Analysis Of Genetic Relationships Research Articles

Genetic relationship analysis and molecular fingerprint identification of the tea germplasms from Guangxi Province, China.

The tea plant (Camellia sinensis) is an evergreen woody plant with a high economic value. Guangxi Province is adjacent to the origin center of the tea plant in southern China. It has abundant germplasm resources and is a historically important tea-producing province. However, there is little information about the genetic diversity, genetic introgression, and fingerprints of the tea germplasms from Guangxi Province. Here, we constructed a phylogenetic tree of 126 tea accessions from Guangxi Province using 20 SSR markers. This tree classified these tea accessions into three subgroups containing 19, 47, and 60 members, respectively. High genetic similarity was observed among the three subgroups, and the genetic diversity of the populations was ranked as follows: subgroup 3 > subgroup 2 > subgroup 1. Furthermore, we analyzed the genetic relationships among 168 tea accessions from Guangxi Province and neighboring provinces. The results of the population structure analysis were highly consistent with the clustering results, and genetic introgression was observed. We identified six SSRs as the core marker set, because they could sufficiently distinguish between all 126 tea accessions. The results provide a crucial theoretical basis for utilization and protection of tea germplasms from Guangxi Province, and will help improve the breeding and popularization of elite tea cultivars.

Analysis of genetic variability and character relationship in rice (Oryza sativa L.) seed and seedling traits

Eight rice genotypes with different genetic backgrounds were evaluated for grain length, grain width, grain length width ratio, grain thickness, 1000 grain weight, seed germination percent, shoot length, root length and root shoot ratio. The genetic variance (δ^2 g), phenotypic variance (δ^2 p), phenotypic covariance (PCV), genotypic coefficient of variation (GCV), heritability (h_b^2), genetic advance (GA), genetic advance in percent of mean (GA %) and correlation coefficient were all calculated. The experiment was conducted using a Randomized Block Design with three replications in a controlled environment in the laboratory of Department of Agriculture at Bangabandhu Sheikh Mujibur Rahman Science and Technology University Gopalganj in June 2021. For all of the studied characters, analysis of variance revealed a significant difference in genotypes. PCV values greater than GCV were found in all of the characteristics, indicating that they were influenced by non-additive gene action rather than environmental factors and that selection for improving these traits would be beneficial. The PCV (41.33) and GCV (41.70) estimates for the root shoot ratio were both high, indicating a wide range of variability for the two component characteristics, shoot length and root length. PCV and GCV values were moderate for grain length width ratio, seed germination percent, shoot length, and root length. The PCV and GCV of most grain characters were low. All of the characters had high heritability, ranging from 90.77 percent to 99.81 percent, except for 1000 grain weight (46.91 percent). Seed germination percent (36.03), shoot length (40.03), root length (35.16) and root shoot ratio (35.16) all had high heritability and high genetic advance in percent of mean (79.25). Grain thickness (8.68) and seed germination percent had the lowest GA% (8.71). Grain length with grain length width ratio, grain width with root shoot ratio, 1000 grain weight with grain width, grain thickness, root length and root shoot ratio were all found to have positive and significant correlations in a character association study. At the genotypic level, the highest positive significant correlation was found between 1000 grain weight and root shoot ratio (r_g= 0.908) and grain length and grain width ratio (r_p=0.900). According to genetic variability and correlation analysis, grain length, grain length width ratio, 1000 grain weight, root length and root shoot ratio could be used as selection indices for further improvement of seed and seedling characters of rice genotypes.

Genetic Diversity and Relationship Analysis of 21 Walnut Varieties Based on SSR Markers

In order to grasp the germplasm resources of walnut in Yunnan province, the genetic diversity and relationship of 21 walnuts varieties commonly planted in Yunnan province were analyzed using SSR fluorescent labeling technology. The results showed that the average number of allelic loci of 12 pairs of primers used in 21 walnut species samples was 7.916 7. The mean number of alleles, Shannon Wiener index (I) and polymorphic information content (PIC) per locus were 4.3516, 1.643 6 and 0.705 5. Twelve pairs of polymorphism information content (PIC) were higher than 0.25, indicating that the 12 pairs of primers had good polymorphism in the samples. In the phylogenetic analysis, the 21 walnut varieties were divided into 7 subgroups, indicating that the 21 walnut varieties had rich genetic diversity, extensive gene exchange and complex genetic background in the breeding process.

