High Rate Of Polymorphism Research Articles

Assessment of Genetic Parameters and Diversity Organization of Ginger Accessions Cultivated in Burkina Faso as Revealed by Microsatellite Markers

Rhizomes of Ginger (Zingiber officinale Rosc.) are widely used as a spice across the world. It has originated from South-east Asia and introduced to many parts of the world, and has been cultivated as a spice and for medicinal purpose. Ginger is a high value crop in Burkina Faso. The genetic diversity organization in ginger species is not well-known in Burkina Faso. Genetic resources are imperative for varietal selection. The importance of genetic resources depends on the levels of their diversity. The present investigation aims to assess the diversity of ginger accessions collected from Burkina Faso. Forty-seven ginger accessions collected from three provinces, Comoé (03), Léraba (14), Kénédougou (30), located in the southwestern zone of Burkina Faso were genotyped for their molecular traits using microsatellite markers. A total of 24 alleles were revealed by electrophoresis. All the simple-sequence repeats (SSR) set primers used revealed high polymorphic rate (100%) with the expected heterozygosity (0.499), showing their ability in assessment of the diversity levels and genetic organization of ginger accessions due to their codominance. The dendrogram obtained by the Neighbor-Joining method revealed three main genetic groups. The genetic differentiation index value (0.313) showed that the accessions of the three provinces were different, with an interesting diversity observed from kénédougou ginger accessions. Information from this study could be used in the development of effective management strategies for the conservation and effective use of the genetic resources within ginger accessions grown in Burkina Faso.

Development and validation of a 40 K liquid SNP array for the mud crab (Scylla paramamosain)

Genomic selection (GS) and genome-wide association studies (GWAS) have been widely implemented to accelerate the genetic improvement of important economic traits. Developing an efficient and reliable high-throughput genotyping tool is the premise and basis of implementing GS and GWAS on the mud crab (Scylla paramamosain). In this study, leveraging the whole-genome resequencing data of 146 mud crabs from the southeast coast of China, a total of 16,714,943 high-quality SNPs were discovered. Based on polymorphic information content and evenly distribution on 49 chromosomes, a total of 40,352 SNPs was selected to develop a 40 K liquid SNP array (named “Xiexin No. 1”) using the genotyping by target sequencing (GBTS) technology. The genotyping performance test showed that this SNP array had a high site polymorphism (over 92.70%) and individual calling rate (97.02%). Furthermore, the mean of SNP concordance, genotype concordance, non-reference sensitivity, and non-reference discrepancy between “Xiexin No. 1” SNP array and resequencing were identified to be 0.986, 0.954, 0.942, and 0.097, respectively. Using this SNP array data, the genomic heritabilities were evaluated as 0.887 ± 0.065, 0.643 ± 0.108, 0.599 ± 0.111, and 0.624 ± 0.111 for body weight (BW), carapace length (CL), carapace length (CW), and body height (BH) in a cultured population (233 crabs). Furthermore, five significant SNPs associated with growth traits were identified by GWAS. After annotation, one candidate gene (XP_027221997.1) associated with BW and one candidate gene (XP_027210446.1) associated with CW and BH were identified. Most importantly, the prediction accuracy of GBLUP for BW, BH, CL, and CW were 0.535 ± 0.064, 0.544 ± 0.101, 0.574 ± 0.087, and 0.585 ± 0.083, with the unbiasedness values of 0.988 ± 0.22, 1.015 ± 0.274, 1.011 ± 0.196 and 1.037 ± 0.235. In conclusion, the “Xiexin No. 1” SNP array provides an efficient and reliable platform for high-quality genotyping, which would greatly promote the genetic studies and thus accelerate the genetic improvement of mud crabs.

