Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis

<p>Abstract</p> <p>Background</p> <p>Heterosis is the superior performance of F₁hybrid progeny relative to the parental phenotypes. Maize exhibits heterosis for a wide range of traits, however the magnitude of heterosis is highly variable depending on the choice of parents and the trait(s) measured. We have used expression profiling to determine whether the level, or types, of non-additive gene expression vary in maize hybrids with different levels of genetic diversity or heterosis.</p> <p>Results</p> <p>We observed that the distributions of better parent heterosis among a series of 25 maize hybrids generally do not exhibit significant correlations between different traits. Expression profiling analyses for six of these hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. The majority of differentially expressed genes in each of the six different hybrids exhibited additive expression patterns, and ~25% exhibited statistically significant non-additive expression profiles. Among the non-additive profiles, ~80% exhibited hybrid expression levels between the parental levels, ~20% exhibited hybrid expression levels at the parental levels and ~1% exhibited hybrid levels outside the parental range.</p> <p>Conclusion</p> <p>We have found that maize inbred genetic diversity is correlated with transcriptional variation. However, sampling of seedling tissues indicated that the frequencies of additive and non-additive expression patterns are very similar across a range of hybrid lines. These findings suggest that heterosis is probably not a consequence of higher levels of additive or non-additive expression, but may be related to transcriptional variation between parents. The lack of correlation between better parent heterosis levels for different traits suggests that transcriptional diversity at specific sets of genes may influence heterosis for different traits.</p

Transcriptional Landscape of the Prenatal Human Brain

Summary The anatomical and functional architecture of the human brain is largely determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and postmitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and human-expanded outer subventricular zones. Both germinal and postmitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in frontal lobe. Finally, many neurodevelopmental disorder and human evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development

Geology of the western Mamaku Plateau and variations in the Mamaku ignimbrite

Pleistocene ignimbrites in the western Mamaku Plateau east of Putaruru consist of the following successively younger formations: (?) Ongatiti Ignimbrite, Ahuroa Ignimbrite, Whakamaru Ignimbrite, Waihou Ignimbrite (new), Waimakariri Ignimbrite (new), Mamaku Ignimbrite. They can be distinguished on the basis of their compositional-, welding-, textural-, and field characteristics. The ignimbrites are separated by unconformities, and intercalated fluvial sedimentary deposits. The three most important units are the Whakamaru, Waimakariri and Mamaku Ignimbrites, which are well exposed and widespread. The Mamaku Ignimbrite covers a surface area of nearly 4300 km² on the Mamaku Plateau. Corresponding vertical changes in lithology, petrography and physical properties near the Rotorua Caldera define two flow members: a lower Sheet 1, and an upper Sheet 2, each of which is about 60 m thick. The ignimbrite constitutes a simple cooling unit which indicates that Sheet 2 was emplaced shortly after Sheet 1. Only one sheet (? Sheet 1) is evident in the western Mamaku Plateau. Welding zonation near-to-source is characterised by a gradual change from a basal glassy lenticulite zone to a nonwelded top. Smith's (1960b) zonal classification ranks the ignimbrite as being partially welded. This condition suggests that total thickness is not necessarily a major factor in the degree of welding of ignimbrites. The phenocryst assemblage of plagioclase, quartz, pyroxene, opaques, hornblende and biotite, is set in a devitrified fine ash matrix, which is an ubiquitous feature of the ignimbrite. Higher modal phenocryst content at the base of each sheet is attributed to compaction. Overall the phenocrysts are uniformly distributed and there is little vertical variation. Seven bulk chemical analyses reveal only minor vertical variations in composition. The near uniform chemical and mineralogical trends suggest nondifferentiation of the source magma. Texturally the Mamaku Ignimbrite is a poorly sorted lapilli ash. The grading of fragments like that shown in "the standard ignimbrite flow unit" is absent. However, the presence of a zone of aligned pumice fragments indicates that laminar flow operated during the later stages of deposition. Two major inferred faults in the western Mamaku Plateau define a western horst, a central graben, and an eastern horst. The eastern horst is postulated to be the southern extension of the axial median horst in the Hauraki Depression and of the Hauraki Rift. Repeated and extended intervals of erosion followed the emplacement of the ignimbrites. Detritus from the eroding sheets was removed by rivers flowing into the Hauraki Depression. Construction of the Mamaku Plateau has largely taken place since the eruption of the Whakamaru Ignimbrite, c.300,000 years ago, and terminated with the eruption of the Mamaku Ignimbrite, c.l40,000 years ago. Excavation of the long deep valleys in the plateau occurred mainly in the latter 42,000 years

Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis-0

Ical BPH values are available in Additional file . Red bars represent BPH for hybrids generated between SS and NSS inbreds, blue bars represent BPH for hybrids generated within SS and NSS inbreds, and grey bars represent BPH for hybrids derived from an inbred line with mixed origin (F2).<p><b>Copyright information:</b></p><p>Taken from "Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis"</p><p>http://www.biomedcentral.com/1471-2229/8/33</p><p>BMC Plant Biology 2008;8():33-33.</p><p>Published online 10 Apr 2008</p><p>PMCID:PMC2365949.</p><p></p

Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis-2

Sed on stringent statistical criteria is plotted against the genetic distance between parents. Spots representing crosses between stiff stalk (SS) and non-stiff stalk (NSS) groups are shown in red, and spots representing crosses within either group are shown in blue. The Pearson's R correlation value and -value of the regression are shown.<p><b>Copyright information:</b></p><p>Taken from "Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis"</p><p>http://www.biomedcentral.com/1471-2229/8/33</p><p>BMC Plant Biology 2008;8():33-33.</p><p>Published online 10 Apr 2008</p><p>PMCID:PMC2365949.</p><p></p

Transcriptional landscape of the prenatal human brain.

The anatomical and functional architecture of the human brain is mainly determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of the mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high-resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser-microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and post-mitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and outer subventricular zones even though the outer zone is expanded in humans. Both germinal and post-mitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in the frontal lobe. Finally, many neurodevelopmental disorder and human-evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development

A comprehensive transcriptional map of primate brain development.

The transcriptional underpinnings of brain development remain poorly understood, particularly in humans and closely related non-human primates. We describe a high-resolution transcriptional atlas of rhesus monkey (Macaca mulatta) brain development that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical division of cortical and subcortical regions associated with human neuropsychiatric disease. Gene expression changes more rapidly before birth, both in progenitor cells and maturing neurons. Cortical layers and areas acquire adult-like molecular profiles surprisingly late in postnatal development. Disparate cell populations exhibit distinct developmental timing of gene expression, but also unexpected synchrony of processes underlying neural circuit construction including cell projection and adhesion. Candidate risk genes for neurodevelopmental disorders including primary microcephaly, autism spectrum disorder, intellectual disability, and schizophrenia show disease-specific spatiotemporal enrichment within developing neocortex. Human developmental expression trajectories are more similar to monkey than rodent, although approximately 9% of genes show human-specific regulation with evidence for prolonged maturation or neoteny compared to monkey