Exploring horticultural traits and disease resistance in Capsicum baccatum through segmental introgression lines.

KEY MESSAGE: Segmental introgression and advanced backcross lines were developed and validated as important tools for improving agronomically important traits in pepper, offering improved sensitivity in detecting quantitative trait loci for breeding. Segmental introgression lines (SILs) and advanced backcross lines (ABs) can accelerate genetics and genomics research and breeding in crop plants. This study presents the development of a complete collection of SILs and ABs in pepper using Capsicum annuum cv. 'CM334' as the recipient parent and Capsicum baccatum 'PBC81', which displays various agronomically important traits including powdery mildew and anthracnose resistance, as donor parent. Using embryo rescue to overcome abortion in interspecific crosses, and marker-assisted selection with genotyping-in-thousands by sequencing (GT-seq) to develop SILs and ABs containing different segments of the C. baccatum genome, we obtained 63 SILs and 44 ABs, covering 94.8% of the C. baccatum genome. We characterized them for traits including powdery mildew resistance, anthracnose resistance, anthocyanin accumulation, trichome density, plant architecture, and fruit morphology. We validated previously known loci for these traits and discovered new sources of variation and quantitative trait loci (QTLs). A total of 15 QTLs were identified, including four for anthracnose resistance with three novel loci, seven for plant architecture, and four for fruit morphology. This is the first complete collection of pepper SILs and ABs validated for agronomic traits and will enhance QTL detection and serve as valuable breeding resources. Further, these SILs and ABs will be useful for comparative genomics and to better understand the genetic mechanisms underlying important agronomic traits in pepper, ultimately leading to improved crop productivity and sustainability.

Fuzzy analytic hierarchy process-based risk priority number for risk assessments of commissioning process of a ring gantry LINAC.

PURPOSE: We propose a fuzzy analytic hierarchy process (AHP)-based risk priority number (RPN) method in failure modes and effects analysis (FMEA) to overcome the shortcomings of traditional RPN-based FMEA. Our research group has previously published the FMEA to mitigate the failure modes (FMs) for the commissioning process of a ring gantry LINAC. However, inter-relationships among FMs were observed in high ranked FMs due to a heavy reliance on imaging system. METHODS: Fuzzy AHP was applied to determine relative weights of risk impacts based on inter-relationships among FMs. Since the time sequence dependency is a major factor for risk factors, a hierarchical structure of AHP was used to reflect the directional impacts such as causal influence and feedback loop. Two fuzzy weighted RPNs, called (RPNW and FRPNW , were calculated depending on the input values of severity (S), occurrence (O), and probability of not being detected (D) from the evaluators. The RPNW used numerical values, whereas the fuzzy values were used for FRPNW . Both RPNs were calculated by multiplying the weighted O, S, and D using the fuzzy AHP method. RESULTS: The differences between the two fuzzy RPN rankings are due to inherent fuzzy uncertainty and deviations in O, S, and D values submitted by the evaluators. Considering all results of traditional and fuzzy-based FMEA, the two most highly ranked FMs were identified: errors in determining the non-isocentric SSD and SSD from MV images because of the unique features of the ring gantry LINAC. CONCLUSION: This study has demonstrated the feasibility of the use of a fuzzy AHP-based RPN to perform comprehensive analysis and prioritization of FMs. The risk analysis using fuzzy AHP can be improved and/or refined based on the department's specific workflow and clinical preferences taking various priority weighting approaches into account.

A major QTL and candidate genes for capsaicinoid biosynthesis in the pericarp of Capsicum chinense revealed using QTL-seq and RNA-seq.

