Rice (Oryza sativa L.) blast disease is one of the most destructive rice diseases in the world. The fungal pathogen, Magnaporthe oryzae, is the causal agent of rice blast disease. Development of resistant cultivars is the most preferred method to achieve sustainable rice production. However, the effectiveness of resistant cultivars is hindered by the genetic plasticity of the pathogen genome. Therefore, information on genetic resistance and virulence stability are vital to increase our understanding of the molecular basis of blast disease resistance. The present study set out to elucidate the resistance pattern and identify potential simple sequence repeat markers linked with rice blast disease. A backcross population (BC2F1), derived from crossing MR264 and Pongsu Seribu 2 (PS2), was developed using marker-assisted backcross breeding. Twelve microsatellite markers carrying the blast resistance gene clearly demonstrated a polymorphic pattern between both parental lines. Among these, two markers, RM206 and RM5961, located on chromosome 11 exhibited the expected 1:1 testcross ratio in the BC2F1 population. The 195 BC2F1 plants inoculated against M. oryzae pathotype P7.2 showed a significantly different distribution in the backcrossed generation and followed Mendelian segregation based on a single-gene model. This indicates that blast resistance in PS2 is governed by a single dominant gene, which is linked to RM206 and RM5961 on chromosome 11. The findings presented in this study could be useful for future blast resistance studies in rice breeding programs.
Naturally, plant habitats are exposed to several potential effects of biotic and different abiotic environmental challenges. Several types of micro-organisms namely; bacteria, viruses, fungi, nematodes, mites, insects, mammals and other herbivorous animals are found in large amounts in all ecosystems, which lead to considerable reduction in crop productivity. These organisms are agents carrying different diseases that can damage the plants through the secretion of toxic-microbial poisons that can penetrate in the plant tissues. Toxins are injurious substances that act on plant protoplast to influence disease development. In response to the stress effect, plants defend themselves by bearing some substances such as phytoalexins. Production of phytoalexins is one of the complex mechanisms through which plants exhibit disease resistance. Several findings specifically on phytoalexins have widen the understanding in the fields of plant biochemistry and molecular biology. However, this review reports the interaction of toxins and phytoalexins in plant-pathogen cycle, research progress on the association of phytoalexins with plant disease resistance as well as the role of the phytoalexins in plant disease control.
Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876.
In plants, pathogen resistance is brought about by the binding of certain transcription factor (TF) proteins to the cis-elements of certain target genes. These cis-elements are present upstream in the motif of the promoters of each gene. This ensures the binding of a specific TF to a specific promoter, therefore regulating the expression of that gene. Therefore, the study of each promoter sequence of all the rice genes would help identify the target genes of a specific TF. Rice 1 kb upstream promoter sequences of 55,986 annotated genes were analyzed using the Perl program algorithm to detect WRKY13 binding motifs (bm). The resulting genes were grouped using Gene Ontology and gene set enrichment analysis. A gene with more than 4 TF bm in their promoter was selected. Ten genes reported to have a role in rice disease resistance were selected for further analysis. Cis-acting regulatory element analysis was carried out to find the cis-elements and confirm the presence of the corresponding motifs in the promoter sequences of these genes. The 3D structure of WRKY13 TF and the corresponding ten genes were built, and the interacting residues were determined. The binding capacity of WRKY13 to the promoter of these selected genes was analyzed using docking studies. WRKY13 was considered for docking analysis based on the prior reports of autoregulation. Molecular dynamic simulations provided more details regarding the interactions. Expression data revealed the expression of the genes that helped provide the mechanism of interaction. Further co-expression network helped to characterize the interaction of these selected disease resistance-related genes with the WRKY13 TF protein. This study suggests downstream target genes that are regulated by the WRKY13 TF. The molecular mechanism involving the gene network regulated by WRKY13 TF in disease resistance against rice fungal pathogens is explored.
