Asynchronous expression of the alcohol and supernatant malate dehydrogenase loci during Barbus hybrid development (Cypriniformes, Teleostei)

The tissue specificity and ontogeny of supernatant malate dehydrogenase (s-MDH) and alcohol dehydrogenase (ADH) are reported for the tiger barb (Barbus tetrazona), the rosy barb (Barbus conchonius) and their reciprocal hybrids. The tissue distribution of s-MDH and ADH isozymes in both species is consistent with spatial profiles reported for other teleosts. The expression of alleles of paternal origin at the s-Mdh-B and Adh loci are delayed in reciprocal hybrids as compared to their expression intraspecifically; suggestive of a low degree of affinity between maternally derived regulatory factors and paternal regulative elements controlling structural gene activation.     

Ontogenetic patterns of enzyme locus expression in Barbus hybrids (Cypriniformes, Teleostei)

The tissue specific patterns and ontogeny of sorbitol dehydrogenase (SDH, EC 1.1.1.14). lactate dehydrogenase (LDH, EC 1.1.1.27) and isocitrate dehydrogenase (IDH, EC 1.1.1.42) are reported for Barbus tetrazona (tiger barb), B. conchonius (rosy barb), B. nigrofasciatus (black ruby barb), B. titteya (cherry barb), B. sachsi (gold barb), and in interspecific hybrids where B. tetrazona is the maternal parent. The spatial and temporal expression of SDH, LDH and IDH isozymes in Barbus is consistent with those reported for other teleosts. As the genetic distance between the parentals used in forming the hybrid increases, allelic expression proceeds from synchronous to asynchronous, with an increasing delay in embryonic gene expression. These observations are consistent with the hypothesis that parental sensor genes differ in their response to maternally controlled regulatory signals; indicative of species specific effector/activator RNA molecule concentrations and sensor/receptor gene induction thresholds.     

鲤鲫人工多倍体谱系中同工酶和蛋白的基因表达

通过对红鲤、红鲫、镜鲤、鲤鲫杂种二倍体一代,二代,鲤鲫杂种三倍体,鲤鲫复合三倍体,鲤鲫杂种四倍体一代,二代的同工酶及蛋白电泳谱型和扫描数据分析表明,在鲤鲫人工多倍体谱系中,亲代的等位基因在杂交子代中共有四种表达模式;（1）两亲本基因在子代中共同表达,即共显表达;（2）父本的基因表达受到部分或完全的抑制,即母本的基因优先得到表达;（3）母本的基因表达受到抑制,父本的基因得到表达;（4）双亲本的基因表达均受到一定程度的抑制或都不表达。其中第一种表达模式是主要的模式。根据以上基因在杂交子代中的表达特点,可用同工酶和蛋白电泳图谱将鲤鲫人工多倍体谱系的各种生物型逐一加以区分。     

酶的基因剂量效应及其对鱼类远缘杂交的影响

亲缘关系较远的杂种二倍体,酶的表达出现父本基因受抑制,双亲基因表达迟缓和母本基因提前表达三种类型的紊乱。由于双亲等位基因不亲和,各等位基因只调控产生1／2的基因产物,从而致使胚胎出现“双单倍体综合症”而在孵化期全部死亡。远缘杂交三倍体由于母本基因剂量加倍,一方面抑制了父本基因的表达,消除了不协调基因活动的干扰,另一方面母本基因产物趋于正常,代谢得以正常进行,杂种后代能成活并正常生长。     

Detection of Parent-of-Origin Specific Expression Quantitative Trait Loci by Cis-Association Analysis of Gene Expression in Trios