Detection of Novel spa Types in Clinical Isolates of Methicillin-Resistant Staphylococcus aureus in Iraq

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a gram-positive bacterium that is an opportunistic pathogen, causing infections in hospital settings and communities. MRSA has become a significant and increasing problem in Iraq. The aim of this study was to evaluate the genetic mutations of MRSA strains, especially in the spa gene, isolated from patients in Wassit, Iraq.Methods and Results: Biochemical tests were conducted to identify S. aureus isolates and then on MRSA. The MRSA was identified by the Chrome Agar method and confirmed by PCR with genotyping of the mecA gene. The disk diffusion method was used to detect antibiotic resistance to three different common antibiotics used at Wassit hospitals. The Vitek-2 compact system was utilized for the detection of the minimum inhibitory concentration (MIC) of vancomycin. All MRSA strains in this study were tested to screen the mecA gene, with 21 strains subjected to the molecular typing method for the spa gene. Out of 166 samples, 132(79.5%) contained S. aureus and 34(20.4%) were identified as MRSA. Genotyping showed that out of 34 MRSA, 31(91.2%) isolates were mecA-positive. The spa gene was detected in 21(61.8%) isolates out of 34 MRSA samples. The spa typing of 21 MRSA samples revealed four different spa types, as follows: t386 (3/14.3%), t3576 (1/4.8%), t10002 (1/4.8%), and t10234 (1/4.8%). High polymorphism rates were shown in isolates of spa type t386. Conclusion: Our data represent the first report to detect novel mutations in the spa gene in the MRSA clinical isolates from Wassit hospitals, Iraq.

Phenotypic and genotypic variability among exotic arabica coffee genotypes using morphological and molecular markers (SRAP)

Coffea arabica is said to have low genetic variability, however more information is still needed about the extent of diversity present in the arabica coffee gene pool by evaluating existing genetic resources present in India. The study therefore was conducted to assess the phenotypic and genotypic variability in arabica coffee germplasm accessions. Significant variation was observed among coffee accessions for the traits studied indicating the presence of diversity. Out of 20 traits, per cent ‘A’ grade bean contributed maximum to the diversity (63.29 %). The 41 arabica coffee accessions were grouped into six clusters. The maximum intra-cluster and inter cluster distance (D2 = 737.34) was revealed by cluster V (7 genotypes) and cluster II and VI (D2 = 8544.21), respectively. Principle Component Analysis displayed 79.50% of variability. Observations on Coffee Leaf Rust disease incidence showed that mean disease severity infection was ranged from 1.34 to 32.67%. On the other hand, molecular analysis of 10 SRAP primers established high rate of polymorphism with an average PIC value of 0.74. The UPGMA clustering grouped arabica coffee genotypes into two major clusters. The similarity matrix coefficient was ranged from 0 to 94%. SRAP marker demonstrated high polymorphism rate can be utilized for future crop improvement program in coffee. Study established high phenotypic but low genetic diversity among the arabica coffee accessions based on morphological and molecular markers, respectively and identified high yielding, coffee leaf rust disease resistant accessions which showed possibility of developing improved varieties through breeding.

Effect of X-rays on Seedling Pigment, Biochemical Profile, and Molecular Variability in Astrophytum spp.

Cacti are important in agricultural economies and one of the most popular horticultural plant groups. The genus Astrophytum is one of the most valuable and desirable cacti for growers and collectors around the world. By selecting the appropriate breeding methods to induce variations in combination with modern biotechnology tools for rapid change detection, it is possible to meet the challenges of the modern world in creating new variability in plants. However, there exists a lack of research concerning the impact of ionizing radiation on cacti. The aim of the study was to assess the effects of X-rays at different doses (0 Gy—control, 15, 20, 25, and 50 Gy) on the dynamics of seed germination in vitro, changes in the color of seedlings, biochemical changes in the content of metabolites and changes at the molecular level in Astrophytum spp. ‘Purple’. A significant effect of X-rays on the induction of genetic variation was observed. Remarkably high polymorphism rates were observed, ranging from 59.09% for primer S12 to a full 100.0% for S3 and S8, as determined by the SCoT (Start-Codon-Targeted) marker. In addition, a large variation in the content of plant pigments (anthocyanins, carotenoids, chlorophyll a, and chlorophyll b) was noted. Additionally, discernible alterations in the color of the tested cactus seedlings, assessed by the RHSCC catalog, were attributed to the impact of ionizing radiation. These findings hold promise for the application of radiomutation breeding in acquiring new cactus cultivars.

