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This article is a Commentary on Yu et al. (2024), 244: 1024–1040.

BACKGROUND: Sclerotinia spp. are generalist fungal pathogens, infecting over 700 plant hosts worldwide, including major crops. While host resistance is the most sustainable and cost-effective method for disease management, complete resistance to Sclerotinia diseases is rare. We recently identified soft basal stem as a potential susceptibility factor to Sclerotinia minor infection in lettuce (Lactuca sativa) under greenhouse conditions. RESULTS: Analysis of stem and root cell wall composition in five L. sativa and one L. serriola accessions with varying growth habits and S. minor resistance levels revealed strong association between hemicellulose constituents, lignin polymers, disease phenotypes, and basal stem mechanical strength. Accessions resistant to basal stem degradation consistently exhibited higher levels of syringyl, guaiacyl, and xylose, but lower levels of fucose in stems. These findings suggest that stem cell wall polymers recalcitrant to breakdown by lignocellulolytic enzymes may contribute to stem strength-mediated resistance against S. minor. CONCLUSIONS: The lignin content, particularly guaiacyl and syringyl, along with xylose could potentially serve as biomarkers for identifying more resistant lettuce accessions and breeding lines. Basal stem degradation by S. minor was influenced by localized microenvironment conditions around the stem base of the plants.

Crown gall disease (Agrobacterium tumefaciens), crown/root rot disease (Phytophthora spp.), root lesion disease (Pratylenchus vulnus) and tree vigor are key traits affecting the productivity and quality of walnuts in California. Unchallenged hybrid rootstocks were analyzed by RNA-seq to examine pre-formed factors affecting these traits. Enrichment analysis of the differentially expressed genes revealed that the increased expression of cell wall biogenesis-related genes plays a key role in susceptibility to A. tumefaciens, susceptibility to Phytophthora spp. and increased vigor. Analysis of the predicted subcellular loci of the encoded proteins revealed that many gene products associated with vigor and susceptibility were targeted to the plasma membrane and extracellular space, connecting these traits to sustaining barrier function. We observed that RNA processing and splicing, along with predicted nuclear targeting, were associated with resistance to A. tumefaciens, resistance to Phytophthora spp. and low vigor. Four genes within the J. microcarpa QTL region for resistance to A. tumefaciens and Phytophthora spp. were represented among our transcripts, with two of the genes being differentially expressed in association with resistance to A. tumefaciens and decreased vigor. No differential expression related to Phytophthora spp. or P. vulnus resistance was observed in this region. Additionally, the J. microcarpa haplotype expressed more transcripts associated with resistance to A. tumefaciens, Phytophthora spp. and low vigor, but not P. vulnus, than the J. regia haplotype. We also report unique and shared hormone and defense responses associated with each trait. This research suggests a link between cell wall biogenesis, vigor and critical root diseases of walnut.

Tomato spotted wilt orthotospovirus (TSWV) causes substantial economic loss to tomato production, and the Sw-5b resistance gene is widely deployed for management. Here, we show (i) the emergence of resistance-breaking (RB) TSWV strains in processing and fresh market tomato production in California over the past ten years, and (ii) evolutionary relationships with RB strains from other areas. A specific RT-PCR test was used to show the C118Y RB strain that emerged in Fresno County in 2016 quickly became predominant in the central production area and remained so through this study. In 2021, the C118Y strain was detected in the Northern production area, and was predominant in 2022. However, in 2023, the C118Y strain was unexpectedly detected in fewer spotted wilt samples from resistant varieties. This was due to emergence of the T120N RB strain, previously known to occur in Spain. A specific RT-PCR test was developed and used to show that the T120N RB strain was predominant in Colusa and Sutter counties (detected in 75-80% of samples), and detected in ~50% of samples from Yolo County. Pathogenicity tests confirmed California isolates of the T120N strain infected Sw-5b tomato varieties and induced severe symptoms. Another RB strain, C118F, was associated with spotted wilt samples of Sw-5 varieties from fresh market tomato production in southern California. Phylogenetic analyses with complete NSm sequences revealed that the C118Y and T120N RB strains infecting resistant processing tomato in California emerged locally, whereas those from fresh market production were more closely related to isolates from Mexico. Thus, widespread deployment of this single dominant resistance gene in California has driven the local emergence of multiple RB strains in different tomato production areas and types. These results further emphasize the need for ongoing monitoring for RB strains, and identification of sources of resistance to these strains.

The rice receptor kinase XA21 confers broad-spectrum resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight disease. To investigate the relationship between the expression level of XA21 and resulting resistance, we generated independent HA-XA21 transgenic rice lines accumulating the XA21 immune receptor fused with an HA epitope tag. Whole-genome sequence analysis identified the T-DNA insertion sites in sixteen independent T0 events. Through quantification of the HA-XA21 protein and assessment of the resistance to Xoo strain PXO99 in six independent transgenic lines, we observed that XA21-mediated resistance is dose dependent. In contrast, based on the four agronomic traits quantified in these experiments, yield is unlikely to be affected by the expression level of HA-XA21. These findings extend our knowledge of XA21-mediated defense and contribute to the growing number of well-defined genomic landing pads in the rice genome that can be targeted for gene insertion without compromising yield.

Over the past two decades Biomedical Engineering has emerged as a major discipline that bridges societal needs of human health care with the development of novel technologies. Every medical institution is now equipped at varying degrees of sophistication with the ability to monitor human health in both non-invasive and invasive modes. The multiple scales at which human physiology can be interrogated provide a profound perspective on health and disease. We are at the nexus of creating avatars (herein defined as an extension of digital twins) of human patho/physiology to serve as paradigms for interrogation and potential intervention. Motivated by the emergence of these new capabilities, the IEEE Engineering in Medicine and Biology Society, the Departments of Biomedical Engineering at Johns Hopkins University and Bioengineering at University of California at San Diego sponsored an interdisciplinary workshop to define the grand challenges that face biomedical engineering and the mechanisms to address these challenges. The Workshop identified five grand challenges with cross-cutting themes and provided a roadmap for new technologies, identified new training needs, and defined the types of interdisciplinary teams needed for addressing these challenges. The themes presented in this paper include: 1) accumedicine through creation of avatars of cells, tissues, organs and whole human; 2) development of smart and responsive devices for human function augmentation; 3) exocortical technologies to understand brain function and treat neuropathologies; 4) the development of approaches to harness the human immune system for health and wellness; and 5) new strategies to engineer genomes and cells.

The fungal pathogen Magnaporthe oryzae causes devastating blast disease in various cereals, including rice (Oryza sativa), wheat (Triticum aestivum), maize (Zea mays), and barley (Hordeum vulgare). Despite previous reports on fungal host specificity, the mechanisms underlying differential host infection strategies remain unclear. This study aimed to identify differentially abundant proteins (DAPs) in the apoplast of rice, barley, and wheat following infection with two M. oryzae pathovars using liquid chromatography-tandem mass spectrometry (LC–MS/MS). LC–MS/MS analysis revealed an enrichment of both M. oryzae and host proteins in the apoplast during the compatible reaction compared to the incompatible reaction. DAPs from M. oryzae involved in the host interaction included secreted extracellular enzymes (e.g., hydrolases), which were significantly increased in the M. oryzae Oryzae (MoO)-infected rice apoplast. Among host proteins, the proportion of protein-modifying enzymes increased in the M. oryzae Triticum (MoT)-infected rice and MoO-infected wheat apoplastic fluids, particularly rice glycosidases, peroxidases, and serine proteases, as well as wheat serine proteases. Furthermore, DAPs from MoL-infected rice were enriched in carbohydrate metabolism, suggesting that carbohydrate metabolism-related proteins may play a vital role in rice resistance to MoL. Additionally, protein-modifying and cytoskeletal proteins, as well as stress-responsive proteins, were enriched in the MoO-infected wheat apoplastic fluid. Finally, DAPs from both MoO- and MoL-infected barley were enriched in hydrogen peroxide catabolism, suggesting that peroxidases may be vital for barley resistance to M. oryzae. The identification of DAPs from both M. oryzae strains and the three host plants offers valuable insights into the host specificity mechanisms of M. oryzae in cereal crops. [ABSTRACT FROM AUTHOR]

