Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum ‘Takanotsume’

日本を代表するトウガラシ「鷹の爪」の全ゲノムを解読 --多様なトウガラシを生み出すための基盤に--. 京都大学プレスリリース. 2023-01-12.Here, we report the genome sequence of a popular Japanese chili pepper landrace, Capsicum annuum ‘Takanotsume’. We used long-read sequencing and optical mapping, together with the genetic mapping technique, to obtain the chromosome-scale genome assembly of ‘Takanotsume’. The assembly consists of 12 pseudomolecules, which corresponds to the basic chromosome number of C. annuum, and is 3, 058.5 Mb in size, spanning 97.0% of the estimated genome size. A total of 34, 324 high-confidence genes were predicted in the genome, and 83.4% of the genome assembly was occupied by repetitive sequences. Comparative genomics of linked-read sequencing-derived de novo genome assemblies of two Capsicum chinense lines and whole-genome resequencing analysis of Capsicum species revealed not only nucleotide sequence variations but also genome structure variations (i.e., chromosomal rearrangements and transposon-insertion polymorphisms) between ‘Takanotsume’ and its relatives. Overall, the genome sequence data generated in this study will accelerate the pan-genomics and breeding of Capsicum, and facilitate the dissection of genetic mechanisms underlying the agronomically important traits of ‘Takanotsume’

Indicator Candidate Traits for Autonomous Fruit Set Ability Under High Temperatures in Capsicum

“Autonomous fruit set” refers to self-pollination and fruit set without pollen vectors such as vibration or insects. Autonomous fruit set under high-temperature stress is an important breeding goal as climate change can reduce fruit yields in Capsicum. We screened Capsicum cultivars for autonomous fruit set ability in a greenhouse environment and investigated pollen germination, viability, pollen grains number, chlorophyll fluorescence (Fv/Fm), style length, anther cone length, and anthesis stage under high temperatures in order to identify indicator traits for screening more genotypes with autonomous fruit set ability. The fruit set of the ‘Takanotsume’ (57.7 ± 20.6%) and ‘Goshiki Kyokko’ (52.2 ± 14.2%) cultivars (both C. annuum) were higher than those of other cultivars. Correlation analysis showed that pollen germination had the highest correlation with fruit set in C. annuum cultivars (r = 0.63). These results indicate that ‘Takanotsume’ and ‘Goshiki Kyokko’ are useful cultivars for novel breeding programs focusing on autonomous fruit sets under high temperatures, and pollen germination in C. annuum was a convincing candidate for an indicator trait of autonomous fruit set ability under high temperatures

SIMULTANEOUS EXTRACTION AND RAPID HPLC BASED QUANTIFICATION OF CROCIN AND SAFRANAL IN SAFFRON (CROCUS SATIVUS L.)

Objective: Saffron (Crocus sativus L.) is one of the most valuable crops with high medicinal values used in many diseases. The aim of the study was to establish the reliability and rapid HPLC method for analysis of crocin and safranal concentration present in stigmata of saffron in the market as well as field grown samples.Methods: Field grown and market stigmata of saffron were used for extraction of crocin and safranal. The linear dynamic ranges were established after validating the robustness of critical method parameters. The Agilent1260-Infinity Quaternary LC system was used for the preparation of calibration standards and quantification of crocin and safranal in C. sativus stigmata.Results: A good linearity was achieved in the range of 10-30 µg for each compound with the determination coefficient (R2). The calibration curves revealed linear regression (r. 0.997) for this rapid HPLC method and limit of quantifications (LOQs) were achieved in the range of 3.4 µg/ml for crocin and 10.2 µg/ml for safranal. The limit of detection (LODs) for all standards was ≤4.2 µg/ml. The range of crocin content (10.43-16.32 mg/g) and safranal (5.19-5.21 mg/g) was estimated in saffron samples.Conclusion: This method may serve the purpose of accurate quantification of crocin and safranal present in the stigmata of the plant in a quick time period.Keywords: Saffron, Crocin, Safranal, Extraction, Quantification, HPL

Fine mapping and identification of candidate genes for the sy-2 locus in a temperature-sensitive chili pepper (Capsicum chinense)

