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As the world’s population grows and food needs diversification, the demand for cereals and horticultural crops with beneficial traits increases. In order to meet a variety of demands, suitable cultivars and innovative breeding methods need to be developed. Breeding methods have changed over time following the advance of genetics. With the advent of new sequencing technology in the early 21st century, predictive breeding, such as genomic selection (GS), emerged when large-scale genomic information became available. GS shows good predictive ability for the selection of individuals with traits of interest even for quantitative traits by using various types of the whole genome-scanning markers, breaking away from the limitations of marker-assisted selection (MAS). In the current review, we briefly describe the history of breeding techniques, each breeding method, various statistical models applied to GS and methods to increase the GS efficiency. Consequently, we intend to propose and define the term digital breeding through this review article. Digital breeding is to develop a predictive breeding methods such as GS at a higher level, aiming to minimize human intervention by automatically proceeding breeding design, propagating breeding populations, and to make selections in consideration of various environments, climates, and topography during the breeding process. We also classified the phases of digital breeding based on the technologies and methods applied to each phase. This review paper will provide an understanding and a direction for the final evolution of plant breeding in the future.

Androgen promotes tumorigenesis in some cancers; however, androgen receptor (AR) is not commonly examined in ovarian cancers (OCs). In this study, we evaluated AR expression among different types of OCs and compared the results to estrogen and progesterone receptors (ER & PR). AR, ER, and PR expressions were assessed in 62 cases which were categorized into: low-grade serous carcinoma (LGSCA), high-grade serous carcinoma (HGSCA), clear cell carcinoma (CCCA), ovarian endometrioid carcinoma (OECA), and granulosa cell tumor (GCT). The hormone receptors were compared and evaluated in relation to p53 and body mass index (BMI) using Fisher's Exact test. In a majority of cases, expression of AR was concordant with ER and/or PR. Positivity for all three receptors was observed in 100% of OECAs. AR expression was seen in 92% of HGSCAs as opposed to 88% and 44% for ER and PR. LGSCAs had expressed AR and ER (100%), and PR (70%). In GCTs, positivity rates were 92%, 62%, and 92% for AR, ER, and PR. In rare cases of HGSCA and CCCA, AR was positive despite negative ER and PR. AR is expressed in a high percentage of OCs, even more frequently than ER and PR in certain high-grade histological types. Overall, our findings are similar to the results of recent studies of AR expression in endometrial cancers. These findings support an important possible role for AR in OCs as a potential marker to serve as a therapeutic target in these malignancies.

Salvia sclarea is a medicinal herb from the Lamiaceae family, valued for its essential oil which contains sclareol, linalool, linalyl acetate, and other compounds. Despite its extensive use, the genetic mechanisms of S. sclarea are not well understood. This study presents a chromosome-level genome assembly of S. sclarea using the Oxford Nanopore Technology, Illumina short reads, and Pore-C technology. The assembled genome spans 499.03 Mbp with a scaffold N50 of 50.5 Mbp, forming 11 pseudochromosomes. The genome assembly was validated by BUSCO analysis, which indicated a high completeness marked at 98.7%. The genome contains 68.73% repetitive sequences, with long terminal repeats (LTRs) accounting for 33.01%. A total of 17,202 protein-coding genes were predicted. Among them, 16,846 genes were annotated in the NCBI NR database, the highest among all databases, covering 97.93% of the predicted genes. The phylogenetic analysis revealed that S. sclarea shares a close evolutionary relationship with S. officinalis within the Salvia genus, while species in the genus have evolved independently within the Lamiaceae family. This high-resolution genome assembly offers fresh insights into the biosynthesis of essential oils and other aromatic compounds in S. sclarea , establishing a basis for genetic preservation.

The agricultural traits that constitute basic plant breeding information are usually quantitative or complex in nature. This quantitative and complex combination of traits complicates the process of selection in breeding. This study examined the potential of genome-wide association studies (GWAS) and genomewide selection (GS) for breeding ten agricultural traits by using genome-wide SNPs. As a first step, a trait-associated candidate marker was identified by GWAS using a genetically diverse 567 Korean (K)-wheat core collection. The accessions were genotyped using an Axiom ® 35K wheat DNA chip, and ten agricultural traits were determined (awn color, awn length, culm color, culm length, ear color, ear length, days to heading, days to maturity, leaf length, and leaf width). It is essential to sustain global wheat production by utilizing accessions in wheat breeding. Among the traits associated with awn color and ear color that showed a high positive correlation, a SNP located on chr1B was significantly associated with both traits. Next, GS evaluated the prediction accuracy using six predictive models (G-BLUP, LASSO, BayseA, reproducing kernel Hilbert space, support vector machine (SVM), and random forest) and various training populations (TPs). With the exception of the SVM, all statistical models demonstrated a prediction accuracy of 0.4 or better. For the optimization of the TP, the number of TPs was randomly selected (10%, 30%, 50% and 70%) or divided into three subgroups (CC-sub 1, CC-sub 2 and CC-sub 3) based on the subpopulation structure. Based on subgroup-based TPs, better prediction accuracy was found for awn color, culm color, culm length, ear color, ear length, and leaf width. A variety of Korean wheat cultivars were used for validation to evaluate the prediction ability of populations. Seven out of ten cultivars showed phenotype-consistent results based on genomics-evaluated breeding values (GEBVs) calculated by the reproducing kernel Hilbert space (RKHS) predictive model. Our research provides a basis for improving complex traits in wheat breeding programs through genomics assisted breeding. The results of our research can be used as a basis for improving wheat breeding programs by using genomics-assisted breeding.