"Huangguan" pears during storage are easily infected by various diseases, which resulted in substantial economic losses due to the decline in production and quality. Being a biocontrol bacterium, Lysobacter enzymogenes MB01 (L. enzymogenes MB01) can bring about the alterations of related defense enzymes, thereby enhancing the shelf life. The genetic changes in samples treated with L. enzymogenes MB01 were discussed by transcriptome. The outcomes indicated that compared to the control, L. enzymogenes MB01 restrained the disease index and total bacterial count and improved the defense enzyme activity. The transcriptome data uncovered the presence of 1975 differentially expressed genes (DEGs). The results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that the majority of DEGs were enriched in plant hormone signal transduction, phenylpropanoid biosynthesis, plant‐pathogen interaction, flavonoid biosynthesis, and stilbenoid, diarylheptanoid, and gingerol biosynthesis. The above results suggested the treatment with L. enzymogenes MB01 induced the disease resistance of pears through regulating multiple genes, which offers a feasible method for protecting fruit against pathogen during storage. [ABSTRACT FROM AUTHOR]

Fusarium wilt, caused by the soilborne fungal pathogen Fusarium oxysporum f. sp. lactucae (FOL), is an economically important disease of lettuce (Lactuca sativa) throughout the world. Four pathogenic races of FOL are reported, though only race 1 is known to exist in the United States. Recently, Californian lettuce growers have expressed increasing concern about Fusarium wilt, as some race 1‐resistant cultivars have exhibited susceptibility, and some susceptible cultivars have displayed reduced disease severity. To determine whether such changes in disease patterns are responses to potentially novel variants, we collected infected plants from commercial fields in the Salinas Valley and Santa Maria regions, isolated the fungus, and conducted a series of pathogenicity tests using a set of FOL race differential cultivars over 2 years (2022 and 2023) in controlled conditions. Pathogenicity tests revealed two new FOL variants that elicited novel disease reaction patterns on the set of differential cultivars that have not been previously described. Isolates Fol621 and Fol621s were less aggressive on race 1‐susceptible Banchu Red Fire, designated Variant‐1. Isolate VSP‐0916 incited severe Fusarium wilt on race 1‐resistant Costa Rica No. 4, designated Variant‐2. Moreover, VSP‐0916 exhibited high aggressiveness and the ability to induce disease in other race 1‐resistant cultivars. This study is the first documentation, to our knowledge, of the occurrence of FOL‐inciting Fusarium wilt on race 1‐resistant lettuce in the United States. Our work provides valuable information critical for the development of Fusarium wilt management strategies, including broad‐spectrum resistance breeding efforts against multiple FOL races. [ABSTRACT FROM AUTHOR]

Russian Snow White (RSW) chickens are characterized by high egg production, extreme resistance to low temperatures, disease resistance, and by the snow-white color of the day-old chicks. Studying the genome of this unique chicken breed will reveal its evolutionary history and help to understand the molecular genetic mechanisms underlying the unique characteristics of this breed, which will open new breeding opportunities and support future studies. We have sequenced and made a de novo assembly of the whole RSW genome using deep sequencing (250×) by the short reads. The genome consists of 40 chromosomes with a total length of 1.1 billion nucleotide pairs. Phylogenetic analysis placed the RSW near the White Leghorn, Fayoumi, and Houdan breeds. Comparison with other chicken breeds revealed a wide pool of mutations unique to the RSW. The functional annotation of these mutations showed the adaptation of genes associated with the development of the nervous system, thermoreceptors, purine receptors, and the TGF-beta pathway, probably caused by selection for low temperatures. We also found adaptation of the immune system genes, likely driven by selection for resistance to viral diseases. Integration with previous genome-wide association studies (GWAS) suggested several causal single nucleotide polymorphisms (SNPs). Specifically, we identified an RSW-specific missense mutation in the RALYL gene, presumably causing the snow-white color of the day-old chicks, and an RSW-specific missense mutation in the TLL1 gene, presumably affecting the egg weight. [ABSTRACT FROM AUTHOR]

Disease outbreaks in aquaculture have recently intensified. In particular, visceral white-nodules disease, caused by Pseudomonas plecoglossicida, has severely hindered the small yellow croaker (Larimichthys polyactis) aquaculture industry. However, research on this disease is limited. To address this gap, the present study employed a 100K SNP chip to genotype individuals from an F1 full-sib family, identify single nucleotide polymorphisms (SNPs), and construct a genetic linkage map for this species. A high-density genetic linkage map spanning a total length of 1395.72 cM with an average interval of 0.08 cM distributed across 24 linkage groups was obtained. Employing post-infection survival time as an indicator of disease resistance, 13 disease resistance-related quantitative trait loci (QTLs) were detected, and these regions included 169 genes. Functional enrichment analyses pinpointed 11 candidate disease resistance-related genes. RT-qPCR analysis revealed that the genes of chmp1a and arg1 are significantly differentially expressed in response to P. plecoglossicida infection in spleen and liver tissues, indicating their pivotal functions in disease resistance. In summary, in addition to successfully constructing a high-density genetic linkage map, this study reports the first QTL mapping for visceral white-nodules disease resistance. These results provide insight into the intricate molecular mechanisms underlying disease resistance in the small yellow croaker. [ABSTRACT FROM AUTHOR]

Anthracnose of the tea plant (Camellia sinensis), caused by Colletotrichum spp., poses a significant threat to both the yield and quality of tea production. To address this challenge, researchers have looked to the application of endophytic bacteria as a natural alternative to the use chemical pesticides, offering potential for enhancing disease resistance and abiotic stress tolerance in tea plants. This study focused on identifying effective microbial agents to combat tea anthracnose caused by Colletotrichum fructicola. A total of 38 Bacillus-like strains were isolated from the tea rhizosphere, with 8 isolates showing substantial inhibitory effects against the mycelial growth of C. fructicola, achieving an average inhibition rate of 60.68%. Among these, strain T3 was particularly effective, with a 69.86% inhibition rate. Through morphological, physiological, and biochemical characterization, along with 16S rRNA gene phylogenetics analysis, these strains were identified as B. inaquosorum (T1 and T2), B. tequilensis (T3, T5, T7, T8, and T19), and B. spizizenii (T6). Biological and molecular assays confirmed that these strains could induce the expression of genes associated with antimicrobial compounds like iturin, fengycin, subtilosin, and alkaline protease, which effectively reduced the disease index of tea anthracnose and enhanced tea plant growth. In conclusion, this study demonstrates that B. inaquosorum, B. tequilensis, and B. spizizenii strains are promising biocontrol agents for managing tea anthracnose. [ABSTRACT FROM AUTHOR]

Root rot is one of the common diseases of Lycium barbarum. Pathogens can cause devastating disasters to plants after infecting host plants. This study investigated the effect of arbuscular mycorrhizal fungi (AMF) Rhizophagus intraradices inoculation on phenylpropane metabolism in L. barbarum and evaluated its resistance to root rot. The experiment was set up with AMF inoculation treatments (inoculated or not) and root rot pathogen-Fusarium solani inoculation treatments (inoculated or not). The results showed that AMF was able to form a symbiosis with the root system of L. barbarum, thereby promoting plant growth significantly and increasing plants' resistance to disease stress. The plant height of AMF-colonized L. barbarum increased by 24.83% compared to non-inoculated diseased plants. After inoculation with AMF, the plant defense response induced by pathogen infection was stronger. When the enzyme activity of the leaves reached the maximum after the onset of mycorrhizal L. barbarum, phenylalanine ammonia-lyase, cinnamic acid-4-hydroxylase, and 4-coumaric acid-CoA ligase increased by 3.67%, 31.47%, and 13.61%, respectively, compared with the non-inoculated diseased plants. The products related to the lignin pathway and flavonoid pathway downstream of phenylpropane metabolism such as lignin and flavonoids were also significantly increased by 141.65% and 44.61% compared to nonmycorrhizal diseased plants. The activities of chitinase and β-1,3-glucanase increased by 36.00% and 57.96%, respectively. The contents of salicylic acid and jasmonic acid were also 17.7% and 31.63% higher than those of nonmycorrhizal plants in the early stage of plant growth, respectively. The results indicated that AMF significantly promoted plant growth and enhanced disease resistance by increasing enzyme activities and the production of lignin and flavonoids. [ABSTRACT FROM AUTHOR]