Diversity analysis of guava (Psidium guajava) germplasm collection

Guava (Psidium guajava L.) is one of the commercially important cultivated fruit crops in India. Guava ranks fifthin production share of fruit crops in the country. During 2014-15, India produced 36.68 lakh tonnes of guava from anarea of 2.68 lakh ha with 13.7 t/ha productivity. In the present investigation, a total 33 genotypes including 6 speciesof Psidium and 28 genotypes of Psidium guajava were characterized using 39 SSR markers. All accessions are beingcultivated at IARI research farm, Pusa campus, New Delhi. Samples were collected from research farm to determinethe overall diversity and to assess the similarity among genotypes using molecular markers. Out of 39 primers 26were reproducible. A total of 64 alleles were produced by 26 primers and number of alleles per locus variedfrom 1 (mPgCIR01, mPgCIR18 and mPgCIR19) to 5 (mPgCIR256) with mean value of 2.34. Gene diversity rangedfrom 0.0377 to 0.6681 with a mean value of 0.2766. Highest gene diversity was observed for primer mPgCIR256(0.6681) and lowest for primer mPgCIR24 (0.0377). SSR primer mPgCIR256 was most informative with high rateof polymorphism as well as number of alleles. Phenotypic correlation indicated the correlated traits with dependentyield trait. PCA and cluster analysis showed a significant phenotypic and genetic diversity among existing cultivars.All accessions were grouped into two major groups and under each group four sub groups. Maximum diversity wasfound in leaf traits, viz. leaf length, leaf breadth, petiole and petiole length. Genetic distance and the dissimilarity matrixshowed three major clusters on the basis of genetic similarity. All these accessions were grouped in to three clusters,viz. A, B and C. While cluster A includes only cultivars, cluster B includes all species except P. friedrichsthalianum.This indicates that, the diversity among and between species is at cluster level. Genetic diversity analysis amongPsidium species showed that P. guajava had more similarity with Psidium guienensis compared to other species.Present investigation indicated the presence of substantial diversity among guava species which can be utilized forfuture guava improvement programmes

Molecular characterization of Passiflora edulis f. flavicarpa Degener with ISSRs markers.

Passiflora edulis it is a specie widely distributed and cultivated in Colombia, with economic potential. Although there is a wide genetic and phenotypic variability, it has not yet been explored through the use of molecular techniques. This study aimed to characterize the structure and genetic diversity of P. edulis cultivars using ISSR markers. The study was carried out using leaf samples from 21 cultivars of P. edulis collected within a productive system in the department of Boyacá, Colombia, using seven ISSR primers. Genetic similarity was used to cluster by the UPGMA method, polymorphic information content (PIC), expected heterozygosity (He), Shannon index (I), gene flow (Nm), and coefficient of genetic differentiation (Gst) were estimated using POPGENE and TFPGA software. The Bayesian model and analysis of molecular variance (AMOVA) were used to assess the genetic structure. Cultivars of P. edulis showed high polymorphism rates. Seven ISSR produced 138 loci. The cluster analysis formed two groups according to the genetic similarity and phenotypic characteristics associated mainly with the fruit. The average value of expected heterozygosity was 0.29 for the total population and 0.27 and 0.22 for groups I and II, respectively. AMOVA indicates higher diversity within groups, but not between groups showing levels of hierarchy different from those considered in this study. Moderate genetic differentiation (Gst=0.12) and high gene flow (Nm=3.91) are observed.

Occurrence of simple sequence repeats in cDNA sequences of safflower (Carthamus tinctorius) reveals the importance of SSR-containing genes for cell biology and dynamic response to environmental cues.

