Search Results (42)

Dollar spot is one of the world’s most widely distributed turfgrass diseases. The pathogen of the disease has been re-identified as a fungus belonging to the genus Clarireedia in the United States, Japan, and China. Since Clarireedia species vary depending on the response to fungicides, hosts, and distribution ranges, it is necessary to re-identify dollar spot in South Korea for effective turfgrass management. In this study, the amplified nucleotide sequences with primer sets of the internal transcribed spacer (ITS) region, Calmodulin (CaM), and Mini-chromosome maintenance complex component 7 (Mcm7) were analyzed to re-identify Clarireedia spp. isolated from creeping bentgrass and Kentucky bluegrass on golf courses in South Korea. The ITS and CaM regions were analyzed through multiple sequence alignments. The isolates were identified as C. paspali, and Clarireedia sp. When cultured on PDA, three groups formed fast growing, cottony colonies with white aerial hyphae that later collapsed and turned tan to brown. Most isolates formed apothecia, but ascospores were not observed. The apothecia formation of C. paspali has never been reported. All isolates exhibited pathogenicity on creeping bentgrass and Kentucky bluegrass. These results indicated that the pathogens causing dollar spot on creeping bentgrass and Kentucky bluegrass in South Korea might be C. paspali and Clarireedia sp. The present study reports the first re-identification of the turfgrass dollar spot pathogen Sclerotinia homoeocarpa into the genus Clarireedia in South Korea. Full article

Overweight and obese individuals show lower mortality rates or better prognoses than those of normal weight in a variety of diseases, a phenomenon called the “obesity paradox”. An inverse association of adiposity with atherosclerosis has been observed in both humans and mice. To dissect phenotypic and genetic connections between the traits, 154 female and 145 male F2 mice were generated from an intercross between BALB/cJ and LP/J apolipoprotein E-deficient mice and fed a Western diet for 12 weeks. Atherosclerotic lesion size in the aortic root, body weight, plasma lipids, and glucose were measured, and genotyping was performed on miniMUGA SNP arrays. Quantitative trait locus (QTL) analyses on all F2 mice with sex as a covariate revealed four significant QTLs on chromosomes (Chr) 3, 6, 13, and 15 for atherosclerosis and three significant QTLs on Chr2, 7, and 15 for body weight. Chr15 QTL for atherosclerosis overlapped with one for body weight near 36 Mb. After adjusting for variation in body weight, Chr15 atherosclerosis QTL was downgraded from significant to suggestive linkage. Body weight was inversely correlated with atherosclerotic lesion sizes and accounted for more variance than a single other risk factor for atherosclerosis among F2 mice. Analysis of public data collected from two backcross cohorts revealed strong correlations between body weight and fat mass in adult mice (r ≥ 0.93; p ≤ 1.6 × 10⁻¹³⁶). Thus, the obesity paradox in atherosclerosis is partially attributable to shared genetic components that have an opposite effect on adiposity and atherosclerosis. Full article

Human viral infections remain a significant global health challenge, contributing to a substantial number of cancer cases worldwide. Among them, infections with oncoviruses such as hepatitis B virus (HBV) and hepatitis C virus (HCV) are key drivers of hepatocellular carcinoma (HCC). Despite the availability of an effective HBV vaccine since the 1980s, millions remain chronically infected due to the persistence of covalently closed circular DNA (cccDNA) as a reservoir in hepatocytes. Current antiviral therapies, including nucleos(t)ide analogs and interferon, effectively suppress viral replication but fail to eliminate cccDNA, underscoring the urgent need for innovative therapeutic strategies. Direct-acting antiviral agents (DAAs), which have revolutionized HCV treatment with high cure rates, offer a promising model for HBV therapy. A particularly attractive target is the intrinsically disordered region (IDR) of the HBx protein, which regulates cccDNA transcription, viral replication, and oncogenesis by interacting with key host proteins. DAAs targeting these interactions could inhibit viral persistence, suppress oncogenic signaling, and overcome treatment resistance. This review highlights the potential of HBx-directed DAAs to complement existing therapies, offering renewed hope for a functional HBV cure and reduced cancer risk. Full article