Cassava (Manihot esculenta Crantz) is a vital carbohydrate source for over 800 million people globally, yet its production in East Africa is severely affected by cassava brown streak disease (CBSD). Genebanks, through ex-situ conservation, play a pivotal role in preserving crop diversity, providing crucial resources for breeding resilient and disease-resistant crops. This study genotyped 234 South American cassava accessions conserved at the CIAT genebank, previously phenotyped for CBSD resistance by an independent group, to perform a genome-wide association analysis (GWAS) to identify genetic variants associated with CBSD resistance. Our GWAS identified 35 single nucleotide polymorphism (SNP) markers distributed across various chromosomes, associated with disease severity or the presence/absence of viral infection. Markers were annotated within or near genes previously identified with functions related to pathogen recognition and immune response activation. Using the SNP candidates, we screened the world's largest cassava collection for accessions with a higher frequency of favorable genotypes, proposing 35 accessions with potential resistance to CBSD. Our results provide insights into the genetics of CBSD resistance and highlight the importance of genetic resources to equip breeders with the raw materials needed to develop new crop varieties resistant to pests and diseases. [ABSTRACT FROM AUTHOR]

MicroRNA‐like RNAs (milRNAs) play a significant role in the infection process by plant‐pathogenic fungi. However, the specific functions and regulatory mechanisms of fungal milRNAs remain insufficiently elucidated. This study investigated the function of Foc‐milR138, an infection‐induced milRNA secreted by Fusarium oxysporum f. sp. cubense (Foc), which is the causal agent of Fusarium wilt of banana. Initially, through precursor gene knockout and phenotypic assessments, we confirmed that Foc‐milR138 acts as a virulent milRNA prominently upregulated during the early stages of Foc infection. Subsequent bioinformatic analyses and transient expression assays in Nicotiana benthamiana leaves identified a host receptor‐like kinase gene, MaLYK3, as the direct target of Foc‐milR138. Functional investigations of MaLYK3 revealed its pivotal role in triggering immune responses of N. benthamiana by upregulating a suite of resistance genes, bolstering reactive oxygen species (ROS) accumulation and callose deposition, thereby fortifying disease resistance. This response was markedly subdued upon co‐expression with Foc‐milR138. Expression pattern analysis further verified the specific suppression of MaLYK3 by Foc‐milR138 during the early root infection by Foc. In conclusion, Foc secretes a virulent milRNA (Foc‐milR138) to enter the host banana cells and inhibit the expression of the plant surface receptor‐like kinase MaLYK3, subverting the disease resistance activated by MaLYK3, and ultimately facilitating pathogen invasion. These findings shed light on the roles of fungal milRNAs and their targets in resistance and pathogenicity, offering promising avenues for the development of disease‐resistant banana cultivars. [ABSTRACT FROM AUTHOR]

Aquaculture is a crucial and rapidly expanding industry in global food production. Fisheries are also an essential socio-economic activity, providing abundant resources and remarkable prospects. However, due to the deteriorating ecological environment, aquatic animals are often exposed to traumatic conditions and are susceptible to bacterial infections that pose significant challenges for aquaculture production. The indiscriminate use of antibiotics in the past has led to the emergence of multidrug-resistant pathogens and sudden outbreaks of infectious diseases, resulting in serious economic losses. Moreover, the use of expensive chemotherapeutic drugs and antibiotics has negative impacts on aquatic environments. Therefore, it is increasingly important to adopt alternative natural agents, such as probiotics and their metabolites, to enhance healthy fish production. Probiotics are microorganisms that have numerous beneficial effects on their hosts. They are environmentally friendly, non-toxic, and cost-effective. This review specifically focuses on the use of Bacillus sp. as probiotics to promote healthy tilapia production in the aquatic sector, while also examining their interactions with the immune system and gut micro-biota. The information presented in this review can guide future research and promote effective and healthy tilapia culture production. [ABSTRACT FROM AUTHOR]

INDETERMINATE DOMAIN (IDD) genes encode plant-specific transcription factors containing a conserved IDD domain with four zinc finger motifs. Previous studies on Arabidopsis IDDs (AtIDDs) have demonstrated that these genes play roles in diverse physiological and developmental processes, including plant architecture, seed and root development, flowering, stress responses, and hormone signaling. Recent studies have revealed important functions of IDDs from rice and maize, especially in regulating leaf differentiation, which is related to the evolution of C4 leaves from C3 leaves. Moreover, IDDs in crops are involved in the regulation of agriculturally important traits, including disease and stress resistance, seed development, and flowering. Thus, IDDs are valuable targets for breeding manipulation. This review explores the role of IDDs in plant development, environmental responses, and evolution, which provides idea for agricultural application. [ABSTRACT FROM AUTHOR]

Carp is a key aquaculture species worldwide. The intensification of carp farming, aimed at meeting the high demand for protein sources for human consumption, has resulted in adverse effects such as poor water quality, increased stress, and disease outbreaks. While antibiotics have been utilized to mitigate these issues, their use poses risks to both public health and the environment. As a result, alternative and more sustainable practices have been adopted to manage the health of farmed carp, including the use of probiotics, prebiotics, phytobiotics, and vaccines to prevent disease outbreaks. Phytobiotics, being both cost-effective and abundant, have gained widespread acceptance. They offer various benefits in carp farming, such as improved growth performance, enhanced immune system, increased antioxidant capacity, stress alleviation from abiotic factors, and enhanced disease resistance. Currently, a focal point of research involves employing molecular approaches to assess the impacts of phytobiotics in aquatic animals. Gene expression, the process by which genetic information encoded is translated into function, along with transcription profiling, serves as a crucial tool for detecting changes in gene expression within cells. These changes provide valuable insights into the growth rate, immune system, and flesh quality of aquatic animals. This review delves into the positive impacts of phytobiotics on immune responses, growth, antioxidant capabilities, and flesh quality, all discerned through gene expression changes in carp species. Furthermore, this paper explores existing research gaps and outlines future prospects for the utilization of phytobiotics in aquaculture. [ABSTRACT FROM AUTHOR]

SUMMARY: 12‐Oxo‐phytodienoic acid reductases (OPRs) perform vital functions in plants. However, few studies have been reported in sugarcane (Saccharum spp.), and it is of great significance to systematically investigates it in sugarcane. Here, 61 ShOPRs, 32 SsOPRs, and 36 SoOPRs were identified from R570 (Saccharum spp. hybrid cultivar R570), AP85‐441 (Saccharum spontaneum), and LA‐purple (Saccharum officinarum), respectively. These OPRs were phylogenetically classified into four groups, with close genes similar structures. During evolution, OPR gene family was mainly expanded via whole‐genome duplications/segmental events and predominantly underwent purifying selection, while sugarcane OPR genes may function differently in response to various stresses. Further, ScOPR2, a tissue‐specific OPR, which was localized in cytoplasm and cell membrane and actively response to salicylic acid (SA), methyl jasmonate, and smut pathogen (Sporisorium scitamineum) stresses, was cloned from sugarcane. In addition, both its transient overexpression and stable overexpression enhanced the resistance of transgenic plants to pathogen infection, most probably through activating pathogen‐associated molecular pattern/pattern‐recognition receptor‐triggered immunity, producing reactive oxygen species, and initiating mitogen‐activated protein kinase cascade. Subsequently, the transmission of SA and hypersensitive reaction were triggered, which stimulated the transcription of defense‐related genes. These findings provide insights into the function of ScOPR2 gene for disease resistance. [ABSTRACT FROM AUTHOR]