Safflower (Carthamus tinctorius) is a diploid crop plant belonging to the family Asteraceae and is well known as one of important oilseed crops due to edible oil containing unsaturated fatty acids. In recent years it is gaining increased attention for food, pharmaceutical and industrial uses, and hence the updating its breeding methods is necessary. Genic simple sequence repeats (SSRs) in addition of being desire molecular markers, are supposed to influence gene function and the respective phenotype. This study aimed to identify SSRs in cDNA sequences and further analysis of the functional features of the SSR-containing genes to elucidate their role in biological and cellular processes. We identified 1,841 SSR regions in 1,667 cDNA sequences. Among all types of repeats, trinucleotide repeats were the most abundant (35.7%), followed by hexanucleotide (29.6%) and dinucleotide repeats (22.0%). Thirty five SSR primer pairs were validated by PCR reaction, detected a high rate of polymorphism (>57%) among safflower accessions, physically mapped on safflower genome and could clearly discriminate the cultivated accessions from wild relatives. The cDNA-derived SSR markers are suitable for evaluation of genetic diversity, linkage and association mapping studies and genome-based breeding programmes. Occurrence of SSR repeats in biologically-important classes of proteins such as kinases, transferases and transcription factors was inferred from functional analyses, which along with variability of their repeat copies, can endow the cell and whole organism the flexibility of facing with continuously changing environment, and indicate a structure-based evolution mechanism of the genome which acts as an up-to-dating tool for the cell and whole origanism, which is realized in GO terms such as involvement of most SSR-containing genes in biological, cellular and metabolic processes, especially in response to stimulus, response to stress, interaction to other organisms and defense responses.

Application of Microsatellite Markers for Genetic Diversity Analysis of Indonesian Local Cattle

Animal genetic resources (AnGR), including cattle, have been valuable national assets that need to be preserved and developed. There are at least 16 recognized breeds of cattle that have been registered as local and new breeds by the Ministry of Agriculture of the Republic of Indonesia. Conservation and development programs of these local cattle breeds require basic information regarding their genetic diversity, relationships, and structures. There are several types of DNA markers that can be used for genetic diversity analysis, such as microsatellite markers. Microsatellites or short tandem repeats (STRs) are a group of DNA sequences consisting of tandemly repeated units (1–6 bp), which are abundant throughout the genome and can be found in both coding and non-coding regions. The primary advantages of microsatellites are that they are inherited in a Mendelian pattern (codominant markers), high polymorphism rates, and high abundances throughout the genome. The aim of this review is to discuss the application of microsatellite markers for genetic diversity analysis in Indonesian local cattle based on 3 indices: number alleles per locus, expected heterozygosity (He), and polymorphisms information content (PIC). There are at least 28 microsatellite markers that have been studied in Indonesian local cattle, with the number of alleles per locus ranging from 2 to 32, He values ranging from 0.100 to 0.985, and PIC values from 0.095 to 0.935. Based on the PIC values, several microsatellites are classified as highly informative, e.g. BM1824, ILST6, TGLA126, TGLA53, TGLA227, TGLA122, ETH225, INRA23, SPS113, SPS115, BM1818, CSSM66, ETH10, INRA005, INRA037, ETH185, HEL017, and ILSTS029. Therefore, these microsatellite markers can be potentially used for future genetic diversity analysis of other breeds of cattle.

Microsatellite analysis in some watermelon (Citrullus lanatus) genotypes

Conservation of genetic resources is essential for the continuation of future crop production. Watermelon (Citrul-lus lanatus), a member of Cucurbitaceae, is widely distributed in tropical and subtropical regions. The aim of this study was to reveal the genetic relationships with the help of microsatellite markers in a watermelon collection free of unnecessary repetitions, and to determine the success of SSR (Simple Sequence Repeats) primers developed in cucurbits. In this study, 96 watermelon genotypes with good agronomic characteristics were used among the geno types collected from different regions of Turkey and purified up to the S4-S6 (self-pollination) stage. In the study, 33 SSR primer pairs were used to determine the genetic relationship between watermelon genotypes. In the study, a total of 67 bands were obtained with SSR primers. As a result of UPGMA (Unweighted Pair Group Method Using Arithmetic Averages) analysis, genotypes showed similarity at the level of 0.84-1.00. The number of alleles detected per primer varied between 1 and 6. In terms of the total number of alleles obtained, CMCT44 (5 units) and Cgb4767 (6 units) loci produced the most alleles. Primers with high polymorphism rate and allele excess were determined, and the possibilities for use in genetic stability analyses, variety differentiation and other genetic analyses were determined.