KEY MESSAGE: A major QTL and candidate genes controlling capsaicinoid content in the pericarp were identified by QTL-seq and RNA-seq in Capsicum chinense. Capsaicinoid biosynthesis was previously thought to be restricted to the placental tissue; however, the recent discovery of their biosynthesis in the pericarp provides new opportunities to increase the capsaicinoid content in pepper fruits. Currently, the genetic mechanisms regulating capsaicinoid biosynthesis in the pericarp remain unknown. Here, we performed quantitative trait loci (QTL) mapping and RNA sequencing (RNA-seq) to reveal the genes controlling capsaicinoid biosynthesis in the pericarp. A whole-genome sequencing-based QTL-seq strategy was employed, identifying a major QTL on chromosome 6. To validate the QTL on chromosome 6, we performed traditional QTL mapping using the same population in QTL-seq with an additional biparental population. A total of 15 QTLs for capsaicinoid content distributed on chromosomes 3, 6, and 11 were newly identified. Among these QTLs, the genetic loci on the lower arm of chromosome 6 were commonly detected in the two mapping populations, corresponding to the location of the major QTL detected using whole-genome sequencing-based QTL-seq. Our RNA-seq analysis identified candidate genes within the common QTL that were differentially expressed in the pungent and non-pungent pericarp tissues. Our results are expected to contribute to the elucidation of the regulation of capsaicinoid biosynthesis. We also demonstrated that a combination of QTL mapping and RNA-seq is helpful for refining the candidate genes of a complicated trait of interest.

A MYB transcription factor is a candidate to control pungency in Capsicum annuum.

KEY MESSAGE: Identification of a novel pungency-controlling gene Pun3, which acts as a master regulator of capsaicinoid biosynthetic genes in Capsicum annuum. Capsaicinoid is a unique compound that gives hot peppers (Capsicum spp.) their spicy taste. The Pun1 and Pun2 loci are known to control pungency in Capsicum species. Whereas Pun1 encodes an acyltransferase, the identity of Pun2 is currently unknown. Here, we used recombinant inbred lines and F2 plants derived from a cross between the non-pungent C. annuum accession 'YCM334' and the pungent C. annuum cultivar 'Tean' to identify a novel non-pungency locus. Inheritance studies showed that non-pungency in C. annuum 'YCM334' is controlled by a single recessive gene, which we named Pun3. Using a high-density SNP map derived from genotyping-by-sequencing, Pun3 was mapped to chromosome 7. By comparing physical information about the Pun3 region in the C. annuum 'Zunla-1' and C. chinense 'PI159236' reference genomes, we identified candidate genes in this target region. One cDNA sequence from 'PI159236' was homologous to an unannotated gene in 'Zunla-1.' This sequence was also homologous to CaMYB31, which is expressed only in 'Tean' and harbors one stop codon in the non-pungent accession 'YCM334.' RNA-Seq analysis showed that major structural genes in the capsaicinoid biosynthetic pathway were significantly downregulated in 'YCM334' compared to pungent pepper. Therefore, CaMYB31 is a candidate gene for Pun3, which may act as a master regulator of capsaicinoid biosynthetic genes in pepper.

Feasibility of image-guided radiotherapy and concurrent chemotherapy for locally advanced nonsmall cell lung cancer.

A retrospective review of 32 patients with stage III nonsmall cell lung cancer who underwent chemoradiation with image-guided radiotherapy (IGRT) was recorded. Acute grade 3-4 hematologic and esophageal toxicities developed in 6 and 13 patients respectively. At a median follow-up of 14.5 months, only one patient developed grade 3 pneumonitis. The median survival was estimated to be 17 months. Five patients (15%) developed loco-regional recurrences, and 17 patients (53%) distant metastases. Grade 3-4 toxicities remained significant during chemoradiation with IGRT. However, the reduced rate of severe pneumonitis despite a high tumor dose is encouraging and needs to be investigated in future prospective studies.

Feasibility of intensity-modulated and image-guided radiotherapy for locally advanced esophageal cancer.

