Waqas Ahmed Malik

Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit

Highlight Maize primary root tissues display extensive transcriptomic plasticity upon water deficit. The most significant adaptive changes in the elongation zone lead to reprogramming of metabolism and cell wall organization.

Comparative Transcriptome Profiling of Maize Coleoptilar Nodes during Shoot-Borne Root Initiation

A microarray analysis reveals 828 unique transcripts with expression related to crown root initiation during coleoptilar node development. Maize (Zea mays) develops an extensive shoot-borne root system to secure water and nutrient uptake and to provide anchorage in the soil. In this study, early coleoptilar node (first shoot node) development was subjected to a detailed morphological and histological analysis. Subsequently, microarray profiling via hybridization of oligonucleotide microarrays representing transcripts of 31,355 unique maize genes at three early stages of coleoptilar node development was performed. These pairwise comparisons of wild-type versus mutant rootless concerning crown and seminal roots (rtcs) coleoptilar nodes that do not initiate shoot-borne roots revealed 828 unique transcripts that displayed RTCS-dependent expression. A stage-specific functional analysis revealed overrepresentation of “cell wall,” “stress,” and “development”-related transcripts among the differentially expressed genes. Differential expression of a subset of 15 of 828 genes identified by these microarray experiments was independently confirmed by quantitative real-time-polymerase chain reaction. In silico promoter analyses revealed that 100 differentially expressed genes contained at least one LATERAL ORGAN BOUNDARIES domain (LBD) motif within 1 kb upstream of the ATG start codon. Electrophoretic mobility shift assay experiments demonstrated RTCS binding for four of these promoter sequences, supporting the notion that differentially accumulated genes containing LBD motifs are likely direct downstream targets of RTCS.

Heterosis-associated proteome analyses of maize (Zea mays L.) seminal roots by quantitative label-free LC–MS

UNLABELLED Heterosis is the superior performance of heterozygous F1-hybrid plants compared to their homozygous genetically distinct parents. Seminal roots are embryonic roots that play an important role during early maize (Zea mays L.) seedling development. In the present study the most abundant soluble proteins of 2-4cm seminal roots of the reciprocal maize F1-hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were quantified by label-free LC-MS/MS. In total, 1918 proteins were detected by this shot-gun approach. Among those, 970 were represented by at least two peptides and were further analyzed. Eighty-five proteins displayed non-additive accumulation in at least one hybrid. The functional category protein metabolism was the most abundant class of non-additive proteins represented by 27 proteins. Within this category 16 of 17 non-additively accumulated ribosomal proteins showed high or above high parent expression in seminal roots. These results imply that an increased protein synthesis rate in hybrids might be related to the early manifestation of hybrid vigor in seminal roots. BIOLOGICAL SIGNIFICANCE In the present study a shot-gun proteomics approach allowed for the identification of 1917 proteins and analysis of 970 seminal root proteins of maize that were represented by at least 2 peptides. The comparison of proteome complexity of reciprocal hybrids and their parental inbred lines indicates an increased protein synthesis rate in hybrids that may contribute to the early manifestation of heterosis in seminal roots. This article is part of a Special Issue entitled: Translational Plant Proteomics.

A High-Resolution Tissue-Specific Proteome and Phosphoproteome Atlas of Maize Primary Roots Reveals Functional Gradients along the Root Axes

Tissue-specific protein and phosphoprotein patterns underlie functional gradients along the maize primary root axis. A high-resolution proteome and phosphoproteome atlas of four maize (Zea mays) primary root tissues, the cortex, stele, meristematic zone, and elongation zone, was generated. High-performance liquid chromatography coupled with tandem mass spectrometry identified 11,552 distinct nonmodified and 2,852 phosphorylated proteins across the four root tissues. Two gradients reflecting the abundance of functional protein classes along the longitudinal root axis were observed. While the classes RNA, DNA, and protein peaked in the meristematic zone, cell wall, lipid metabolism, stress, transport, and secondary metabolism culminated in the differentiation zone. Functional specialization of tissues is underscored by six of 10 cortex-specific proteins involved in flavonoid biosynthesis. Comparison of this data set with high-resolution seed and leaf proteome studies revealed 13% (1,504/11,552) root-specific proteins. While only 23% of the 1,504 root-specific proteins accumulated in all four root tissues, 61% of all 11,552 identified proteins accumulated in all four root tissues. This suggests a much higher degree of tissue-specific functionalization of root-specific proteins. In summary, these data illustrate the remarkable plasticity of the proteomic landscape of maize primary roots and thus provide a starting point for gaining a better understanding of their tissue-specific functions.