Лістеріоз: огляд проблеми, презентація клінічного випадку лістеріозного сепсису у 4-місячної дитини

Лістеріоз — це інфекційне захворювання, спричинене мікроорганізмами Listeria monocytogenes. Зараження людини може відбуватися фекально-оральним, аерогенним, трансплацентарним шляхами. Захворюваність в Україні на лістеріоз реєструється на спорадичному рівні, у вигляді поодиноких випадків, не пов’язаних між собою. Лістеріозу властиві висока летальність та поліморфізм клінічних проявів. Клініка хвороби характеризується поліорганністю: ураженням центральної нервової системи, септичними проявами, абортами, маститами; лістеріоз також може перебігати у формі безсимптомного носійства. У разі ураження нервової системи з’являються ознаки менінгіту, менінгоенцефаліту або абсцесу мозку. Актуальність проблеми діагностики та лікування лістеріозу обумовлена спорадичністю захворювання, поліморфізмом клінічних проявів, труднощами етіологічної верифікації діагнозу. Особливістю наведеного випадку стала принципова діагностична помилка при встановленні діагнозу: дитині не був встановлений сепсис. Лістеріоз у цієї дитини мав прогредієнтний перебіг з формуванням септичної форми. Проте лістеріоз — це рідкісна інфекція, тому прижиттєво було складно запідозрити саме цю інфекцію.

Determination of salt tolerance levels and genetic relationships of Vicia sativa cultivars using gene targeted functional markers

The objectives of the present study were to determine salt tolerance levels of 12 different common vetch (Vicia sativa L.) cultivars at germination stage in the presence of 250 mM NaCl and to reveal genetic relationships based on gene targeted functional markers (GTFMs) associated with salt tolerance. The results revealed the presence of a significant genetic variation among the cultivars although s alt stress significantly reduced all germination parameters tested. The cultivar Ozveren was the most salt tolerant with 20.1% reduction in final germination percentage compared to control seeds while cultivars Alınoglu, Ayaz and Bakir did not germinate. The maximum delays in germination rate (G50 = 3.78 days) and synchrony (G10-90 = 3.45 days) were obtained from the cultivars Urkmez and Ozveren, respectively. The GTFMs provided a total of 53.1% polymorphism. The primers of MtSOS2 gene gave the highest numbers of alleles per primer pair while the highest polymorphism rate (77.8%) was obtained from the MtP5CS gene. The first three components of principal component analysis explained 57.63% of total variation. This study concluded that the cultivars determined to be salt tolerant and sensitive at germination stage distributed into three main clades determined by UPGMA analysis while the GTFMs associated with salt tolerance successfully determined the genetic relationships of common vetch cultivars.

Molecular epidemiology of Paracoccidiodes spp. recovered from patients with paracoccidioidomycosis in a teaching hospital from Minas Gerais State of Brazil.

IntroductionParacoccidioidomycosis (PCM) is caused by several species of the Paracoccidioides genus which can be differentiated by interspecific genetic variations, morphology and geographic distribution. Intraspecific variability correlation with clinical and epidemiological aspects of these species still remains unclear. This study aimed to sequence the loci GP43, exon 2 and ARF of 23 clinical isolates of Paracoccidioides spp. from patients in the Southeast Region of Brazil.Methodology and main findingsGenBank was used to compare the present (23) with previous described sequences (151) that included ARF and GP43. It was identified a high polymorphism rate among the 23 isolates in comparison to the other 151. Among the isolates, 22 (95.66%) were S1/P. brasiliensis and 1 (4.34%) was identified as PS2/P. americana. A total of 45 haplotypes were found as follows: 19 from S1/P. brasiliensis (13 from the present study), 15 from P. lutzii, 6 from PS2/P. americana (1 from the present study), 3 from PS3/P. restrepiensis and 2 from PS4/P. venezuelensis. Moreover, exclusive haplotypes according to clinical origin and geographical area were found. S1/P. brasiliensis (HD = 0.655 and K = 4.613) and P. lutzii (HD = 0.649 and K = 2.906) presented the highest rate of polymorphism among all species, from which 12 isolates of the present study were clustered within S1b/P. brasiliensis. The GP43 locus showed a higher variability and was found to be the main reason for the species differentiation.ConclusionsThe results herein decribed show a high intraspecific genetic variability among S1/P. brasiliensis isolates and confirm the predominance of this species in the Southeast region of Brazil. The finding of exclusive haplotypes according to clinical origin and geographical area would suggest correlation between the molecular profile with the clinical form and geographic origin of patients with PCM.

