DNA Molecular Markers Research Articles

A rapid recognition method of Auricularia auricula varieties based on near-infrared spectral characteristics

Edible fungus is one of the significant foods for human beings. The rapid recognition of fruit body phenotypic characteristics is of great significance, theoretical and practical value for the classification of edible fungus, evaluation of germplasm resources, breeding, and intelligent cultivation. The existing morphological-physiological phenotype detection for edible fungus’ growth process is not systematic enough and lack of rapid and accurate detection methods for the fruit body varieties of Auricularia auricula. At present, the operation process of DNA molecular marker technology is complex, time-consuming, laborious, and expensive, moreover, the traditional artificial judgment of fruit body varieties based on naked-eye observation and experience easily led to errors and inaccuracy. Therefore, a rapid recognition method of Auricularia auricula varieties was proposed based on the characteristics of near-infrared spectroscopy. First, the four Auricularia auricula varieties of Cheng D, Hei Feng, Hei Shan, and Xu 1 were taken as the research objects, the near-infrared spectral data of Auricularia auricula were scanned by Fourier transform near-infrared spectrometer (Tango). Second, the detrend(DT)method was used to pre-process the raw spectral data. Then the competitive adaptive reweighted sampling (CARS) algorithm was applied to extract 131 effective characteristic wavenumbers from the pre-processed spectral data. Finally, the radial basis function (RBF) neural network of type 131-12-4 was constructed to recognize Auricularia auricula varieties. The research results showed that the accuracy of DT-CARS-RBF model for recognizing Auricularia auricula varieties was 99.32%, the root mean square error value was 0.0908, and the running time was 0.000956 s. This achievement established a rapid, efficient, and accurate method for the recognition of Auricularia auricula varieties, which provided a theoretical basis and technical support for the rapid of Auricularia auricula varieties for the classification of edible fungus and evaluation of germplasm resources, breeding, and cultivation.

MP56-07 PREDICTORS OF RESPONSE FOLLOWING NEOADJUVANT CISPLATIN BASED CHEMOTHERAPY FOR MUSCLE INVASIVE UROTHELIAL BLADDER CANCER USING MOLECULAR PROFILE

You have accessJournal of UrologyCME1 May 2022MP56-07 PREDICTORS OF RESPONSE FOLLOWING NEOADJUVANT CISPLATIN BASED CHEMOTHERAPY FOR MUSCLE INVASIVE UROTHELIAL BLADDER CANCER USING MOLECULAR PROFILE Ahmed Elkarta, Ahmed Elhefnawy, Hassan Abol-Enein, and Ahmed Shokeir Ahmed ElkartaAhmed Elkarta More articles by this author , Ahmed ElhefnawyAhmed Elhefnawy More articles by this author , Hassan Abol-EneinHassan Abol-Enein More articles by this author , and Ahmed ShokeirAhmed Shokeir More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002639.07AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Despite Neoadjuvant chemotherapy (NAC) before radical cystectomy (RC) improves 5-year survival by 5-10% many patients who receive NAC didn’t get survival benefit and bear the burden of side effects only. Literature has an increasing evidence of the potential role of DNA damage repair (DDR) genes & molecular markers to predict NAC response, however, Currently still no clinically applied reliable predictors for NAC response, as results were cuffed by small number of patients, retrospective nature & heterogeneity of NAC regimen received. We studied molecular predictors in a prospective study with unified NAC regimen. METHODS: Between December 2019 and August 2021, tumor biopsies were obtained from patients with urothelial MIBC (T2-4a N0 M0) who were fit for RC and eligible for cisplatinum based NAC. Patients received Gemcitabine & Cisplatinum for at least 3 cycles. m-RNA expression levels of DDR (BRACA1, ERCC1) & CTR gene in resected tissue were measured. The response to chemotherapy was assessed following NAC by MRI & pathologically. Patients with stage ≤pT1 were considered responders. Bivarite and multivariate analysis were used to define predictors for NAC response before RC. Receiver operating characteristic (ROC) curve was used to delineate cutoff value copes with the best sensitivity and specificity for significant continuous data. RESULTS: 95 patients were included in the study with mean age (SD) 63.04 (6.98) years and the majority were males (91.6%). 36 patients (37.9%) showed complete pathological response to NAC. Bivariate analysis showed that higher mRNA expression level of CTR, lower radiological stage preoperatively and lower mRNA gene expression levels of BRACA1 and ERCC1 were associated with good response to NAC preoperatively. The best cutoff value for mRNA expression of these genes was delineated in Table 1. Lower levels of gene expression of BRACA1, ERCC1& higher expression of CTR were the only factors which remained statistically significant in multivariate analysis by logistic regression (Table 1). CONCLUSIONS: Molecular profile has a decisive role in identifying patients who will get benefit from preoperative NAC. Lower mRNA expression levels of the genes ERCC1 (≤3.65), BRACA1 (≤3.21) in addition to higher gene expression of CTR (>14.2) were predictors for good response to cisplatinum based NAC in MIBC. Source of Funding: No source of funding © 2022 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 207Issue Supplement 5May 2022Page: e974 Advertisement Copyright & Permissions© 2022 by American Urological Association Education and Research, Inc.MetricsAuthor Information Ahmed Elkarta More articles by this author Ahmed Elhefnawy More articles by this author Hassan Abol-Enein More articles by this author Ahmed Shokeir More articles by this author Expand All Advertisement PDF DownloadLoading ...