Research has demonstrated that strigolactones (SLs) mediate plant disease resistance; however, the basal mechanism is unclear. Here, we provide key genetic evidence supporting how SLs mediate plant disease resistance. Exogenous application of the SL analog, rac-GR24, increased Arabidopsis thaliana resistance to virulent Pseudomonas syringae. SL-biosynthetic mutants and overexpression lines of more axillary growth 1 (MAX1, an SL-biosynthetic gene) enhanced and reduced bacterial susceptibility, respectively. In addition, rac-GR24 promoted bacterial pattern flg22-induced callose deposition and hydrogen peroxide production. SL-biosynthetic mutants displayed reduced callose deposition but not hydrogen peroxide production under flg22 treatment. Moreover, rac-GR24 did not affect avirulent effector-induced cell death between Col-0 and SL-biosynthetic mutants. Furthermore, rac-GR24 increased the free salicylic acid (SA) content and significantly promoted the expression of pathogenesis-related gene 1 related to SA signaling. Importantly, rac-GR24- and MAX1-induced bacterial resistance disappeared completely in Arabidopsis plants lacking both callose synthase and SA. Taken together, our data revealed that callose and SA are two important determinants in SL-mediated plant disease resistance, at least in Arabidopsis. [ABSTRACT FROM AUTHOR]

Soybean, one of the most important oil seed crops known for its high-quality oil and protein content, is widely grown and consumed worldwide. However, the crop is severely affected by various biotic and abiotic factors, of which diseases are by far the most important, resulting in significant yield losses each year. The major diseases affecting soybean production include soybean rust, soybean mosaic virus, anthracnose, charcoal rot, Sclerotinia stem rot (white mold), seedling diseases, sudden death syndrome, frogeye leaf spot, and Stem canker. Development of soybean varieties resistant to these diseases using modern biotechnology techniques is a viable option to increase genetic potential and boost soybean production. This paper, hence, aims to explore the application of functional genomics in improving resistance to various diseases in soybean. Therefore, this paper provides a comprehensive overview of the progress made in improving soybean resistance to major diseases by using the various approaches of modern biotechnological tools such as molecular markers, QTL/gene mapping, omics technology, freely available online databases, genome editing, genetic modification, and marker-assisted breeding. This review also highlights future directions that may be important for genomics-based research programs to improve disease resistance in soybean while increasing production.Article Highlights: Summarizes main discoveries and findings. Offers in-depth explorations of various genetic loci. Identifies direction for future progress. [ABSTRACT FROM AUTHOR]

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In the realm of agricultural sustainability, the utilization of plant genetic resources for enhanced disease resistance is paramount. Preservation efforts in genebanks are justified by their potential contributions to future crop improvement. To capitalize on the potential of plant genetic resources, we focused on a barley core collection from the German ex situ genebank and contrasted it with a European elite collection. The phenotypic assessment included 812 plant genetic resources and 298 elites, with a particular emphasis on four disease traits (Puccinia hordei , Blumeria graminis hordei , Ramularia collo-cygni , and Rhynchosporium commune). An integrated genome-wide association study, employing both Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) and a linear mixed model, was performed to unravel the genetic underpinnings of disease resistance. A total of 932 marker–trait associations were identified and assigned to 49 quantitative trait loci. The accumulation of novel and rare resistance alleles significantly bolstered the overall resistance level in plant genetic resources. Three plant genetic resources donors with high counts of novel/rare alleles and exhibiting exceptional resistance to leaf rust and powdery mildew were identified, offering promise for targeted pre-breeding goals and enhanced resilience in future varieties. Our findings underscore the critical contribution of plant genetic resources to strengthening crop resilience and advancing sustainable agricultural practices. [ABSTRACT FROM AUTHOR]

Background: DIR (Dirigent) proteins play important roles in the biosynthesis of lignin and lignans and are involved in various processes such as plant growth, development, and stress responses. However, there is less information about VvDIR proteins in grapevine (Vitis vinifera L). Results: In this study, we used bioinformatics methods to identify members of the DIR gene family in grapevine and identified 18 VvDIR genes in grapevine. These genes were classified into 5 subfamilies based on phylogenetic analysis. In promoter analysis, various plant hormones, stress, and light-responsive cis-elements were detected. Expression profiling of all genes following Colletotrichum gloeosporioides infection and phytohormones (salicylic acid (SA) and jasmonic acid (JA)) application suggested significant upregulation of 17 and 6 VvDIR genes, respectively. Further, we overexpressed the VvDIR4 gene in Arabidopsis thaliana and grapes for functional analysis. Ectopic expression of VvDIR4 in A. thaliana and transient expression in grapes increased resistance against C. gloeosporioides and C. higginsianum, respectively. Phenotypic observations showed small disease lesions in transgenic plants. Further, the expression patterns of genes having presumed roles in SA and JA signaling pathways were also influenced. Lignin contents were measured before and after C. higginsianum infection; the transgenic A. thaliana lines showed higher lignin content than wild-type, and a significant increase was observed after C. higginsianum infection. Conclusions: Based on the findings, we surmise that VvDIR4 is involved in hormonal and lignin synthesis pathways which regulate resistance against anthracnose. Our study provides novel insights into the function of VvDIR genes and new candidate genes for grapevine disease resistance breeding programs. [ABSTRACT FROM AUTHOR]

Post‐flowering diseases (PFDs), such as ear rot, stalk rot and smut, affect maize yield and quality by damaging the reproductive organs, stalks and seeds. We hypothesized that quantitative trait loci (QTL) associated with different PFDs colocalize and share similar defence mechanisms. Hence, to find a stable consensus meta‐QTL (MQTL) for single or multiple PFDs, MQTL analysis was performed. QTL conferring resistance to PFD reported in 31 independent studies were collated to develop a consensus map. As many as 49 MQTL conferring PFD resistance were projected using appropriate algorithms. Most MQTL regions encompass genes encoding a wide range of defence‐related proteins. MQTL1.1 and MQTL10.5 included QTL/genes for resistance to all PFDs, which supported our hypothesis. Candidate genes for PFDs in MQTL7.1 were associated with pathogenesis‐related 1 protein and mitogen‐activated protein kinase (MAPK) signalling. MQTL5.2 encompassed chalcone flavanone isomerase and cinnamoyl coenzyme A (CoA) reductase genes involved in flavonoid and phenylpropanoid biosynthesis, respectively. Furthermore, MQTL10.4 was found to harbour genes encoding E3 ubiquitin ligase, WRKY‐TF11, calcium‐binding domains and zinc finger motifs. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis reiterated the role of genes within MQTL7.1 in the MAPK signalling pathway, phytohormone signal transduction and plant–pathogen interaction. Hence, we propose that these genes are potential candidates for PFD resistance. Furthermore, 75% of the genes within the MQTL showed orthology with sorghum and rice, indicating that these genes were conserved across species. The role of 27 MQTL, including the six most significant MQTL, was confirmed with reported genome‐wide association study (GWAS) results. Thus, the hotspots associated with PFDs identified in our study could be reliably used in marker‐assisted breeding for PFD resistance. [ABSTRACT FROM AUTHOR]

Summary Aegilops umbellulata serve as an important reservoir for novel biotic and abiotic stress tolerance for wheat improvement. However, chromosomal rearrangements and evolutionary trajectory of this species remain to be elucidated. Here, we present a comprehensive investigation into Ae. umbellulata genome by generating a high‐quality near telomere‐to‐telomere genome assembly of PI 554389 and resequencing 20 additional Ae. umbellulata genomes representing diverse geographical and phenotypic variations. Our analysis unveils complex chromosomal rearrangements, most prominently in 4U and 6U chromosomes, delineating a distinct evolutionary trajectory of Ae. umbellulata from wheat and its relatives. Furthermore, our data rectified the erroneous naming of chromosomes 4U and 6U in the past and highlighted multiple major evolutionary events that led to the present‐day U‐genome. Resequencing of diverse Ae. umbellulata accessions revealed high genetic diversity within the species, partitioning into three distinct evolutionary sub‐populations and supported by extensive phenotypic variability in resistance against several races/pathotypes of five major wheat diseases. Disease evaluations indicated the presence of several novel resistance genes in the resequenced lines for future studies. Resequencing also resulted in the identification of six new haplotypes for Lr9, the first resistance gene cloned from Ae. umbellulata. The extensive genomic and phenotypic resources presented in this study will expedite the future genetic exploration of Ae. umbellulata, facilitating efforts aimed at enhancing resiliency and productivity in wheat. [ABSTRACT FROM AUTHOR]