This study evaluated the synergistic effects of dietary Bacillus subtilis WB60 and mannanoligosaccharide (MOS) in juvenile Japanese eel, Anguilla japonica. Seven treatment diets were formulated to contain three different levels of B. subtilis (0.0, 0.5, and 1.0 × 107 CFU/g diet denoted as BS0, BS0.5, and BS1, respectively) with two MOS levels (0 and 5 g/kg diet denoted as M0 and M5, respectively), and one diet with oxytetracycline (OTC) at 5 g/kg diet. Each diet (BS0M0 (CON), BS0M5, BS0.5M0, BS0.5M5, BS1M0, BS1M5, and OTC) was fed to triplicate groups of 20 fish averaging 9.00 ± 0.11 g (mean ± SD) for eight weeks. Average weight gain, feed efficiency, specific growth rate and protein efficiency ratio of fish fed the BS0.5M5 and BS1M5 diets were significantly higher than those of fish fed CON, BS0.5M0 and OTC diets (P 0.05). Therefore, the results for growth performance, non-specific immune responses, intestinal morphology, and disease resistance demonstrated that supplementation of B. subtilis at 0.5 × 107 CFU/g diet and mannanoligosaccharide at 5 g/kg diet could have beneficial synergistic effects in Japanese eel. The isolated probiotic from eel and the selected prebiotic could lead to the development of a specific and potential synbiotic in Japanese eel aquaculture.
Since their domestication, Brassica oilseed species have undergone progressive transformation allied with the development of breeding and molecular technologies. The canola (Brassica napus) crop has rapidly expanded globally in the last 30 years with intensive innovations in canola varieties, providing for a wider range of markets apart from the food industry. The breeding efforts of B. napus, the main source of canola oil and canola meal, have been mainly focused on improving seed yield, oil quality, and meal quality along with disease resistance, abiotic stress tolerance, and herbicide resistance. The revolution in genetics and gene technologies, including genetic mapping, molecular markers, genomic tools, and gene technology, especially gene editing tools, has allowed an understanding of the complex genetic makeup and gene functions in the major bioprocesses of the Brassicales, especially Brassica oil crops. Here, we provide an overview on the contributions of these technologies in improving the major traits of B. napus and discuss their potential use to accomplish new improvement targets.
The emergence of diseases such as white spot disease has become a threat to Penaeus monodon cultivation. Although there have been a few studies utilizing RNA-Seq, the cellular processes of host-virus interaction in this species remain mostly anonymous. In the present study, P. monodon was challenged with WSSV by intramuscular injection and survived for 12 days. The effect of the host gene expression by WSSV infection in the haemocytes, hepatopancreas and muscle of P. monodon was studied using Illumina HiSeq 2000. The RNA-Seq of cDNA libraries was developed from surviving WSSV-challenged shrimp as well as from normal healthy shrimp as control. A comparison of the transcriptome data of the two groups showed 2,644 host genes to be significantly up-regulated and 2,194 genes significantly down-regulated as a result of the infection with WSSV. Among the differentially expressed genes, our study discovered HMGB, TNFSF and c-Jun in P. monodon as new potential candidate genes for further investigation for the development of potential disease resistance markers. Our study also provided significant data on the differential expression of genes in the survived WSSV infected P. monodon that will help to improve understanding of host-virus interactions in this species.
Maize dwarf mosaic virus (MDMV) is a serious maize pathogen, epidemic worldwide, and one of the most common virus diseases for monocotyledonous plants, causing up to 70% loss in corn yield globally since 1960. MDMV belongs to the genus Potyvirus (Potyviridae) and was first identified in 1964 in Illinois in corn and Johnsongrass. MDMV is a single stranded positive sense RNA virus and is transmitted in a non-persistent manner by several aphid species. MDMV is amongst the most important virus diseases in maize worldwide. This review will discuss its genome, transmission, symptomatology, diagnosis and management. Particular emphasis will be given to the current state of knowledge on the diagnosis and control of MDMV, due to its importance in reducing the impact of maize dwarf mosaic disease, to produce an enhanced quality and quantity of maize.
Madagascar periwinkle is an ornamental and a medicinal plant, and is also an indicator plant that is highly susceptible to phytoplasma and spiroplasma infections from different crops. Periwinkle lethal yellows, caused by Spiroplasma citri, is one of the most devastating diseases of periwinkle. The response of plants to S. citri infection is very little known at the transcriptome level. In this study, quantitative real-time PCR (RT-qPCR) was used to investigate the expression levels of four selected genes involved in defense and stress responses in naturally and experimentally Spiroplasma citri infected periwinkles. Strictosidine β-glucosidase involved in terpenoid indole alkaloids (TIAs) biosynthesis pathway showed significant upregulation in experimentally and naturally infected periwinkles. The transcript level of extensin increased in leaves of periwinkles experimentally infected by S. citri in comparison to healthy ones. A similar level of heat shock protein 90 and metallothionein expression was observed in healthy, naturally and experimentally spiroplasma-diseased periwinkles. Overexpression of Strictosidine β-glucosidase demonstrates the potential utility of this gene as a host biomarker to increase the fidelity of S. citri detection and can also be used in breeding programs to develop stable disease-resistance varieties.