Key message The sy-2 temperature-sensitive gene from Capsicum chinense was fine mapped to a 138.8-kb region at the distal portion of pepper chromosome 1. Based on expression analyses, two putative F-box genes were identified as sy-2 candidate genes. Abstract Seychelles-2 (sy-2) is a temperature-sensitive natural mutant of Capsicum chinense, which exhibits an abnormal leaf phenotype when grown at temperatures below 24 °C. We previously showed that the sy-2 phenotype is controlled by a single recessive gene, sy-2, located on pepper chromosome 1. In this study, a high-resolution genetic and physical map for the sy-2 locus was constructed using two individual F2 mapping populations derived from a cross between C. chinense mutant sy-2 and wild-type No. 3341. The sy-2 gene was fine mapped to a 138.8-kb region between markers SNP 5-5 and SNP 3-8 at the distal portion of chromosome 1, based on comparative genomic analysis and genomic information from pepper. The sy-2 target region was predicted to contain 27 genes. Expression analysis of these predicted genes showed a differential expression pattern for ORF10 and ORF20 between mutant and wild-type plants; with both having significantly lower expression in sy-2 than in wild-type plants. In addition, the coding sequences of both ORF10 and ORF20 contained single nucleotide polymorphisms (SNPs) causing amino acid changes, which may have important functional consequences. ORF10 and ORF20 are predicted to encode F-box proteins, which are components of the SCF complex. Based on the differential expression pattern and the presence of nonsynonymous SNPs, we suggest that these two putative F-box genes are most likely responsible for the temperature-sensitive phenotypes in pepper. Further investigation of these genes may enable a better understanding of the molecular mechanisms of low temperature sensitivity in plants.OAIID:RECH_ACHV_DSTSH_NO:T201625254RECH_ACHV_FG:RR00200001ADJUST_YN:EMP_ID:A076900CITE_RATE:3.9FILENAME:TAG(2016) Fine mapping and identification of candidate genes for sy2.pdfDEPT_NM:식물생산과학부EMAIL:[email protected]_YN:YFILEURL:https://srnd.snu.ac.kr/eXrepEIR/fws/file/c773c8d3-fc79-496f-af60-fa1b9b2e214e/linkCONFIRM:

Differential Encoding of Factors Influencing Predicted Reward Value in Monkey Rostral Anterior Cingulate Cortex

Background: The value of a predicted reward can be estimated based on the conjunction of both the intrinsic reward value and the length of time to obtain it. The question we addressed is how the two aspects, reward size and proximity to reward, influence the responses of neurons in rostral anterior cingulate cortex (rACC), a brain region thought to play an important role in reward processing. Methods and Findings: We recorded from single neurons while two monkeys performed a multi-trial reward schedule task. The monkeys performed 1–4 sequential color discrimination trials to obtain a reward of 1–3 liquid drops. There were two task conditions, a valid cue condition, where the number of trials and reward amount were associated with visual cues, and a random cue condition, where the cue was picked from the cue set at random. In the valid cue condition, the neuronal firing is strongly modulated by the predicted reward proximity during the trials. Information about the predicted reward amount is almost absent at those times. In substantial subpopulations, the neuronal responses decreased or increased gradually through schedule progress to the predicted outcome. These two gradually modulating signals could be used to calculate the effect of time on the perception of reward value. In the random cue condition, little information about the reward proximity or reward amount is encoded during the course of the trial before reward delivery, but when the reward is actually delivered the responses reflect both the reward proximity and reward amount

Effects of Growth Phase and Ultraviolet-B Pretreatment in Perilla Leaves on the Two-Spotted Spider Mite

Perilla, Perilla frutescens (L.) Britton var. crispa (Thunb.) H. Deane, is traditionally cultivated as an edible/medicinal crop in East Asia. Its essential oil contains many bioactive compounds that are expected to have high pharmacological functionality, as well as antimicrobial and insecticidal activity. Spider mites are a major pest group for perilla cultivation. The two-spotted spider mite, Tetranychus urticae Koch, possesses divergent detoxification enzymes and has developed resistance against most acaricides. The essential oil content of perilla halves from the pre-flowering phase to the flowering phase, and ultraviolet (UV)-B radiation generally increases defense compounds. To clarify the effects of this change in essential oil content and the effects of UV-B pretreatment, we investigated the developmental success and egg production of T. urticae on leaves from the preflowering and flowering phases cultivated with and without nighttime UV-B irradiation. Both the parameters significantly increased on leaves from the flowering phase in comparison with that from the preflowering phase, suggesting that constitutively produced essential oil provided protection against mite pests in a growth phase-specific manner. The defense system also extended the developmental period of mites on red perilla leaves, but not on green perilla leaves, in preflowering phase. Although egg production was lower on red perilla leaves pretreated with UV-B, no negative effects were caused on the developmental success and duration on red and green perilla and the egg production on green perilla by UV-B pretreatment. Our findings reveal a significant impact of investment allocation of perilla plants and a small contribution of UV-B irradiation to the plant defense system

Endogenous post-transcriptional gene silencing of flavone synthase resulting in high accumulation of anthocyanins in black dahlia cultivars.