Sunflower (Helianthus annuus) is a globally significant field crop, and disease resistance is crucial for ensuring yield stability and crop quality. Verticillium dahliae is a notorious soilborne pathogen that causes Verticillium Wilt (VW) and threatens sunflower production worldwide. In this study, we conducted a comprehensive assessment of sunflower resistance to V. dahliae across 231 sunflower cultivar lines, from the Sunflower Association Mapping (SAM) population. We employed EMMAX and ridge regression best linear unbiased prediction (rrBLUP) and identified 148 quantitative trait loci (QTLs) and 23 putative genes associated with V. dahliae resistance, including receptor like kinases, cell wall modification, transcriptional regulation, plant stress signalling and defense regulation genes. Our enrichment and quantitative real-time PCR validation results highlight the importance of membrane vesicle trafficking in the sunflower immune system for efficient signaling and defense upon activation by V. dahliae. This study also reveals the polygenic architecture of V. dahliae resistance in sunflowers and provides insights for breeding sunflower cultivars resistant to VW. This research contributes to ongoing efforts to enhance crop resilience and reduce yield losses due to VW, ultimately benefiting sunflower growers and the agricultural sector. [ABSTRACT FROM AUTHOR]

This study aimed to identify potential probiotic strains of Bacillus subtilis from healthy fish gut microbiota for application in aquaculture. The effects of dietary B. subtilis administration on growth performance, serum enzyme activity, immune gene expression, and disease resistance in darkbarbel catfish (Pelteobagrus fulvidraco) were investigated. The isolate, identified through gene sequencing and biochemical tests, demonstrated resilience to pH 3.0% and 6.0% bile, and exhibited extracellular protease, cellulose, lipase, and amylase production. Darkbarbel catfish were fed diets with varying B. subtilis concentrations (0 CFU/kg [T0], 107 CFU/kg [T1], 108 CFU/kg [T2], and 109 CFU/kg [T3]). After 8 weeks, significant increases (p < 0.05) were observed in final body weight, weight gain rate, specific growth rate, serum lysozyme, serum superoxide dismutase, alkaline phosphatase, and total antioxidant capacity, whereas malondialdehyde levels significantly decreased. Feeding darkbarbel catfish with B. subtilis diets increased immunoglobulin M (IgM) and C3 gene expression (p < 0.05), indicating a positive impact on the fish's immune system. The strain upregulated interleukin 10 (IL‐10) and transforming growth factor‐β (TGF‐β) expression and downregulated TNF‐α and IL‐1β, suggesting potential anti‐inflammatory effects. Following a 7‐day challenge with Aeromonas hydrophila, fish fed with B. subtilis exhibited lower mortality, with higher survival rates in the T2 and T3 groups. In conclusion, supplementing darkbarbel catfish diets with B. subtilis effectively enhances growth performance, immune response, and disease resistance. [ABSTRACT FROM AUTHOR]

Backround: In recent years, with the increasing demand for seedless grape varieties that have lower production costs, are disease resistant/tolerant and require less chemical pesticides, the embryo recovery technique has begun to be used more in table grape breeding studies. However, the desired high success rate has not yet been achieved in these studies. Although there are different reasons for this, especially the grape varieties selected for cross-breeding and the timing of transferring the embryos to medium are among the most important reasons. In this study, focusing on these two important factors, the embryos obtained from different hybridization combinations were transferred to agar medium at different weeks for 4 years and the most successful combination and time were determined. In addition, seedless and large berry grape varieties and some seeded varieties that are resistant/tolerant to fungal diseases were selected as parents because they can provide resistance to disease infections in vitro and thus increase the success rate. Results: The results obtained from the study showed that the selected variety and combination significantly affected the success rate in embryo rescue. Especially in combinations with the 'Yalova Seedless' variety as the female parent, more successful results were obtained compared to combinations of other varieties. When 'Yalova Seedless' variety was pollinated with pollen of 'Red Globe', 'Muscat Bailey A' and 'Exalta' varieties, more seedlings were obtained with the help of embryo rescue. The results obtained over four years showed that the best sampling time after pollination was the eighth week and then the seventh week. Conclusions: According to the results obtained, it has been shown that the selected varieties and the sampling time significantly affect the success rate in embryo rescue studies. Therefore, higher success rates can be achieved in comprehensive breeding studies in which they will be included as pollinators, especially in different seeded varieties that are resistant to diseases and have larger berry size. [ABSTRACT FROM AUTHOR]

Sheath blight, caused by the fungus Rhizoctonia solani, is a major problem that significantly impacts rice production and can lead to substantial yield losses. The disease has become increasingly problematic in recent years due to the widespread use of high-yielding semi-dwarf rice cultivars, dense planting, and heavy application of nitrogenous fertilizers. The disease has become more challenging to manage due to its diverse host range and the lack of resistant cultivars. Despite utilizing traditional methods, the problem persists without a satisfactory solution. Therefore, modern approaches, including advanced breeding, transgenic methods, genome editing using CRISPR/Cas9 technology, and nanotechnological interventions, are being explored to develop rice plants resistant to sheath blight disease. This review primarily focuses on these recent advancements in combating the sheath blight disease. [ABSTRACT FROM AUTHOR]

Stripe rust and powdery mildew are serious diseases that severely decrease the yield of wheat. Planting wheat cultivars with powdery mildew and stripe rust resistance genes is the most effective way to control these two diseases. Introducing disease resistance genes from related species into the wheat genome via chromosome translocation is an important way to improve wheat disease resistance. In this study, nine novel T1RS.1AL translocation lines were developed from the cross of wheat cultivar Chuannong25 (CN25) and a Chinese rye Qinling. The results of non-denaturing fluorescence in situ hybridization and PCR showed that all new lines were homozygous for the T1RS.1AL translocation. These new T1RS.1AL translocation lines exhibited strong resistance to stripe rust and powdery mildew. The cytogenetics results indicated that the resistance of the new lines was conferred by the 1RS chromosome arms, which came from Qinling rye. The genetic analysis indicated that there were new dominant resistance genes on the 1RS chromosome arm resistant to stripe rust and powdery mildew, and their resistance patterns were different from those of Yr9, Pm8, and Pm17 genes. In addition, the T1RS.1AL translocation lines generally exhibited better agronomic traits in the field relative to CN25. These T1RS.1AL translocations have great potential in wheat-breeding programs in the future. [ABSTRACT FROM AUTHOR]

The rice cultivar ‘JJ644wx’ was developed to improve disease resistance and lodging tolerance of Korean japonica glutinous rice cultivars. ‘JJ644wx’ was derived from a cross between ‘HR27814-B-47-1-1’ (‘Sinjinbaek’), a multiple disease-resistant mid-late maturing elite line, and ‘HR29676-AC29’, a medium-maturing glutinous line with lodging tolerance. To shorten the breeding period, an anther culture method was applied to F1 plants. ‘JJ644wx’ was selected through the pedigree method, yield trials, and local adaptability tests, with high selection pressure for disease resistance and lodging tolerance. The heading date of ‘JJ644wx’ was August 11th, four days later than that of ‘Sinseonchal’. ‘JJ644wx’ exhibited strong tolerance to lodging with a short culm length. The 1,000-grain weight of brown rice of ‘JJ644wx’ was heavier than that of ‘Sinseonchal’, and its yield was 553 kg/10a, which was 10% higher than that of ‘Sinseonchal’. ‘JJ644wx’ had a higher milling performance than ‘Sinseonchal’, but a lower head rice ratio due to a higher percentage of broken rice. ‘JJ644wx’ tended to be situated between ‘Sinseonchal’ and ‘Dongjinchal’ in terms of pasting and texture characteristics. ‘JJ644wx’ is the only Korean japonica glutinous rice cultivar resistant to the most virulent bacterial blight race, K3a; it also showed resistance to rice blast and stripe virus. ‘JJ644wx’ is expected to be a valuable resource that could contribute to improving the cultivation stability of Korean japonica glutinous rice in response to climate change (Registration No. 9606). [ABSTRACT FROM AUTHOR]