Aqueous and methanol extracts of lemon Citrus limon peel, Euphorbia hirta (aerial parts), and fenugreek Trigonella foenum-graecum seeds were tested for their in vitro antimicrobial activities against the bacterium Aeromonas hydrophila. A swab paper disk method showed that the methanol extract of E. hirta (EHE) had the largest inhibition zone and the lowest minimal inhibitory concentration compared to all other herbal extracts. Based on these results, EHE was included in the diets of Sharptooth Catfish Clarias gariepinus at 0 (control), 2, 5, or 7 g/kg of diet (experiment 1). Each treatment was conducted in triplicate, with 30 fish (mean weight ± SE = 9.4 ± 0.4 g) in each replicate. After 30 d, the growth, feed intake, hepatosomatic index (HSI), and plasma biochemical parameters were measured. With a separate batch of Sharptooth Catfish, the efficacy of the EHE diets in conferring fish resistance to A. hydrophila over 30 d was compared to that of a diet containing oxytetracycline (OTC; experiment 2). Six treatments were conducted in triplicate groups of 30 fish (mean weight ± SE = 9.0 ± 0.3 g); the Control fish were fed the control diet and were not injected with A. hydrophila, while the Control-AH and OTC-AH groups were infected with A. hydrophila and were fed either the control diet or the diet containing OTC at 1 g/199 g. The other three treatments included fish that were injected with A. hydrophila but fed diets with increasing EHE at 2, 5, or 7 g/kg. Experiment 1 showed no change to growth, feeding efficiency, HSI, or plasma biochemical parameters. In experiment 2, however, fish that were fed dietary EHE at 5 g/kg had significantly lower mortality than the Control-AH group, with further resistance observed for fish fed EHE at 7 g/kg. Dietary OTC was more effective than EHE as a prophylactic to A. hydrophila infection in Sharptooth Catfish. Nevertheless, EHE can potentially be a valuable dietary supplement to improve the resistance of Sharptooth Catfish to A. hydrophila infection. Received May 3, 2017; accepted August 24, 2017.
Commelinales belongs to the commelinids clade, which also comprises Poales that includes the most important monocot species, such as rice, wheat, and maize. No reference genome of Commelinales is currently available. Water hyacinth (Pontederia crassipes or Eichhornia crassipes), a member of Commelinales, is one of the devastating aquatic weeds, although it is also grown as an ornamental and medical plant. Here, we present a chromosome-scale reference genome of the tetraploid water hyacinth with a total length of 1.22 Gb (over 95% of the estimated size) across 8 pseudochromosome pairs. With the representative genomes, we reconstructed a phylogeny of the commelinids, which supported Zingiberales and Commelinales being sister lineages of Arecales and shed lights on the controversial relationship of the orders. We also reconstructed ancestral karyotypes of the commelinids clade and confirmed the ancient commelinids genome having 8 chromosomes but not 5 as previously reported. Gene family analysis revealed contraction of disease-resistance genes during polyploidization of water hyacinth, likely a result of fitness requirement for its role as a weed. Genetic diversity analysis using 9 water hyacinth lines from 3 continents (South America, Asia, and Europe) revealed very closely related nuclear genomes and almost identical chloroplast genomes of the materials, as well as provided clues about the global dispersal of water hyacinth. The genomic resources of P. crassipes reported here contribute a crucial missing link of the commelinids species and offer novel insights into their phylogeny.
Bacterial leaf blight (BLB) is one of the major rice diseases in Malaysia. This disease causes substantial yield loss as high as 70%. Development of rice varieties which inherited BLB resistant traits is a crucial approach to promote and sustain rice industry in Malaysia. Hence, this study aims were to enhance BLB disease resistant characters of high yielding commercial variety MR219 through backcross breeding approach with supporting tool of marker-assisted selection (MAS). Broad spectrum BLB resistance gene, Xa7 from donor parent IRBB7 were introgressed into the susceptible MR219 (recurrent parent) using two flanking markers ID7 and ID15. At BC3F4, we managed to generate 19 introgressed lines with homozygous Xa7 gene and showed resistant characteristics as donor parent when it was challenged with Xanthomonas oryzae pv. oryzae through artificial inoculation. Recurrent parent MR219 and control variety, MR263 were found to be severely infected by the disease. The improved lines exhibited similar morphological and yield performance characters as to the elite variety, MR219. Two lines, PB-2-107 and PB-2-34 were chosen to be potential lines because of their outstanding performances compared to parent, MR219. This study demonstrates a success story of MAS application in development of improved disease resistance lines of rice against BLB disease.