Parent-of-origin (PofO) effects, such as imprinting are a phenomenon in which homologous chromosomes exhibit differential gene expression and epigenetic modifications according to their parental origin. Such non-Mendelian inheritance patterns are generally ignored by conventional association studies, as these tests consider the maternal and paternal alleles as equivalent. To identify regulatory regions that show PofO effects on gene expression (imprinted expression Quantitative Trait Loci, ieQTLs), here we have developed a novel method in which we associate SNP genotypes of defined parental origin with gene expression levels. We applied this method to study 59 HapMap phase II parent-offspring trios. By analyzing mother/father/child trios, rules of Mendelian inheritance allowed the parental origin to be defined for ～95% of SNPs in each child. We used 680,475 informative SNPs and corresponding expression data for 92,167 probe sets from Affymetrix GeneChip Human Exon 1.0 ST arrays and performed four independent cis-association analyses with the expression level of RefSeq genes within 1 Mb using PLINK. Independent analyses of maternal and paternal genotypes identified two significant cis-ieQTLs (p<10(-7)) at which expression of genes SFT2D2 and SRRT associated exclusively with maternally inherited SNPs rs3753292 and rs6945374, respectively. 28 additional suggestive cis-associations with only maternal or paternal SNPs were found at a lower stringency threshold of p<10(-6), including associations with two known imprinted genes PEG10 and TRAPPC9, demonstrating the efficacy of our method. Furthermore, comparison of our method that utilizes independent analyses of maternal and paternal genotypes with the Likelihood Ratio Test (LRT) showed it to be more effective for detecting imprinting effects than the LRT. Our method represents a novel approach that can identify imprinted regulatory elements that control gene expression, suggesting novel PofO effects in the human genome.     

Gene activation of alcohol dehydrogenase in danio hybrids

The regulation of alleles encoding the enzyme alcohol dehydrogenase (ADH) was investigated in F1Brachydanio hybrids (zebra danio female x spotted danio male) by acrylamide gel electrophoresis. Both parental species showed a single, cathodal band of species-specific ADH. During development at 26 degrees C, hybrid fry showed a preferential activation of the maternally derived Adh allele. It is suggested that the low activity of the paternally derived allele may result from an incompatibility between maternal regulatory factors and the paternal regulative element controlling gene expression.     

Genomic imprinting,disrupted placental expression,and speciation

The importance of regulatory incompatibilities to the early stages of speciation remains unclear. Hybrid mammals often show extreme parent‐of‐origin growth effects that are thought to be a consequence of disrupted genetic imprinting (parent‐specific epigenetic gene silencing) during early development. Here, we test the long‐standing hypothesis that abnormal hybrid growth reflects disrupted gene expression due to loss of imprinting (LOI) in hybrid placentas, resulting in dosage imbalances between paternal growth factors and maternal growth repressors. We analyzed placental gene expression in reciprocal dwarf hamster hybrids that show extreme parent‐of‐origin growth effects relative to their parental species. In massively enlarged hybrid placentas, we observed both extensive transgressive expression of growth‐related genes and biallelic expression of many genes that were paternally silenced in normal sized hybrids. However, the apparent widespread disruption of paternal silencing was coupled with reduced gene expression levels overall. These patterns are contrary to the predictions of the LOI model and indicate that hybrid misexpression of dosage‐sensitive genes is caused by other regulatory mechanisms in this system. Collectively, our results support a central role for disrupted gene expression and imprinting in the evolution of mammalian hybrid inviability, but call into question the generality of the widely invoked LOI model.     

Fetal Genotyping in Maternal Blood by Digital PCR: Towards NIPD of Monogenic Disorders Independently of Parental Origin

PurposeTo date, non-invasive prenatal diagnosis (NIPD) of monogenic disorders has been limited to cases with a paternal origin. This work shows a validation study of the Droplet Digital PCR (ddPCR) technology for analysis of both paternally and maternally inherited fetal alleles. For the purpose, single nucleotide polymorphisms (SNPs) were studied with the only intention to mimic monogenic disorders.MethodsNIPD SNP genotyping was performed by ddPCR in 55 maternal plasma samples. In 19 out of 55 cases, inheritance of the paternal allele was determined by presence/absence criteria. In the remaining 36, determination of the maternally inherited fetal allele was performed by relative mutation dosage (RMD) analysis.ResultsddPCR exhibited 100% accuracy for detection of paternal alleles. For diagnosis of fetal alleles with maternal origin by RMD analysis, the technology showed an accuracy of 96%. Twenty-nine out of 36 were correctly diagnosed. There was one FP and six maternal plasma samples that could not be diagnosed.DiscussionIn this study, ddPCR has shown to be capable to detect both paternal and maternal fetal alleles in maternal plasma. This represents a step forward towards the introduction of NIPD for all pregnancies independently of the parental origin of the disease.     