Currently, the disease control in cucumber mainly depends on agrochemicals, which is not an environmentally benign strategy. Biocontrol bacteria not only resist plant pathogens but also promote plant growth, which is ecofriendly and sustainable option. A biocontrol bacterial strain BJ-5 was screened using Corynespora cassiicola as the target pathogen, and BJ-5 was determined to be Paenarthrobacter nitroguajacolicus by morphological and molecular methods. The effect of BJ-5 on C. cassiicola was studied, including the spore germination, cell membrane permeability and infected cucumbers. BJ-5 inhibited the germination of C. cassiicola spores in vitro and led to atrophy and deformation of the C. cassiicola budding tubes. BJ-5 caused the relative extracellular conductivity of C. cassiicola mycelia to increase compared with the control. Additionally, BJ-5 reduced the severity of cucumber corynespora leaf spot of cucumber infected with C. cassiicola. The inhibition efficacy of BJ-5 suspension as a foliar spray against cucumber corynespora leaf spot reached 63% inhibition, which is higher than a 5000-fold dilution of Luna-Son SC fungicide. In addition, BJ-5 was tested on the emergence of cucumber seedlings, recording the biomass and photosynthesis of cucumber during the growth period. BJ-5 at 1.5 x 105 CFU·mL-1 promoted the germination of cucumber seeds and increased biomass and photosynthesis at the adult plant stage. Also, the secondary metabolites of BJ-5 were determined. BJ-5 could produce chitinases, siderophore, cellulase, amylase and protease in the respective medium. Finally, adaptation assay of BJ-5 showed good salt tolerance and good adaptability in alkaline conditions, and that BJ-5 retains inhibition of fungi activity at higher temperatures. This is the first report of the biocontrol by P. nitroguajacolicus with antagonism to C. cassiicola and promote cucumber growth. This study indicates that P. nitroguajacolicus may serve as potential biocontrol agents against cucumber corynespora leaf spot fungus. [ABSTRACT FROM AUTHOR]

Germin-like proteins (GLPs) play crucial roles in disease resistance, stress tolerance, and plant defense responses in various crop species. This review explores the intricate role of GLP gene expression and its modulation by cis-acting regulatory elements (CAREs) under biotic and abiotic stress in major crops. In rice, OsGLP2-1 and OsGLP3-7 have been identified as positive regulators of disease resistance. Similarly, TaGLP genes in wheat and VvGLP3 in grapes have been associated with powdery mildew resistance. Additionally, ZmGLP1 in maize and StGLP5 in potato contribute to defense against Bipolaris maydis and salt stress, respectively. AhGLPs in peanuts respond to drought stress, while GmGLP10 in soybean demonstrates a response to Sclerotinia sclerotiorum infection. Research in cotton has unveiled GhABP19 and GhGLP2 as GLPs involved in plant defense responses to wilt disease. Analysis of GLP gene promoters has revealed the presence of stress-responsive CAREs that modulate gene expression under biotic and abiotic stresses. Transgenic overexpression of GLP genes in different plant species, such as potato, tobacco, and Arabidopsis, has resulted in enhanced resistance to fungal pathogens, oxidative stress, and abiotic stresses. CRISPR/Cas9 genome editing has provided insights into UV-B stress response mechanisms. Promising outcomes from transgenic studies and CRISPR genome editing present exciting opportunities to improve disease resistance and stress tolerance in crops. These findings significantly enhance our understanding of the critical roles played by GLPs in crop resilience, paving the way for the development of stress-resistant crops to ensure sustainable global food security. [ABSTRACT FROM AUTHOR]

(1) Background: This study aimed to evaluate the potential of short-chain fatty acids as functional ingredients to improve the immune status and disease resistance of European seabass (Dicentrarchus labrax) juveniles. (2) Methods: For that purpose, triplicate groups of fish with an initial body weight of 15.2 ± 0.03 g were fed isoproteic (43% crude protein) and isolipidic (18% crude lipids) diets supplemented with sodium acetate (SA), sodium propionate (SP), and sodium butyrate (SB) at two inclusion levels: 0.25% and 0.50%. An unsupplemented diet was used as a control. After 56 days of feeding with the experimental diets, fish were intraperitoneally (i.p.) injected with 100 µL of Vibrio anguillarum (1.2 × 107 Colony Forming Units (CFU)/mL) and mortality was recorded for 3 weeks. At the end of the trial, there were no differences in survival between the treatment groups and the control, but survival was higher in fish fed the diet supplemented with SB 0.50 than SP 0.25 (93.3 vs. 66.7%). Compared to the pre-challenge values, and regardless of diet composition, all hematological parameters (hemoglobin, hematocrit, red blood cells, white blood cells) measured decreased after 4 h of bacterial challenge, except for neutrophils which were increased. Independently of diet composition, lysozyme and nitric oxide decreased at 4 and 24 h post infection. Compared to the control, diets supplemented with SA and SP promoted an up-regulation of both pro- and anti-inflammatory cytokines at 4 h after the challenge, while the diets supplemented with SB promoted an up-regulation of pro- and anti-inflammatory cytokines at 24 h after the challenge. (3) Conclusions: Overall, present results suggest that SA and SP provide a fast response to a bacterial challenge in European sea bass juveniles, while SB provides increased survival. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are small, non-coding RNAs that are expressed in a tissue- and temporal-specific manner during development. They have been found to be highly conserved during the evolution of different species. miRNAs regulate the expression of several genes in various organisms, with some regulating the expression of multiple genes with similar or completely unrelated functions. Frequent disease and insect pest infestations severely limit agricultural development. Thus, cultivating resistant crops via miRNA-directed gene regulation in plants, insects, and pathogens is an important aspect of modern breeding practices. To strengthen the application of miRNAs in sustainable agriculture, plant endogenous or exogenous miRNAs have been used for plant breeding. Consequently, the development of biological pesticides based on miRNAs has become an important avenue for future pest control methods. However, selecting the appropriate miRNA according to the desired target traits in the target organism is key to successfully using this technology for pest control. This review summarizes the progress in research on miRNAs in plants and other species involved in regulating plant disease and pest resistance pathways. We also discuss the molecular mechanisms of relevant target genes to provide new ideas for future research on pest and disease resistance and breeding in plants. [ABSTRACT FROM AUTHOR]

Global agricultural production must quadruple by 2050 to fulfil the needs of a growing global population, but climate change exacerbates the difficulty. Cereals are a very important source of food for the world population. Improved cultivars are needed, with better resistance to abiotic stresses like drought, salt, and increasing temperatures, and resilience to biotic stressors like bacterial and fungal infections, and pest infestation. A popular, versatile, and helpful method for functional genomics and crop improvement is genome editing. Rapidly developing genome editing techniques including clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) are very important. This review focuses on how CRISPR/Cas9 genome editing might enhance cereals' agronomic qualities in the face of climate change, providing important insights for future applications. Genome editing efforts should focus on improving characteristics that confer tolerance to conditions exacerbated by climate change (e.g. drought, salt, rising temperatures). Improved water usage efficiency, salt tolerance, and heat stress resilience are all desirable characteristics. Cultivars that are more resilient to insect infestations and a wide range of biotic stressors, such as bacterial and fungal diseases, should be created. Genome editing can precisely target genes linked to disease resistance pathways to strengthen cereals' natural defensive systems. The world population is increasing day by day. Cereals are a good source of energy for this increasing population. Climate changes exert pressure on agriculture and hinder overall production. Genome editing techniques such as CRISPR/Cas have been extensively used to improve crops. In this review, we summarise the different genome editing techniques, their advantages, and disadvantages. This article belongs to the Collection Functional Genomics for Developing Climate Resilient Crops. [ABSTRACT FROM AUTHOR]

Macrophomina phaseolina, the causal agent of charcoal rot, is one of the most destructive soil-borne pathogens that affect the global strawberry industry. Resistant cultivars are critical for ensuring the profitability of strawberry production without the protection historically provided by methyl bromide. Previously, three loci, namely, FaRMp1, FaRMp2, and FaRMp3, associated with quantitative resistance to Macrophomina phaseolina have been identified and validated across diverse populations and environments. Among those, the locus with the largest effect, FaRMp3, was initially detected in crosses with an exotic Fragaria xananassa selection. We introgressed the favorable FaRMp3 allele into elite germplasm in the University of Florida strawberry breeding program already segregating for FaRMp1 and FaRMp2 and confirmed its phenotypic effects across various genetic backgrounds. Subsequently, we developed a high-throughput genotyping assay to facilitate the transfer and selection of FaRMp3 in breeding populations via marker-assisted selection. Given that three quantitative trait loci (QTL) contribute to partial resistance to Macrophomina phaseolina, stacking them within a single genotype presents a potential strategy for enhancing resistance. We screened 564 individuals that segregate for favorable alleles at all three QTL to assess their effects singly and in combination across multiple genetic backgrounds and production seasons. Inoculated field trials revealed that the three QTL cumulatively enhanced resistance levels, and that two-way QTL combinations including FaRMp3 provide increased protection against the pathogen. Pyramiding all three loci achieved the strongest resistance and could provide substantial economic value to the strawberry industry. [ABSTRACT FROM AUTHOR]

