Probing the endosperm gene expression landscape in Brassica napus

<p>Abstract</p> <p>Background</p> <p>In species with exalbuminous seeds, the endosperm is eventually consumed and its space occupied by the embryo during seed development. However, the main constituent of the early developing seed is the liquid endosperm, and a significant portion of the carbon resources for the ensuing stages of seed development arrive at the embryo through the endosperm. In contrast to the extensive study of species with persistent endosperm, little is known about the global gene expression pattern in the endosperm of exalbuminous seed species such as crucifer oilseeds.</p> <p>Results</p> <p>We took a multiparallel approach that combines ESTs, protein profiling and microarray analyses to look into the gene expression landscape in the endosperm of the oilseed crop <it>Brassica napus</it>. An EST collection of over 30,000 entries allowed us to detect close to 10,000 unisequences expressed in the endosperm. A protein profile analysis of more than 800 proteins corroborated several signature pathways uncovered by abundant ESTs. Using microarray analyses, we identified genes that are differentially or highly expressed across all developmental stages. These complementary analyses provided insight on several prominent metabolic pathways in the endosperm. We also discovered that a transcription factor <it>LEAFY COTYLEDON </it>(<it>LEC1</it>) was highly expressed in the endosperm and that the regulatory cascade downstream of <it>LEC1 </it>operates in the endosperm.</p> <p>Conclusion</p> <p>The endosperm EST collection and the microarray dataset provide a basic genomic resource for dissecting metabolic and developmental events important for oilseed improvement. Our findings on the featured metabolic processes and the <it>LEC1 </it>regulatory cascade offer new angles for investigation on the integration of endosperm gene expression with embryo development and storage product deposition in seed development.</p

Selection for improved energy use efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes

To increase both the yield potential and stability of crops, integrated breeding strategies are used that have mostly a direct genetic basis, but the utility of epigenetics to improve complex traits is unclear. A better understanding of the status of the epigenome and its contribution to agronomic performance would help in developing approaches to incorporate the epigenetic component of complex traits into breeding programs. Starting from isogenic canola (Brassica napus) lines, epilines were generated by selecting, repeatedly for three generations, for increased energy use efficiency and drought tolerance. These epilines had an enhanced energy use efficiency, drought tolerance, and nitrogen use efficiency. Transcriptome analysis of the epilines and a line selected for its energy use efficiency solely revealed common differentially expressed genes related to the onset of stress tolerance-regulating signaling events. Genes related to responses to salt, osmotic, abscisic acid, and drought treatments were specifically differentially expressed in the drought-tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine-4 of histone 3, further supported the phenotype by targeting drought-responsive genes and facilitating the transcription of the differentially expressed genes. From these results, we conclude that the canola epigenome can be shaped by selection to increase energy use efficiency and stress tolerance. Hence, these findings warrant the further development of strategies to incorporate epigenetics into breeding

BRAD, the genetics and genomics database for Brassica plants

<p>Abstract</p> <p>Background</p> <p>Brassica species include both vegetable and oilseed crops, which are very important to the daily life of common human beings. Meanwhile, the Brassica species represent an excellent system for studying numerous aspects of plant biology, specifically for the analysis of genome evolution following polyploidy, so it is also very important for scientific research. Now, the genome of <it>Brassica rapa </it>has already been assembled, it is the time to do deep mining of the genome data.</p> <p>Description</p> <p>BRAD, the Brassica database, is a web-based resource focusing on genome scale genetic and genomic data for important Brassica crops. BRAD was built based on the first whole genome sequence and on further data analysis of the Brassica A genome species, <it>Brassica rapa </it>(Chiifu-401-42). It provides datasets, such as the complete genome sequence of <it>B. rapa</it>, which was <it>de novo </it>assembled from Illumina GA II short reads and from BAC clone sequences, predicted genes and associated annotations, non coding RNAs, transposable elements (TE), <it>B. rapa </it>genes' orthologous to those in <it>A. thaliana</it>, as well as genetic markers and linkage maps. BRAD offers useful searching and data mining tools, including search across annotation datasets, search for syntenic or non-syntenic orthologs, and to search the flanking regions of a certain target, as well as the tools of BLAST and Gbrowse. BRAD allows users to enter almost any kind of information, such as a <it>B. rapa </it>or <it>A. thaliana </it>gene ID, physical position or genetic marker.</p> <p>Conclusion</p> <p>BRAD, a new database which focuses on the genetics and genomics of the Brassica plants has been developed, it aims at helping scientists and breeders to fully and efficiently use the information of genome data of Brassica plants. BRAD will be continuously updated and can be accessed through <url>http://brassicadb.org</url>.</p

Exploring glucosinolates diversity in Brassicaceae: a genomic and chemical assessment for deciphering abiotic stress tolerance

