Agri Gene最新文献

Feed efficiency is a complex trait influenced by several genes and biological processes. However, there is limited knowledge about the genes and pathways involved in this trait. KCNJ11, related to the insulin secretion pathway, was shown to be a functional candidate gene for beef quality traits in Nelore. Given its role in energy metabolism, we evaluated the effects of KCNJ11 gene expression level on feed efficiency-related, carcass and growth traits in Nelore steers. Skeletal muscle KCNJ11 mRNA levels were positively and significantly associated with dry matter intake (DMI), total digestible nutrients consumption (TDN), average daily gain (ADG), and relative growth rate (RGR) from a general linear mixed model approach. Co-expression analysis, using RNA sequencing data obtained from Longissimus dorsi (LD) muscle of 30 Nelore steers, identified key signalling pathways related to the regulation of energy metabolisms, such as mitogen-activated protein kinases and insulin pathways. Our findings indicate a linear relationship between KCNJ11 gene expression and the phenotypic measures for feed intake, weight gain, and relative growth rate in Nelore steers, but not for residual feed intake or fat deposition traits.

The Matang Mangrove Forest Reserve (MMFR) in Malaysia has been acknowledged as the best sustainably-managed mangrove forest in the world. The management employed a 30-year rotation cycle to enable harvest of mangrove timbers, followed by replanting and series of thinnings. Information on soil microbial diversity and its functional capability in managed mangrove is scarce. To this end, we analysed high-throughput metagenomic datasets from two sites at MMFR with distinct features: the Virgin Jungle Forest and the harvested Productive Zone. Taxonomic classification of sequencing reads using metagenomics RAST (MG-RAST) revealed distinct differences at phylum and class level for bacteria present in both samples. Productive zone, which consisted of managed forest blocks, exhibited total organic carbon content that was 18.7 times higher than that of Virgin Jungle Forest. The Productive Zone microbial community was overabundant in genes related to carbohydrate metabolism, especially enzymes involved in the degradation and utilization of polysaccharides from plant cell wall. Functional analysis focusing on carbohydrate degrading enzymes revealed an array of enzymes involved in hemicellulose, cellulose and pectin utilization enzymes in Matang mangrove metagenomes. Overall, differences in taxonomic composition and function profile of soil microorganisms were observed between Productive Zone and Virgin Jungle Forest. The results presented in this study have important implications in understanding managed mangrove microbial assemblage and provide important resources for the discovery of bacterial species and enzymes involved in litter processing.

Cardamom (Elettaria cardamomum Maton) is an economically valuable spice crop and the essential oil of cardamom possesses splendid medicinal properties. To get insight into the domestication related traits and varied gene regulation, differential expression profiling of wild and cultivar cardamom was performed by analyzing the transcriptome data available for cardamom. Functional annotation using seven different publicly available databases identified significant genes coding for enzymes participating in monoterpenoid biosynthesis. Differential expression profile of cultivar and wild genotypes of cardamom exhibited 132 unigenes as differentially expressed (log2 > 4) with 105 up regulated and 27 down regulated genes in cultivars comparing with its wild genotype. Expression analysis showed wild cardamom has increased drought stress tolerance, defense response, and various plant growth regulations. Most of the genes coding for enzymes participating in flavanoid biosynthesis were up regulated, while resistance related genes (cinnamoyl CoA reductase) and few genes involved in the monoterpenoid biosynthetic pathway were down regulated in cultivars when compared to its wild progenitor. Transcriptome data were validated and correlated using qPCR using 10 randomly selected differentially expressed genes. Our study is the first application of next generation RNA-seq to explore the genes involved in various metabolic pathways and quantification of transcript expression levels in cultivar and wild cardamom genotypes.

