Download with Google Download with Facebook. In comparison, 47% (78/166) of genes with unexpected allelic ratios were nonsyntenic in cortex, 41% (73/177) in the elongation zone, 58% (118/202) in the meristematic zone, and 39% (124/321) in the stele (Fig. B and C, Overlap of genes with unexpected allelic ratio between the four different primary root tissues in B73xMo17 (B) and in Mo17xB73 (C). F1 progeny of such inbred lines are often more vigorous than their parents, a phenomenon known as heterosis. Heterosis, or hybrid vigor, describes the superior performance of heterozygous F1 hybrid progeny relative to the average of their homozygous parental inbred lines (midparent heterosis) or the better performing parent (best parent heterosis; Falconer and Mackay, 1996). The numbers in parentheses indicate the total number of genes with unexpected allelic ratio in the corresponding root tissue. Similar results were observed in early maize ear inflorescences (Ding et al., 2014). A similar observation was made in the four maize primary root tissues, where nonsyntenic genes were significantly overrepresented among genes displaying SPE patterns (Paschold et al., 2014). Now, we're building on the success of prior editions to provide an even more effective fourth edition. 3). In summary, nonsyntenic genes were significantly overrepresented among nonadditive, differential, and unexpected allelic expression patterns relative to their prevalence among all expressed genes. 4B). (2000) “Stresses; external conditions that adversely affect growth, development or productivity”-----Plant Physiology It has been demonstrated that maize genotypes with higher root cortical aerenchyma formation have growth advantages over genotypes with lower root cortical aerenchyma formation under certain conditions (Postma and Lynch, 2011). Another remarkable observation was the high degree of conservation of both the nonadditively expressed genes and those showing unexpected allelic expression ratios between the two reciprocal hybrids (Fig. PLANT PHYSIOLOGY Chapter 11 Transport in Plants Chapter 12 Mineral Nutrition Chapter 13 Photosynthesis in Higher Plants Chapter 14 Respiration in Plants Chapter 15 Plant Growth and Development. Library, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. A, Number of genes showing unexpected allelic ratios in both hybrids (plain: B73xMo17; shaded: Mo17xB73) for each primary root tissue. While the reciprocal hybrids, which contain an identical nuclear genome, did not display any differentially expressed genes, the genetically distinct parents displayed a high degree of differential gene expression. 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. gene expression in these hybrids was significantly different from the mean of expression of the two parental inbred lines. Advances in Plant Physiology Vol 17 . Advances in Plant Physiology Vol 15 . Volumes for 1972- include also scientists from the East European countries. The 64 cDNA libraries were loaded on two flow cells according to a split plot design (supplemental table S1 in Paschold et al., 2014). Download List of Library Books and Periodicals book written by Montreal. All Rights Reserved. Google Drive is a safe place for all your files. Get any books you like and read everywhere you want. 4C). 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). Genes that exhibited either above high-parent (36 genes in B73xMo17; 17 genes in Mo17xB73) or below low-parent (147 genes in B73xMo17; 36 genes in Mo17xB73) expression in the hybrids were assigned to the expression classes 5 to 8. Hence, nonsyntenic genes were substantially underrepresented among all expressed genes relative to their fraction of all genes present in FGSv2. … Similarly, mapping of Mo17 genomic sequences to the B73 reference genome revealed that only 63% of the sequences were identical in both genotypes (Wei and Wang, 2013). What is plant stress? In a second step, gene expression levels of the hybrid were compared with midparent values (MPV) to determine the number of nonadditively expressed genes. 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). Anatomy & Physiology. 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. The overlapping genes between the two hybrids within each tissue are highlighted by the darker color. 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. 