Study of Genetic Diversity of the Aphid Predator Hippodamia variegata (Goeze) in Different Areas of Syria Using SRAP markers

This study was conducted in 2020 at the Laboratory of Biotechnology, Agronomy Department and Research Center for Biological Control Studies, Faculty of Agriculture, Damascus University. This study aimed to determine the genetic diversity of the variegated ladybug aphid predator Hippodamia variegata (Goeze) (Coleoptera: Coccinellidae) collected from different regions in Syria using the SRAP technique (Sequence-related Amplified polymorphism). The number of amplified fragments was 101 bands, 99 of which were polymorphic with a polymorphism rate of 97.99%. The number of polymorphic fragments ranged between two bands by using the primers pair SRAP-12 and 13 bands by using the primers pair SRAP-1, with an average of 6.6 bands for each primers pair. The lowest polymorphism rate was 83.33% for primers pairs SRAP-4 and SRAP-9, whereas the highest polymorphism rate was 100% for the rest of the primers pairs. The results obtained on the degree of genetic diversity of the predator's individuals H. variegata showed that the highest value for percent disagreement values was 0.904 between samples from Damascus and Latakia (Fedio) and Homs and Latakia (Fedio), whereas the lowest value for percent disagreement values was 0.271 between samples from Damascus and Sweida. The phylogenetic tree showed that the studied populations were divided according to their geographical distribution into two main groups; the first group included samples collected from the regions of Damascus, Sweida, and Homs with a genetic distance of 15.51, whereas the second group included samples collected from the regions of Tartous, Jabla (Beit Yashout), and Lattakia (Fedio) with a genetic distance of 11.08. This is the first study to determine genetic diversity of H. variegata in Syria. Keywords: Genetic diversity, predator, Hippodamia variegata, SRAP, Syria

Distinct Retrotransposon Evolution Profile in the Genome of Rabbit (Oryctolagus cuniculus).

Although the rabbit genome has already been annotated, it is mobilome remains largely unknown. Here, multiple pipelines were used to de novo mine and annotate the mobilome in rabbit. Four families and 19 subfamilies of LINE1s, two families and nine subfamilies of SINEs, and 12 ERV families were defined in rabbit based on sequence identity, structural organization, and phylogenetic tree. The analysis of insertion age and polymerase chain reaction suggests that a number of families are very young and may remain active, such as L1B, L1D, OcuSINEA, and OcuERV1. RepeatMasker annotation revealed a distinct transposable element landscape within the genome, with approximately two million copies of SINEs, representing the greatest proportion of the genome (19.61%), followed by LINEs (15.44%), and LTRs (4.11%), respectively, considerably different from most other mammal mobilomes except hedgehog and tree shrew, in which LINEs have the highest proportion. Furthermore, a very high rate of insertion polymorphisms (>85%) for the youngest subfamily (OcuSINEA1) was identified by polymerase chain reaction. The majority of retrotransposon insertions overlapped with protein-coding regions (>80%) and lncRNA (90%) genes. Genomic distribution bias was observed for retrotransposons, with those immediately upstream (−1 kb) and downstream (1 kb) of genes significantly depleted. Local GC content in 50-kb widows had significantly negative correlations with LINE (rs=−0.996) and LTR (rs=−0.829) insertions. The current study revealed a distinct mobilome landscape in rabbit, which will assist in the elucidation of the evolution of the genome of lagomorphs, and even other mammals.

