Assessing the Potential for Genome-Assisted Breeding in Red Perilla Using Quantitative Trait Locus Analysis and Genomic Prediction.

Red perilla is an important medicinal plant used in Kampo medicine. The development of elite varieties of this species is urgently required. Medicinal compounds are generally considered target traits in medicinal plant breeding; however, selection based on compound phenotypes (i.e., conventional selection) is expensive and time consuming. Here, we propose genomic selection (GS) and marker-assisted selection (MAS), which use marker information for selection, as suitable selection methods for medicinal plants, and we evaluate the effectiveness of these methods in perilla breeding. Three breeding populations generated from crosses between one red and three green perilla genotypes were used to elucidate the genetic mechanisms underlying the production of major medicinal compounds using quantitative trait locus analysis and evaluating the accuracy of genomic prediction (GP). We found that GP had a sufficiently high accuracy for all traits, confirming that GS is an effective method for perilla breeding. Moreover, the three populations showed varying degrees of segregation, suggesting that using these populations in breeding may simultaneously enhance multiple target traits. This study contributes to research on the genetic mechanisms of the major medicinal compounds of red perilla, as well as the breeding efficiency of this medicinal plant.

Genetic diversity of viruses infecting cnidium plants (Cnidium officinale) in Japan.

Cnidium vein yellowing virus (CnVYV), cnidium virus X (CnVX), cucumber mosaic virus (CMV) and cnidium virus 1 (CnV1) were detected at extremely high levels in Cnidium officinale plants showing viral symptoms collected from Iwate and Hokkaido Prefectures, Japan. The complete nucleotide sequence of the newly detected CnVYV and CnV1, and genetic diversity of the cnidium-infecting viruses (CnVYV, CnVX, and CnV1) indicated that South Korean and Japanese cnidium plants had close relationship with each other. All three viruses can infect vegetatively propagated perennials and are vertically transmitted once infection occurs. Supplementary Information: The online version contains supplementary material available at 10.1007/s13337-023-00835-w.

Efficient fertilization in the cultivation of Angelica acutiloba (Siebold & Zucc.) Kitag. in Hokkaido: Effect of amount of supplied nitrogen on growth, yield, and quality of A. acutiloba.

Angelica acutiloba (Siebold & Zucc.) Kitag., the source plant of the crude drug Angelicae acutilobae radix, is traditionally cultivated in western regions of Japan. Since A. acutiloba is now also grown in Hokkaido, the northernmost prefecture of the country, the cultivation method, especially the quantity of fertilizer, needs to be adapted because of the cooler climate and shorter growing period. In this study, we compared plant growth and harvest yield of A. acutiloba cultivated with different amounts of nitrogen (N) fertilizer. When plants were fertilized with 24 kg N/10 a, the aerial part was lush, and the diameter at the top of the root was about 1.3 times thicker than that in plants treated with 12 kg N/10 a. On the other hand, the weight of the harvested root grown with 24 kg N/10 a was slightly, although not significantly, less than that in plants grown with 12 kg N/10 a. In addition, we found that the content of (Z)-ligustilide, a major essential oil contained in A. acutiloba root, is affected by nitrogen application. Interestingly, it increased with increasing amounts of supplied nitrogen. However, the importance of Angelicae acutilobae radix as the crude drug is not limited to its (Z)-ligustilide content, and there are also other crucial quality features, such as having thick lateral roots, which were generated in this study with a moderate nitrogen application. We conclude that about 12 kg N/10 a is the optimal amount of nitrogen for healthy growth of A. acutiloba in Hokkaido.

Genome analysis and genetic transformation of a water surface-floating microalga Chlorococcum sp. FFG039.

Microalgal harvesting and dewatering are the main bottlenecks that need to be overcome to tap the potential of microalgae for production of valuable compounds. Water surface-floating microalgae form robust biofilms, float on the water surface along with gas bubbles entrapped under the biofilms, and have great potential to overcome these bottlenecks. However, little is known about the molecular mechanisms involved in the water surface-floating phenotype. In the present study, we analysed the genome sequence of a water surface-floating microalga Chlorococcum sp. FFG039, with a next generation sequencing technique to elucidate the underlying mechanisms. Comparative genomics study with Chlorococcum sp. FFG039 and other non-floating green microalgae revealed some of the unique gene families belonging to this floating microalga, which may be involved in biofilm formation. Furthermore, genetic transformation of this microalga was achieved with an electroporation method. The genome information and transformation techniques presented in this study will be useful to obtain molecular insights into the water surface-floating phenotype of Chlorococcum sp. FFG039.

Absence of in vivo selection for K13 mutations after artemether-lumefantrine treatment in Uganda.