Late blight (LB), Phytophthora infestans (PI) as pathogen, is the most devastating disease limiting potato production globally. In the Tropic highlands it can reduce yields by >50%. Cooperation-88 (C88) is a potato variety with high levels of durable resistance to PI, even after being widely grown for over 20 years. To more fully understand the mechanism of the resistance to PI of this variety, we inoculated detached leaves of young C88 plants with PI isolate XA-4 (super race with vir 1–11). Samples of one day post pathogen inoculation (1 dpi), 3 dpi, 5 dpi and control treated with sterile water were collected and frozen with liquid nitrogen. Transcriptomes of these 4 samples were sequenced by the next-generation sequencing platform Illumina Hiseq 2000. Totally ~68 M clean reads were obtained. With the genome of S. phureja clone DM1–3 516R44 as reference, these clean reads were processed by GO analysis, KEGG pathway enrichment analysis and differential expression analysis. PI inoculation of C88 leaves resulted in the following: a) in the 3 pathogen inoculated samples, 3950 were differentially regulated compared to those in the control; c) at 1 dpi increased expression genes were nearly double the number of decreased expression genes; d) 665 genes were differentially expressed in every treatments; e) gene expression levels in photosynthesis and the chloroplast were mostly diminished. The high durable late blight resistance C88 is composed of: a) 344 expressed R genes; b) 9 pathogenesis-related genes, particularly osmotin gene and endochitinase gene expressions increased dramatically with PI inoculation; c) thirty genes for phenolic compounds synthesis expressions increased with PI inoculation from small to large multiples compared to the control; and d) R genes need pathogenesis proteins and phenolic compounds to have superior durable resistance to PI.

Molecular marker based selection has become the method of choice to find undiscoverable natural variations and induced mutations in plants. Routine gel based molecular marker screening procedures involve complex steps which require considerable investment of time, money and efforts. Most often, genomic configuration of a plant species complicates the ultimate output of such screening programme. Therefore, a reliable and rapid high-throughput method is required to facilitate ease in identification of variants in a large number of samples. Here we demonstrate the application of a high-resolution melting (HRM) method to detect gamma radiation induced mutants of sugarcane (Saccharum spp.) which is a complex aneu-polyploidy plant. We have screened nine distinct mutants using sequence-tagged microsatellite site (STMS) markers and the analyses based on gel electrophoresis and HRM curve were compared. All the six STMS microsatellite markers coupled with HRM analysis were found highly informative and generated a unique melting curve for each of the marker tested. Of these, two markers NKSCSSR 22 and NKSCSSR 42 exhibited differential melting curve among the mutants and these results were well correlated with the gel based banding pattern. Taken together these results highlighted potential of HRM based marker screening and demonstrated reliability and robustness in detecting induced mutations in a complex polyploidy plant like sugarcane.

In the present study, ontogenetic expression of different innate immune genes in the Toll pathway of tiger shrimp, Penaeus monodon, such as TLR, myeloid differentiation factor 88 (MyD88) and tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6), was investigated in different developmental stages. Ontogenetic expression by real-time PCR revealed constitutive expression of these genes in all the developmental stages selected. TLR expression was found to be the highest in PL4, whereas MyD88 and TRAF6 showed the highest expression in eggs. The ubiquitous expression of TLR, MyD88 and TRAF6 in different developmental stages of P. monodon indicates the role of these genes in protecting the animals during early development. Immersion challenge of PL 18 with V. harveyi resulted in significant upregulation of TRAF6 at all time-points and significant upregulation of TLR at most of the time-points selected; however, MyD88 showed differential modulation pattern. In contrast to the bacterial challenge, WSSV infection in PL18 did not show any significant change in the expression of TRAF6, except for a downregulation observed at 12 to 48 hpi. However, TLR and MyD88 showed moderate increase in their expression, especially at late time-points. The responses of these genes to V. harveyi and WSSV immersion challenges in the juveniles (average body weight 3 g) of P. monodon were investigated in selected tissues including gill, hepatopancreas, and different parts of gastrointestinal tract such as foregut (stomach), midgut and hindgut. Temporal expression analysis revealed complete downregulation of PmMyD88 at most of the time-points in the gill following V. harveyi challenge and significant induction of PmTRAF6 at all time-points following WSSV infection. Immersion challenge with V. harveyi resulted in enhanced expression of TRAF6 in stomach and MyD88 in hepatopancreas showed similar pattern of expression post-WSSV challenge. Other tissues showed varying levels of induction of these genes at different time-points following pathogen challenge. The results of the present study suggest that both bacterial and viral challenges through immersion modulates the genes involved in the Toll pathway, and this might play an important role in the immune defense of post-larvae and juveniles of P. monodon.