The Frequencies of Allele Distribution of CYP2C9 and CYP2C19 Gene Polymorphisms in Healthy Papuan Population, Indonesia

This study's objective was to determine the distribution of allele frequencies of CYP2C9 and CYP2C19 gene polymorphisms among the Papuan population, known as the second-largest ethnic group in Indonesia. According to recent research, there is a decrease in CYP2C9 and CYP2C19 produced by humans globally, including in Indonesia. These gene polymorphisms aid in the transmission of various endogenous and exogenous drugs in the human body. Material and Methods: A sum of 99 subjects, comprising 73 male and 26 female subjects aged 20-30 years, were used for this research. PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) analysis using AvaII, NsiI, and SfaNI enzymes tested for the genotypes CYP2C9 and CYP2C19 administered. The distribution of genotypes was calculated in the population (P<0.05) using the Hardy-Weinberg equilibrium. The Faculty of Medicine Gadjah Mada University's Medical and Health Research Ethics Committee (MHREC) accepted this research with written consent. The results revealed that in Papua subjects, CYP2C9*2 (rs1799853) and CYP2C19*17 (rs12248560) alleles were absent while in 17 percent of the population CYP2C9*3 (rs1057910) allele frequency was. In conclusion, CYP2C9*3 has the highest polymorphism rate in Indonesia, with the absence of CYP2C9*2 and CYP2C19*17. Therefore, genetic drift can occur within this ethnic group. Keywords: Genotyping; Papuan ethnic; Pharmacogenetics; Polymorphisms

Implication of the Cytochrome <i>P-450c17α</i> (<i>CYP17α</i>) Gene in the Tumor Progression of Uterine Fibroids in Senegalese Women

Uterine fibroids, also known as leiomyomas, uterine myomas or fibroleiomyomas, are benign, encapsulated uterine tumors consisting of smooth muscle fibers of the uterus and connective tissue, the most common in the female genital tract. They affect 20 to 25% of women of childbearing age and are 3 to 9 times more common in black women than in white women, and nearly 70% of those close to 50 years of age. Uterine myomas are a real public health problem. The cost of treating them is expensive and the only treatment deemed effective is surgery. The rapid progression of leiomyomas during the childbearing years and regression after menopause indicate that estrogen plays a key role as a growth factor for these tumors. To contribute to the knowledge of the etiological factors involved in the tumor process of uterine fibroids, the study of the <i>Cytochrome P-450c17α</i> gene (<i>CYP17α</i>), involved in the hydroxylation of estrogen, has been carried out. Our study population consisted of 57 patients with uterine fibroids. After sampling (tumour tissue and peripheral blood), molecular analysis were done (DNA extraction, PCR-sequencing). Raw data were submitted to Mutation Surveyor 5.0.1 for mutation identification and AlamutVisual 2.12 software. The pathogenicity of each non-synonymous mutation was evaluated using Polyphen-2, Mutation Taster and SIFT. After cleaning, correction and alignment of sequences with BioEdit 7.0.8.0, genetic diversity, genetic differentiation and polymorphism of the gene <i>CYP17α</i> in correlation with epidemiological factors were determined with DNASP 5.10.01, MEGA 7.0.14, Arlequin 3.5.3.1 and the statistical software RStudio 3.5.1. Our results showed 84 mutations characterizing a high rate of tumor tissue polymorphism but also a genetic difference between tumor and peripheral blood. The mutation c.-34T>C which is located in the 5' promoter region at 34 bp upstream of the translation initiation site was found in patients with uterine fibroids. No genetic structuring of the <i>CYP17α</i> gene according to clinico-pathological parameters was observed. In conclusion, the cytochrome P450 enzymes responsible for highly specific reactions in the steroid biosynthesis pathway are gaining interest as molecular targets, given their role clé́ in the formation of various very potent endogenous steroid hormones. Indeed, current treatments for tumors, particularly fibroids, are mainly surgical and expensive. It is therefore essential to develop and evaluate alternatives to surgical procedures.

