Seed size: a priority trait in cereal crops Kesavan, Markkandan; Song, Jong Tae; Seo, Hak Soo
Physiologia plantarum,
February 2013, Letnik:
147, Številka:
2
Journal Article
Recenzirano
Crop production and productivity must be increased to provide a balanced diet for the global population. The entire genome sequences of crop species allow the elucidation of genes that regulate ...important traits related to the final crop seed yield, which frequently depends mainly on seed size. Seed size is a major factor that controls seed quantity and it is strongly affected by various biotic, abiotic and genetic factors. Epigenetic marks in the genome and phytohormones are also important factors affecting seed growth and development. Several genes are known to be involved in the control of seed size, but their interaction and functional characterization have yet to be resolved. In this review, we discuss the different factors that govern seed size in cereal crops and Arabidopsis.
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•Microbial acclimatization improved lipidic-waste utilization in acidogenic fermentation.•Firmicutes, Bacteroidetes, and Cloacimonetes were abundant in the acclimatized ...microbiome.•Hydrogen productivity enhanced to 46 mL d−1 after acclimatization.•Hydrogenogenic acidogenesis and carboxylic chain elongation produced C4–C7 fatty acids.
Lipidic-waste such as fat, oil, and grease (FOG) are promising substrates for achieving higher bioenergy yields. An inadequate presence of an effective microbiome in the anaerobic digesters is the bottleneck for the proper utilization of FOG. Gradual introduction of FOG (0.2%, 1.2%, and 2.4% as volatile solids) in acidogenic fermentation showed a significant improvement in hydrogen yield (72%), compared to the control, after 2.4% FOG loading. Volatile solid (VS) reduction reached up to 65% in high FOG reactors with complete removal of major unsaturated fatty acids. Removal of saturated fatty acids increased to 90%. Improvement in hydrogen productivity (46 mL d−1) occurred during step-wise loading of 2.4% FOG to the acclimatized microbiome. The metabolic shift toward carboxylic chain elongation produced C4 and C6 fatty acids at concentrations of 1.61 mM and 0.90 mM, respectively in the acidogenic reactors. High-throughput sequencing of 16S rRNA amplicons revealed that the acclimatization process enriched the phylum Firmicutes (90%), followed by Bacteroidetes (12%) and Cloacimonetes (11%). The abundance of these phyla and their respective genera confirmed their preeminent role in hydrolysis, hydrogenogenic acidogenesis, and carboxylic chain elongation to produce hydrogen and C4–C7 fatty acids. Thus, we suggest that the improvement of hydrogen production using a microbiome acclimatized to FOG, and simultaneous production of high value organics (C4–C7 fatty acids), could facilitate the greater efficacy of the acidogenic fermentation.
Lentinula edodes is one of the most popular edible mushroom species in the world and contains useful medicinal components, such as lentinan. The light-induced formation of brown film on the ...vegetative mycelial tissues of L. edodes is an important process for ensuring the quantity and quality of this edible mushroom. To understand the molecular mechanisms underlying this critical developmental process in L. edodes, we characterized the morphological phenotypic changes in a strain, Chamaram, associated with abnormal brown film formation and compared its genome-wide transcriptional features.
In the present study, we performed genome-wide transcriptome analyses of different vegetative mycelium growth phenotypes, namely, early white, normal brown, and defective dark yellow partial brown films phenotypes which were exposed to different light conditions. The analysis revealed the identification of clusters of genes specific to the light-induced brown film phenotypes. These genes were significantly associated with light sensing via photoreceptors such as FMN- and FAD-bindings, signal transduction by kinases and GPCRs, melanogenesis via activation of tyrosinases, and cell wall degradation by glucanases, chitinases, and laccases, which suggests these processes are involved in the formation of mycelial browning in L. edodes. Interestingly, hydrophobin genes such as SC1 and SC3 exhibited divergent expression levels in the normal and abnormal brown mycelial films, indicating the ability of these genes to act in fruiting body initiation and formation of dikaryotic mycelia. Furthermore, we identified the up-regulation of glycoside hydrolase domain-containing genes in the normal brown film but not in the abnormal film phenotype, suggesting that cell wall degradation in the normal brown film phenotype is crucial in the developmental processes related to the initiation and formation of fruiting bodies.