Novel gene expression patterns in hybrid embryos between species with different modes of development

SUMMARY Cross-species hybrids between eggs of the direct-developing sea urchin, Heliocidaris erythrogramma , and sperm from its congeneric indirect-developing species, Heliocidaris tuberculata, show restoration of features of the paternal feeding pluteus larva, including the gut, and pluteus spicular skeleton. Unlike other reported sea urchin cross-species hybrids, Heliocidaris hybrids express genes derived from both maternal and paternal species at high levels. Ectodermal cell types, which differ radically between the two parental species, are of intermediate form in the hybrids. Gene expression patterns in hybrid embryo tissues represent a number of combinations of parental gene expression patterns: genes that are not expressed in one paternal species, but are expressed in hybrids as in the expressing parent; genes that show additive expression patterns plus novel sites of expression; a gene that is misexpressed in the hybrids; and genes expressed identically in both parents and in hybrids. The results indicate that both conserved and novel gene regulatory interactions are present. Only one gene, CyIII actin , has lost cell-type-specific regulation in the hybrids. Hybrids thus reveal that disparate parental genomes, each with its own genic regulatory system, can produce in combination a novel gene expression entity with a unique ontogeny. This outcome may derive from conserved gene regulatory regions in downstream genes of both parental species responding in conserved ways to higher-level regulators that determine modular gene expression territories.     

Analysis of mechanisms regulating the expression of parental alleles at the GPD locus in mule erythrocytes

Erythrocyte glucose-6-phosphate dehydrogenase (G6PD) was examined by 13% starch gel electrophoresis in 74 mules (42 females and 32 males), 35 donkeys, and ten horses. The quantitative expression of the parental alleles at the Gpd locus varies greatly in female mules from the hemizygous expression of the maternal allele to that of the paternal. The data obtained indicate that the X chromosomes are randomly inactivated in female mules. No selective advantage of a cell population with a maternally (or paternally) derived X active was found in female mule erythrocytes. It is suggested that the phenotypic variability in the expression of the parental Gpd alleles is related to the random proportions established between cells having either a maternal or paternal X active in an initiator (stem) cell group giving rise to erythroid tissue. Initiator cell numbers estimated for erythroid tissue (six or seven) are close to those reported for human females and intergeneric fox hybrids. These numbers may vary depending on the duration of the time of determination and the division rate of initiator cells at determination.     

Cytogenetic studies on the origin and species differentiation of the Philippine medaka, Oryzias luzonensis

The origin and species differentiation of the Philippine medaka, Oryzias luzonensis , was studied by means of karyotype analyses and interspecific hybridyzations. The karyotype revealed 2n = 48 consisting of 24 pairs of biarmed chromosomes (NF = 96). Characteristic C-bands were found in three sub-metacentric pairs. Nucleolar organizer regions (NORs) were detected on the short arms of the satellited sub-metacentric pair. Estimated DNA-value was 1.9 pg per nucleus. Interspecific crosses revealed that O. luzonensis was allied most closely to O. latipes (biarmed chromosome type), less closely to O. celebensis (fused chromosome type), and least closely to O. melastigma and O.javanicus (monoarmed chromosome type), which are distributed in east Asia, the Sulawesi, and south-west Asia and west side of south-east Asia, respectively. The external appearance of O. luzonensis was also more similar to that of O. latipes . From these results, we concluded that O. luzonensis is a member of the biarmed chromosome group and the nearest relative to O. latipes . Thus, the Philippine medaka seems to be of east Asiatic origin, having migrated to northern Luzon from the China continent via Formosa.     

