Nuclear and cytoplasmic contributions to intraspecific divergence in an annual legume

The genetic architecture of trait differentiation was evaluated between two ecologically distinct populations of Chamaecrista fasciculata. Individuals from Maryland and Illinois populations were crossed to create 10 types of seed: Maryland and Illinois parents, reciprocal F1 and F2 hybrids, and backcrosses to Maryland and to Illinois on reciprocal F1 hybrids. Reciprocal crosses created hybrid generation seeds with both Maryland and Illinois cytoplasmic backgrounds. Experimental individuals were grown in a common garden near the site of the Maryland population. In the garden, plants from the Illinois population flowered, set fruit, and died earlier than those from Maryland, likely reflecting adaptations to differences in growing season length between the two populations. Although reproductive components at the flower and whole plant level differed between the two populations, reproductive output as measured by fruit and seed production was similar. Cytoplasmic genes had a subtle but pervasive effect on population differentiation; hybrids with Maryland cytoplasm were significantly differentiated from those with Illinois cytoplasm when all characters were evaluated jointly. The nuclear genetic architecture of population differentiation was evaluated with joint scaling tests. Depending on the trait, both additive and nonadditive genetic effects contributed to population differentiation. Intraspecific genetic differentiation in this wild plant species appears to reflect a complex genetic architecture that includes the contribution of additive, dominance, and epistatic components in addition to subtle cytoplasmic effects.     

Parent-of-origin specific QTL--a possibility towards understanding reciprocal effects in chicken and the origin of imprinting

Reciprocal effects for sexual maturity, egg production, egg quality traits and viability are well known in poultry crosses. They have been used in an optimal way to form profitable production hybrids. These effects have been hypothesized to originate from sex-linked genes, maternal effects or a combination of both. However, these may not be the only explanations for reciprocal effects. Recent mapping of quantitative trait loci (QTL) has revealed autosomal areas with parent-of-origin specific effects in the chicken. In mammals, parental imprinting, i.e. the specifically regulated expression of either maternal or paternal allele in the offspring, is the main cause of such effects. The most commonly accepted hypothesis for the origin of imprinting, the conflict hypothesis, assumes a genetic conflict of interest between the maternal and paternal genomes regarding the allocation of resources to the offspring. It also intrinsically implies that imprinting should not occur in oviparous taxa. However, new molecular genetic information has raised a need to review the possible involvement of imprinting or some related phenomena as a putative cause of reciprocal effects in poultry. Comparative mapping provides strong evidence for the conservation of orthologous imprinted gene clusters on chicken macrochromosomes. Furthermore, these gene clusters exhibit asynchronous DNA replication, an epigenetic mark specific for all imprinted regions. It has been proposed that these intrinsic chromosomal properties have been important for the evolution of imprinted gene expression in the mammalian lineage. Many of the mapped parent-of-origin specific QTL effects in chicken locate in or close to these conserved regions that show some of the basic features involved in monoallelic expression. If monoallelic expression in these regions would be observed in birds, the actual mechanism and cause may be different from the imprinting that evolved later in the mammalian lineage. In this review we discuss recent molecular genetic results that may provide tools for understanding of reciprocal differences in poultry breeding and the evolution of imprinting.     

Epigenetic targeting in the mouse zygote marks DNA for later methylation: a mechanism for maternal effects in development