Molecular Characteristics and Genetic Diversity of Fasciola Hepatica from Sheep in Xinjiang, China.

IntroductionFasciola hepatica is a trematode infecting ruminants worldwide and occasionally affecting other animal species, including humans. It causes significant economic losses. Geographic distribution and patterns of infection must be considered before control and management measures are developed for this parasite. DNA molecular markers are useful for the identification of flukes and elucidation of their genetic evolution. Therefore, the population structure of F. hepatica was studied using this method in sheep in Xinjiang, China.Material and MethodsThe molecular characteristics, genetic relationships within the population and dispersal patterns of F. hepatica isolates were analysed based on the cox1 and nad1 genes. The population structure of F. hepatica from three regions of Xinjiang was explored and a neutrality test was conducted.ResultsThe cox1 and nad1 genes have 21 and 42 variable sites, respectively, which can be classified into 34 and 33 haplotypes. Median-joining network and phylogenetic tree analyses showed that there was no significant variation in F. hepatica isolates between the three geographical regions. Analysis of variance revealed that the genetic variation of F. hepatica was mainly present within the populations. The neutrality test indicated that the populations were relatively stable but the Hami population may have undergone short-term expansion.ConclusionThis study revealed for the first time the molecular characteristics, genetic diversity and dispersal patterns of F. hepatica isolates from sheep in Xinjiang, thus providing new insights into the genetic variation and haplotype diversity of F. hepatica from indigenous sheep.

Morphologic and Molecular Evaluation of Papaya Strains (Carica papaya L.) Under Mediterranean Conditions

Papaya is high in nutrients, delicious flavours, and potent antioxidants like lycopene; all of these bio constituents may reduce the risk of a variety of ailments, particularly those associated with ageing, such as heart disease and cancer. The papaya (Carica papaya L.) despite having a lengthy farming history and important germplasm, little is known about its genetic basis and variety. In response to environmental changes, the results of papaya strain diversity show variation in yield, vegetative traits, morphological characteristics of flowers, fruits, and leaves. To characterise the genetic assessment, morphological, agronomical traits, and an inter-simple sequence repeat (ISSR) molecular marker were studied across 9 papaya strains. For the past three decades, DNA Molecular markers have been used. The DNA contours provide data on the strains, display the entire genome, and showing difference in both the encrypting and non-encrypting regions, as well as polymorphism. A mix of morphologic, chemical, and molecular characteristics of papaya strains can be used to well measure the degree of variety and correlation among papaya strains. The primers UBC812 and UBC825 performed the best for identifying and estimating the diversity of papaya accessions, followed by UBC864, UBC809, UBC811 and HB-13. The 9 papaya strains were classified into two clusters using UPGMA cluster analysis and a similarity coefficient obtained from ISSR markers. Among the nine papaya strains, the pair S3 and S7 had the highest similarity (0.97). The morphological characteristics are similar to molecular analysis. This work provided a quick and steadfast method for estimating variability among different Papaya strains, which breeders could use to improve papaya.