Coleoptile is a sheath-like structure unique to monocots and is easily observed in sorghum. Colored coleoptiles have been shown to protect plants against abiotic and biotic stresses. The purpose of this study was to identify factors controlling coleoptile color in sorghum. We phenotyped the sorghum mini core accessions for coleoptile color in two environments, determined the anthocyanin content of each color of selected accessions, carried out a genome-wide association analysis and identified a candidate gene. The phenotypic analysis showed that 95 (40% of 235) accessions were green, 28 (12%) were purple and 42 (18%) were red in both 2022 and 2023. About 12% of the accessions changed from green to red due to environmental conditions. The anthocyanin content analysis showed a positive correlation between intensity of coleoptile color and anthocyanin levels. A genome-wide association analysis identified two candidate genes, Sobic.006G175700 and Sobic.006G175500, mapped to this trait in a single locus on chromosome 6. An orthologous comparison, together with mapping, sequence analysis and qPCR, identified Sobic.006G175700 as Rs1, the gene determining the sorghum coleoptile color. The haplotype analysis with SNPs from both coding and upstream regions of Sobic.006G175700 indicates that the predominant haplotypes can differentiate between green and colored coleoptile colors. This information can be used for marker-assisted selection of desired coleoptile colors in sorghum. Full article

This paper investigates the application of genetic algorithms (GAs) for hyperparameter optimisation in deep reinforcement learning (RL), focusing on the Deep Q-Learning (DQN) algorithm. This study aims to identify approaches that enhance RL model performance through the effective exploration of the configuration space. By comparing different GA methods for selection, crossover, and mutation, this study focuses on deep RL models. The results indicate that GA techniques emphasising the exploration of the configuration space yield significant improvements in optimisation efficiency, reducing training time and enhancing convergence. The most effective GA improved the fitness function value from 68.26 (initial best chromosome) to 979.16 after 200 iterations, demonstrating the efficacy of the proposed approach. Furthermore, variations in specific hyperparameters, such as learning rate, gamma, and update frequency, were shown to substantially affect the DQN model’s learning ability. These findings suggest that exploration-driven GA strategies outperform GA approaches with limited exploration, underscoring the critical role of selection and crossover methods in enhancing DQN model efficiency and performance. Moreover, a mini case study on the CartPole environment revealed that even a 5% sensor dropout impaired the performance of a GA-optimised RL agent, while a 20% dropout almost entirely halted improvements. Full article

Drought is a destructive abiotic stress that affects all critical stages of peanut growth such as emergence, flowering, pegging, and pod filling. The development of a drought-tolerant variety is a sustainable strategy for long-term peanut production. The U.S. mini-core peanut germplasm collection was evaluated for drought tolerance to the middle-season drought treatment phenotyping for pod weight, pod count, relative water content (RWC), specific leaf area (SLA), leaf dry matter content (LDMC), and drought rating. A genome-wide association study (GWAS) was performed to identify minor and major QTLs. A total of 144 QTLs were identified, including 18 significant QTLs in proximity to 317 candidate genes. Ten significant QTLs on linkage groups (LGs) A03, A05, A06, A07, A08, B04, B05, B06, B09, and B10 were associated with pod weight and pod count. RWC stages 1 and 2 were correlated with pod weight, pod count, and drought rating. Six significant QTLs on LGs A04, A07, B03, and B04 were associated with RWC stages 1 and 2. Drought rating was negatively correlated with pod yield and pod count and was associated with a significant QTL on LG A06. Many QTLs identified in this research are novel for the evaluated traits, with verification that the pod weight shared a significant QTL on chromosome B06 identified in other research. Identified SNP markers and the associated candidate genes provide a resource for molecular marker development. Verification of candidate genes surrounding significant QTLs will facilitate the application of marker-assisted peanut breeding for drought tolerance. Full article

The sweet oranges [C. sinensis (L.) Osbeck] produced in India are mainly consumed fresh as a table fruit and in the form of freshly extracted juice. Currently, a fraction of the fruit is processed into products like orange juice, concentrates, pulp, and other value-added products. Seedless varieties are preferred both by the consumers and by the processing industry; however, indigenously developed seedless sweet orange cultivars are not available. Citrus triploids are usually seedless due to their abnormal meiosis and embryo abortion. A research study was undertaken at CCRI Nagpur to develop triploid seedless plants of the local sweet orange cultivar Mosambi through endosperm culture in the shortest possible time by dovetailing various techniques. Various steps, viz., endosperm excision, standardization of media for callus initiation, somatic embryogenesis, shoot/root differentiation, mini-grafting, and validation of the triploid status through flow cytometry, chromosome counting, and other morphological parameters, were standardized, and seven confirmed triploid plants were finally produced. An evaluation of fruit quality parameters during the 2022 and 2023 fruiting seasons revealed that the fruits of the triploid sweet orange trees were commercially seedless. This is the first reported comprehensive study on the successful development of commercially seedless plants of the sweet orange cultivar Mosambi. The fruits of the triploid plants showed desirable fruit quality parameters in terms of their seed number (3 to 5.9/fruit), higher vitamin C content (34.4 to 42.66 mg), and lower limonene content (7.77 to 11.34 µg/mL). These triploid plants have the potential to gain recognition as a distinct variety. Full article