Most of the tomato (Solanum lycopersicum) varieties currently used in organic farming were bred for conventional farming, often characterized by high-input use. These varieties do not perform as well in low-input organic systems, generating the need to develop varieties that are adapted to organic management systems. This project focused on improving flavor, disease resistance, and yield, all identified as key traits by organic tomato farmers in the Upper Midwest, USA. Ten advanced tomato breeding lines and two check varieties were developed and evaluated for 16 traits in organic high tunnel systems in 2020 and 2021. The line CSDE-F6.47 averaged 6.32 kg/plant and obtained high flavor intensity and overall flavor scores (3.78 and 3.69 out of 5, respectively). The line JBDE-F5.31 was another outstanding line, with a yield of 5.18 kg/plant, with good flavor intensity (3.32) and overall flavor (2.92) scores. Broad-sense heritability of marketable weight per plant was high (0.91), and the genetic variance was also high, which shows the opportunity to continue to increase the marketable weight in lines with excellent flavor. A significant positive correlation was found between overall flavor and °Brix (0.56), and titratable acidity (0.70), indicating that both measurements can be good predictors of overall flavor. The most promising lines will be further evaluated on-farm to evaluate their potential as releasable varieties. [ABSTRACT FROM AUTHOR]

Wheat is the predominant crop worldwide, contributing approximately 20% of protein and calories to the human diet. However, the yield potential of wheat faces limitations due to pests, diseases, and abiotic stresses. Although conventional breeding has improved desirable traits, the use of modern transgenesis technologies has been limited in wheat in comparison to other crops such as maize and soybean. Recent advances in wheat gene cloning and transformation technology now enable the development of a super wheat consistent with the One Health goals of sustainability, food security, and environmental stewardship. This variety combines traits to enhance pest and disease resistance, elevate grain nutritional value, and improve resilience to climate change. In this review, we explore ways to leverage current technologies to combine and transform useful traits into wheat. We also address the requirements of breeders and legal considerations such as patents and regulatory issues. [ABSTRACT FROM AUTHOR]

Summary: The nuclear factor Y (NF‐Y) transcription factors play important roles in plant development and physiological responses. However, the relationship between NF‐Y, plant hormone and plant stress resistance in tropical crops remains unclear. In this study, we identified MeNF‐YC15 gene in the NF‐Y family that significantly responded to Xanthomonas axonopodis pv. manihotis (Xam) treatment. Using MeNF‐YC15‐silenced and ‐overexpressed cassava plants, we elucidated that MeNF‐YC15 positively regulated disease resistance to cassava bacterial blight (CBB). Notably, we illustrated MeNF‐YC15 downstream genes and revealed the direct genetic relationship between MeNF‐YC15 and 1‐aminocyclopropane‐1‐carboxylic acid (ACC) oxidase (MeACO1)‐ethylene module in disease resistance, as evidenced by the rescued disease susceptibility of MeNF‐YC15 silenced cassava plants with ethylene treatment or overexpressing MeACO1. In addition, the physical interaction between 2C‐type protein phosphatase 1 (MePP2C1) and MeNF‐YC15 inhibited the transcriptional activation of MeACO1 by MeNF‐YC15. In summary, MePP2C1‐MeNF‐YC15 interaction modulates ethylene biosynthesis and cassava disease resistance, providing gene network for cassava genetic improvement. [ABSTRACT FROM AUTHOR]

Grass carp was an important economic fish for freshwater aquaculture. The exploring and utilization of high-quality grass carp germplasm resources were important for ensuring a domestic supply of high-quality aquatic protein. However, natural grass carp populations in China were facing severe threats because of the effects of frequent human activities, water environment damage, overfishing, etc. Against this background, high-quality grass carp germplasm resources were the foundation for the healthy and sustainable development of the grass carp aquaculture industry, so systematic collection, preservation, identification, evaluation, protection, and utilization of them carry great strategic importance. This paper summarizes major research results of grass carp in morphology, cytogenetics, molecular population genetics, etc. It not only introduced genetic improvement techniques such as gynogenesis, hybrid breeding, and polyploid breeding, but also discussed the existing research on the protection measures of grass carp germplasm resources. On this basis, the paper proposed new methods to improve the protection of grass carp germplasm and create improved varieties, which could provide high-quality resources for the sustainable development of the grass carp industry. [ABSTRACT FROM AUTHOR]

Microbial volatile organic compounds (mVOCs) and its potentiality in plant growth and development is still an unexplored area. The in vitro study on bipartite plate showed inhibition of Fusarium oxysporum f.sp lycopersici (FOL) by volatiles of Trichoderma asperellum BHU P1 and Ochrobactrum sp. BHU-PB1 over control. The seed germination and seedling growth was recorded maximum in plant exposed to VOCs of Ochrobactrum sp. in both magenta box (in vitro) and pot (in vivo) experiment. The growth parameters as seed germination, shoot length, root length, fresh weight, dry weight, number of lateral roots and number of leaflets was compared to be higher in microbial volatile metabolites treated plants as compared to control. Disease incidence in T. asperellum and Ochrobactrum sp. volatile treated tomato plants were 43.66% and 41.33%, respectively at 20 days post inoculation (dpi) whereas untreated control showed disease incidence up to 79.16%. GC–MS analysis of volatile metabolite of T. asperellum BHU P1 detected 42 compounds and Ochrobactrum sp. BHU-PB1 detected 50 compounds over PDB and NB control. HPLC analysis of volatile treated tomato leaves showed enhanced concentration of gallic acid, t-chlorogenic acid, rutin, p-caumeric acid, cinnamic acid, ferulic acid, capsacin, salicylic acid, syringic acid and quercetin over control at 0, 48 and 72 h of FOL challenge. Above observations led to the conclusion that tomato roots which perceived the volatiles of Ochrobactrum sp. BHU-PB1 showed better plant growth promotion and enhanced plant defense, revealed by higher phenolic compound production followed by T. asperellum BHU P1 volatile treated plant. [ABSTRACT FROM AUTHOR]

The priority in oilseed rape (Brassica napus L.) research and breeding programs worldwide is to combine different features to develop cultivars tailored to specific applications of this crop. In this study, forms with a modified fatty acid composition of seed oil were successfully combined with a source of resistance to Plasmodiophora brassicae Wor., a harmful protist-causing clubroot. Three HO-type recombinants in F6–F12 generations with oleic acid content of 80.2–82.1% and one HOLL-type F6 inbred mutant recombinant (HOmut × LLmut), with a high oleic acid content (80.9%) and reduced linolenic acid content (2.3%), were crossed with the cultivar Tosca, resistant to several pathotypes of P. brassicae. The work involved genotyping with the use of DNA markers specific for allelic variants of desaturase genes responsible for the synthesis of oleic and linolenic fatty acids, CAPS (FAD2 desaturase, C18:1), and SNaPshot (FAD3 desaturase, C18:3), respectively. Of 350 progenies in the F3 generation, 192 (55%) were selected for further studies. Among them, 80 HO (≥ 72%) lines were identified, 10 of which showed resistance to at least one up to four P. brassicae pathotypes. Thirty lines in the selected progeny contained high oleic acid and less than 5% linolenic acid; eight of them belonged to the HOLL type conferring resistance to at least one pathotype. Two HO lines and two HOLL lines were resistant to four pathotypes. The resulting HO-CR and HOLL-CR inbred lines with altered seed oil fatty acid composition and resistance to P. brassicae represent unique oilseed rape material with the desired combination of valuable traits. [ABSTRACT FROM AUTHOR]

Abstract Cassava (Manihot esculenta Crantz) is a vital carbohydrate source for over 800 million people globally, yet its production in East Africa is severely affected by cassava brown streak disease (CBSD). Genebanks, through ex-situ conservation, play a pivotal role in preserving crop diversity, providing crucial resources for breeding resilient and disease-resistant crops. This study genotyped 234 South American cassava accessions conserved at the CIAT genebank, previously phenotyped for CBSD resistance by an independent group, to perform a genome-wide association analysis (GWAS) to identify genetic variants associated with CBSD resistance. Our GWAS identified 35 single nucleotide polymorphism (SNP) markers distributed across various chromosomes, associated with disease severity or the presence/absence of viral infection. Markers were annotated within or near genes previously identified with functions related to pathogen recognition and immune response activation. Using the SNP candidates, we screened the world’s largest cassava collection for accessions with a higher frequency of favorable genotypes, proposing 35 accessions with potential resistance to CBSD. Our results provide insights into the genetics of CBSD resistance and highlight the importance of genetic resources to equip breeders with the raw materials needed to develop new crop varieties resistant to pests and diseases.

