Premium PDF Package . Gene lists for all analyzed expression patterns in the four tissues of the primary maize roots. Mapping Mo17 reads to the B73 genome introduces a slight bias because Mo17 reads that contain polymorphisms beyond the parameters defined above are at disadvantage of being aligned to the B73 genome sequence. Remarkably, when comparing gene expression levels between hybrids and one parent in the four primary root tissues, in all instances more differentially expressed genes were preferentially expressed in hybrids than in the parental inbred line (Fig. These tissues are located at opposite poles of the root, and the high number of differentially expressed genes underscores the dissimilarity between these primary root tissues. The RNA-seq dataset analyzed in this study was generated in our research group and described in detail by Paschold et al. Similar results were observed in early maize ear inflorescences (Ding et al., 2014). Significantly, nonsyntenic genes that evolved after the last whole genome duplication of a maize progenitor from genes with synteny to sorghum (Sorghum bicolor) were highly overrepresented among differential, nonadditive, and allelic expression patterns compared with the fraction of these genes among all expressed genes. Distantly related maize ( Zea mays ) inbred lines display an exceptional degree of genomic diversity. Hence, this pattern represents a special instance of the dominance model of complementation on the gene expression level. The first commercial hybrid maize was introduced in the 1930s (Duvick, 2005). A similar distribution of the differentially expressed genes between the two maize inbred lines and their reciprocal hybrids was previously reported for aboveground tissues of 11-d-old maize seedlings (Stupar et al., 2008) and for whole primary roots of the same developmental stage as described here (Paschold et al., 2012). 3). This observation supports the notion that altered allelic activity in hybrids could contribute to nonadditive gene expression (Paschold et al., 2012). In total, 739 unique genes displaying unexpected allelic expression ratios were identified in this study (Supplemental Data File S1). DOI: https://doi.org/10.1104/pp.16.00262. This indicates that nonsyntenic genes are instrumental to cope with the selective fluctuating environment, which requires constant adaptations to new conditions. Similar values were observed for nonadditively expressed genes in the remaining three primary root tissues investigated: cortex 61% (407/666), meristematic zone 60% (667/1,115), and stele 63% (435/686). Download The Publishers Trade List Annual book written by , available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Introduction to Plant Physiology became the best-selling first edition plant physiology text of the 1990's! Compatible with any devices. Beside these syntenic maize genes, the genome of modern maize is complemented by a set of nonsyntenic genes that lack syntenic orthologs in other grass species (Schnable et al., 2011). Free PDF. Raw sequencing data are stored at the Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) under accession number SRP029742. Genes with unexpected allelic expression in the hybrids. the development of root cortical aerenchyma. B, Proportion of nonsyntenic genes among genes showing unexpected allelic ratios (shaded) in the hybrids relative to all expressed genes containing an SNP (not shaded) in each of the four primary root tissues. To directly assess the influence of light on the physiological status of green oilseeds in planta, Brassica napus and soybean ( Glycine max ) seeds were rapidly dissected from plants growing in the light or dark. The number of differentially expressed genes while controlling the FDR at 5% and with a cutoff of |log2(FC)| > 1 are displayed. J.A.B., A.P., and F.H. Plant physiology is the study of plant function and behaviour, encompassing all the dynamic processes of growth, metabolism, reproduction, defence, and communication that account for plants being alive (Salisbury & Ross, 1992; Baluška et al., 2006; Scott, 2008). our understanding of the factors affecting the growth and productivity of grasslands has trailed in the shadow of the determined efforts made to improve our knowledge of cereals and, to a somewhat lesser extent, legumes. The pairwise comparisons between two genotypes resulting in an adjusted p ≤ 0.05 were used for the classification of the gene expression in the hybrid. It will therefore be interesting to see in future experiments if the overrepresentation of cell death and apoptosis genes in the cortex is a general feature of maize hybrids and if this observation is related to an increase in root cortical aerenchyma in hybrids. The comparison of the nonadditively expressed genes with unexpected allelic ratios between the two reciprocal hybrids B73xMo17 and Mo17xB73 within each primary root tissue revealed that a significantly higher number of these genes is common in both hybrids than expected. We thank Hans-Peter Piepho (Institute for Crop Sciences, Biostatistics Unit, University of Hohenheim, Stuttgart, Germany) for advice in statistical questions. The distance between each pair of samples was estimated as the root-mean-square deviation for the top 500 genes with the largest standard deviations between samples. Syntenic genes were shaped by more than 5 million years of natural selection (Blanc and Wolfe, 2004b). In summary, nonsyntenic genes were significantly overrepresented among nonadditive, differential, and unexpected allelic expression patterns relative to their prevalence among all expressed genes. These tendencies were observed for all comparisons and were statistically significant for 22 of 24 comparisons (Fig. In this study, approximately 8% of all expressed genes were nonadditively expressed, which is similar to results previously observed in whole primary maize roots of the same developmental stage (Paschold et al., 2012). 