This study systematically analysed the expression patterns of light-induced browning-related genes in L. edodes. Our findings provide information for further investigations of browning formation mechanisms in L. edodes and a foundation for future L. edodes breeding.
Seed size is one of the most important traits determining the yield of cereal crops. Many studies have been performed to uncover the mechanism of seed development. However, much remains to be ...understood, especially at the molecular level, although several genes involved in seed size have been identified. Here, we show that rice Grain Width 2 (GW2), a RING-type E3 ubiquitin ligase, can control seed development by catalyzing the ubiquitination of expansin-like 1 (EXPLA1), a cell wall-loosening protein that increases cell growth. Microscopic examination revealed that a
mutant had a chalky endosperm due to the presence of loosely packed, spherical starch granules, although the grain shape was normal. Yeast two-hybrid and in vitro pull-down assays showed a strong interaction between GW2 and EXPLA1. In vitro ubiquitination analysis demonstrated that EXPLA1 was ubiquitinated by GW2 at lysine 279 (K279). GW2 and EXPLA1 colocalized to the nucleus when expressed simultaneously. These results suggest that GW2 negatively regulates seed size by targeting EXPLA1 for degradation through its E3 ubiquitin ligase activity.
The complete mitogenome of the cotton leafhopper, Amrasca biguttula biguttula Ishida, 1913, was sequenced and annotated. The mitogenome is 14,474 bp long and contains 37 genes, including 13 ...protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, as well as a control region. The nucleotide composition of the mitogenome is as follows: A, 39.17%; T, 39.3%; C, 11.13%; and G, 10.39%. The total length of the 13 PCGs is 10,496 bp, which encodes 3503 amino acids. All PCGs start with the ATG codon, except for ATA, ATC, GTG, and ATT. Most of the PCGs stop with TGA, and the remaining with CCT, GAA, GGT, TCA, CCA, CTA, TTA, AAA, ATT, or ATA. The phylogenetic tree shows that A. biguttula biguttula belongs to Empoascini of the subfamily Typhlocybinae, but is different from other species within the subfamily.
Abalone (Haliotis discus hannai) is one of the most valuable marine aquatic species in Korea, Japan and China. Tremendous exposure to bacterial infection is common in aquaculture environment, ...especially by Vibrio sp. infections. It's therefore necessary and urgent to understand the mechanism of H. discus hannai host defense against Vibrio parahemolyticus infection. However studies on its immune system are hindered by the lack of genomic resources. In the present study, we sequenced the transcriptome of control and bacterial challenged H. discus hannai tissues. Totally, 138 MB of reference transcriptome were obtained from de novo assembly of 34 GB clean bases from ten different libraries and annotated with the biological terms (GO and KEGG). A total of 10,575 transcripts exhibiting the differentially expression at least one pair of comparison and the functional annotations highlight genes related to immune response, cell adhesion, immune regulators, redox molecules and mitochondrial coding genes. Mostly, these groups of genes were dominated in hemocytes compared to other tissues. This work is a prerequisite for the identification of those physiological traits controlling H. discus hannai ability to survive against Vibrio infection.
Although the genome sequence of cucumber is publicly available, only a limited number of functional markers are in store for developing gynoecious hybrids using Indian genotypes. This study reported ...novel SNPs and InDels in the exonic regions of genes involved in gynoecy using two parents and their hybrid with genotyping-by-sequencing (GBS) by generating 3.547 Gb of raw data. Using NSDC reference genome GCA_000004075.2, a total of 40,143, 181,008 and 43,612 SNPs were identified, among which 514 were polymorphic between male and female parents but monomorphic between the male parent and the hybrid (confirming hybridity). We further identified that, out of those 514 SNPs, 74 were within the exonic regions of the sex-specific genes. The most interesting functional marker in this study was SNP 2,13,85,488, identified in the gene CsaV3_6G037780 G3I-38214 on chromosome 6, encoding 1-aminocyclopropane-1-carboxylate oxidase 1 (ACS1), which plays a key role in female flower production, as indicated in CuCyc with the PathoLogic algorithm. The InDel analysis also identified a variation inside the gene CsaV3_6G304050 G3I-37940, encoding histone lysine N-methyl transferase, involved in flowering and female gametophyte development. Thus, this study has identified gynoecy-specific functional markers; upon further validation, these markers will accelerate the evolution of gynoecious hybrids in India and global cucumber breeding programs.
