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Carotenoids are essential for plant and animal nutrition, and are important factors in the variation of pigmentation in fruits, leaves, and flowers. Tomato is a model crop for studying the biology and biotechnology of fleshy fruits, particularly for understanding carotenoid biosynthesis. In commercial tomato cultivars and germplasms, visual phenotyping of the colors of ripe fruits can be done easily. However, subsequent analysis of metabolic profiling is necessary for hypothesizing genetic factors prior to performing time-consuming genetic analysis. We used high performance liquid chromatography (HPLC), employing a C30 reverse-phase column, to efficiently resolve nine carotenoids and isomers of several carotenoids in yellow, orange, and red colored ripe tomatoes. High content of lycopene was detected in red tomatoes. The orange tomatoes contained three dominant carotenoids, namely δ-carotene, β-carotene, and prolycopene. The yellow tomatoes showed low levels of carotenoids compared to red or orange tomatoes. Based on the HPLC profiles, genes responsible for overproducing δ-carotene and prolycopene were described as lycopene ε-cyclase and carotenoid isomerase, respectively. Subsequent genetic analysis using DNA markers for segregating population and germplasms were conducted to confirm the hypothesis. This study establishes the usefulness of metabolic profiling for inferring the genetic determinants of fruit color.

Genetic resistance to plant viruses has been used for at least 80 years to control agricultural losses to viral diseases. To date, hundreds of naturally occurring genes for resistance to plant viruses have been reported from studies of both monocot and dicot crops, their wild relatives, and the plant model, Arabidopsis. The isolation and characterization of a few of these genes in the past decade have resulted in detailed knowledge of some of the molecules that are critical in determining the outcome of plant viral infection. In this chapter, we have catalogued genes for resistance to plant viruses and have summarized current knowledge regarding their identity and inheritance. Insofar as information is available, the genetic context, genomic organization, mechanisms of resistance and agricultural deployment of plant virus resistance genes are also discussed.

Bacterial canker caused by Clavibacter michiganensis ( Cm ) is one of the most economically important vascular diseases causing unilateral leaf wilting, stem canker, a bird’s-eye lesion on fruit, and whole plant wilting in tomato. There is no commercially available cultivar with bacterial canker resistance, and genomics-assisted breeding can accelerate the development of cultivars with enhanced resistance. Solanum lycopersicum “Hawaii 7998” was found to show bacterial canker resistance. A Quantitative trait loci (QTL)-seq was performed to identify the resistance loci using 909 F 2 individuals derived from a cross between S. lycopersicum “E6203” (susceptible) and “Hawaii 7998,” and a genomic region (37.24–41.15 Mb) associated with bacterial canker resistance on chromosome 6 ( Rcm6 ) was found. To dissect the Rcm6 region, 12 markers were developed and several markers were associated with the resistance phenotypes. Among the markers, the Rcm6-9 genotype completely matched with the phenotype in the 47 cultivars. To further validate the Rcm6 as a resistance locus and the Rcm6-9 efficiency, subsequent analysis using F 2 and F 3 progenies was conducted. The progeny individuals with homozygous resistance allele at the Rcm6-9 showed significantly lower disease severity than those possessing homozygous susceptibility alleles. Genomes of five susceptible and two resistant cultivars were analyzed and previously known R-genes were selected to find candidate genes for Rcm6 . Nucleotide-binding leucine-rich repeat, receptor-like kinase, and receptor-like protein were identified to have putative functional mutations and show differential expression upon the Cm infection. The DNA markers and candidate genes will facilitate marker-assisted breeding and provide genetic insight of bacterial canker resistance in tomato.