The transgenic sequences in the mouse line TKZ751 are demethylated on a DBA/2 inbred strain background but become highly methylated at postimplantation stages in offspring of a cross with a BALB/c female. In the reciprocal cross the transgene remains demethylated suggesting that imprinted BALB/c methylation modifiers or egg cytoplasmic factors are responsible for this striking maternal effect on de novo methylation. Reciprocal pronuclear transplantation experiments were carried out to distinguish between these mechanisms. The results indicate that a maternally-derived oocyte cytoplasmic factor from BALB/c marks the TKZ751 sequences at fertilization; this mark and postzygotic BALB/c modifiers are both required for de novo methylation of the target sequences at postimplantation stages. Using genetic linkage analyses we mapped the maternal effect to a locus on chromosome 17. Moreover, seven postzygotic modifier loci were identified that increase the postimplantation level of methylation. Analysis of interactions between the maternal and the postzygotic loci shows that both are needed for de novo methylation in the offspring. The combined experiments thus reveal a novel epigenetic marking process at fertilization which targets DNA for later methylation in the foetus. The most significant consequence is that the genotype of the mother can influence the epigenotype of the offspring by this marking process. A number of parental and imprinting effects may be explained by this epigenetic marking.     

Maternal effects and generation mean analysis of seed-oil content in cotton (Gossypium hirsutum L.)

Summary The nature of gene action and of maternal influence governing cottonseed oil attributes were determined with four lines, two each with high and low seed-oil percentage. For this purpose, P1, P2, F0, F1, F2 and alternative sets of BC1 and BC2 generations were analysed in six cross-combinations and their reciprocals. Marginal extents of heterosis for seed-oil percentage were noticeable in F1, with inbreeding depression in F2. Data from reciprocal backcrosses provided evidence in favour of maternal rather than cytoplasmic effects of seed-oil development. Relatively higher extents of heterosis, sizeable inbreeding depression and reciprocally unequal F2 averages were characteristic of the seed index trait, which often showed a reversal of effects from F1 to F2. Reverse reciprocal backcrosses exhibited some differences, including greater resemblance between the types, (A/B)A and (B/A)A, in addition to variable dose effects in seed index. Thus, the differences between F1 seed index values were not due to cytoplasmic influence. Positive heterotic effects for seed-oil index, especially among the backcrosses, ranged between 16.08% and 47.29% over midparent averages. Genetic component estimates from analysis of similar sets of crosses differing only in reciprocal backcrosses, and also from sets of reciprocal crosses between any two parental combinations, were inconsistent. Scaling tests detected presence of epistasis within and between a majority of cross-combinations. Despite reciprocal differences, additive gene effects for seed-oil percentage were significant in 7 out of 24 crosses, representing high x low, low x high and low x low seed-oil parents. Those were, however, accompanied by significant dominance effects of higher order. In crosses involving low seed-oil percentage parents SA1060 and SA229, all six components were detected significant, with opposite effects of dominance and dominance x dominance epistatic components. Significant additive components were also detected for seed index and seed-oil index in 7 and 5 out of 24 crosses, respectively. In the inheritance of seed index and seed-oil index, dominance effects were more important. Epistatic components of additive x additive, and to a lesser extent, those of dominant x dominant were found significant.     

Genetic analysis of reciprocal differences in the inheritance of in vitro characters in pearl millet

Reciprocal differences persist in nature because of the unequal contribution of cytoplasmic determinants from male and female gametes to the zygote. The inheritance of genetic differences is an important factor that influences various traits, including somatic embryogenesis and regeneration in vitro. In this report, we estimate the cytoplasmic and maternal effects in pearl millet and their adequacy in describing the observed reciprocal differences based on an in depth study of the parents, F₂s and reciprocal backcross progenies needed for fitting genetical models. Our study revealed that of the two characters examined, embryogenic callus quantity and regeneration frequency, the former showed a greater proportion of cytoplasmic nuclear interaction whereas the latter showed a greater role of nuclear factors. Additive-maternal effects influenced total callus quantity and dominance-maternal effects influenced total callus quantity, embryogenic callus quantity and regeneration frequency. Dwarfing was associated with the production of large quantities of embryogenic callus that had visually recognizable characteristics. The phenotypic nature of dwarf parents (green dwarf with long narrow leaves) with a genetic basis for a given character controlled by nuclear and cytoplasmic determinants can be exploited for other breeding programs.     