Genetic information of reproduction and growth is essential for sustainable molluscan fisheries and aquaculture management. However, there is limited knowledge regarding the reproductive activity of ...the commercially important Pacific abalone
. We performed de novo transcriptome sequencing of the ganglia in sexually immature and mature female Pacific abalone to better understand the sexual maturation process and the underlying molecular mechanisms. Of the ~305 million high-quality clean reads, 76,684 transcripts were de novo-assembled with an average length of 741 bp, 28.54% of which were annotated and classified according to Gene Ontology terms. There were 256 differentially expressed genes between the immature and mature abalone. Tandem mass spectrometry analysis, as compared to the predicted-peptide database of abalone ganglia transcriptome unigenes, identified 42 neuropeptide precursors, including 29 validated by peptidomic analyses. Label-free quantification revealed differential occurrences of 18 neuropeptide families between immature and mature abalone, including achatin, FMRFamide, crustacean cardioactive peptide, and pedal peptide A and B that were significantly more frequent at the mature stage. These results represent the first significant contribution to both maturation-related transcriptomic and peptidomic resources of the Pacific abalone ganglia and provide insight into the roles of various neuropeptides in reproductive regulation in marine gastropods.
Antimicrobial peptides/proteins (AMPs) are present in all types of organisms, from microbes and plants to vertebrates and invertebrates such as insects. The grasshopper
is an insect species that is ...widely consumed around the world for its broad medicinal value. However, the lack of available genetic information for this species is an obstacle to understanding the full potential of its AMPs. Analysis of the
transcriptome and expression profile is essential for extending the available genetic information resources. In this study, we determined the whole-body transcriptome of
and analyzed the potential AMPs induced by bacterial immunization. A high-throughput RNA-Seq approach generated 94,348 contigs and 66,555 unigenes. Of these unigenes, 36,032 (54.14%) matched known proteins in the NCBI database in a BLAST search. Functional analysis demonstrated that 38,219 unigenes were clustered into 5,499 gene ontology terms. In addition, 26 cDNAs encoding novel AMPs were identified by an in silico approach using public databases. Our transcriptome dataset and AMP profile greatly improve our understanding of
genetics and provide a huge number of gene sequences for further study, including genes of known importance and genes of unknown function.
In recent years, insects have been used in animal-based foods for sustainable live-stock management and in the human diet as therapeutic foods. These insects are classified as edible and are widely ...consumed around the world for their broad medicinal and nutritional values. Antimicrobial peptides/proteins (AMPs) confer resistance to microbial pathogens and contribute to the immune function of insects. The emma field cricket (Teleogryllus emma) is widely consumed around the world for its broad-spectrum therapeutic effects. However, the absence of genetic information on T. emma is an obstacle to understanding the diversity and activity of its AMPs. Hence, deep sequencing of the T. emma transcriptome and expression profiling are essential. We report whole-body de novo transcriptome profiling of T. emma and analysis of its potential bacterial immunization-induced AMPs. We assembled 18.2 Gb of Illumina reads, generated 102,311 transcripts (minimum length: >500 bp, N50: 2585 bp), and identified 67,838 unigenes. Of these unigenes, 39,937 (58.87%) matched known proteins in a Basic Local Alignment Search Tool search of the National Center for Biotechnology Information database. Functional analysis demonstrated that the 39,937 unigenes clustered under 5707 Gene Ontology terms. In addition, we identified 10 cDNAs encoding new AMPs via an in-silico approach using public databases. Our transcriptome data set and AMP profile greatly improve the understanding of T. emma genetics and provide a huge number of gene sequences, including those for genes of known and unknown function, for further study.
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•First RNA-seq based transcriptome of immunized Teleogryllus emma immune response.•The de novo assembly T. emma transcriptome revealed more contig length.•Promising T. emma-derived antimicrobial peptides (AMPs) were identified.
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