DNA barcoding based on 16S mitochondrial DNA (mtDNA) Molecular Marker of Mangrove Clams from the Selected Sites of Davao Region, Philippines

Aims: The taxonomic identification of mangrove clams was confirmed using DNA barcoding based on 16S mitochondrial DNA (mtDNA) genome.
 Study design: DNA was extracted from adductor muscle of mangrove clams sample. Purified DNA were sequenced and barcode was generated.
 Place and duration of the study: The mangrove clams samples used in the study were collected from Malita, Davao Occidental; Santa Cruz, Davao Del Sur; Mati, Davao Oriental, Philippines from January 2021 to June 2021.
 Methodology: DNA was extracted from adductor muscle of mangrove clams using the Promega GoTaq PCR kit. The extracted DNA were then purified and viewed using the Gel Electrophoresis. The Purified DNA samples were then sequenced and various softwares were then utilized namely sequenced assembly and alignment namely Basic Local Search Tool (BLAST) and Barcode Of Life Database(BOLD) and phylogenetic tree was generated.
 Results: There are two species morphologically identified as Anodontia philippiana (Reeve, 1850) and Austriella corrugata (Deshayes, 1843) from Davao region. BLAST search established the two species to be closely related to Anodontia (Cavatidens) omissa (Iredale, 1930) and Phacoides pectinatus (Gmelin, 1791), also a member of the Lucinidae family.
 Conclusion: In this study, the taxonomic identification of the two mangrove clams were further elucidated using the 16S mitochondrial DNA marker.

High Genetic Diversity of 16 Indian lettuce (Lactuca indica L.) Accessions from Vietnam.

<b>Background and Objective:</b> Plant genetic resources provide the raw material for crop improvement and plant breeding program largely depends on it. Therefore, the evaluation of plant genetic resources plays a critical role in crop improvement and also in conserving valuable genetic resources for the future. In this study, the genetic diversity of 16 <i>Lactuca indica</i> L. accessions collected in Vietnam was investigated by using ISSR and RAPD markers. <b>Materials and Methods:</b> Genetic diversity of 16 <i>Lactuca sativa</i> L. genotypes collected in Vietnam were evaluated using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR) molecular markers. <b>Results:</b> In this study, 42 RAPD and ISSR primers were initially used, of which 12 and 9 primers, respectively were finally selected as they produced scorable patterns. RAPD markers produced a total of 113 loci, out of which 52 loci (45.96%) were polymorphic. The average percentage of the polymorphic band for RAPD primer is 45.96% and the genetic similarity based on simple matching coefficient ranged from 69.0-94.7%. ISSR analysis detected a total of 60 loci, out of which 22 loci (36.32%) were polymorphic and the genetic similarity ranged from 56.7-95.0%. In general, ISSR markers amplified fewer loci and showed lower variation in the percentage of polymorphism compares to the RAPD assay. <b>Conclusion:</b> These results indicate that the 16 collected Indian lettuce genotypes are genetically diverse. Because of these genetic diversities, the collected genotypes could be used for preserving or crossing programs to improve this precious medicinal plant in Vietnam.

Study of non-pollution cultivation techniques of organic ecotype of melon crops considering population characteristics.

Due to the requirement of melon yield, the cultivated seeds are overused with pesticides during the melon planting process, and the population characteristics are not considered, resulting in serious soil pesticide pollution during the melon planting process. Therefore, this study proposes an organic ecological pollution-free cultivation technology of melon considering population characteristics. The population characteristics of melon crops were determined by DNA molecular marker technology. On this basis, the organic ecotype pollution-free matrix of melon crops was formulated, and the bulk density, total porosity and aeration porosity of the matrix were determined. The MNL model method was used to control the spraying amount of melon cultivation, and the light condition of the melon growing environment was determined by the leaf fluorescence of melon crops. There were significant differences in plant height, stem diameter and leaf area between melons grown in the studied substrate and common soil. With the change of planting days, the height of the melon grown in this technology was always higher than that of the melon grown in common soil, and the maximum value was about 20 cm. As planting days changed, the stem thickness of melon crops grown with the substrate was initially lower than that of common soil, but quickly exceeded the thickness of common soil over time. The surface areas of the third and fourth leaves of the melon crops grown according to this technology varied with the days of planting. Early differences between the two substrates were not significant. However, in later stages, melons grow faster. In the early stage of melon production, the chlorophyll content of pollution-free cultivation was higher than that of common cultivation methods. The flowering period was the period with the highest chlorophyll content in both cultivation techniques. However, the highest content of melon chlorophyll under this technology was about 2.0 mg, and the highest content of melon chlorophyll under common cultivation technology was about 1.4 mg, which verifies the effectiveness of the method. It has been verified that pollution-free cultivation technology can effectively improve the growth efficiency of melon crops and ensure the quality of melon cultivation.