Nepenthes is a genus comprising carnivorous tropical pitcher plants that have evolved trapping organs at the tip of their leaves for nutrient acquisition from insect trapping. Recent studies have applied proteomics approaches to identify proteins in the pitcher fluids for better understanding the carnivory mechanism, but protein identification is hindered by limited species-specific transcriptomes for Nepenthes. In this study, the proteomics informed by transcriptomics (PIT) approach was utilized to identify and compare proteins in the pitcher fluids of Nepenthes ampullaria, Nepenthes rafflesiana, and their hybrid Nepenthes × hookeriana through PacBio isoform sequencing (Iso-Seq) and liquid chromatography-mass spectrometry (LC-MS) proteomic profiling. We generated full-length transcriptomes from all three species of 80,791 consensus isoforms with an average length of 1,692 bp as a reference for protein identification. The comparative analysis found that transcripts and proteins identified in the hybrid N. × hookeriana were more resembling N. rafflesiana, both of which are insectivorous compared with omnivorous N. ampullaria that can derive nutrients from leaf litters. Previously reported hydrolytic proteins were detected, including proteases, glucanases, chitinases, phosphatases, nucleases, peroxidases, lipid transfer protein, thaumatin-like protein, pathogenesis-related protein, and disease resistance proteins. Many new proteins with diverse predicted functions were also identified, such as amylase, invertase, catalase, kinases, ligases, synthases, esterases, transferases, transporters, and transcription factors. Despite the discovery of a few unique enzymes in N. ampullaria, we found no strong evidence of adaptive evolution to produce endogenous enzymes for the breakdown of leaf litter. A more complete picture of digestive fluid protein composition in this study provides important insights on the molecular physiology of pitchers and carnivory mechanism of Nepenthes species with distinct dietary habits.
To identify gene polymorphisms that differ between Malays, Han Chinese and South Indians, and to identify candidate genes for the investigation of their role in protecting Malays from Helicobacter pylori (H. pylori) infection.
Salmonella enterica serovar Enteritidis infection is a common concern in poultry production for its negative effects on growth as well as food safety for humans. Identification of molecular markers that are linked to resistance to Salmonella Enteritidis may lead to appropriate solutions to control Salmonella infection in chickens. This study investigated the association of candidate genes with resistance to Salmonella Enteritidis in young chickens. Two native breeds of Malaysian chickens, namely, Village Chickens and Red Junglefowl, were evaluated for bacterial colonization after Salmonella Enteritidis inoculation. Seven candidate genes were selected on the basis of their physiological role in immune response, as determined by prior studies in other genetic lines: natural resistance-associated protein 1 (NRAMP1), transforming growth factor β3 (TGFβ3), transforming growth factor β4 (TGFβ4), inhibitor of apoptosis protein 1 (IAP1), caspase 1 (CASP1), lipopolysaccharide-induced tumor necrosis factor (TNF) α factor (LITAF), and TNF-related apoptosis-inducing ligand (TRAIL). Polymerase chain reaction-RFLP was used to identify polymorphisms in the candidate genes; all genes exhibited polymorphisms in at least one breed. The NRAMP1-SacI polymorphism correlated with the differences in Salmonella Enteritidis load in the cecum (P = 0.002) and spleen (P = 0.01) of Village Chickens. Polymorphisms in the restriction sites of TGFβ3-BsrI, TGFβ4-MboII, and TRAIL-StyI were associated with Salmonella Enteritidis burden in the cecum, spleen, and liver of Village Chickens and Red Junglefowl (P < 0.05). These results indicate that the NRAMP1, TGFβ3, TGFβ4, and TRAIL genes are potential candidates for use in selection programs for increasing genetic resistance against Salmonella Enteritidis in native Malaysian chickens.
The indigenous populations from Peninsular Malaysia, locally known as Orang Asli, continue to adopt an agro-subsistence nomadic lifestyle, residing primarily within natural jungle habitats. Leading a hunter-gatherer lifestyle in a tropical jungle environment, the Orang Asli are routinely exposed to malaria. Here we surveyed the genetic architecture of individuals from four Orang Asli tribes with high-density genotyping across more than 2.5 million polymorphisms. These tribes reside in different geographical locations in Peninsular Malaysia and belong to three main ethno-linguistic groups, where there is minimal interaction between the tribes. We first dissect the genetic diversity and admixture between the tribes and with neighboring urban populations. Later, by implementing five metrics, we investigated the genome-wide signatures for positive natural selection of these Orang Asli, respectively. Finally, we searched for evidence of genomic adaptation to the pressure of malaria infection. We observed that different evolutionary responses might have emerged in the different Orang Asli communities to mitigate malaria infection.