BACKGROUND: In this study the feasibility of intensity-modulated radiotherapy (IMRT) and tomotherapy-based image-guided radiotherapy (IGRT) for locally advanced esophageal cancer was assessed. METHODS: A retrospective study of ten patients with locally advanced esophageal cancer who underwent concurrent chemotherapy with IMRT (1) and IGRT (9) was conducted. The gross tumor volume was treated to a median dose of 70 Gy (62.4-75 Gy). RESULTS: At a median follow-up of 14 months (1-39 months), three patients developed local failures, six patients developed distant metastases, and complications occurred in two patients (1 tracheoesophageal fistula, 1 esophageal stricture requiring repeated dilatations). No patients developed grade 3-4 pneumonitis or cardiac complications. CONCLUSIONS: IMRT and IGRT may be effective for the treatment of locally advanced esophageal cancer with acceptable complications.

Feasibility of image-guided radiotherapy based on helical tomotherapy to reduce contralateral parotid dose in head and neck cancer.

BACKGROUND: To evaluate the feasibility of image-guided radiotherapy based on helical Tomotherapy to spare the contralateral parotid gland in head and neck cancer patients with unilateral or no neck node metastases. METHODS: A retrospective review of 52 patients undergoing radiotherapy for head and neck cancers with image guidance based on daily megavoltage CT imaging with helical tomotherapy was performed. RESULTS: Mean contralateral parotid dose and the volume of the contralateral parotid receiving 40 Gy or more were compared between radiotherapy plans with significant constraint (SC) of less than 20 Gy on parotid dose (23 patients) and the conventional constraint (CC) of 26 Gy (29 patients). All patients had PTV coverage of at least 95% to the contralateral elective neck nodes. Mean contralateral parotid dose was, respectively, 14.1 Gy and 24.7 Gy for the SC and CC plans (p < 0.0001). The volume of contralateral parotid receiving 40 Gy or more was respectively 5.3% and 18.2% (p < 0.0001) CONCLUSION: Tomotherapy for head and neck cancer minimized radiotherapy dose to the contralateral parotid gland in patients undergoing elective node irradiation without sacrificing target coverage.

Effectiveness of prophylactic retropharyngeal lymph node irradiation in patients with locally advanced head and neck cancer.

BACKGROUND: The aim of the study is to assess the effectiveness of intensity-modulated radiotherapy (IMRT) or image-guided radiotherapy (IGRT) for the prevention of retropharyngeal nodal recurrences in locally advanced head and neck cancer. METHODS: A retrospective review of 76 patients with head and neck cancer undergoing concurrent chemoradiation or postoperative radiotherapy with IMRT or IGRT who were at risk for retropharyngeal nodal recurrences because of anatomic site (hypopharynx, nasopharynx, oropharynx) and/or the presence of nodal metastases was undertaken.The prevalence of retropharyngeal nodal recurrences was assessed on follow-up positron emission tomography (PET)-CT scans. RESULTS: At a median follow-up of 22 months (4-53 months), no patient developed retropharyngeal nodal recurrences. CONCLUSION: Prophylactic irradiation of retropharyngeal lymph nodes with IMRT or IGRT provides effective regional control for individuals at risk for recurrence in these nodes.

[4-(2-tert-But-oxy-2-oxoeth-oxy)naph-thalen-1-yl]diphenyl-sulfonium trifluoro-methane-sulfonate.

In the cation of the title salt, C(28)H(27)O(3)S(+)·CF(3)O(3)S(-), the dihedral angle between the naphthalene ring system and the -C(=O)-O- plane is 80.39 (9)°. The three methyl groups of the tert-butyl group are each disordered over two orientations with an occupancy ratio of 0.712 (18):0.288 (18).

5,5'-[1,4-Phenyl-enebis(methyl-enesulfanedi-yl)]bis-[1,3,4-thia-diazol-2(3H)-one] dimethyl sulfoxide disolvate.

The asymmetric unit of the title compound, C(12)H(10)N(4)O(2)S(4)·2C(2)H(6)OS, contains one half of the p-xylene mol-ecule and one dimethyl sulfoxide mol-ecule. The p-xylene mol-ecule is located about a crystallographic inversion centre. In the mol-ecule, the thia-diazole and benzene rings are almost perpendicular to one another, with a dihedral angle of 88.95 (6)°. In the crystal, an N-H⋯O hydrogen bond is observed between the two components. The dimethyl sulfoxide mol-ecule is disordered over two orientations with an occupancy ratio of 0.879 (1):0.121 (1).