Analysis of the chloroplast genomes of four Pinus species in Northeast China: Insights into hybrid speciation and identification of DNA molecular markers

Analysis of the chloroplast genomes of four Pinus species in Northeast China: Insights into hybrid speciation and identification of DNA molecular markers

Hard tick species (Acari: Ixodidae) and infestation in two livestock agroecosystems from Antioquia, Colombia.

Tick infestation affects about 80% of livestock globally while transmitting various pathogens causing high economic losses. This study aimed to determine the degree of tick infestation in two regions, North and Middle Magdalena in Antioquia, Colombia, to identify the ixodid tick species found and the associated risk factors. A cross-sectional study was carried out in 48 farms distributed in six municipalities of Antioquia. Two paddocks and eight bovines per farm were evaluated to estimate tick infestation (adults, nymphs, and larvae). Tick species were identified through a morphological and molecular analysis based on partial sequences of data obtained from DNA molecular markers, two mitochondrial (16S rRNA and COI), and one genomic DNA gene (18S rRNA). A multivariate Poisson regression model was applied to estimate the associated risk factors with ticks in cattle. Rhipicephalus microplus, Amblyomma patinoi and Dermacentor nitens were present in the livestock agroecosystems in the Middle Magdalena region; the highest incidence of tick infestation in cows and paddocks was reported in the municipality of Puerto Triunfo. The livestock agroecosystems in Middle Magdalena were characterized by a higher presence of adult R. microplus in cattle. Larval infestation of R. microplus, followed by D. nitens, was also found in paddocks. The multivariate analysis showed that the origin of cattle was the main risk factor associated with the presence of ticks (i.e., when cattle came from outside the farm). Cattle movement between farms in Middle Magdalena can contribute to the spread of ticks in this region.

Assessment of genome stability of pfleFB hybrid generations through molecular DNA markers

Using PEG-mediated protoplast fusion, a total of nine pfle somatic hybrids were developed between Pleurotus florida and Lentinula edodes. Only six could developed fruit bodies and the second generation was made of each through tissue culture isolate from their fruit bodies. The first generation were denoted as pfle1p, pfle1q, pfle1v, pfle 1s, pfle1o and the second generation were as pfle1pFB, pfle1qFB, pfle1vFB, pfle 1sFB, pfle1oFB. The genetic closeness, stability and variance is analyzed compared to their first parental strains using nine RAPD molecular markers. Amplified PCR bands were scored analyzed using SPSS software version 19. Polymorphisms were found calculating a total of 104 bands is 94.23% where the highest polymorphism was observed in RAPD-02, RAPD- 03, RAPD-08 and SS-11. Maximum bands (16) were generated by SRS-06 and minimum in SRS-05, ranged from 330 bp – 3000 bp and 450 bp – 2000 bp, respectively. Jaccards proximity matrix was generated from the scored data followed by dendogram including two generations with parents, using single linkage. The proximity matrix was ranged from 8.00-60.00. Two parental strains P. florida and L. edodes found to be most distantly related among all, where pfle 1pFB, pfle 1rFB were very close in genetic distance and another two hybrid lines, pfle 1vFB, pfle 1qFB were also showed the same. It was observed that the nearest neighbor showed a little variance genetically, but the hybrid lines are mostly similar with their second generation.