Novel yellow azo pyridone dye derivatives were synthesized for use in image-sensor color filters. The synthesized compounds have a basic chemical structure composed of azo, hydroxy, amide, and nitrile groups as well as different halide groups. New materials were evaluated on the basis of their optical, thermal, and surface properties under conditions mimicking those of a commercial device fabrication process. A comparison of their related performance revealed that, among the four prepared compounds, 5-((4,6-dichlorocyclohexa-2,4-dien-1-yl)diazenyl)-6-hydroxy-1,4-dimethyl-2-oxo-1,2-dihydropyridine-3-carbonitrile (Cl-PAMOPC) exhibited the best performance as an image-sensor color filter material, including a solubility greater than 0.1 wt% in propylene glycol monomethyl ether acetate solvent, a high decomposition temperature of 263 °C, and stable color difference values of 4.93 and 3.88 after a thermal treatment and a solvent-resistance test, respectively. The results suggest that Cl-PAMOPC can be used as a green dye additive in an image-sensor colorant.

Plant breeding has a long history of developing new varieties that have ensured the food security of the human population. During this long journey together with humanity, plant breeders have successfully integrated the latest innovations in science and technologies to accelerate the increase in crop production and quality. For the past two decades, since the completion of human genome sequencing, genomic tools and sequencing technologies have advanced remarkably, and adopting these innovations has enabled us to cost down and/or speed up the plant breeding process. Currently, with the growing mass of genomic data and digitalized biological data, interdisciplinary approaches using new technologies could lead to a new paradigm of plant breeding. In this review, we summarize the overall history and advances of plant breeding, which have been aided by plant genomic research. We highlight the key advances in the field of plant genomics that have impacted plant breeding over the past decades and introduce the current status of innovative approaches such as genomic selection, which could overcome limitations of conventional breeding and enhance the rate of genetic gain.

The expression of androgen receptor (AR) is not commonly tested or studied in uterine cancers, unlike estrogen receptor (ER) and progesterone receptor (PR) which are positive in most endometrial carcinomas. In this series, we evaluated the expression of AR and its comparison to ER and PR in different types of endometrial cancers and have reviewed the literature. The status of AR, ER, and PR expression were evaluated in 71 cases which were categorized into endometrial endometrioid cancer (EEC), non-endometrioid endometrial cancers (NEEC), and metastatic carcinomas of endometrium. Expression of the receptors were compared to each other as well as to mismatch repair proteins (MMR), p53, and body mass index (BMI) using Fisher's Exact test in the StatPlus software. In EECs, the positivity was 97% for all the three receptors. In NEEC, positivity rates were 68%, 48%, and 35% for AR, ER, and PR respectively. In Metastatic carcinomas, AR and ER positivity was seen in 100% while PR was positive in 75% of the cases. In all cancers, the rates were 17% (11/66) for MMR loss, 57% (30/53) for p53 aberrant expression, and 76% (54/71) for the patients with BMI of [greater than or equal to] 25 (kg/m2). AR is expressed in a high percentage of endometrial cancers. Its significance is more evident in high-grade NEEC where ER and PR may not be expressed. These findings warrant further evaluation of AR expression and candidacy of this pathway as a potential therapeutic target in endometrial cancers.

Synovial sarcoma and malignant peripheral nerve sheath tumor pose a significant diagnostic challenge given similar histomorphology. The distinction is further complicated by similar immunophenotype and especially by occasional synovial sarcomas that present as intraneural tumors. Although the presence of a t(X;18) rearrangement or expression of TLE1 can help confirm the diagnosis of synovial sarcoma, negative results for these tests are not diagnostic of malignant peripheral nerve sheath tumor. The SOX10 transcription factor, a putative marker of neural crest differentiation, may have diagnostic utility in this differential, but immunohistochemical data are limited. The goal of the present study was to determine the diagnostic utility of SOX10 to discriminate between synovial sarcoma and malignant peripheral nerve sheath tumor. Forty-eight cases of malignant peripheral nerve sheath tumor, all from patients with documented neurofibromatosis, and 97 cases of genetically confirmed synovial sarcoma, including 4 intraneural synovial sarcomas, were immunohistochemically stained for SOX10. The stain was scored for intensity and fraction of cells staining. Thirty-two of 48 malignant peripheral nerve sheath tumors (67%) were SOX10-positive. The majority of malignant peripheral nerve sheath tumors showed ≥2+ staining, but staining did not correlate with grade. By contrast, only 7/97 (7%) synovial sarcomas were SOX10-positive. Only three synovial sarcomas showed ≥2+ staining but, importantly, two of these were intraneural synovial sarcoma. Therefore, SOX10 is a specific (93%), albeit not very sensitive (67%), diagnostic marker to support a diagnosis of malignant peripheral nerve sheath tumor over synovial sarcoma. Furthermore, the stain needs to be interpreted with caution in intraneural tumors in order to avoid a potential diagnostic pitfall. It remains to be determined whether SOX10-positive cells in intraneural synovial sarcoma represent entrapped Schwann cells, synovial sarcoma cells or both.