Nagpur mandarin is a popular table fruit across India and is exported to various countries. Only 1% of the total production is processed into various products. The development of seedless cultivars will boost agricultural incomes by enhancing the potential for export and processing. At present, only a couple of commercially seedless varieties are available, but these have yet to become popular. A research study was undertaken to quickly develop a high-quality seedless variety of Nagpur mandarin by combining the available technologies, viz., endosperm rescue, somatic embryogenesis, and mini-grafting, at CCRI, Nagpur. Complete plantlets of C. reticulata Blanco cv. Nagpur mandarin was successfully regenerated from hybrid endosperm tissue via somatic embryogenesis after attempting various permutations and combinations of media at various stages of regeneration, right from the primary callus to complete plantlet production. Maximum response (93.33%) and survival (91.67%) for primary callus induction were obtained in Murashige and Tucker (MT) + Malt Extract (ME) + Casein Hydrolysate (CH) (500 mg/L) +2,4-dichlorophenoxyacetic acid (2,4-D) (2 mg/L) medium. Maximum stimulation for embryogenesis and morphogenesis occurred in 2MT + CH (500 mg/L) + adenine sulfate (ad.s) (2 mg/L) + Benzyl Adenine (BA) (0.25 mg/L). The highest response (95.84%) for shoot differentiation occurred in MT + adenine sulphate (2 mg/L) + Gibberellic Acid (GA3) (1 mg/L) + BA (1 mg/L) (94.85%). The surviving plantlets were tested for ploidy status through flow Cytometry, chromosomal counting/cytogenetic technique, leaf morphology, stomatal characteristics, and the appearance of prominent thorns. In initial evaluation trials, the fruits of the triploid field-planted trees were found to be commercially seedless. These results demonstrated the recovery of stable triploids from the hybrid endosperm via somatic embryogenesis, which is the first of its kind in the field of Citrus triploid breeding in India. Full article

The world population’s growing demand for food is expected to increase dramatically by 2050. The agronomic productivity for food is severely affected due to biotic and abiotic constraints. At a global level, insect pests alone account for ~20% loss in crop yield every year. Deployment of noxious chemical pesticides to control insect pests always has a threatening effect on human health and environmental sustainability. Consequently, this necessitates for the establishment of innovative, environmentally friendly, cost-effective, and alternative means to mitigate insect pest management strategies. According to a recent study, using chloroplasts engineered with double-strand RNA (dsRNA) is novel successful combinatorial strategy deployed to effectively control the most vexing pest, the western flower thrips (WFT: Frankliniella occidentalis). Such biotechnological avenues allowed us to recapitulate the recent progress of research methods, such as RNAi, CRISPR/Cas, mini chromosomes, and RNA-binding proteins with plastid engineering for a plausible approach to effectively mitigate agronomic insect pests. We further discussed the significance of the maternal inheritance of the chloroplast, which is the major advantage of chloroplast genome engineering. Full article

Plant mitochondrial genomes (mitogenomes) exhibit fluid genome architectures, which could lead to the rapid erosion of genome synteny over a short evolutionary time scale. Among the species-rich orchid family, the leafy Cymbidium lancifolium and leafless Cymbidium macrorhizon are sister species with remarkable differences in morphology and nutritional physiology. Although our understanding of the evolution of mitochondria is incomplete, these sister taxa are ideal for examining this subject. In this study, the complete mitogenomes of C. lancifolium and C. macrorhizon, totaling 704,244 bp and 650,751 bp, respectively, were assembled. In the 2 mitogenomes, 38 protein-coding genes, 18 cis- and 6 trans-spliced introns, and approximately 611 Kb of homologous sequences are identical; overall, they have 99.4% genome-wide similarity. Slight variations in the mitogenomes of C. lancifolium and C. macrorhizon in repeat content (21.0 Kb and 21.6 Kb, respectively) and mitochondrial DNA of plastid origin (MIPT; 38.2 Kb and 37.5 Kb, respectively) were observed. The mitogenome architectures of C. lancifolium and C. macrorhizon are complex and comprise 23 and 22 mini-circular chromosomes, respectively. Pairwise comparisons indicate that the two mitogenomes are largely syntenic, and the disparity in chromosome numbers is likely due to repeat-mediated rearrangements among different chromosomes. Notably, approximately 93.2 Kb C. lancifolium mitochondrial sequences lack any homology in the C. macrorhizon mitogenome, indicating frequent DNA gains and losses, which accounts mainly for the size variation. Our findings provide unique insights into mitogenome evolution in leafy and leafless plants of sister species and shed light on mitogenome dynamics during the transition from mixotrophy to mycoheterotrophy. Full article