Molecular diversity analysis of rice (Oryza sativa L.) genotypes using RAPD and SSR marker

Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR) molecular markers were used for detecting the genetic variability of 20 rice genotypes using 79 SSRs and 30 RAPD primers. Among primers used, a set of 16 SSR and 14 RAPD markers showed polymorphism, and banding patterns were scored as 1 (present) or 0 (absent) in the datasheet which was further analyzed by using Jaccard’s similarity coefficient and SAHN clustering. The number of alleles, PIC value, and heterozygosity for individual 16 SSR and 14 RAPD markers were used to assess the degree of polymorphism among the rice genotypes. A total of 36 polymorphic loci were found in 16 polymorphic SSR markers and 77 polymorphic loci were observed in 14 polymorphic RAPD markers. The number of alleles produced per locus ranged from 2 (RM447, RM21, RM171, RM237, RM25, RM283, RM510, RM259, RM334, RM433, RM489, and RM212) to 3 (RM263, RM152, RM413, and RM3331) in 16 SSRs markers and 3 (OPR-05) to 9 (OPR-02 and OPC-06) in 14 RAPD. In SSRs, the PIC value diverse from 0.30 (RM447) to 0.58 (RM152) with an average of 0.38 per locus and an average value of heterozygosity (0.49). RAPD analysis showed an average PIC value of 0.78. Based on the information generated, the 20 rice genotypes were grouped into two main clusters in both the analysis of the marker. In SSR markers analysis, cluster I comprised 4 genotypes and cluster II comprised 16 genotypes and in RAPD cluster I was shown 2 genotypes and cluster II show 18 genotypes.

ОПРЕДЕЛЕНИЕ РАЗМЕРА НУКЛЕИНОВЫХ КИСЛОТ БАКТЕРИОФАГОВ PS.S-7 УЛГАУ И PS.S-27 УЛГАУ

The article presents results of studies on specification of the size of nucleic acids of Ps.s-7 UlGAU and Ps.s-27 UlGAU bacteriophages. The relevance of the research on classification of bacteriophages by type and size of nucleic acid is substantiated in the introduction of the article. It was established, by the method of extraction on magnetic particles and phenol-chloroform extraction, that the maximum calculated size for the DNA of Ps.s-7 UlGAU bacteriophage (isolated from a soil sample, characteristics: lytic activity, determined by the Gracio method, - 2.0 ± 0.1x109 pfu / ml, by Appelman's method - 10-8, drip test - n9; spectrum of lytic action - 85.7%) was 38137 bp, for Ps.s-27 UlGAU bacteriophage (isolated from a soil sample, characteristics: 1.0 ± 0.1x109 pfu / ml according to Grazio, according to Appelman - 10-8 , drop test - n9; spectrum of lytic action was 85.7%) DNA size was 23744 bp. The studies used a DNA molecular weight marker Quick-Load Extend DNA 500-48500 bp, a Nanodrop 2000 / 2000c spectrophotometer (ThermoFisher), and a PAGE electrophoresis technique. The obtained data will make it possible to specify the phylogenetic relationship of Ps.s-7 UlGAU and Ps.s-27 UlGAU bacteriophages with bacteriophages annotated in the NCBI database, using Protein BLAST, active against phytopathogenic Pseudomonas syringae bacteria, causing tumor neoplasms, rotting, growth cessation and death of a part of plants cultivated by humans without decay, chlorosis, necrosis, etc.

Morphoagronomic and molecular characterization of Euterpe oleracea accessions from eastern Brazilian Amazon

Açaí (Euterpe oleracea Mart.) - a common tropical palm has high social, economic, and environmental importance in the Amazon region. In the light of increasing exploration to obtain the fruit and heart of this palms, comprehensive studies are warranted for conservation and genetic improvement. Here, we characterized açaí accessions using phenological, morphological, and agronomic descriptors and random amplified polymorphic DNA (RAPD) molecular markers for joint selection of accessions with greater productivity. Hundred accessions were analyzed using 18 morphoagronomic descriptors and 13 RAPD markers. The spathe and inflorescence emission phases during flowering and fruiting showed seasonality. Based on the coefficient of variation and mean squared error, the accessions exhibited high variability in the tested morphoagronomic descriptors and were distributed into seven groups. Fruit, seed, and pulp weights were important descriptors for the distinction of accessions and identification of those with greater productivity. The accessions presented >85% similarity, and 85 accessions, distributed in nine subgroups, could not be differentiated using RAPD markers. There was no correlation between grouping based on morphometric descriptors and RAPD markers. Panicle weight was 3.9-9.0 kg in 15 accessions and 100-fruit pulp weight was 35-50 g in six accessions. Therefore, accessions with high productivity could be selected.