A statistical model for estimating maternal-zygotic interactions and parent-of-origin effects of QTLs for seed development

Proper development of a seed requires coordinated exchanges of signals among the three components that develop side by side in the seed. One of these is the maternal integument that encloses the other two zygotic components, i.e., the diploid embryo and its nurturing annex, the triploid endosperm. Although the formation of the embryo and endosperm contains the contributions of both maternal and paternal parents, maternally and paternally derived alleles may be expressed differently, leading to a so-called parent-of-origin or imprinting effect. Currently, the nature of how genes from the maternal and zygotic genomes interact to affect seed development remains largely unknown. Here, we present a novel statistical model for estimating the main and interaction effects of quantitative trait loci (QTLs) that are derived from different genomes and further testing the imprinting effects of these QTLs on seed development. The experimental design used is based on reciprocal backcrosses toward both parents, so that the inheritance of parent-specific alleles could be traced. The computing model and algorithm were implemented with the maximum likelihood approach. The new strategy presented was applied to study the mode of inheritance for QTLs that control endoreduplication traits in maize endosperm. Monte Carlo simulation studies were performed to investigate the statistical properties of the new model with the data simulated under different imprinting degrees. The false positive rate of imprinting QTL discovery by the model was examined by analyzing the simulated data that contain no imprinting QTL. The reciprocal design and a series of analytical and testing strategies proposed provide a standard procedure for genomic mapping of QTLs involved in the genetic control of complex seed development traits in flowering plants.     

Parental effects on growth in Solanum conditioned at multiple levels

Summary Reciprocal crosses were made between plants that had nuclear genes of S.tuberosum L. ssp tuberosum combinated, by recurrent backrossing, with cytoplasmic factors of S. phureja Juz. & Buk. and, separately, of S. tuberosum ssp. andigena (Juz. & Buk.) Hawkes. Significant differences in growth between 19 of 23 intra-cytoplasmic reciprocal progenies occurred in vigor at one or more growth stages during the season and/or in yield as measured by tuber number and weight. If no transmission of cytoplasmic factors occurred through the pollen, the cytoplasmic factors of the parents were the same, and these reciprocal differences were caused by parental chromosomal gene mechanisms such as maternal effect, pollen-tube selection, and/or imprinting. Early seedling vigor was, in some cases, associated with greater seed weight, but this did not account for all of the reciprocal contrasts. The data do not show whether these parental effects are a result of maternal and/or paternal effects. Analysis to determine whether parental effect was a single gene character or alleles expressed at two levels, or multi-genic and so expressed at multiple levels, was based on a study of progeny of ten parents that were used in more than one reciprocal pair combination. The data showed that the parents could be classified at eight successive levels of relative effectiveness as staminate or pistillate parents. Of 23 crosses, 19 showed significant differences between reciprocal progenies that were consistent with this eight-level array. The data support the interpretation that parental effect is a multi-genic character.Authorized for publication as paper No. 163 of the Department of Horticulture     

Population differentiation in the beetleTribolium castaneum. I. Genetic architecture

We used joint-scaling analyses in conjunction with rearing temperature variation to investigate the contributions of additive, non-additive, and environmental effects to genetic divergence and incipient speciation among 12 populations of the red flour beetle, Tribolium castaneum, with small levels of pairwise nuclear genetic divergence (0.033 < Nei's D < 0.125). For 15 population pairs we created a full spectrum of line crosses (two parental, two reciprocal F1's, four F2's, and eight backcrosses), reared them at multiple temperatures, and analyzed the numbers and developmental defects of offspring. We assayed a total of 219,388 offspring from 5147 families. Failed crosses occurred predominately in F2's, giving evidence of F2 breakdown within this species. In all cases where a significant model could be fit to the data on offspring number, we observed at least one type of digenic epistasis. We also found maternal and cytoplasmic effects to be common components of divergence among T. castaneum populations. In some cases, the most complex model tested (additive, dominance, epistatic, maternal, and cytoplasmic effects) did not provide a significant fit to the data, suggesting that linkage or higher order epistasis is involved in differentiation between some populations. For the limb deformity data, we observed significant genotype-by-environment interaction in most crosses and pure parent crosses tended to have fewer deformities than hybrid crosses. Complexity of genetic architecture was not correlated with either geographic distance or genetic distance. Our results support the view that genetic incompatibilities responsible for postzygotic isolation, an important component of speciation, may be a natural but serendipitous consequence of nonadditive genetic effects and structured populations.     