37 Full PDFs related to this paper. However, there is a major gap in understanding the nature of protein interactions and pathway complexes needed to mediate carotenogenesis. However, among all expressed genes in the different tissues, only between 30% (cortex) and 33% (meristematic zone) were nonsyntenic. A previous study of our research group revealed dynamic root tissue-specific patterns of single-parent expression (SPE), an extreme instance of expression complementation in which genes are expressed in both reciprocal hybrids but only in one parental inbred line (Paschold et al., 2014). Get started today. For all studied types of expression - differential, nonadditive, and allelic - substantial tissue-specific plasticity was observed. 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. eur-lex.europa.eu. In this study, this dataset was surveyed to determine tissue-specific nonadditive, differential, and allelic gene expression patterns and the relation of these expression patterns to the phylogenetic origin of these genes. Pairwise comparison of gene expression levels revealed a high number of differentially expressed genes between the two parental inbred lines B73 and Mo17 but no differentially expressed genes between the genetically identical reciprocal hybrids of a specific tissue (Fig. Supplemental Data File S1. Free PDF. Functional categorization of nonsyntenic nonadditively expressed genes in the reciprocal hybrids. The overlap of both nonadditive and allelic expression patterns in the reciprocal hybrids significantly exceeded the expected values. Consistent with the definition of the gene expression pattern of class 4, no nonadditively expressed genes were observed in this class. Significant differences (α ≤ 5%) between the two bars per comparison are indicated by an asterisk. Incredibly. Additionally, a hierarchical cluster analysis was performed using the Euclidean distance of the average values of the four tissues and genotypes. 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). C, Proportion of nonsyntenic genes among differentially expressed genes [FDR ≤ 5%; |log2(FC)| > 1] (not shaded) between the four different genotypes B73 (B), Mo17 (M), B73xMo17 (BM), and Mo17xB73 (MB) in cortex, stele, elongation, and meristematic zone relative to all expressed genes in all genotypes (shaded). For each tissue, the observed number of common genes in both hybrids significantly exceeded the number of genes expected purely by chance. Maize (Zea mays) is one of the most prolific crops with a global production of 1.02 billion tons in 2014. Download Free PDF. Therefore, the model included a fixed effect for genotype and block and a normally distributed random error term. Comparisons of the duplicated regions of the genome of modern maize with orthologous regions of the unduplicated genomes of rice (Oryza sativa) and sorghum (Sorghum bicolor) indicated that the maize genome had lost many of its duplicated genes (Haberer et al., 2005). Singular enrichment analysis computed overrepresented categories in these two gene sets by comparing them with GO terms in the set of all expressed genes using Fisher’s exact test (Du et al., 2010). Raw sequencing data are stored at the Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) under accession number SRP029742. The determination of nonadditively expressed genes was performed for each of the nine gene expression classes separately. We determined if the evolutionary origin of genes correlates with the intraspecific transcriptome diversity between parental inbred lines B73 and Mo17 and their reciprocal hybrids. For each hybrid, a contrast was fitted within the linear mixed model framework of limma to compare the estimated log-expression value of the hybrid to the mean of the log-expression values of both parents. For B73xMo17, this comparison indicated that 74% to 84% of the genes with unexpected allelic ratios were exclusively expressed in one primary root tissue and only 1.3% of these genes were common in all four root tissues (Fig. simple text with good understanding Addeddate 2014-04-17 14:45:48 Identifier PlantPhysiologyTaizZeiger1 Identifier-ark ark:/13960/t4pk30r1f Ocr ABBYY FineReader 9.0 Ppi 600 Scanner Internet Archive HTML5 Uploader 1.5.2. plus-circle Add Review. To identify overrepresented biological and molecular functions among the nonsyntenic genes with nonadditive and allelic expression patterns, a Gene Ontology (GO) analysis was performed. Moreover, in B73xMo17, the molecular processes “iron ion binding” and “tetrapyrrole binding” with its subcategory “heme binding” were significantly enriched. Munish K Bansal. eur-lex.europa.eu. Intermediate numbers of differentially expressed genes were observed in comparisons of hybrids with one of the parental inbred lines. Supplemental Table S3. Along the longitudinal axis, maize roots are structurally divided into a subterminal meristematic zone at the terminal end, followed by the elongation and differentiation zones (Hochholdinger, 2009).