Locating illicit discharges in storm sewers in urban areas using multi-parameter source tracking: Field validation of a toolbox composite index to prioritize high risk areas

In urban areas served by separate sewerage systems, illicit connections to the storm drain system from residences or commercial establishments are frequent whether these misconnections were made accidentally or deliberately. As a result, untreated and contaminated wastewater enters into storm sewers leading to pollution of receiving waters and non-compliance with water quality standards. Typical procedures for detecting illicit connections to the storm sewer system are time consuming and expensive, especially in a highly urbanised area. In this study, we investigated the use of human wastewater micropollutants WWMPs (caffeine, theophylline, and carbamazepine) and advanced DNA molecular markers (human specific Bacteroides HF183 and mitochondrial DNA) as anthropogenic tracers in order to assist identifying potential cross connections.Water samples from storm outfalls and storm sewer pipes in three urban subcatchments were collected in dry weather from 2013 to 2018. All samples contained various concentrations of these markers especially HF183, caffeine and theophylline, suggesting that the storm pipe system studied is widely contaminated by sanitary sewers. None of the traditional indicators or markers tested is sufficient alone to determine the origin of fecal pollution. In a highly urbanised area, the combination of at least three specific human markers was needed in order to locate the residential section with likely misconnections. The human specific Bacteroides HF183, and theophylline appeared to be the most effective markers (along with E. coli) of crossconnections, whereas carbamazepine can provide an indication of contamination through sanitary sewer exfiltration. A composite sewer cross-connection index was developed, and eight misconnected houses were identified and corrected. The index approach enables the reduction of false positives that could lead to expensive interventions to identify cross-connected households. The results show the multiparameter source tracking toolbox as an effective method to identify sewer cross connections for sustainable storm water management.

Drought Tolerance and Application of Marker-Assisted Selection in Sorghum

Simple SummarySorghum is a climate-resilient crop grown in limited rainfall areas globally. However, climate change has increased temperature and shortened rainfall durations, which has constrained crop yield. We reviewed mechanisms of drought tolerance and application of marker-assisted selection in sorghum. Marker-assisted selection uses DNA molecular markers to map quantitative trait loci (QTL) associated with stay-green. Stg1, Stg2, Stg3, Stg4, Stg3A, and Stg3B QTLs associated with stay-green and high yield, have been mapped in sorghum. These QTLs are used for introgression into the senescent sorghum varieties through marker-assisted backcrossing.Sorghum is an important staple food crop in drought prone areas of Sub-Saharan Africa, which is characterized by erratic rainfall with poor distribution. Sorghum is a drought-tolerant crop by nature with reasonable yield compared to other cereal crops, but such abiotic stress adversely affects the productivity. Some sorghum varieties maintain green functional leaves under post-anthesis drought stress referred to as stay-green, which makes it an important crop for food and nutritional security. Notwithstanding, it is difficult to maintain consistency of tolerance over time due to climate change, which is caused by human activities. Drought in sorghum is addressed by several approaches, for instance, breeding drought-tolerant sorghum using conventional and molecular technologies. The challenge with conventional methods is that they depend on phenotyping stay-green, which is complex in sorghum, as it is constituted by multiple genes and environmental effects. Marker assisted selection, which involves the use of DNA molecular markers to map QTL associated with stay-green, has been useful to supplement stay-green improvement in sorghum. It involves QTL mapping associated with the stay-green trait for introgression into the senescent sorghum varieties through marker-assisted backcrossing by comparing with phenotypic field data. Therefore, this review discusses mechanisms of drought tolerance in sorghum focusing on physiological, morphological, and biochemical traits. In addition, the review discusses the application of marker-assisted selection techniques, including marker-assisted backcrossing, QTL mapping, and QTL pyramiding for addressing post-flowering drought in sorghum.

Development and application of microsatellite DNA molecular markers for the laboratory red crucian carp (Carassius auratus) strain C1HD

Development and application of microsatellite DNA molecular markers for the laboratory red crucian carp (Carassius auratus) strain C1HD

Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety "SSR41" and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1.

Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the “Yugu1” variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, “SSR41”, which is morphologically similar to, and readily cross-pollinates with, “Yugu1”. High-throughput resequencing of “SSR41” identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used “SSR41” and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.