Black pepper is an important commodity crop in Malaysia that generates millions of annual revenue for the country. However, black pepper yield is affected by slow decline disease caused by a soil-borne fungus Fusarium solani. RNA sequencing transcriptomics approach has been employed in this study to explore the differential gene expression in susceptible Piper nigrum L. and resistant Piper colubrinum Link. Gene expression comparative analysis of the two pepper species has yielded 2,361 differentially expressed genes (DEGs). Among them, higher expression of 1,426 DEGs was detected in resistant plant. These DEGs practically demonstrated the major branches of plant-pathogen interaction pathway (Path: ko04626). We selected five groups of defence-related DEGs for downstream qRT-PCR analysis. Cf-9, the gene responsible for recognizing fungal avirulence protein activity was found inexpressible in susceptible plant. However, this gene exhibited promising expression in resistant plant. Inactivation of Cf-9 could be the factor that causes susceptible plant fail in recognition of F. solani and subsequently delay activation of adaptive response to fungal invasion. This vital study advance the understanding of pepper plant defence in response to F. solani and aid in identifying potential solution to manage slow decline disease in black pepper cultivation.
The natural rubber latex extracted from the bark of Hevea brasiliensis plays various important roles in today's modern society. Following ultracentrifugation, the latex can be separated into 3 layers: C-serum, lutoids, and rubber particles. Previous studies have shown that a large number of proteins are present in these 3 layers. However, a complete proteome for this important plant is still unavailable. Protein sequences have been recently translated from the completed draft genome database of H. brasiliensis, leading to the creation of annotated protein databases of the following H. brasiliensis biosynthetic pathways: photosynthesis, latex allergens, rubberwood formation, latex biosynthesis, and disease resistance. This research was conducted to identify the proteins contained within the latex by way of de novo sequencing from mass spectral data obtained from the 3 layers of the latex. Peptides from these proteins were fragmented using collision-induced dissociation, higher-energy collisional dissociation, and electron-transfer dissociation activation methods. A large percentage of proteins from the biosynthetic pathways (63% to 100%) were successfully identified. In addition, a total of 1839 unique proteins were identified from the whole translated draft genome database (AnnHBM).
This investigation describes the impacts of dietary provisioning with astaxanthin on hemato-biochemistry, non-specific immunity, and disease resistance of the Asian seabass, Lates calcarifer, against the virulent Vibrio alginolyticus; with specific reference to dose-response associations and variations over different post-infection periods (0-, 7-, and 14-day). Triplicate groups of fish weighing 28 g, on average, were fed various diets (C, the control or astaxanthin-free; AXT50, 50 mg astaxanthin kg-1 diet; AXT100, 100 mg astaxanthin kg-1 diet; and AXT150, 150 mg astaxanthin kg-1 diet) for 90 days and subsequently challenged with V. alginolyticus at the end of the feeding period. Experimental infection unveiled that supplemented fish demonstrated significant improvements (P
At the present time, no artificial larval diet is capable of entirely fulfilling the dietary requirements of several larval fish and crustacean species. Zooplankton live food is the basic foundation of fish larviculture, and successful rearing of fish larvae still heavily depends on an adequate supply of nutritious live food. Despite being important, the production protocols of copepods and cladocerans (Moina) are still underdeveloped in hatcheries. Rotifers and Artemia are the most commonly used live foods. However, these live foods are evidently lacking in crucial nutrient constituents. Hence, through nutrient enrichment, live food with the nutritional profile that meets the requirements of fish larvae can be produced. With the aim to maximize the effectiveness of production to optimize profitability, it is important to evaluate and improve culture techniques for the delivery of micro- and macro-nutrients as feed supplements to larvae in aquaculture systems. Bioencapsulation and enrichment are the evolving techniques in aquaculture that are commonly employed to enhance the nutritional quality of live food by integrating nutrients into them, which subsequently improves the growth, survival, and disease resistance of the consuming hosts. This review aims to highlight some of the approaches and methods used to improve the nutritional quality of live food by modifying their nutrient composition, which could have immense promise in the enhancement of aquatic animal health.