The Elucidation of the Interactome of 16 Arabidopsis bZIP Factors Reveals Three Independent Functional Networks

The function of the bZIP transcription factors is strictly dependent on their ability to dimerize. Heterodimerization has proven to be highly specific and is postulated to operate as a combinatorial mechanism allowing the generation of a large variety of dimers with unique qualities by specifically combining a small set of monomers; an assumption that has not yet been tested systematically. Here, the interaction pattern and the transactivation properties of 16 Arabidopsis thaliana bZIPs are examined in transiently transformed Arabidopsis protoplasts to deliver a perspective on the relationship between bZIP dimerization and function. An interaction matrix of bZIPs belonging to the C, G, H, and S1 bZIP groups was resolved by Bimolecular Fluorescent Complementation (BiFC) coupled to quantitative flow cytometric analysis, while an extensive GUS reporter gene assay was carried out to determine the effect of different bZIP pairs on the expression of four different known bZIP-targeted promoters. Statistical data treatment and complementary bioinformatic analysis were performed to substantiate the biological findings. According to these results, the 16 bZIPs interact in three isolated networks, within which their members dimerize non-specifically and exhibit a significant level of functional redundancy. A coherent explanation for these results is supported by in silico analysis of differences in the length, structure and composition of their leucine zippers and appears to explain their dimerization specificity and dynamics observed in vivo quite well. A model in which the bZIP networks act as functional units is proposed.

Stability of Single-Parent Gene Expression Complementation in Maize Hybrids upon Water Deficit Stress

Single-parent expression genes are nonsyntenic and stable throughout fluctuating water availability, underscoring their role in the early developmental manifestation of heterosis in maize. Heterosis is the superior performance of F1 hybrids compared with their homozygous, genetically distinct parents. In this study, we monitored the transcriptomic divergence of the maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal F1 hybrid progeny in primary roots under control and water deficit conditions simulated by polyethylene glycol treatment. Single-parent expression (SPE) of genes is an extreme instance of gene expression complementation, in which genes are active in only one of two parents but are expressed in both reciprocal hybrids. In this study, 1,997 genes only expressed in B73 and 2,024 genes only expressed in Mo17 displayed SPE complementation under control and water deficit conditions. As a consequence, the number of active genes in hybrids exceeded the number of active genes in the parental inbred lines significantly independent of treatment. SPE patterns were substantially more stable to expression changes by water deficit treatment than other genotype-specific expression profiles. While, on average, 75% of all SPE patterns were not altered in response to polyethylene glycol treatment, only 17% of the remaining genotype-specific expression patterns were not changed by water deficit. Nonsyntenic genes that lack syntenic orthologs in other grass species, and thus evolved late in the grass lineage, were significantly overrepresented among SPE genes. Hence, the significant overrepresentation of nonsyntenic genes among SPE patterns and their stability under water limitation might suggest a function of these genes during the early developmental manifestation of heterosis under fluctuating environmental conditions in hybrid progeny of the inbred lines B73 and Mo17.

A Clustering-based Test for Nonadditivity in an Unreplicated Two-way Layout

When there are several replicates available at each level combination of two factors, testing nonadditivity can be done by the usual two-way ANOVA method. However, the ANOVA method cannot be used when the experiment is unreplicated (one observation per cell of the two-way classification). Several tests have been developed to address nonadditivity in unreplicated experiments starting with Tukeys (1949) one-degree-of-freedom test for nonadditivity. Most of them assume that the interaction term has a multiplicative form. But such tests have low power if the assumed functional form is inappropriate. This leads to tests which do not assume a specific form for the interaction term. This paper proposes a new method for testing interaction which does not assume a specific form of interaction. The proposed test has the advantage over the earlier tests that it can also be used for incomplete two-way tables. A simulation study is performed to evaluate the power of the proposed test and compare it with other well-known tests.

On a new family of shifted logarithmic transformations

Most parametric statistical methods are based on a set of assumptions: normality, linearity and homoscedasticity. Transformation of a metric response is a popular method to meet these assumptions. In particular, transformation of the response of a linear model is a popular method when attempting to satisfy the Gaussian assumptions on the error components in the model. A particular problem with common transformations such as the logarithm or the Box–Cox family is that negative and zero data values cannot be transformed. This paper proposes a new transformation which allows negative and zero data values. The method for estimating the transformation parameter consider an objective criteria based on kurtosis and skewness for achieving normality. Use of the new transformation and the method for estimating the transformation parameter are illustrated with three data sets.

On generalized exponential transformations for proportions

ABSTRACT Transformation of the response is a popular method to meet the usual assumptions of statistical methods based on linear models such as ANOVA and t-test. In this paper, we introduce new families of transformations for proportions or percentage data. Most of the transformations for proportions require 0 < x < 1 (where x denotes the proportion), which is often not the case in real data. The proposed families of transformations allow x = 0 and x = 1. We study the properties of the proposed transformations, as well as the performance in achieving normality and homoscedasticity. We analyze three real data sets to empirically show how the new transformation performs in meeting the usual assumptions. A simulation study is also performed to study the behavior of new families of transformations.