普通小麦F_1杂种Glu-1基因表达过程中的共显性,基因组互作和剂量效应

普通小麦F_1杂种Glu-1基因表达过程中的共显性,基因组互作和剂量效应@潘幸来$山西农业科学院棉花研究所!运城044000小麦;;基因表达;;基因组     

Genome‐wide screen of genes imprinted in sorghum endosperm,and the roles of allelic differential cytosine methylation

Imprinting is an epigenetic phenomenon referring to allele‐biased expression of certain genes depending on their parent of origin. Accumulated evidence suggests that, while imprinting is a conserved mechanism across kingdoms, the identities of the imprinted genes are largely species‐specific. Using deep RNA sequencing of endosperm 14 days after pollination in sorghum, 5683 genes (29.27% of the total 19 418 expressed genes) were found to harbor diagnostic single nucleotide polymorphisms between two parental lines. The analysis of parent‐of‐origin expression patterns in the endosperm of a pair of reciprocal F₁ hybrids between the two sorghum lines led to identification of 101 genes with ≥ fivefold allelic expression difference in both hybrids, including 85 maternal expressed genes (MEGs) and 16 paternal expressed genes (PEGs). Thirty of these genes were previously identified as imprinted in endosperm of maize (Zea mays), rice (Oryza sativa) or Arabidopsis, while the remaining 71 genes are sorghum‐specific imprinted genes relative to these three plant species. Allele‐biased expression of virtually all of the 14 tested imprinted genes (nine MEGs and five PEGs) was validated by pyrosequencing using independent sources of RNA from various developmental stages and dissected parts of endosperm. Forty‐six imprinted genes (30 MEGs and 16 PEGs) were assayed by quantitative RT–PCR, and the majority of them showed endosperm‐specific or preferential expression relative to embryo and other tissues. DNA methylation analysis of the 5’ upstream region and gene body for seven imprinted genes indicated that, while three of the four PEGs were associated with hypomethylation of maternal alleles, no MEG was associated with allele‐differential methylation.     

Comparison of the spatial and temporal expression of supernatant malate dehydrogenase in Barbus hybrids (Cypriniformes, Teleostei)

The tissue specificity and ontogeny of supernatant malate dehydrogenase (s-MDH) are reported for the tiger barb, cherry barb, and their reciprocal hybrids. The tissue distribution of s-MDH isozymes in Barbus is consistent with the patterns reported in other teleosts. The expression of the Mdh-B locus is correlated with the initial muscle contractions of the developing embryos. It is suggested that the state of muscle cell differentiation may be the stimulus necessary for the expression of this locus in Barbus. Expression of maternal and paternal alleles at the B locus are synchronously delayed in reciprocal hybrids, as compared to their expression intraspecifically.     

Widespread disruption of genomic imprinting in adult interspecies mouse (Mus) hybrids

Mammalian interspecies hybrids exhibit parent-of-origin effects in that offspring of reciprocal matings, even though genetically identical, frequently exhibit opposite phenotypes, especially in growth. This was also observed in hybridization with the genus Mus. These parent-of-origin effects suggested that imbalance in the expression of imprinted genes, which are expressed differentially, depending on their transmission through the maternal or paternal germline, and/or differential loss-of-imprinting (LOI) could underlie these opposite growth phenotypes in reciprocal mammalian hybrids. Here we report that tissue-specific LOI occurs in adult Mus hybrids. Contrary to expectations, LOI patterns were not consistent with a direct influence of altered expression levels of imprinted genes on growth. Bisulfite sequencing revealed that reactivation of maternal alleles of Peg3 and Snrpn in specific tissues was accompanied by partial demethylation at their potential imprinting control regions. We propose that abnormal reprogramming after fertilization and during preimplantation development is in part responsible for hybrid dysgenesis, for which a strong epigenetic basis has been demonstrated.     