Platelet-activating factor (PAF) is a potent inflammatory mediator that activates the PAF receptor, which induces additional PAF production. Animal studies have shown that PAF induces inflammatory and neuropathic pain, including dysesthesia, a prodromal symptom of neuropathic pain. However, in humans, the association between PAF and pain remains unknown. Phospholipase A2 Group VII (PLA2G7) hydrolyzes PAF to eliminate PAF activity. The present study investigated the association between the PLA2G7 rs1051931 nonsynonymous polymorphism (T/C, Val379Ala), which decreases the PAF-degrading activity of PLA2G7 in plasma, and postoperative pain-related phenotypes in humans. The study included 303 patients who underwent sagittal split ramus osteotomy at Tokyo Dental College and were assessed for dysesthesia and 332 patients who underwent laparoscopic gynecologic surgery at Juntendo University Hospital and were assessed for postoperative pain using the Numeric Rating Scale (NRS). PLA2G7 rs1051931 was significantly associated with dysesthesia (p = 0.0491) and NRS scores (p = 0.0243). Carriers of the CC genotype of PLA2G7 rs1051931 were more likely to have dysesthesia and higher NRS scores than carriers of the TT + TC genotypes. Carriers of the CC genotype of PLA2G7 rs1051931 reportedly had lower PAF-degrading activity in plasma, thereby increasing the amount of PAF. The increase in PAF possibly leads to dysesthesia and postoperative pain in humans.

Postoperative nausea and vomiting (PONV) after orthognathic surgery is a serious postoperative complication. The cholinergic receptor muscarinic 3 ( CHRM3 ) rs2165870 and tachykinin receptor 1 ( TACR1 ) rs3755468 single-nucleotide polymorphisms (SNPs) have been reported to be involved in PONV. We evaluated the impact of these SNPs on PONV in a Japanese population who underwent orthognathic surgery under PONV prophylaxis with the 5-hydroxytryptamine (serotonin) receptor 3A receptor antagonist ondansetron. In 121 patients, dexamethasone was administered after intubation, followed by ondansetron before the end of surgery. An 11-point numeric rating scale (NRS) score for PONV (0–2 h or 2–24 h after anesthesia endpoint [a.a.e.]) and the presence or absence of metoclopramide administration (0–2 h or 2–24 h a.a.e.) were evaluated. If patients complained of PONV and had an NRS score ≥ 4, then metoclopramide was administered intravenously for PONV rescue. Patients were genotyped for the CHRM3 rs2165870 and TACR1 rs3755468 SNPs, followed by the statistical analysis of associations between these SNPs and phenotypes. AA carriers of CHRM3 rs2165870 received metoclopramide at a significantly higher rate ( P  = 2.48 × 10 − 2 ) and had higher NRS scores ( P  = 3.40 × 10 − 2 ) under a diminished influence of ondansetron than GG and GA carriers. CC carriers of TACR1 rs3755468 had significantly higher NRS scores under the sufficient influence of ondansetron than CT and TT carriers ( P  = 9.97 × 10 − 3 ). Numeric rating scale scores showed a significant interaction between “time” (the effect of ondansetron) and “genotype” (two-way analysis of variance, P  = 4.39 × 10 − 2 ). AA carriers of CHRM3 rs2165870 were significantly associated with “time” ( P  = 3.26 × 10 − 2 ), and CC carriers of TACR1 rs3755468 were not ( P  > 0.05). These results suggest that ondansetron significantly affects nausea that is associated with CHRM3 , whereas it has a minimal effect on nausea that is associated with TACR1 . This indicates that nausea that is associated with CHRM3 is qualitatively different from nausea that is associated with TACR1 . Ondansetron mainly exerts its effects outside the blood-brain barrier, which may lead to differential impacts on nausea that is associated with CHRM3 and TACR1 . These findings may provide future directions for tailor-made preventive measures against PONV that depend on high-risk genotypes of the CHRM3 rs2165870 and TACR1 rs3755468 SNPs.