N-(5-Sulfanyl-idene-4,5-dihydro-1,3,4-thia-diazol-2-yl)acetamide dimethyl sulfoxide disolvate.

In the title compound, C(4)H(5)N(3)OS(2)·2C(2)H(6)OS, the five-membered heterocyclic ring and the N-(C=O)-C plane of the acetamide group are essentially co-planar, with a dihedral angle of 1.25 (3)°. Inter-molecular N-H⋯O hydrogen bonds between the acetamide compound and the dimethyl sulfoxide mol-ecules stabilize the crystal structure. The two dimethyl sulfoxide mol-ecules are each disordered over two positions with occupancy ratios of 0.605 (2):0.395 (2) and 0.8629 (18):0.1371 (18).

5-Amino-1,3,4-thia-diazol-2(3H)-one.

The asymmetric unit of the title compound, C(2)H(3)N(3)OS, contains three independent mol-ecules which are essentially planar, with r.m.s. deviations of 0.011 (2)-0.027 (2) Šfrom the mean plane defined by the seven non-H atoms. In the crystal, N-H⋯N and N-H⋯O hydrogen bonds link the mol-ecules into a sheet parallel to the (111) plane.

5-({3-[(5-Amino-1,3,4-thia-diazol-2-yl)sulfanylmeth-yl]benz-yl}sulfan-yl)-1,3,4-thia-diazol-2-amine.

In the title compound, C(12)H(12)N(6)S(4), the two terminal thia-diazole rings are twisted with respect to the central benzene ring, making dihedral angles of 54.28 (4) and 76.56 (3)°. The dihedral angle between the two thia-diazole rings is 27.77 (4)°. Inter-molecular N-H⋯N hydrogen bonds stabilize the crystal packing, linking the mol-ecules into a tape along the b axis.

5-Eth-oxy-1,3,4-thia-diazole-2(3H)-thione.

In the title compound, C(4)H(6)N(2)OS(2), the dihedral angle between the five-membered heterocyclic ring and the plane of the eth-oxy group is 4.9 (2)°. The 1,3,4-thiadiazole-2-thione unit is planar, with an r.m.s. deviation of 0.011 Šfrom the corresponding squares plane defined by the seven constituent atoms. In the crystal, pairs of N-H⋯S hydrogen bonds link the mol-ecules into inversion dimers.

Genetic mapping revealed that the Pun2 gene in Capsicum chacoense encodes a putative aminotransferase.

Several genes regulating capsaicinoid biosynthesis including Pun1 (also known as CS), Pun3, pAMT, and CaKR1 have been studied. However, the gene encoded by Pun2 in the non-pungent Capsicum chacoense is unknown. This study aimed to identify the Pun2 gene by genetic mapping using interspecific (C. chacoense × Capsicum annuum) and intraspecific (C. chacoense × C. chacoense) populations. QTL mapping using the interspecific F2 population revealed two major QTLs on chromosomes 3 and 9. Two bin markers within the QTL regions on two chromosomes were highly correlated with the capsaicinoid content in the interspecific population. The major QTL, Pun2_PJ_Gibbs_3.11 on chromosome 3, contained the pAMT gene, indicating that the non-pungency of C. chacoense may be attributed to a mutation in the pAMT gene. Sequence analysis revealed a 7 bp nucleotide insertion in the 8th exon of pAMT of the non-pungent C. chacoense. This mutation resulted in the generation of an early stop codon, resulting in a truncated mutant lacking the PLP binding site, which is critical for pAMT enzymatic activity. This insertion co-segregated with the pungency phenotype in the intraspecific F2 population. We named this novel pAMT allele pamt11 . Taken together, these data indicate that the non-pungency of C. chacoense is due to the non-functional pAMT allele, and Pun2 encodes the pAMT gene.