Discovery of Genome-Wide DNA Polymorphisms and Resistance-Relative Genes in Chaling Wild Rice (Oryza rufipogon Griff.) by Whole-Genome Sequencing

Chaling common wild rice (Chaling CWR, Oryza rufipogon Griff.) is a kind of germplasm resource which possesses abundant genetic diversity and plays a pivotal role in improving cultivated rice. In this research, we used next-generation sequencing technology to reveal the genome sequence of Chaling CWR and investigate its elite genes. The results showed that the average coverage was 93.99%. 1,743,368 single-nucleotide polymorphism (SNP) and 387,381 insertion and deletion (InDel) variants have been detected in Chaling CWR compared with the Nipponbare genome. The variant density was found to be highest in chromosome 10 and lowest in chromosome 5, with an average density of 467.08 SNPs/100 kb and 109.59 InDels/100 kb across the whole genome. 109,684 non-synonymous SNPs were identified in 14,315 genes, and 26,051 InDels were detected in the coding regions. We further classified these genes based on the protein domains that were involved in host defense mechanisms and in the analysis of 37 NBS-LRRs, 71 LRRs, 136 NB-ARCs, 119 PKs, 19 WRKY transcription factors, and 25 resistant protein genes. Among the putative R-genes, Pish, Pita, Pi25, Pi9, Pi21, Pid2, Pikm, and Xa21 were further identified, as exhibiting high rates of polymorphism. Results from this study provide a foundation for future basic research and marker-assisted breeding of rice resistance.

Sequence-Activity Relationships for the Snf7 Insecticidal dsRNA in Chrysomelidae.

The responsiveness of insects to oral delivery of insecticidal dsRNA has been shown to be dependent on dsRNA length and sequence match. Previous work with the western corn rootworm (WCR, Diabrotica virgifera virgifera; Coleoptera: Chrysomelidae) demonstrated that at least one ≥21 nt match must be present in the DvSnf7 dsRNA of approximately ≥60 base-pairs (bp) for activity. Further data is needed on the activity of <21 nt matches along with characterization of relationship between activity and the number of ≥21 nt matches. To characterize the sequence–activity relationship for insecticidal dsRNA further, the activity of orthologous Snf7 dsRNAs with 19, 20, and 21 nt contiguous matches against WCR was compared. Neither 19 nor 20 nt sequence matches were active, supporting that a ≥21 nt sequence match is required for activity. The relationship between the number of 21 nt matches with activity of Snf7 dsRNA orthologs from several Chrysomelid species was characterized using WCR and Colorado potato beetle (CPB, Leptinotarsa decemlineata; Coleoptera Chrysomelidae). For WCR, there was a strong relationship between an increasing number of 21 nt matches and increased activity (i.e., lower LC50 values). A similar relationship was observed for CPB with an exception for a single ortholog, which may be related to the exceptionally high rate of polymorphisms in CPB. Overall, these results demonstrate a general relationship between the number of 21 nt matches and activity, and this relationship could be used to inform a testing and assessment plan for an ecological risk assessment for an insecticidal dsRNA.

Spliceosomal Introns: Features, Functions, and Evolution

Spliceosomal introns, which have been found in most eukaryotic genes, are non-coding sequences excised from pre-mRNAs by a special complex called spliceosome during mRNA splicing. Introns occur in both protein- and RNA-coding genes and can be found in coding and untranslated gene regions. Because intron sequences vary greatly due to a high rate of polymorphism, the functions of intron had been for a long time associated only with alternative splicing, while intron evolution had been viewed not as an evolution of an individual genomic element, but rather considered within a framework of the evolution of the gene intron-exon structure. Here, we review the theories of intron origin, evolutionary events in the exon-intron structure, such as intron gain, loss, and sliding, intron functions known to date, and mechanisms by which changes in the intron features (length and phase) can affect the regulation of gene-mediated processes.