4; Supplemental Tables S1 and S2). Supplemental Data File S1. Using the allelic read counts, the hypothesis test that the ratio of the expression of the parental alleles in both inbred lines equals to the ratio of the expression of the parental alleles in a specific hybrid was performed by applying the contrasts.fit function in limma (Smyth, 2005). Compatible with any devices. The surrounding cortical parenchyma consists of the endodermis, multiple layers of cortex tissue, and the epidermis that connects the root to the rhizosphere. This observation is supported by similar distributions of differentially expressed genes identified between the four root tissues in the four genotypes (Fig. Plant Physiology & Metabolism.pdf - Google Drive ... Sign in 1A), based on a RNA-seq dataset from our laboratory (Paschold et al., 2014). Although the maize tetraploidy with subsequent genome fractionation occurred already between 5 and 12 million years ago, there is evidence that biased gene loss and expression continues today (Woodhouse et al., 2010; Schnable et al., 2011). Acknowledged experts have therefore been selected as contributors to provide an up-to-date review of their own specialized areas. Significant differences (α ≤ 5%) compared with all expressed genes are indicated with an asterisk. All Rights Reserved. In this study, we investigated how the genetic divergence of the maize inbred lines B73 and Mo17 and their F1 hybrid progeny is reflected in differential, nonadditive, and allelic expression patterns in primary root tissues. However, there is a major gap in understanding the nature of protein interactions and pathway complexes needed to mediate carotenogenesis. ® Contributors and consultants vi. Functional categorization of nonsyntenic nonadditively expressed genes in the reciprocal hybrids. The genome of an ancient maize progenitor underwent several duplications, including that of a paleopolyploid ancestor (Paterson et al., 2004) and an additional whole genome duplication ∼5 to 12 million years ago (Blanc and Wolfe, 2004a; Swigonová et al., 2004). S2). The highest number of nonadditively expressed genes was observed in gene expression class 1 (between 205 in cortex and 432 in meristematic zone) and class 3 (between 201 in meristematic zone and 339 in elongation zone; Supplemental Table S2). or. Gene expression levels in the hybrids were classified according to nine gene expression classes defined previously (Paschold et al., 2012). Cells in the differentiation zone display diverse functions. The activation state of malate dehydrogenase, which reflects reduced thioredoxin and NADP/NADPH ratios, was found to … Download Annual Review of Plant Physiology and Plant Molecular Biology book written by , available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Fast Download Speed ~ Commercial & Ad Free. Get any books you like and read everywhere you want. Copyright © 2020 by The American Society of Plant Biologists, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany. … 10 Immune system; 11 … Lower numbers of nonadditively expressed genes were observed in gene expression class 2 and the classes to which genes with extreme expression patterns were assigned to (classes 5–8). Enter multiple addresses on separate lines or separate them with commas. However, in this dataset this bias is very small. 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). B, Hierarchical cluster analysis of normalized read counts among all four replicates of each RNA-seq sample. Moreover, the low correlation of the cortex and stele can be explained by the functional differences of the disparate cell types present in these tissues (Saleem et al., 2010). Advances in Plant Physiology Vol 17 . Intermediate numbers of differentially expressed genes were observed in comparisons of hybrids with one of the parental inbred lines. As illustrated by these correlation analyses, overall gene expression is more divergent between different tissues of a genotype than between different genotypes within a tissue. Less differentially expressed genes were estimated between adjacent tissues, whereas high numbers of differentially expressed genes were observed in comparisons of the differentiation zone with the meristematic or elongation zone. The number of differentially expressed genes while controlling the FDR at 5% and with a cutoff of |log2(FC)| > 1 are shown. To determine the number of differentially expressed genes between the four different primary root tissues, six pairwise comparisons were performed per genotype (Fig. Among the genes with unexpected allelic ratios, between 26 (Mo17xB73, elongation zone) and 58 (B73xMo17, meristematic zone) genes showed nonadditive gene expression patterns (Supplemental Table S1). Subsequently, the subset of genes showing expression levels that deviate significantly from the midparent value was determined in these nine classes. Gene expression classification in the reciprocal hybrids within each tissue. We do not capture any email address. Seeds of many plant species are green during embryogenesis. However, among all expressed genes in the different tissues, only between 30% (cortex) and 33% (meristematic zone) were nonsyntenic. Sara I. Zandalinas; Ron Mittler; Damián Balfagón; Vicent Arbona; Aurelio Gómez‐Cadenas; Pages: 2-12; First Published: 2 January 2017 However, in spite of its low profile, grassland research has resulted