KEY MESSAGE : Disease resistance against xylem-colonizing pathogenic bacteria in crops. Plant pathogenic bacteria cause destructive diseases in many commercially important crops. Among these bacteria, eight pathogens, Ralstonia solanacearum, Xanthomonas oryzae pv. oryzae, X. campestris pv. campestris, Erwinia amylovora, Pantoea stewartii subsp. stewartii, Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. actinidiae, and Xylella fastidiosa, infect their host plants through different infection sites and paths and eventually colonize the xylem tissues of their host plants, resulting in wilting symptoms by blocking water flow or necrosis of xylem tissues. Noticeably, only a relatively small number of resistant cultivars in major crops against these vascular bacterial pathogens except X. oryzae pv. oryzae have been found or generated so far, although these pathogens threaten productivity of major crops. In this review, we summarize the lifestyles of major xylem-colonizing bacterial pathogens and then discuss the progress of current research on disease resistance controlled by qualitative disease resistance genes or quantitative trait loci against them. Finally, we propose infection processes of xylem-colonizing bacterial pathogens as one of possible reasons for why so few qualitative disease resistance genes against these pathogens have been developed or identified so far in crops.

Tomato yellow leaf curl virus (TYLCV) is a disease that is damaging to tomato production worldwide. Resistance to TYLCV has been intensively investigated, and single resistance genes such as Ty-1 have been widely deployed in breeding programs. However, resistance-breaking incidences are frequently reported, and achieving durable resistance against TYLCV in the field is important. In this study, gene-specific markers for Ty-2 and ty-5, and closely-linked markers for Ty-4 were developed and applied to distinguish TYLCV resistance in various tomato genotypes. Quantitative infectivity assays using both natural infection in the field and artificial inoculation utilizing infectious TYLCV clones in a growth chamber were optimized and performed to investigate the individual and cumulative levels of resistance. We confirmed that Ty-2 could also be an effective source of resistance for TYLCV control, together with Ty-1. Improvement of resistance as a result of gene-pyramiding was speculated, and breeding lines including both Ty-1 and Ty-2 showed the strongest resistance in both field and artificial infections.

Cannabis sativa L. cv. ‘Cheungsam’ is an industrial hemp plant of Republic of Korea origin, primarily cultivated for fiber and seed production. In vitro seed germination and tissue culture are valuable tools for developing various biotechnological techniques. In the present study, we aimed to develop a tissue culture process for hemp plants using Cheungsam as a model plant and examine the secondary metabolites produced from its callus. We also developed a method to prepare pathogen-free seedlings from field-derived seeds using hydrogen peroxide (H2O2) solution as a liquid germination medium. Treating seedlings with removed seed coat in 3% H2O2 significantly reduced the contamination rate. Callus formation and de novo organogenesis of shoots and roots from callus were successfully achieved using cotyledon and leaf tissues prepared from the pathogen-free seedlings. The most effective in vitro regeneration results were obtained using the Murashige and Skoog (MS) medium supplemented with certain targeted growth regulators. An optimal combination of 0.5 mg/L thidiazuron (TDZ) and 1.0 mg/L 1-naphthalene acetic acid proved highly effective for callus induction. The addition of 0.5 mg/L TDZ in the MS medium significantly stimulated shoot proliferation, while robust root development was best supported by MS medium supplemented with 2.5 mg/L indole-3-butyric acid for both cotyledon and leaf explants. Finally, gas chromatography–mass spectrometry (GC–MS) analysis of ethanol extract from Cheungsam leaf callus revealed the presence of different secondary metabolites, including 9-octadecenamide, methyl salicylate, dodecane, tetradecane, and phenol, 2,4-bis-(1,1-dimethylethyl). This study provides a comprehensive de novo regeneration protocol for Cheungsam plants and insight into the secondary metabolite profiles of its callus.

