profiles, suggesting that the beta-carotene oxygenase subtypes have evolved functional divergences. We suggest that teleost fish have evolved and maintained an extended repertoire of beta-carotene oxygenases compared to the investigated Sarcopterygii species, and hypothesize that the main driver behind this functional divergence is the exposure to a diverse set of carotenoids in the aquatic environment.