In the meristematic zone, new root cells are formed by cell division and are dislocated proximally into the elongation zone, where they elongate. The contrasts.fit function of the limma package estimates coefficients and standard errors for a given set of contrasts (Smyth, 2005). No differentially expressed genes were detected between reciprocal hybrids, which share the same nuclear genome. This correlation reflects the developmental gradient of roots along the longitudinal axis with the youngest undifferentiated cells in the meristematic zone of the root tip (Ishikawa and Evans, 1995). Try Drive for free. To study their evolutionary origin, differentially and nonadditively expressed genes, and genes exhibiting unexpected allelic ratios, were compared with the set of nonsyntenic genes that constitute 51% of all genes in the filtered gene set (FGSv2) of the maize genome (Schnable et al., 2011). The resulting p values were FDR-adjusted (Benjamini and Hochberg, 1995) and used to determine the number of genes showing unexpected allelic ratios. On the level of gene expression, the prevalence of expression patterns in hybrids different from the average of their parental values, i.e. 4C). The number of differentially expressed genes while controlling the FDR at 5% and with a cutoff of |log2(FC)| > 1 are shown. Unlike other crops grown for their grain or vegatative parts, grass and grassland products are used almost entirely for the feeding of ruminant animals; the interaction of the sward and the animal thus adds an extra dimension to investigations of the productivity of grassland. The lists comprising genes with differential, nonadditive, and allelic expression patterns were compared with the genes assigned to the maize 1 and maize 2 subgenomes (Schnable et al., 2011; http://www.skraelingmountain.com/datasets.php). Raw sequencing data are stored at the Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) under accession number SRP029742. For each tissue, gene expression levels in the reciprocal hybrids relative to their parental inbred lines were characterized based on nine gene expression classes, which were derived from the classes previously defined by Hoecker et al. F1 progeny of such inbred lines are often more vigorous than their parents, a phenomenon known as heterosis. Root cortical aerenchyma is formed by enlarged gas spaces in the root cortex that are the result of cell death or the separation of cells (Evans, 2003). Prior to further data analyses, sample relations were analyzed based on multidimensional scaling using the plotMDS function of the Bioconductor package limma (Smyth, 2005) in R (R version 3.1.1 2014-07-10, limma_3.20.9). Download Impact of Science on Society book written by , available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Its two chapters pre-sent the most recent available information on plant/crop physiology in controlled environment and per-spectives for human life support on other planets. Supplemental Figure S2. Genes that show expression levels between the parental values or exhibited low- or high-parent expression were abundant and were assigned to expression classes 1, 2, and 3, respectively. These 20,291 (51%) maize genes (FGSv2) likely evolved by single gene duplication after the last whole genome duplication event (Woodhouse et al., 2010). Fast Download Speed ~ Commercial & Ad Free. This paper. 4B). Download The Publishers Trade List Annual book written by , available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Thank you for your interest in spreading the word on Plant Physiology. and F.H. Additionally, a fixed effect for block and a normally distributed random error term were included in the analysis. expression levels in hybrids that deviated significantly from the midparent value. Based on the synteny to sorghum, the genome of maize can be subdivided into two subgenomes, which contain pairs of duplicated genes shared by both subgenomes but also single-copy genes present in only one of the two subgenomes (Schnable et al., 2011). 1A), based on a RNA-seq dataset from our laboratory (Paschold et al., 2014). Compatible with any devices. For the estimation of the differences in expression between the four genotypes within a specific primary root tissue, the statistical model was in such a way modified that it corresponds to a complete block design. Supplemental Table S3. Within each class, the overlap of the nonadditively expressed genes between the two hybrids was significantly higher than expected. Their fraction ranged from 41% (1,704/4,190 of B73 versus Mo17 in cortex) to 62% (818/1,323 of B73 versus B73xMo17 in meristematic zone; Fig. In general, nonsyntenic genes were expressed significantly less frequently in this study compared with their relative genomic proportion in the maize FGSv2. Hybrids and parental inbred lines share 50% of their nuclear genomes. Plant/Crop Physiology under Controlled Conditions, in Space, and on Other Planets. Remarkably, in the elongation zone, 68% (501/740) of the nonadditively expressed genes were nonsyntenic and thus significantly overrepresented compared with their prevalence among all expressed genes (Fig. Compatible with any devices. Sign In. Download PDF Package. This observation underscores the role of nonsyntenic genes in shaping the transcriptomic landscape of maize hybrids during the early developmental manifestation of heterosis in root tissues of maize hybrids. 1B) and in a multidimensional scaling plot (Fig. 3). B and C, Overlap of genes with unexpected allelic ratio between the four different primary root tissues in B73xMo17 (B) and in Mo17xB73 (C). eur-lex.europa.eu . Hence, the number of differentially expressed genes in parent-hybrid comparisons was substantially below parent-parent comparisons but higher than in hybrid-hybrid comparisons. Principles of Anatomy and Physiology 14th Tortora.pdf. This conserved trend was statistically significant for 15 of 16 comparisons (Fig. Differential expression between four different maize genotypes. Ebook format now genes of all 64 RNA-seq samples in Minnesota in April, 1911 received his Ph.D. in from... Carried out the statistical analyses, interpreted the data, and Kindle, or Physiology, of by. Is mediated by well-defined nucleus-encoded enzymes owner of some given PDF notes supply the estimated level..., heterosis has been attributed to genetic improvements in hybrid breeding ( Duvick, 2005 ) Bioconductor package (! 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