maternally expressed gene1 Is a novel maize endosperm transfer cell-specific gene with a maternal parent-of-origin pattern of expression

Growth of the maize (Zea mays) endosperm is tightly regulated by maternal zygotic and sporophytic genes, some of which are subject to a parent-of-origin effect. We report here a novel gene, maternally expressed gene1 (meg1), which shows a maternal parent-of-origin expression pattern during early stages of endosperm development but biallelic expression at later stages. Interestingly, a stable reporter fusion containing the meg1 promoter exhibits a similar pattern of expression. meg1 is exclusively expressed in the basal transfer region of the endosperm. Further, we show that the putatively processed MEG1 protein is glycosylated and subsequently localized to the labyrinthine ingrowths of the transfer cell walls. Hence, the discovery of a parent-of-origin gene expressed solely in the basal transfer region opens the door to epigenetic mechanisms operating in the endosperm to regulate certain aspects of nutrient trafficking from the maternal tissue into the developing seed.     

Evidence for cytoplasmic inheritance of a developmental organizer affecting growth habit and leaf shape in Antirrhinum majus

A cross between two distinct, true-breeding plants of Antirrhinum majus L. showed an unexpected pattern of inheritance of growth habit in the F2, which was extended to both growth habit and leaf shape in the F3 generation of all the plants traced further. All the F3 families, offspring of individual F2 plants, were very uniform for both growth habit and leaf shape traits but differed distinctly from each other in these respects. The backcrosses of selected F3 and F4 families to the original parents in the cross did not segregate for the distinctive family phenotypes. This led to the postulate that a cytoplasmic factor was involved in the regulation and/or integration of genetic information concerned with growth habit/leaf shape. The similarity of the reciprocal backcrosses of the F3 and F4 families led to the further postulate that the proposed cytoplasmic factor was specified by both the maternal and paternal parents to a similar degree. That the gene component was segregating normally was shown by the inheritance of four marker genes for flower colour, colour pattern and flower shape.     

Developmental Genetic Analysis of Brown Rice Weight Under Different Environmental Conditions in indica Rice

Analysis of genetic main effects and genotype×environment (GE) interaction effects for brown rice weight (BRW) at four different filling stages in indica rice ( Oryza sativa L.) was conducted for two-year experimental data by using developmental genetic models and corresponding statistical approaches for quantitative traits of seeds in cereal crops. It was indicated that the genetic main effects and their GE interaction effects of triploid endosperm, cytoplasmic and diploid maternal plant genes were important for BRW at different filling stages of rice, especially for endosperm or maternal additive main effects and their additive interaction effects. Because of the higher additive effects and additive interaction effects for BRW at different filling stages, the better improving effects for this trait could be expected by selection in rice breeding. The results of conditional genetic variance components showed that the new expression of quantitative genes in endosperm and maternal plant for BRW was mostly found at all different filling stages of rice. The gene expression, however, was most active at the early filling stages especially for the first (1-7 d) and the second filling stages (8-14 d after flowering). The phenomena that some genes were spasmodically expressible among filling stages of rice were detected for some genetic effects especially for net cytoplasmic main effects or its interaction effects and net dominance main effects. Predicted genetic effects at different filling stages of rice showed that some parents such as V20 and Zuo 5 were better than others for improving the BRW.     

Methods for detection of parent-of-origin effects in genetic studies of case-parents triads.