Black color in flowers is a highly attractive trait in the floricultural industry, but its underlying mechanisms are largely unknown. This study was performed to identify the bases of the high accumulation of anthocyanidins in black cultivars and to determine whether the high accumulation of total anthocyanidins alone leads to the black appearance. Our approach was to compare black dahlia (Dahlia variabilis) cultivars with purple cultivars and a purple flowering mutant of a black cultivar, using pigment and molecular analyses. Black cultivars characteristically exhibited low lightness, high petal accumulation of cyanidin and total anthocyanidins without flavones, and marked suppression of flavone synthase (DvFNS) expression. A comparative study using black and purple cultivars revealed that neither the absence of flavones nor high accumulation of total anthocyanidins is solely sufficient for black appearance, but that cyanidin content in petals is also an important factor in the phenotype. A study comparing the black cultivar 'Kokucho' and its purple mutant showed that suppression of DvFNS abolishes the competition between anthocyanidin and flavone synthesis and leads to accumulation of cyanidin and total anthocyanidins that produce a black appearance. Surprisingly, in black cultivars the suppression of DvFNS occurred in a post-transcriptional manner, as determined by small RNA mapping

A basic helix-loop-helix transcription factor DvIVS determines flower color intensity in cyanic dahlia cultivars.

The study was aimed to identify the factors that regulate the intensity of flower color in cyanic dahlia (Dahlia variabilis), using fifteen cultivars with different color intensities in their petals. The cultivars were classified into three groups based on their flavonoid composition: ivory white cultivars with flavones; purple and pink cultivars with flavones and anthocyanins; and red cultivars with flavones, anthocyanins, and chalcones. Among the purple, pink, and ivory white cultivars, an inverse relationship was detected between lightness, which was used as an indicator for color intensity and anthocyanin content. A positive correlation was detected between anthocyanin contents and the expression of some structural genes in the anthocyanin synthesis pathway that are regulated by DvIVS, a basic helix-loop-helix transcription factor. A positive correlation between anthocyanin content and expression of DvIVS was also found. The promoter region of DvIVS was classified into three types, with cultivars carrying Type 1 promoter exhibited deep coloring, those carrying Type 2 and/or Type 3 exhibited pale coloring, and those carrying Type 1 and Type 2 and/or Type 3 exhibited medium coloring. The transcripts of the genes from these promoters encoded full-length predicted proteins. These results suggested that the genotype of the promoter region in DvIVS is one of the key factors determining the flower color intensity

Petal Color Is Associated with Leaf Flavonoid Accumulation in a Labile Bicolor Flowering Dahlia (Dahlia variabilis) ‘Yuino’

Bicolor flowering dahlias generally produce inflorescences with bicolor petals characterized by a colored basal part and a white tip; however, they frequently produce single-colored petals. This petal color lability prevents uniform production of cut or pot flowers of bicolor dahlias and reduces the economic value of bicolor cultivars. In this study, to reveal the underlying mechanism and control color lability, the pattern of occurrence of single-colored petals was characterized in a red–white bicolor flowering cultivar ‘Yuino’. ‘Yuino’ produced inflorescences with bicolor petals, red petals, and both red and bicolor petals. Red petals occurred almost always at the outer whorls or sectorally in a mixed inflorescence, similar to a chimera or a lateral mutant. The occurrence of red petals was higher in field experiments during May to December than in greenhouse experiments during October to next July. We identified the “R-line” plant, which produced red petals with high frequency during the winter to spring cultivation; this characteristic to produce red petals with high frequency was retained through vegetative propagation. There were strong relationships between inflorescence color and leaf phenotype; red petal-producing plants accumulated flavonoids in leaves, whereas only bicolor petal-producing plants tended not to accumulate flavonoid in leaves. This suggests that petal color of ‘Yuino’ is associated with flavonoid synthetic potential in shoot. Therefore, a phenotypic difference is observed not only in petal colors but also at the whole plant level

Comparative Analysis of Chrysanthemum Stunt Viroid Accumulation and Movement in Two Chrysanthemum (Chrysanthemum morifolium) Cultivars with Differential Susceptibility to the Viroid Infection

Chrysanthemum stunt viroid (CSVd) was inoculated into two chrysanthemum (Chrysanthemum morifolium) cultivars, the CSVd-susceptible cultivar Piato and the CSVd-resistant cultivar Mari Kazaguruma. For CSVd inoculation, grafting and Agrobacterium-mediated inoculation were used. In grafting experiments, CSVd was detectable in Mari Kazaguruma after grafting onto infected Piato, but after removal of infected rootstocks, CSVd could not be detected in the uppermost leaves. In agroinfection experiments, CSVd systemic infection was observed in Piato but not in Mari Kazaguruma. However, agro-inoculated leaves of Mari Kazaguruma accumulated circular CSVd RNA to levels equivalent to those in Piato at 7 days post-inoculation. In situ detection of CSVd in inoculated leaves revealed that CSVd was absent in phloem of Mari Kazaguruma, while CSVd strongly localized to this site in Piato. We hypothesize that CSVd resistance in Mari Kazaguruma relates not to CSVd replication but to CSVd movement in leaves