Cowpea aphids (Aphis craccivora Koch) double as a direct damaging pest and a virus vector to cowpea, threatening the economic yield of the crop. Given the multiple ecotypes, different alleles have been implicated in aphid resistance, necessitating the identification of key genes involved. The present study implemented a genome-wide scan using 365 cowpea mini-core accessions to decipher loci involved in resistance to aphid ecotype from Kano, Nigeria. Accessions were artificially inoculated with A. craccivora in insect-proof cages and damage severity assessed at 21 days after infestation. Significant phenotypic differences based on aphid damage severity were registered among the accessions. Skewed phenotypic distributions were depicted in the population, suggesting the involvement of major genes in the control of resistance. A genome-wide scan identified three major regions on chromosomes Vu10, Vu08 and Vu02, and two minor ones on chromosomes Vu01 and Vu06, that were significantly associated with aphid resistance. These regions harbored several genes, out of which, five viz Vigun01g233100.1, Vigun02g088900.1, Vigun06g224900.1, Vigun08g030200.1 and Vigun10g031100.1 were the most proximal to the peak single nucleotide polymorphisms (SNPs) positions. These genes are expressed under stress signaling, mechanical wounding and insect feeding. The uncovered loci contribute towards establishing a marker-assisted breeding platform and building durable resistance against aphids in cowpea. Full article

The increased virulence of infectious bursal disease virus (IBDV) is a threat to the chicken industry. The construction of novel herpesvirus of turkey-vectored (HVT) vaccines expressing VP2 of virulent IBDV may be a promising vaccine candidate for controlling this serious disease in chickens. We generated a novel infectious clone of HVT Fc-126 by inserting mini-F sequences in lieu of the glycoprotein C (gC) gene. Based on this bacterial artificial chromosome (BAC), a VP2 expression cassette containing the pMCMV IE promoter and a VP2 sequence from the virulent IBDV NJ09 strain was inserted into the noncoding area between the UL55 and UL56 genes to generate the HVT vector VP2 recombinant, named HVT-VP2-09. The recovered vectored mutant HVT-VP2-09 exhibited higher titers (p = 0.0202 at 36 h) or similar growth kinetics to the parental virus HVT Fc-126 (p = 0.1181 at 48 h and p = 0.1296 at 64 h). The high reactivation ability and strong expression of VP2 by HVT-VP2-09 in chicken embryo fibroblasts (CEFs) were confirmed by indirect immunofluorescence (IFA) and Western blotting. The AGP antibodies against IBDV were detected beginning at 3 weeks post-inoculation (P.I.) of HVT-VP2-09 in 1-day-old SPF chickens. Seven of ten chickens immunized with HVT-VP2-09 were protected post-challenge (P.C.) with the virulent IBDV NJ09 strain. In contrast, all chickens in the challenge control group showed typical IBD lesions in bursals, and eight of ten died P.C. In this study, we demonstrated that (i) a novel HVT BAC with the whole genome of the Fc-126 strain was obtained with the insertion of mini-F sequences in lieu of the gC gene; (ii) HVT-VP2-09 harboring the VP2 expression cassette from virulent IBDV exhibited in vitro growth properties similar to those of the parental HVT virus in CEF cells; and (iii) HVT-VP2-09 can provide efficient protection against the IBDV NJ09 strain. Full article