When affected probands and their biological parents are genotyped at a candidate gene or a marker, the resulting case-parents-triad data enable powerful tests for linkage in the presence of association. When linkage disequilibrium has been detected in such a study, the investigator may wish to look further for possible parent-of-origin effects. If, for example, the transmission/disequilibrium test restricted to fathers is statistically significant, whereas that restricted to mothers is not, the investigator might interpret this as evidence for nonexpression of the maternally derived disease gene-that is, imprinting. This report reviews existing methods for detection of parent-of-origin effects, showing that each can be invalid under certain scenarios. Two new methods are proposed, based on application of likelihood-based inference after stratification on both the parental mating type and the inherited number of copies of the allele under study. If there are no maternal genetic effects expressed prenatally during gestation, the parental-asymmetry test is powerful and provides valid estimation of a parent-of-origin parameter. For diseases for which there could be maternal effects on risk, the parent-of-origin likelihood-ratio test provides a robust alternative. Simulations based on an admixed population demonstrate good operating characteristics for these procedures, under diverse scenarios.     

Genetic variation in dosage effects in maize aneuploids.

In maize (Zea mays L.), the consequences of aneuploidy have been well documented, however, genetic variation in the responses to aneuploidy has not been examined. Using simple B-A translocation stocks to generate a dosage series involving segments from 14 chromosome arms, we tested for the presence of genetic variation for dosage responses in maize by examining reciprocal and maternal genotype effects on the dosage responses. Reciprocal effects examined whether there were differences between two distinctly different inbred backgrounds, Mo17Ht and B73Ht, in how they responded to loss or gain of a B73Ht segment in the Mo17Ht x B73Ht (TB) F1 cross versus a Mo17Ht segment in the B73Ht x Mo17Ht (TB) F1 cross. Maternal genotype effects questioned whether different inbred backgrounds, Sc41R, T8, and either Mo17Ht or B73Ht (depending on the male), when used as females responded differently to the loss or gain of a chromosome arm segment from the same male (either B73Ht TB or Mo17Ht TB) in an F1 cross. Numerous examples of reciprocal and maternal genetic effects were identified in this study. Most of the genetic effects were due to differences in magnitude of response rather than direction; however, tassel-branch number involving the 5S chromosome segment in the B73Ht male background and the 7L chromosome segment in the Mo17Ht male background showed a trend toward the maternal genotype effects being due to differences in the direction of the response. Key words : quantitative traits, corn, B-A translocations, dosage analysis.     

普通玉米籽粒性状的遗传效应分析

采用二倍体种子遗传模型及其分析方法,研究了５个玉米籽粒性状的直接效应、母体效应和细胞质效应．分析结果表明,各性状的遗传同时受种子直接效应和母体效应的影响,细胞质基因对百粒重和粒宽具有极显著影响．除粒长、粒厚的直接显性效应与母体显性效应间的协方差外,直接效应与母体效应间的协方差均不显著．因此,通过母体植株的表现可对这些性状进行有效的选择．Ｓ_２２和 ８７－１是改良粒重的优良亲本．选择粒较宽的自交系作母本有利于提高后代选系及Ｆ_１的百粒重．     

Complex inheritance of larval adaptation in Plutella xylostella to a novel host plant

Studying the genetics of host shifts and range expansions in phytophagous insects contributes to our understanding of the evolution of host plant adaptation. We investigated the recent host range expansion to pea, in the pea-adapted strain (P-strain) of the crucifer-specialist diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae). Larval survivorship on the novel host plant pea and a typical crucifer host (kale) was measured in reciprocal F(1), F(2) and backcrosses between the P-strain and a strain reared only on crucifers (C-strain). Reciprocal F(1) hybrids differed: offspring from P-strain mothers survived better on pea, indicating a maternal effect. However, no evidence for sex-linkage was found. Backcrosses to the P-strain produced higher survivorship on pea than C-strain backcrosses, suggesting recessive inheritance. In a linkage analysis with amplified fragment length polymorphism markers using P-strain backcrosses, two, four and five linkage groups contributing to survival on pea were identified in three different families respectively, indicating oligogenic inheritance. Thus, the newly evolved ability to survive on pea has a complex genetic basis, and the P-strain is still genetically heterogeneous and not yet fixed for all the alleles enabling it to survive on pea. Survivorship on kale was variable, but not related to survivorship on pea. This pattern may characterize the genetic inheritance of early host plant adaptation in oligophagous insect species.     