Abstract Soybean, one of the most important oil seed crops known for its high-quality oil and protein content, is widely grown and consumed worldwide. However, the crop is severely affected by various biotic and abiotic factors, of which diseases are by far the most important, resulting in significant yield losses each year. The major diseases affecting soybean production include soybean rust, soybean mosaic virus, anthracnose, charcoal rot, Sclerotinia stem rot (white mold), seedling diseases, sudden death syndrome, frogeye leaf spot, and Stem canker. Development of soybean varieties resistant to these diseases using modern biotechnology techniques is a viable option to increase genetic potential and boost soybean production. This paper, hence, aims to explore the application of functional genomics in improving resistance to various diseases in soybean. Therefore, this paper provides a comprehensive overview of the progress made in improving soybean resistance to major diseases by using the various approaches of modern biotechnological tools such as molecular markers, QTL/gene mapping, omics technology, freely available online databases, genome editing, genetic modification, and marker-assisted breeding. This review also highlights future directions that may be important for genomics-based research programs to improve disease resistance in soybean while increasing production.

Clubroot caused by Plasmodiophora brassicae is an important disease of crucifer crops worldwide. This study aimed to establish an efficient screening method to determine resistant cultivars of Chinese cabbage against P. brassicae. To do this, we investigated the virulence of seven P. brassicae isolates using seedlings of susceptible Chinese cabbage cultivar. The isolates exhibited different virulence in the plants and were divided into three groups based on their virulence. When we explored the disease occurrence in Chinese cabbage seedlings according to photoperiod after inoculation of P. brassicae and incubation temperature, the plants with all-day light showed higher disease severity than seedlings cultivated under 14 hr of light a day. The occurrence of clubroot disease was most severe at 25°C, followed by 20°C and 18°C, but the fresh weight of clubroot of the seedlings cultivated at 20°C was the highest, followed by plants grown at 25°C and 18°C. When the seedlings of two commercial resistant cultivars were inoculated with the mixed spore suspensions of two different pathotype isolates of P. brassicae, disease severity increased as the spore concentration of the susceptible P. brassicae isolate among the two strains increased, suggesting that the clubroot development by different pathotype isolates was independent and not influenced by each other. Taken together, our results provide a faster and more accurate screening methods to determine the resistance of Chinese cabbage against P. brassicae.

Abstract Background DIR (Dirigent) proteins play important roles in the biosynthesis of lignin and lignans and are involved in various processes such as plant growth, development, and stress responses. However, there is less information about VvDIR proteins in grapevine (Vitis vinifera L). Results In this study, we used bioinformatics methods to identify members of the DIR gene family in grapevine and identified 18 VvDIR genes in grapevine. These genes were classified into 5 subfamilies based on phylogenetic analysis. In promoter analysis, various plant hormones, stress, and light-responsive cis-elements were detected. Expression profiling of all genes following Colletotrichum gloeosporioides infection and phytohormones (salicylic acid (SA) and jasmonic acid (JA)) application suggested significant upregulation of 17 and 6 VvDIR genes, respectively. Further, we overexpressed the VvDIR4 gene in Arabidopsis thaliana and grapes for functional analysis. Ectopic expression of VvDIR4 in A. thaliana and transient expression in grapes increased resistance against C. gloeosporioides and C. higginsianum, respectively. Phenotypic observations showed small disease lesions in transgenic plants. Further, the expression patterns of genes having presumed roles in SA and JA signaling pathways were also influenced. Lignin contents were measured before and after C. higginsianum infection; the transgenic A. thaliana lines showed higher lignin content than wild-type, and a significant increase was observed after C. higginsianum infection. Conclusions Based on the findings, we surmise that VvDIR4 is involved in hormonal and lignin synthesis pathways which regulate resistance against anthracnose. Our study provides novel insights into the function of VvDIR genes and new candidate genes for grapevine disease resistance breeding programs.

Abstract Backround In recent years, with the increasing demand for seedless grape varieties that have lower production costs, are disease resistant/tolerant and require less chemical pesticides, the embryo recovery technique has begun to be used more in table grape breeding studies. However, the desired high success rate has not yet been achieved in these studies. Although there are different reasons for this, especially the grape varieties selected for cross-breeding and the timing of transferring the embryos to medium are among the most important reasons. In this study, focusing on these two important factors, the embryos obtained from different hybridization combinations were transferred to agar medium at different weeks for 4 years and the most successful combination and time were determined. In addition, seedless and large berry grape varieties and some seeded varieties that are resistant/tolerant to fungal diseases were selected as parents because they can provide resistance to disease infections in vitro and thus increase the success rate. Results The results obtained from the study showed that the selected variety and combination significantly affected the success rate in embryo rescue. Especially in combinations with the ‘Yalova Seedless’ variety as the female parent, more successful results were obtained compared to combinations of other varieties. When ‘Yalova Seedless’ variety was pollinated with pollen of ‘Red Globe’, ‘Muscat Bailey A’ and ‘Exalta’ varieties, more seedlings were obtained with the help of embryo rescue. The results obtained over four years showed that the best sampling time after pollination was the eighth week and then the seventh week. Conclusions According to the results obtained, it has been shown that the selected varieties and the sampling time significantly affect the success rate in embryo rescue studies. Therefore, higher success rates can be achieved in comprehensive breeding studies in which they will be included as pollinators, especially in different seeded varieties that are resistant to diseases and have larger berry size.

The use of the gene pool of wild relatives for expanding the genetic diversity of common wheat is an important task of breeding programs. However, the practical application of common wheat lines with alien genetic material is constrained by the lack of information on chromosomal rearrangements and the negative impact of the transferred material on agronomically important traits. This research is aimed at studying 14 introgression lines with the T2DL.2DS-2SS translocation and the 5S(5D) substitution from Aegilops speltoides obtained from crossing common wheat varieties (Aurora, Krasnodarskaya 99, Nika Kubani) with the genome-substituted form Avrodes (BBAASS). Hybrid lines with different combinations of T2DL.2DS-2SS and T1BL.1RS translocations and 5S(5D) substitution were characterized by resistance to leaf and yellow rusts, productivity components and technological qualities of grain. The assessment of the varieties’ resistance to rust diseases showed that Krasnodarskaya 99, Nika Kubani and the Aurora variety, which is a carrier of the T1BL.1RS translocation, are highly susceptible to diseases, while the presence of the T2DL.2DS-2SS translocation and the 5S(5D) substitution, both together and separately, provides resistance to fungal pathogens. The analysis of the lines using markers designed for known resistance genes of Ae. speltoides did not reveal the presence of the Lr28, Lr35 and Lr51 genes in the lines. The results suggest that the genetic material of Ae. speltoides transferred to chromosomes 2D and 5D contains new resistance genes. To determine the effect of the T2DL.2DS-2SS translocation and the 5S(5D) substitution on the productivity and technological qualities of grain, the lines were assessed by weight of 1000 grains, grain weight and number of ears per 1 m2, by protein and gluten content, gluten quality and general baking evaluation. A positive effect was determined upon the weight of 1000 grains, protein and gluten content. There were no significant differences in other characteristics. The T2DL.2DS-2SS trans-location and the 5S(5D) substitution did not have a negative effect on the productivity and technological quality of grain, and are of interest for breeding practice.