in considerable advances in our knowledge in the last 20 years, and we feel that this book provides a timely opportunity to bring together some of this work in a review of what is primarily the ecophysiology of the temperate grass crop. 2). Furthermore, nonsyntenic genes were significantly overrepresented among genes differentially expressed between the four genotypes compared with all expressed genes (Fig. Fundamentals of Plant Physiology book. On the proteome level, a similar distribution of differentially accumulated proteins between the same four primary root tissues of B73 seedlings at the same developmental stage was observed (Marcon et al., 2015). expression levels in hybrids that deviated significantly from the midparent value. Distribution of nonsyntenic genes among different classes of genes. gene expression in these hybrids was significantly different from the mean of expression of the two parental inbred lines. In Order to Read Online or Download Advances In Plant Physiology Vol 9 Full eBooks in PDF, EPUB, Tuebl and Mobi you need to create a Free account. Similarly, nonsyntenic genes were significantly overrepresented among the genes with unexpected allelic expression ratios relative to all expressed genes with single nucleotide polymorphisms (SNPs) in each of the four root tissues (Fig. Furthermore, unexpected allelic expression patterns were observed in hybrids that deviated from the allelic ratios of their parents (Guo et al., 2004; Stupar and Springer, 2006; Springer and Stupar, 2007; Paschold et al., 2012; Song et al., 2013). NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. www.plantphysiol.org/cgi/doi/10.1104/pp.16.00262. 5C). Download Advances in Botanical Research book written by Reginald Dawson Preston, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Genes with ambiguous gene expression levels in the hybrids were assigned to class 9. We cannot guarantee that every book is in the library! In brief, primary roots of a length of 2 to 4 cm of the inbred lines B73, Mo17, and their reciprocal hybrids B73xMo17 and Mo17xB73 were separated into meristematic zone, elongation zone, cortex, and stele. In transverse orientation, the stele with the pericycle as its outermost cell layer contains xylem and primary phloem elements functioning in the transport of water, nutrients, and photosynthates. Finally, in the elongation zone, the molecular process “aspartic-type peptidase activity” and its subcategory “aspartic-type endopeptidase activity” were overrepresented among the nonsyntenic nonadditively expressed genes in Mo17xB73. According to this classification scheme most of the expressed genes in the hybrids revealed no significant difference in their expression relative to their parents (class 4). This Decision is addressed to Professor J. Geuns, KUL, Laboratory of Plant Physiology, Kardinaal Mercierlaan 92, 3001 Heverlee, Belgium. Anatomy & Physiology. eur-lex.europa.eu. 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. conceived the research; J.A.B. 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. In the past 50 years, global maize production has increased almost 5-fold (http://faostat3.fao.org/). Additionally, a hierarchical cluster analysis was performed using the Euclidean distance of the average values of the four tissues and genotypes. Pulp and Paper Research Institute of Canada. The Web-based agriGO platform (http://bioinfo.cau.edu.cn/agriGO/analysis.php) was used to assign GO functional categories to nonsyntenic genes with nonadditive and allelic expression patterns. In all four genotypes, the relative number of differentially expressed genes in the six comparisons was similar. This paper. Nonsyntenic Genes Drive Tissue-Specific Dynamics of Differential, Nonadditive, and Allelic Expression Patterns in Maize Hybrids, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Unraveling the genetic basis of hybrid vigor, Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes, Functional divergence of duplicated genes formed by polyploidy during, The effects of cross- and self-fertilization in the vegetable kingdom, Heterosis in early maize ear inflorescence development: a genome-wide transcription analysis for two maize inbred lines and their hybrid, Evolutionary genetics of genome merger and doubling in plants, agriGO: a GO analysis toolkit for the agricultural community, Genetic progress in yield of United States maize (, Genome-wide transcript analysis of maize hybrids: allelic additive gene expression and yield heterosis, Allelic variation of gene expression in maize hybrids, Structure and architecture of the maize genome, The maize root system: morphology, anatomy and genetics, Manifestation of heterosis during early maize (, Analysis of nonadditive protein accumulation in young primary roots of a maize (, Specialized zones of development in roots, Genome-wide genetic changes during modern breeding of maize, Dominance of linked factors as a means of accounting for heterosis, voom: Precision weights unlock linear model analysis tools for RNA-seq read counts, The phylogenetic relationships of US maize germplasm, A high-resolution tissue-specific proteome and phosphoproteome atlas of maize primary roots reveals functional gradients along the root axes, Note on the sampling error of the difference between correlated proportions or percentages, Complementation contributes to transcriptome complexity in maize (, Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids, Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics, Root cortical aerenchyma enhances the growth of maize on soils with suboptimal availability of nitrogen, phosphorus, and potassium, Identification and