Quantitative genetic studies of A/B zeins using a new model to test non-allelic interactions

A genetic model developed by Bogyo et al. (1988) for quantitatively inherited triploid endosperm characters (an extension of the well-known Mather-Jinks model) is not well-suited for estimating epistatic interaction effects because it requires the assumption that, in segregating loci, all alleles positively affecting a particular character are in one of the inbred parental lines. To better explain zein inheritance in maize, a new model was developed not relying on this assumption. This model was tested by quantitative analysis of A/B zeins, the predominant prolamin storage proteins of maize, using reversed phase high-performance liquid chromatography of two inbred lines, their reciprocal F₁ crosses, the F₂ generation, backcrosses, and reciprocal backcrosses to both parent lines. The model required epistatic components to be included for an excellent fit for most protein peaks.Scientific Paper No. 3 Program in Statistics, Washington State University, Pullman WA 99164. The mention of firm names or trade products does not imply that they are endorsed or recommended by the US Department of Agriculture over other firms or similar products not mentioned     

Genetics of behavioural and morphological differences between parapatric subspecies of Chorthippus parallelus (Orthoptera: Acrididae)

The grasshoppers Chorthippus parallelus parallelus and C. p. erythropus form a narrow hybrid zone in the Pyrenees. They differ in several characters of the pattern and structure of male stridulation and in the morphology of the stridulatory file. These characters are considered to be involved in the species' mate recognition system.
Crosses have been made between a Pyrenean C. p. erythropus population and two C. p. parallelus populations, one in the Pyrenees and one in the Massif Central. Reciprocal Fls and backcrosses have been examined for a set of stridulation and associated morphological characters. The crosses confirm that the subspecific differences have a genetic basis and suggest that they are polygenically determined. However the mode of inheritance is not simple. There is evidence for dominance and epistatic effects and for sex-linkage or maternal effects. Genetic correlations exist between some pairs of characters in the backcrosses.
These results are discussed in the context of the hybrid zone and in relation to the general problem of the evolutionary divergence of mate recognition systems.     

Desiccation resistance in interspecific Drosophila crosses. Genetic interactions and trait correlations

We used crosses between two closely related Drosophila species, Drosophila serrata and D. birchii, to examine the genetic basis of desiccation resistance and correlations between resistance, physiological traits, and life-history traits. D. serrata is more resistant to desiccation than D. birchii, and this may help to explain the broader geographical range of the former species. A comparison of F2's from reciprocal crosses indicated higher resistance levels when F2's originated from D. birchii mothers compared to D. serrata mothers. However, backcrosses had a resistance level similar to that of the parental species, suggesting an interaction between X-linked effects in D. serrata that reduce resistance and autosomal effects that increase resistance. Reciprocal differences persisted in hybrid lines set up from the different reciprocal crosses and tested at later generations. Increased desiccation resistance was associated with an increased body size in two sets of hybrid lines and in half-sib groups set up from the F4's after crossing the two species, but size associations were inconsistent in the F2's. None of the crosses provided evidence for a positive association between desiccation resistance and glycogen levels, or evidence for a tradeoff between desiccation resistance and early fecundity. However, fecundity was positively correlated with body size at both the genetic and phenotypic levels. This study illustrates how interspecific crosses may provide information on genetic interactions between traits following adaptive divergence, as well as on the genetic basis of the traits.