Brassica is one of the most economically important genus of the Brassicaceae family, encompassing several key crops like Brassica napus (cabbage) and broccoli (Brassica oleraceae var. italica). This family is well known for their high content of characteristic secondary metabolites such as glucosinolates (GLS) compounds, recognize for their beneficial health properties and role in plants defense. In this work, we have looked through gene clusters involved in the biosynthesis of GLS, by combining genomic analysis with biochemical pathways and chemical diversity assessment. A total of 101 Brassicaceae genes involved in GLS biosynthesis were identified, using a multi-database approach. Through a UPGMA and PCA analysis on the 101 GLS genes recorded, revealed a separation between the genes mainly involved in GLS core structure synthesis and genes belonging to the CYP450s and MYBs gene families. After, a detailed phylogenetic analysis was conducted to better understand the disjunction of the aliphatic and indolic genes, by focusing on CYP79F1–F2 and CYP81F1–F4, respectively. Our results point to a recent diversification of the aliphatic CYP79F1 and F2 genes in Brassica crops, while for indolic genes an earliest diversification is observed for CYP81F1–F4 genes. Chemical diversity revealed that Brassica crops have distinct GLS chemo-profiles from other Brassicaceae genera; being highlighted the high contents of GLS found among the Diplotaxis species. Also, we have explored GLS-rich species as a new source of taxa with great agronomic potential, particularly in abiotic stress tolerance, namely Diplotaxis, the closest wild relatives of Brassica crops.info:eu-repo/semantics/publishedVersio

Soybean Breeding on Seed Composition Trait

Soybean is a most important crop providing edible oil and plant protein source for human beings, in addition to animal feed because of high protein and oil content. This review summarized the progresses in the QTL mapping, candidate gene cloning and functional analysis and also the regulation of soybean oil and seed storage protein accumulation. Furthermore, as soybean genome has been sequenced and released, prospects of multiple omics and advanced biotechnology should be combined and applied for further refine research and high-quality breeding

Plant Comparative Transcriptomics Reveals Functional Mechanisms and Gene Regulatory Networks Involved in Anther Development and Male Sterility

Gene transcription and transcriptional regulation are crucial biological processes in all cellular life. Through the next-generation sequencing (NGS) technology, transcriptome data from different tissues and developmental stages can be easily obtained, which provides us a powerful tool to reveal the transcriptional landscape of investigated tissue(s) at special developmental stage(s). Anther development is an important process not only for sexual plant reproduction but also for genic male sterility (GMS) used in agriculture production. Plant comparative transcriptomics has been widely used to uncover molecular mechanism of GMS. Here, we focused on researches of anther developmental process and plant GMS genes by using comparative transcriptomics method. In detail, the contents include the following: (1) we described the commonly used flowchart in comparative transcriptomics; (2) we summarized the comparative strategies used to analyze transcriptome data; (3) we presented a case study on a maize GMS gene, ZmMs33; (4) we described the methods and results previously reported on gene co-expression and gene regulatory networks; (5) we presented the workflow of a case study on gene regulatory network reconstruction. The further development of comparative transcriptomics will provide us more powerful theoretical and application tools to investigate molecular mechanism underlying anther development and plant male sterility

Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants

Simple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plant Chlamydomonas reinhardtii were detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available at http://www.pssrd.info/. We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future

Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants’ demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production

Exploring the genetic landscape of nitrogen uptake in durum wheat: genome-wide characterization and expression profiling of NPF and NRT2 gene families

Nitrate uptake by plants primarily relies on two gene families: Nitrate transporter 1/peptide transporter (NPF) and Nitrate transporter 2 (NRT2). Here, we extensively characterized the NPF and NRT2 families in the durum wheat genome, revealing 211 NPF and 20 NRT2 genes. The two families share many Cis Regulatory Elements (CREs) and Transcription Factor binding sites, highlighting a partially overlapping regulatory system and suggesting a coordinated response for nitrate transport and utilization. Analyzing RNA-seq data from 9 tissues and 20 cultivars, we explored expression profiles and co-expression relationships of both gene families. We observed a strong correlation between nucleotide variation and gene expression within the NRT2 gene family, implicating a shared selection mechanism operating on both coding and regulatory regions. Furthermore, NPF genes showed highly tissue-specific expression profiles, while NRT2s were mainly divided in two co-expression modules, one expressed in roots (NAR2/NRT3 dependent) and the other induced in anthers and/ovaries during maturation. Our evidences confirmed that the majority of these genes were retained after small-scale duplication events, suggesting a neo- or sub-functionalization of many NPFs and NRT2s. Altogether, these findings indicate that the expansion of these gene families in durum wheat could provide valuable genetic variability useful to identify NUE-related and candidate genes for future breeding programs in the context of low-impact and sustainable agriculture