BACKGROUND: Individual drug treatment may select resistant parasites in the human body, a process termed in vivo selection. Some single nucleotide polymorphisms in Plasmodium falciparum chloroquine-resistance transporter (pfcrt) and multidrug resistance gene 1 (pfmdr1) genes have been reportedly selected after artemether-lumefantrine treatment. However, there is a paucity of data regarding in vivo selection of P. falciparum Kelch propeller domain (pfkelch13) polymorphisms, responsible for artemisinin-resistance in Asia, and six putative background mutations for artemisinin resistance; D193Y in ferredoxin, T484I in multiple resistance protein 2, V127M in apicoplast ribosomal protein S10, I356T in pfcrt, V1157L in protein phosphatase and C1484F in phosphoinositide-binding protein. METHODS: Artemether-lumefantrine efficacy study with a follow-up period of 28 days was conducted in northern Uganda in 2014. The above-mentioned genotypes were comparatively analysed before drug administration and on days; 3, 7, and 28 days after treatment. RESULTS: In 61 individuals with successful follow-up, artemether-lumefantrine treatment regimen was very effective with PCR adjusted efficacy of 95.2%. Among 146 isolates obtained before treatment, wild-type alleles were observed in 98.6% of isolates in pfkelch13 and in all isolates in the six putative background genes except I356T in pfcrt, which had 2.4% of isolates as mixed infections. In vivo selection study revealed that all isolates detected in the follow-up period harboured wild type alleles in pfkelch13 and the six background genes. CONCLUSION: Mutations in pfkelch13 and the six background genes may not play an important role in the in vivo selection after artemether-lumefantrine treatment in Uganda. Different mechanisms might rather be associated with the existence of parasites after treatment.

Application of a cell microarray chip system for accurate, highly sensitive, and rapid diagnosis for malaria in Uganda.

Accurate, sensitive, rapid, and easy operative diagnosis is necessary to prevent the spread of malaria. A cell microarray chip system including a push column for the recovery of erythrocytes and a fluorescence detector was employed for malaria diagnosis in Uganda. The chip with 20,944 microchambers (105 µm width and 50 µm depth) was made of polystyrene. For the analysis, 6 µl of whole blood was employed, and leukocytes were practically removed by filtration through SiO2-nano-fibers in a column. Regular formation of an erythrocyte monolayer in each microchamber was observed following dispersion of an erythrocyte suspension in a nuclear staining dye, SYTO 21, onto the chip surface and washing. About 500,000 erythrocytes were analyzed in a total of 4675 microchambers, and malaria parasite-infected erythrocytes could be detected in 5 min by using the fluorescence detector. The percentage of infected erythrocytes in each of 41 patients was determined. Accurate and quantitative detection of the parasites could be performed. A good correlation between examinations via optical microscopy and by our chip system was demonstrated over the parasitemia range of 0.0039-2.3438% by linear regression analysis (R(2) = 0.9945). Thus, we showed the potential of this chip system for the diagnosis of malaria.

Effects of different microhabitas on growth and four kinds of volatile oil components of Atractylodes lancea / 中国中药杂志

To investigate the suitable site environment for Atractylodes lancea, field trials in different niches was carried out, and the seedling growth, biomass and volatile oil components in different microhabitas was studied. The study found that the survival rate, plant height, volatile oil content of those which growing under the bamboo were significantly higher than those exposed in the open field. The survival rate understory was (76 ± 15.1) %, plant height understory was (77 ± 14. 8) cm and the summation of the four kinds of volatile oil content understory reached up to 4.09%; The same evaluation values of these indicators of the four faces in the open field respectively: survival rate is 30%, plant height was (77 ± 14.8) cm and the summation of the four kinds of volatile oil content was 2.24%. But, the yield of the understory (41 ± 22.3) g was significantly lower than those four faces in the open field (104.5 g) on the contrary. For the four open field towards, the yield of the east facing, which organic matter and other nutritional conditions were better than others, was significantly higher than those in the other facings. A. lancea was found to be an anti-poor and shading-like or growing in east facing slope herb through the correlation analysis of light, temperature, soil and leaf nutrients with seedling growth, biomass and volatile oil components. It also reminds us that the understory herb with high survival rate, low incidence, low management costs, and high medicinal ingredients, although it's production is not so high, but it can be improved by increased organic fertilizer. So the ecological planting patterns which can intercropping herbs with the forest was proposed.

Large-scale survey for novel genotypes of Plasmodium falciparum chloroquine-resistance gene pfcrt.