Dividing the child

The evolution of genomic imprinting is viewed as a problem of economic optimization that is analyzed using the tools of evolutionary game theory. We specifically consider genetic conflicts over the allocation of maternal resources between present and future offspring. Five sets of genes, with the same interests within sets but distinct interests between sets, are considered as agents: maternal alleles (Mater), paternal alleles (Pater), unimprinted offspring alleles (Filius), and imprinted offspring alleles of maternal and paternal origin (Matris and Patris). Fitness functions are derived for each agent and the parameter space in which there is conflict defined. Three potential conflicts are considered: between mother and offspring (Mater v.s. Filius); between alleles of maternal and paternal origin within offspring (Matris v.s. Patris) and between mothers and the paternally derived alleles of offspring (Mater v.s. Patris).     

Study of mitochondrial genomes of allopllasmic recombinant wheat lines constructed on the basis of barley-wheat hybrids Hordeum geniculatum all. (= H. marinum subsp. gussoneanum) (2n = 28) x x Triticum aestivum L. (2n = 42) with using of RELP and PCR analyses

Using RELP analysis with three probes homologous to specific regions of mitochondrial DNA genes and PCR analysis of the mitochondrial recombining-repeat-sequence 18S/5S region of cereals, five alloplasmic wheat lines of different origin and fertility expression were studied. These lines are self-pollinated progeny of BC1-BC4 generations of barley-wheat hybrids Hordeum geniculatum All. (2n = 28) x Triticum aestivum L. (2n = 42). It was found that recombinant alloplasmic lines characterized by partial fertility contain either maternal (barley) DNA fragments or maternal and paternal (wheat) DNA fragments simultaneously (heteroplasmy). In lines with stable expression of self-fertility, fragments of only paternal mitochondrial DNA were detected. It is assumed that in alloplasmic lines, there is the interrelation between the presence of definite fragments of the mitochondrial genome belonging to either parental type and fertility expression.     

Nonadditive expression and parent-of-origin effects identified by microarray and allele-specific expression profiling of maize endosperm

Plant endosperm cells have a nuclear ratio of two maternal genomes to one paternal genome. This 2 to 1 dosage relationship provides a unique system for studying the additivity of gene expression levels in reciprocal hybrids. A combination of microarray profiling and allele-specific expression analysis was performed using RNA isolated from endosperm tissues of maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal hybrids at two developmental stages, 13 and 19 d after pollination. The majority of genes exhibited additive expression in reciprocal hybrids based on microarray analyses. However, a substantial number of genes exhibited nonadditive expression patterns, including maternal like, paternal like, high parent like, low parent like, and expression patterns outside the range of the parental inbreds. The frequency of hybrid expression patterns outside of the parental range in maize endosperm tissue is much higher than that observed for vegetative tissues. For a set of 90 genes, allele-specific expression assays were employed to monitor allelic bias and regulatory variation. Eight of these genes exhibited evidence for maternally or paternally biased expression at multiple stages of endosperm development and are potential examples of differential imprinting. Our data indicate that parental effects on gene expression are much stronger in endosperm than in vegetative tissues.     

Chromosome constitution of in vitro segregated haploid and diploid cells of the mouse

The composition in segregated haploid sets of paternal and maternal chromosomes has been studied in order to verify whether their composition is uniparental of mixed, fixed or variable. Primary cultures where prepared using kidneys from hybrids of strains of Mus musculus in which the parental chromosomes are distinguishable; the maternal set consists of 20 teleocentric chromosomes, the paternal set of 9 metacentric chromosomes, derived by Robertsonian fusion and 2 telocentrics. Applying Seabright's banding technique, an analysis of segregated haploid and diploid cells, which have originated spontaneously through polyploidisation-segregation processes was carried out. It was concluded that the haploid sets have a variable composition of paternal and maternal chromosomes.