Among abiotic stresses, salt stress is the most complicated problem posing a major challenge for maintaining world food supplies as well as food security as it covers 1125 m ha globally and 6.73 m ha in India. It is very essential to increase rice productivity in salt-affected soils for food security and sustainability in salt-affected environments. The pass port data of 9000 rice Germplasm has been established for 30 traits and a mini core of 1500 lines has been developed. Approximately 20,000 rice lines have been screened for salinity and sodicity for both seedling and reproductive stages. The highly tolerant rice lines are being used in breeding programme to enhance the genetic diversity. The six QTLs in chromosomes 1, 2, 8, 9, 10 has been identified for the Na/K ratio, spikelet fertility and grain yield for the reproductive stage salt tolerance. The Saltol QTL has been transferred to Indian mega rice varieties namely, Pusa44 and Sarjoo52, to improve the salinity tolerance at the seedling stage. Similarly, the qSSISFHS8.1 (QTL for spikelet fertility) QTL is being transferred into mega rice varieties namely, PR114, Pusa44 and Sarjoo52, to improve the salinity tolerance at the reproductive stage. The marker assisted selection accelerates the breeding activities to develop the salt-tolerant varieties as well as transfer the QTLs to HVYs through marker assisted back cross breeding. The Central Soil Salinity Research Institute (CSSRI) has developed 13 salt-tolerant rice varieties, namely CSR10, CSR13, CSR23, CSR27, Basmati CSR30, CSR36, CSR43, CSR46, CSR49, CSR52, CSR56, CSR60 and CSR76, through conventional breeding approaches to increase the productivity of salt-affected soils for resource poor farmers. The popularity of these salt-tolerant rice varieties can be ascertained from the facts that large quantity of breeder seeds (1056 quintals) and truthfully labelled seeds (3126 quintals) has been produced and sold during last 22 years (2000–2021), more demand from the farmers and large area app. One point two million hectares is covered by these salt-tolerant rice varieties every year. Numerous salt-tolerant rice lines are being developed at CSSRI to cope with salt-affected soils and enable sustainable agriculture under salt-affected soils. Full article

An enhancer trap (ET) mediated by a transposon is an effective method for functional gene research. Here, an ET system based on a PB transposon that carries a mini Krt4 promoter (the keratin4 minimal promoter from zebrafish) and the green fluorescent protein gene (GFP) has been used to produce zebrafish ET lines. One enhancer trap line with eye-specific expression GFP named EYE was used to identify the trapped enhancers and genes. Firstly, GFP showed a temporal and spatial expression pattern with whole-embryo expression at 6, 12, and 24 hpf stages and eye-specific expression from 2 to 7 dpf. Then, the genome insertion sites were detected by splinkerette PCR (spPCR). The Krt4-GFP was inserted into the fourth intron of the gene itgav (integrin, alpha V) in chromosome 9 of the zebrafish genome, with the GFP direction the same as that of the itgav gene. By the alignment of homologous gene sequences in different species, three predicted endogenous enhancers were obtained. The trapped endogenous gene itgav, whose overexpression is related to hepatocellular carcinoma, showed a similar expression pattern as GFP detected by in situ hybridization, which suggested that GFP and itgav were possibly regulated by the same enhancers. In short, the zebrafish enhancer trap lines generated by the PB transposon-mediated enhancer trap technology in this study were valuable resources as visual markers to study the regulators and genes. This work provides an efficient method to identify and isolate tissue-specific enhancer sequences. Full article

Dyslipidemia is considered a risk factor for type 2 diabetes (T2D), yet studies with statins and candidate genes suggest that circulating lipids may protect against T2D development. Apoe-null (Apoe^-/-) mouse strains develop spontaneous dyslipidemia and exhibit a wide variation in susceptibility to diet-induced T2D. We thus used Apoe^-/- mice to elucidate phenotypic and genetic relationships of circulating lipids with T2D. A male F2 cohort was generated from an intercross between LP/J and BALB/cJ Apoe^-/- mice and fed 12 weeks of a Western diet. Fasting, non-fasting plasma glucose, and lipid levels were measured and genotyping was performed using miniMUGA arrays. We uncovered a major QTL near 60 Mb on chromosome 15, Nhdlq18, which affected non-HDL cholesterol and triglyceride levels under both fasting and non-fasting states. This QTL was coincident with Bglu20, a QTL that modulates fasting and non-fasting glucose levels. The plasma levels of non-HDL cholesterol and triglycerides were closely correlated with the plasma glucose levels in F2 mice. Bglu20 disappeared after adjustment for non-HDL cholesterol or triglycerides. These results demonstrate a causative role for dyslipidemia in T2D development in mice. Full article