To evaluate the involvement of translation initiation factors eIF4E and eIFiso4E in Chilli veinai mottle virus (ChiVMV) infection in pepper, we conducted a genetic analysis using a segregating population derived from a cross between Capsicum annuum 'Dempsey' containing an eIF4E mutation (pvr1²) and C. annuum 'Perennial' containing an eIFiso4E mutation (pvr6). C. annuum 'Dempsey' was susceptible and C. annuum 'Perennial' was resistant to ChiVMV. All F₁ plants showed resistance, and F₂ individuals segregated in a resistant-susceptible ratio of 166:21, indicating that many resistance loci were involved. Seventy-five F₂ and 329 F₃ plants of 17 families were genotyped with pvr1² and pvr6 allele-specific markers, and the genotype data were compared with observed resistance to viral infection. All plants containing homozygous genotypes of both pvr1² and pvr6 were resistant to ChiVMV, demonstrating that simultaneous mutations in eIF4E and eIFiso4E confer resistance to ChiVMV in pepper. Genotype analysis of F₂ plants revealed that all plants containing homozygous genotypes of both pvr1² and pvr6 showed resistance to ChiVMV. In protein-protein interaction experiments, ChiVMV viral genome-linked protein (VPg) interacted with both eIF4E and eIFiso4E. Silencing of eIF4E and eIFiso4E in the VIGS experiment showed reduction in ChiVMV accumulation. These results demonstrated that ChiVMV can use both eIF4E and eIFiso4E for replication, making simultaneous mutations in eIF4E and eIFiso4E necessary to prevent ChiVMV infection in pepper.

Doil Choi and colleagues report the genome sequence of the hot pepper, Capsicum annuum , as well as the resequencing of two cultivated peppers and a wild species, Capsicum chinense . Comparative genomic analysis across Solanaceae provides insights into genome expansion, pungency, ripening and disease resistance in hot peppers. Hot pepper ( Capsicum annuum ), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense . The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.

Naturally existing variation in the eukaryotic translation initiation factor 4E (eIF4E) homolog encoded at the pvr1 locus in Capsicum results in recessively inherited resistance against several potyviruses. Previously reported data indicate that the physical interaction between Capsicum-eIF4E and the viral genome-linked protein (VPg) is required for the viral infection in the Capsicum-Tobacco etch virus (TEV) pathosystem. In this study, the potential structural role(s) of natural variation in the eIF4E protein encoded by recessive resistance alleles and their biological consequences have been assessed. Using high-resolution three-dimensional structural models based on the available crystallographic structures of eIF4E, we show that the amino acid substitution G107R, found in many recessive plant virus resistance genes encoding eIF4E, is predicted to result in a substantial modification in the protein binding pocket. The G107R change was shown to not only be responsible for the interruption of VPg binding in planta but also for the loss of cap binding ability in vitro, the principal function of eIF4E in the host. Overexpression of the Capsicum-eIF4E protein containing the G107R amino acid substitution in Solanum lycopersicum indicated that this polymorphism alone is sufficient for the acquisition of resistance against several TEV strains.

Diseases caused by members of the Potyviridae family currently threaten pepper crops (Capsicum annuum L.) worldwide. A series of monogenic recessive resistance genes that control potyvirus resistance at the pvr1 locus in Capsicum species are widely known and used in pepper breeding programs, each allele with a differential resistance spectrum affecting a distinct range of viral strains across three viruses, Tobacco etch virus (TEV), Pepper mottle virus and Potato virus Y. In this study, we systematically analyzed the resistant spectra, and the level of the resistance each allele confers using a set of pepper genotypes homozygous or heterozygous for the following alleles; Pvr1 super(+), pvr1, pvr1 super(1) and pvr1 super(2). The resistance alleles at the pvr1 locus show recessive inheritance when combined with a susceptible allele in F1 progenies. However, our results show that resistance in this system is, in fact, not always fully recessive and establish a hierarchy of allelic interactions We identified the resistance phenotype in F sub(1) progenies generated by combining a complete resistant allele with an incomplete resistance allele against TEV strains implying that the resistance alleles at the pvr1 shows dominant inheritance when combined with an incomplete resistance allele. Resistance alleles against TEV-HAT, pvr1 and pvr1 super(2), show dominance inheritance when each is combined with pvr1 super(1). The resistance allele, pvr1, shows dominance inheritance when combined with pvr1 super(2) against TEV-N. These results clarify the allelic relationship between resistance alleles at the pvr1 locus displaying different resistance spectra, and will assist breeders to select the preferred combinations of the resistance alleles to obtain durable resistance against multiple potyviral strains.