characterization of a repertoire of genes differentially expressed in developing top ear shoots between a superior hybrid and its parental inbreds in, Specification of cortical parenchyma and stele of maize primary roots by asymmetric levels of auxin, cytokinin, and cytokinin-regulated proteins, Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss, The B73 maize genome: complexity, diversity, and dynamics, The RIN: an RNA integrity number for assigning integrity values to RNA measurements, Linear models and empirical bayes methods for assessing differential expression in microarray experiments, Bioinformatics and Computational Biology Solutions Using R and Bioconductor, Global RNA sequencing reveals that genotype-dependent allele-specific expression contributes to differential expression in rice F, Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize, Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis, All possible modes of gene action are observed in a global comparison of gene expression in a maize F, Close split of sorghum and maize genome progenitors, Comparative expression profiling in meristems of inbred-hybrid triplets of maize based on morphological investigations of heterosis for plant height, A computational workflow to identify allele-specific expression and epigenetic modification in maize, Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs, Developmental Programming of Thermonastic Leaf Movement, BRASSINOSTEROID-SIGNALING KINASE5 Associates with Immune Receptors and Is Required for Immune Responses, Deetiolation Enhances Phototropism by Modulating NON-PHOTOTROPIC HYPOCOTYL3 Phosphorylation Status, Clade I TGACG-Motif Binding Basic Leucine Zipper Transcription Factors Mediate BLADE-ON-PETIOLE-Dependent Regulation of Development, by The American Society of Plant Biologists, http://ftp.maizesequence.org/release-5b/filtered-set/, http://schnablelab.plantgenomics.iastate.edu/software, http://www.skraelingmountain.com/datasets.php, http://bioinfo.cau.edu.cn/agriGO/analysis.php. Taiz Plant Physiology (ISBN 0878938230).pdf - Google Drive ... Sign in Create a free account to download. 5A; Supplemental Data File S1). Cross-comparison of the differentially expressed genes between the different root tissues among the four maize genotypes B73, Mo17, and their reciprocal hybrids showed that between 44% (cortex versus stele) and 68% (cortex versus meristematic zone) of differentially expressed genes were conserved among the four genotypes (Supplemental Fig. Hence, roots represent gradients of development, with very young undifferentiated cells at the distal end near the root cap and fully differentiated cells toward the proximal end of the root (Hochholdinger, 2009). Only for the nonsyntenic nonadditively expressed genes of the cortex and the elongation zone, significantly enriched GO terms were identified (Supplemental Table S3). The overlapping genes between the two hybrids within each tissue are highlighted by the darker color. These 20,291 (51%) maize genes (FGSv2) likely evolved by single gene duplication after the last whole genome duplication event (Woodhouse et al., 2010). Get started today. Guyton and Hall is a book for First Year MBBS Students and is the best and recommended book for Physiology. (2008a). Anatomy& Physiology. 1B). We demonstrated that nonsyntenic genes were highly overrepresented among nonadditive and allelic expression patterns in hybrids, suggesting a possible role of these genes in the early developmental manifestation of heterosis in maize roots. The phenomenon of heterosis was first scientifically reported by Charles Darwin after he compared the performance of self-pollinated maize progeny to cross-pollinated maize plants (Darwin, 1876). Diese Entscheidung ist an Professor J. Geuns, KUL - Pflanzenphysiologisches Labor, Kardinal Mercierlaan 92, 3001 Heverlee, Belgien, gerichtet. ↵1 This work was supported by the Deutsche Forschungsgemeinschaft (Grant HO2249-9/3 to F.H.). In total, 19,365 genes, representing 49% of the 39,656 maize genes of the filtered gene set (FGSv2), were assigned to these two subgenomes (Schnable et al., 2011). In contrast, the highest numbers of differentially expressed genes were observed in the comparisons of the meristematic zone with cortex and with stele. Easy! In all inbred versus hybrid comparisons, a significantly higher number of differentially expressed genes was preferentially expressed in the hybrids. We are not the owner of some given pdf notes. and F.H. Supplemental Table S2. Library, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. For each pairwise comparison, two color-coded bars illustrate the genotype preference of the differentially expressed genes. Hypothesis tests were performed using the contrasts.fit function of the Bioconductor package limma (Smyth, 2005). It is a sub-discipline of botany. In total, 1,056 and 824 nonadditively expressed genes were exclusively identified in the hybrids B73xMo17 and Mo17xB73, respectively. The number of genes for which these ratios were significantly different (unexpected allelic ratios) is summarized in Figure 4A. These numbers reflect the genetic relationship of the analyzed genotypes. Differentially expressed genes (DEGs) were identified on the basis of six pairwise comparisons between the four analyzed maize genotypes: B73 (B, purple), Mo17 (M, dark blue), B73xMo17 (BM, blue), and Mo17xB73 (MB, light blue) for each of the four primary root tissues: meristematic zone (A), elongation zone (B), stele (C), and cortex (D). Volumes for 1972- include also scientists from the East European countries. Taiz & Zeiger- Plant Physiology. 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