BACKGROUND: In Plasmodium falciparum, resistance to chloroquine (CQ) is conferred by a K to T mutation at amino acid position 76 (K76T) in the P. falciparum CQ transporter (PfCRT). To date, at least 15 pfcrt genotypes, which are represented by combinations of five amino acids at positions 72-76, have been described in field isolates from various endemic regions. To identify novel mutant pfcrt genotypes and to reveal the genetic relatedness of pfcrt genotypes, a large-scale survey over a wide geographic area was performed. METHODS: Sequences for exon 2 in pfcrt, including known polymorphic sites at amino acid positions 72, 74, 75 and 76, were obtained from 256 P. falciparum isolates collected from eight endemic countries in Asia (Bangladesh, Cambodia, Lao P.D.R., the Philippines and Thailand), Melanesia (Papua New Guinea and Vanuatu) and Africa (Ghana). A haplotype network was constructed based on six microsatellite markers located -29 kb to 24 kb from pfcrt in order to examine the genetic relatedness among mutant pfcrt genotypes. RESULTS: In addition to wild type (CVMNK at positions 72-76), four mutant pfcrt were identified; CVIET, CVIDT, SVMNT and CVMNT (mutated amino acids underlined). Haplotype network revealed that there were only three mutant pfcrt lineages, originating in Indochina, Philippines and Melanesia. Importantly, the Indochina lineage contained two mutant pfcrt genotypes, CVIET (n = 95) and CVIDT (n = 14), indicating that CVIDT shares a common origin with CVIET. Similarly, one major haplotype in the Melanesian lineage contained two pfcrt genotypes; SVMNT (n = 71) and CVMNT (n = 3). In Africa, all mutant pfcrt genotypes were the CVIET of the Indochina lineage, probably resulting from the intercontinental migration of CQ resistance from Southeast Asia. CONCLUSIONS: The number of CQ-mutant lineages observed in this study was identical to that found in previous studies. This supports the hypothesis that the emergence of novel CQ resistance is rare. However, in the mutant pfcrt genotypes, amino acid changes at positions 72, 74 and 75 appear to have recently been generated at least several times, producing distinct pfcrt mutant genotypes. The occurrence of new mutations flanking K76T may yield stronger resistance to CQ and/or a higher fitness than the original pfcrt mutant.

Transmission disequilibrium test and haplotype analysis of the NOTCH4 gene in Japanese patients with schizophrenia.

A recent study reported that the NOTCH4 gene was highly associated with schizophrenia in the British population. To confirm this association for another population, a case-control study was conducted and a transmission disequilibrium test (TDT) analysis was performed on a group of Japanese subjects (235 pairs of schizophrenia patients and controls, and 78 trios consisting of probands and their parents) using two single nucleotide polymorphisms and three microsatellite markers for the NOTCH4 gene. Haplotype analysis was also studied in case-control and family based data sets. In all markers except for (CTG)n (P = 0.012, before correction for multiple testing), no differences were found in the case-control study. The TDT analysis also revealed only a weak transmission disequilibrium in (TTAT)n (genotype-wise P = 0.012). The finding of the present study could not support the original findings that the NOTCH4 gene itself is associated with susceptibility to schizophrenia.

[Assessment of post-administration body distribution of toremifene and tamoxifen, and their administration regimens].

Toremifene is an anti-estrogenic drug like tamoxifen. We assessed the body distributions after administration of toremifene and tamoxifen in order to evaluate their treatment regimens by measuring the concentrations in tissues. It is known that, after toremifene (TOR) or tamoxifen (TAM) is consecutively administered to breast cancer patients, TOR or TAM and their main active N-desmethyl-metabolites (TOR-1 or TAM-1) are detected in sera, tumor tissues, and lymph nodes. Accordingly, after we administered toremifene or tamoxifen to primary breast cancer patients previous to surgery, we measured the concentrations of TOR, TOR-1, TAM, TAM-1 in sera, tumor tissues, and lymph nodes. We found that the concentrations of TOR and TOR-1 in sera, tumors, and lymph nodes reached a peak about 2 weeks after administration of toremifene 40 mg. Likewise, the concentrations of TAM and TAM-1 in sera, tumors, and lymph nodes reached a peak about 2 weeks after administration of tamoxifen, although the peak levels were lower than those of TOR or TOR-1. The concentrations of TAM-1 in lymph nodes were significantly and positively correlated to the duration of administration of TAM, and it was predicted that the concentration of TAM-1 in lymph nodes would reach a steady state at more than 4 weeks after administration of tamoxifen. The concentrations of TOR and TOR-1 were higher in tumors and lymph nodes than in sera. Furthermore, the concentrations of TOR and TOR-1 were significantly higher than those of TAM and TAM-1 in sera and tumors, respectively. Moreover, the concentration in tissue increased in a dose-dependent manner with administration of toremifene 120 mg. There were no significant differences between breast cancers positive and negative for estrogen receptors, with regard to the concentrations of TOR and TOR-1 in either sera, tumors, or lymph nodes. In conclusion, it would be expected that treatment with toremifene might be more effective for breast cancer than that with tamoxifen.