Establishment of an Efficient Micropropagation System for Humulus lupulus L. cv. Cascade and Confirmation of Genetic Uniformity of the Regenerated Plants through DNA Markers

The demand for virus-free hop planting material has increased in the last few years due to its multipurpose uses. The present study aimed to establish an effective protocol for clonal propagation of cv. Cascade using only the cytokinins as PGRs in all stages of micropropagation: (i) in vitro culture initiation using single-node micro-cuttings inoculated on modified Murashige and Skoog (MSm) medium solidified with Plant agar and supplemented with 0.5 mg L−1 6-benziyladenine (BA) with 76% recorded viability of nodal explants; (ii) in vitro multiplication of multinodal shoots on MSm medium gelled with Plant agar and supplemented with different types and concentrations of cytokinins: 2 mg L−1 kinetin (KIN), 0.7 mg L−1 1-(2-Chloro-4-pyridyl)-3-phenylurea) (1 CPPU), 2 mg L−1 meta-topoline (mT) and 0.5 mg L−1 BA, which was the best variant for shoot proliferation (9.48 ± 0.78 shoots/explant); (iii) rooting and acclimatization with the best results obtained by ex vitro rooting and acclimatization of plants in the same stage in perlite (96.00 ± 0.60% acclimatized rooted plants with 100% survival under greenhouse conditions). The true-to-type nature of in vitro raised plants with the mother plant was assessed by Random Amplified Polymorphic DNA (RAPD) and Start Codon Target Polymorphism (SCoT) molecular markers, and then their genetic uniformity were confirmed.

GENETIC DIVERSITY EEL Anguilla marmorata BY RAPD IN THUA THIEN HUE PROVINCE, VIETNAM

Anguilla marmorata is a species with high economic value and increasingly interested by organizations and scientists. So far, many of the eel's biological characteristics remain mysterious, and they are often classified according to morphological features such as pigmentation patches, number of vertebrae, ... It is even difficult to distinguish one individual from another in some species, especially in the larval stage. In this study, the Random amplification of polymorphic DNA (RAPD) molecular marker was used to evaluate the genetic diversity of 48 eels collected in Thua Thien Hue province. Results showed that the genetic diversity of individuals in the Eel population studied is quite high. With 8 random primers via PCR, 77 DNA tapes with 76 polymorphic tapes were obtained, the tape size ranged from 170-2,500 bp, in which primer S10 showed the highest diversity with an average Ho value of 0.563, followed by primer S8 (Ho = 0.558). The lowest diversity was in the OPD5 primer (Ho = 0.300). The OPG17 primer is the primer that produces the most polymorphic tapes (13/13 tapes) and the S3 primer for the least amplified tapes polymorphism (9/10 DNA tapes). The diversity coefficient in each random primer ranged from about 0.300 to 0.563, with an average of 0.433. The genetic variation in the Eel population is random. Genetic variation can be attributed mainly to different eel breeding conditions and origins. Genetic similarity coefficients among the Eels varied from 0.660 to 0.910 and were divided into two main groups in genetic similarity coefficient 0.660.

Variants of ADPGK gene and its effect on the male reproductive organ parameters and sperm count in Hu sheep

ADP-dependent glucokinase (ADPGK) plays an important role instead of hexokinase in regulating energy metabolism via the Embden–Meyerhof–Parnas Pathway. And energy provided via glycolysis promotes testis development and spermatogenesis. In this study, 466 Hu sheep were screened for mutations in the ADPGK gene to examine the association of the ADPGK gene polymorphisms with the testis traits and spermatogenesis. The NC_056060.1: g.31295 C > T SNP was found in the 3′-UTR region, resulting in two genotypes CC and TC type with genotypic frequencies of 0.66 and 0.34, respectively. This mutation was significantly associated with testis weight, testis long circumference, testis short girth, epididymis weight, and sperm concentration (p < 0.05). Moreover, TC genotype individuals had an increased tendency in the expression of the ADPGK gene and had significant reproductive performance advantages compared with CC genotype individuals in the study. And compared with the small testes (<50 g), the ADPGK gene expression of big testes (>160 g) increased significantly. This indicates an association between the ADPGK gene and reproductive organ parameters and sperm count in selected Hu sheep breed, and this SNP may serve as an effective DNA molecular marker for marker-assisted selection in Hu sheep breeding programs.