Switchgrass (Panicum virgatum L.) is a perennial fodder grass and well known as a model renewable bioenergy crop. The plant's high production of biomass for biofuel supply is due to its fast-growing and wide adaptation properties. Very little studies and data are available about microRNAs (miRNAs) in this important biofuel crop. This situation demands to focus and identify new miRNAs and also to study their expressional analysis. In current research, a combination of computational and expressional approaches is applied to profile and characterize miRNAs in switchgrass and analyze some of them under drought stress. A total of 158 new miRNAs belonging to 83 families are identified and characterized from switchgrass expressed sequence tags (ESTs) and genomic survey sequences (GSS). In addition, five pre-miRNA clusters as well as four sense and antisense pre-miRNAs are also predicted from these newly identified miRNAs. Furthermore, 39 miRNAs were randomly selected and subjected to quantitative real-time RT-PCR expressional studies in root, leaf and stem of switchgrass under drought stress. A set of 13, 20 and 25 miRNAs are found as drought responding miRNAs in root, stem and leaf respectively. A total of 894 putative targets are also predicted for 158 switchgrass' miRNAs. These targets play roles in metabolism, transcription factor, signaling pathways, growth & development, stress-related, transport protein and other vital processes. Such findings in switchgrass improved the baseline data of miRNAs and their targets. This data can be utilized to fine-tune this important bioenergy crop under biotic and abiotic stresses. Furthermore, it can also be used for the improvement of biofuel properties of the plant.

As an important legume, common bean (Phaseolus vulgaris L.) is widely utilized as a staple crop and as a source of protein, minerals and vitamins for resource-poor populations in the tropics and in subtropical regions. However, substantial amounts of common beans may be lost due to infestations by bruchids and nematodes, among other pests. With the discovery of arcelins, a class of seed proteins, a biotechnological approach to addressing attacks by bruchids may be developed. Arcelins are components of a multigene family encoded by the APA locus [arcelin (Arc)/Phytohemagglutinin (PHA)/α-Amylase Inhibitor (αAI)] and have been shown to confer resistance to bruchids. Here we present an overview of the APA locus and briefly discuss the function of the components that make up this gene family, while linking this to the biocidal effects of the arcelin proteins and their biotechnological potential in the control of bruchids in common bean and other leguminous crops.

MicroRNAs (miRNAs) are a class of endogenous non-coding, small RNAs that are associated with the regulation of gene expression in eukaryotes. In plants, few miRNAs are highly conserved, that may have the same ancestor in the early stages of evolution. This fact allows the detection of conserved miRNAs in various plant species, especially in those that lack genome sequence information. Though the draft genome of the orphan crop, Lens culinaris Medik. (Lentil) is published, its complete genome assembly is still underway. In this computational study, an EST and GSS based comparative genomics approach were conducted to identify miRNAs in Lentils. The adopted approach was on the basis of a search for sequence similarity followed by series of filtering steps to provide reliable and precise results, eliminating the false-positive predictions. This study reports 24 miRNAs from 10,190 ESTs and 715 GSSs in Lentil. Further, it was also sought to pinpoint the 83 likely target genes of Lentil miRNAs and their most probable functions using Legume Information Resource (LIS) annotation pipeline. The newly identified miRNAs were mainly found to regulate the genes that encode transcription factors and key enzymes involved in metabolic processes as well as oxidation-reduction processes. Many of target genes were found to have an association with plant growth and development, stress response, defense and hormone signaling pathways. The miRNAs accounted is presumed to advance Lentil miRNAome in future as this computational study puts forward, first-ever, view towards miRNA research in Lentil.