Investigation of genetic factors regulating chlorophyll and carotenoid biosynthesis in red pepper fruit.

Chlorophylls and carotenoids are synthesized in the chloroplast and chromoplast, respectively. Even though the two pigments are generated from the same precursor, the genetic correlation between chlorophyll and carotenoid biosynthesis has not yet been fully understood. We investigated the genetic correlation of chlorophyll and carotenoid biosynthesis during fruit ripening. Two recombinant inbred lines populations, "Long Sweet" × "AC2212" ("LA") RILs derived from a cross between Capsicum annuum "Long Sweet" with light-green and light-red fruit and C. annuum "AC2212" with dark-green and brown-fruit and "3501 (F)" × "3509 (C)" ("FC") RILs from C. annuum "3501" with dark-green and dark-red fruit and C. annuum "3509" with intermediate green and light-red fruit, were used. As the fruit ripened, three accessions produced high levels of xanthophyll. The dark-green immature fruit accumulated more total carotenoids than the light-green fruit. This trend corresponded to the expression pattern of 1-deoxy-d-xylulose 5-phosphate synthase (DXS) and CaGLK2 genes during fruit development. The expression levels of DXS and CaGLK2 in the dark-green accession "3501" were significantly higher than those of "3509" and "Long Sweet" during the early stages of fruit development. Furthermore, the genotype analysis of the transcription factor controlling chloroplast development (CaGLK2) in LA RILs revealed that CaGLK2 expression affected both carotenoid and chlorophyll contents. The single nucleotide polymorphism (SNP) linkage maps were constructed using genotyping-by-sequencing (GBS) for the two populations, and QTL analysis was performed for green fruit color intensity and carotenoid content. The QTL (LA_BG-CST10) for capsanthin content in LA RILs located at 24.4 to 100.4 Mbp on chromosome 10 was overlapped with the QTL (FC15-Cap10) for capsanthin content in FC RILs. Three QTLs for capsanthin content, American spice trade association (ASTA) value, and immature green fruit color intensity were also overlapped from 178.2 to 204 Mbp on chromosome 10. At the location, 151.6 to 165 Mbp on chromosome 8, QTLs (FC15-tcar8, FC17-ASTA8.1, and FC17-ASTA8.2) for total carotenoid content and ASTA value were discovered, and this region contained 2-C-methyl-d-erythritol 4-phosphate cytidylyltransferase (MCT), which is involved in the MEP pathway. This result is the first report to show the correlation between carotenoid and chlorophyll biosynthesis in pepper. This research will expand our understanding of the mechanism of the chloroplast-to-chromoplast transition and the development of high pigment pepper varieties.

High-quality chromosome-scale genomes facilitate effective identification of large structural variations in hot and sweet peppers.

Pepper (Capsicum annuum) is an important vegetable crop that has been subjected to intensive breeding, resulting in limited genetic diversity, especially for sweet peppers. Previous studies have reported pepper draft genome assemblies using short read sequencing, but their capture of the extent of large structural variants (SVs), such as presence-absence variants (PAVs), inversions, and copy-number variants (CNVs) in the complex pepper genome falls short. In this study, we sequenced the genomes of representative sweet and hot pepper accessions by long-read and/or linked-read methods and advanced scaffolding technologies. First, we developed a high-quality reference genome for the sweet pepper cultivar 'Dempsey' and then used the reference genome to identify SVs in 11 other pepper accessions and constructed a graph-based pan-genome for pepper. We annotated an average of 42 972 gene families in each pepper accession, defining a set of 19 662 core and 23 115 non-core gene families. The new pepper pan-genome includes informative variants, 222 159 PAVs, 12 322 CNVs, and 16 032 inversions. Pan-genome analysis revealed PAVs associated with important agricultural traits, including potyvirus resistance, fruit color, pungency, and pepper fruit orientation. Comparatively, a large number of genes are affected by PAVs, which is positively correlated with the high frequency of transposable elements (TEs), indicating TEs play a key role in shaping the genomic landscape of peppers. The datasets presented herein provide a powerful new genomic resource for genetic analysis and genome-assisted breeding for pepper improvement.

Effectiveness of image-guided radiotherapy for locally advanced rectal cancer.

BACKGROUND: Image-guided radiotherapy (IGRT) combines precise target visualization with optimal delivery of radiation dose to spare normal tissue from radiation and may potentially reduce side-effects and long-term treatment complications. We have assessed the effectiveness of IGRT for locally advanced rectal cancer. METHODS: A retrospective review of 22 patients with locally advanced rectal cancer who underwent preoperative chemoradiation was conducted. RESULTS: Nineteen patients (median age, 69 years) underwent surgical resection after chemoradiation. All 19 patients achieved complete resection with negative margins. Seven patients (32%) had no residual tumor in the surgical specimen. One patient had grade 4 gastrointestinal toxicity and hematological toxicity probably related to inadvertent overdosing of capecitabine. The median survival for the whole group-patients who had pCR and those who did not have pCR-was 14, 17, and 15 months, respectively. CONCLUSIONS: Image-guided radiotherapy provided effective treatment for locally advanced rectal cancer with minimal toxicity and should be investigated in future prospective trials.

Feasibility of tomotherapy for Graves' ophthalmopathy: Dosimetry comparison with conventional radiotherapy.

PURPOSE: To compare the dosimetry of tomotherapy and the conventional half-beam technique (HBT) or non-split beam technique (NSBT) for target coverage and radiation dose to the lacrimal glands and lens. PATIENTS AND METHODS: A retrospective review of 7 patients with Graves' ophthalmopathy who had radiotherapy because of disease progression on high steroid dose is reported: 3 patients were treated with tomotherapy and 4 patients with HBT. RESULTS: Compared to HBT, tomotherapy may provide better target coverage and significant reduction of radiation dose to the lacrimal glands and a higher dose to the lens. The NSBT improved target coverage but resulted in significantly higher doses to the lens and lacrimal glands. CONCLUSION: Tomotherapy may provide better coverage of the target volume and may be more effective in reducing severe exophthalmos compared to the conventional radiotherapy technique.

Population Structure and Genetic Diversity of Cucurbita moschata Based on Genome-Wide High-Quality SNPs.

Pumpkins (Cucurbita moschata) are one of the most important economic crops in genus Cucurbita worldwide. They are a popular food resource and an important rootstock resource for various Cucurbitaceae. Especially, C. moschata is widely used as a rootstock for the commercial production of bloomless cucumbers in East Asia. Since the genetic diversity of the commercial rootstock varieties is narrow, there has been an increasing demand for the trait development of abiotic and biotic stress tolerance breeding. In this study, 2071 high-quality SNPs that were distributed evenly across 20 chromosomes of pumpkins were discovered through the genotyping-by-sequencing (GBS) analysis of 610 accessions of C. moschata germplasm with a global origin. Using these SNPs, various analyses of the genetic diversity and the population structure were performed. Three subgroups were clustered from the germplasm collection, which included East Asia, Africa, and America, and these areas were included the most in each subgroup. Among those groups, accessions from Africa and South Asia showed the highest genetic diversity, which was followed by the Mexico accessions. This result reflected that large gene pools that consist of various native landraces have been conserved in those of countries. Based on the genetic diversity, we finally constructed the C. moschata core collection, which included 67 representative accessions from the 610 germplasms. Five morphological traits that are important in commercial grafting and rootstock seed production, which include the cotyledon length, the cotyledon width, the hypocotyl length, the internode length, and the number of female flowers, were investigated for three years and used to confirm the validity of the core collection selection. The results are expected to provide valuable information about the genetic structure of the worldwide C. moschata germplasm and help to create new gene pools to develop genetically diverse rootstock breeding materials.