Genetic diversity and relationships among salvia species by ISSR markers

Species identification is fundamentally important within the fields of conservation, biology, biogeography and ecology. Salvia species are herbaceous, biennial or annual, strongly aromatic. Inter-Simple sequence repeats (ISSR) molecular markers were used for evaluate genetic diversity and relationship analysis of 30 Salvia species. Ten selected ISSR primers amplified 116 loci, respectively, of which all were polymorphic. The obtained average polymorphism information content 0.39, average band informativeness 10.5 and the marker index 3.1 revealed high genetic diversity prevailing among Salvia accessions. The dendrogram was constructed based on ISSR separated the individuals into sub-clusters in accordance with their species. Our results indicated that ISSR markers can be used as a reliable and informative technique for evaluation of genetic diversity and relationships among Salvia species. The objectives of present study are: 1) can ISSR markers identify Salvia species, 2) what is the genetic of these taxa in Iran, and 3) to investigate the species inter-relationship?

Identification and Genetic Relationship Analysis of <i>Torreya</i> Based on nrDNA ITS Sequence

In order to evaluate the identification ability of nrDNA ITS sequences on Torreya , this study used ITS sequence and four different analysis methods (BLAST, K2P genetic distance, SNP analysis, NJ tree) to identify species of Torreya , and established phylogenetic trees to discuss their phylogenetic relationships. The results showed that the length of 48 ITS sequences was 1 095 bp~1 105 bp, the average intraspecies genetic distance was 0.001 6 and the average interspecies genetic distance was 0.015 0. At the species level, BLAST alignment and NJ tree had the highest efficiency in Torreya . The SNP loci analysis could effectively identify T. grandis cv . ‘ Merrillii ’ and T. grandis . The analysis of genetic relationship showed that all the other species of Torreya were single-line branches, but the quince tree of T. yunnanensis and T. fargesii were clustered into a cluster in the ML tree, indicating that the two were closely related. This provided evidence for the nuclear genome sequence proposed the incorporation of T. yunnanensis and T. fargesii . This study showed that ITS sequence could be used as a DNA barcode for the identification of Torreya , and providing reference for the identification and systematic relationship of Torreya.

Comparison of identity by descent estimates with Plink and refinedIBD in dogs

Article Details: Received: 2020-05-26 | Accepted: 2020-07-10 | Available online: 2020-12-31 https://doi.org/10.15414/afz.2020.23.04.213-216 With the availability of dense SNP genotype data various types of estimation methods were developed to estimate relatedness of any two individuals, even in absence of traditional pedigrees. One of the most prominent method was the identity by descent (IBD), widely used in genetic diversity studies. IBD itself could be estimate using different approaches and software that might provide different results. The purpose of this study was to compare the estimates from two established software, probabilistic approach by Plink and a non-probabilistic approach based on haplotypes by refinedIBD. High density SNP genotypes from 98 Leonberger dogs were used to estimate IBD coefficients based on two data types: with one of the SNP markers in high linkage disequilibrium removed, as required by Plink, and SNP markers subjected only to standard quality control, as required by refinedIBD. The Pearson correlation coefficients from pairwise estimates were 0.97 when estimated with the same software and 0.84 between the two software and data types, as required by the respective user manuals. The numerical differences were clustered around zero (i.e. no to little difference) for half of the pairwise comparisons, and up to ±0.1 for the vast majority of cases. The most extreme differences were consistently estimated higher by Plink. Because of these differences a follow up investigation should be done, including pedigrees, as well as simulated data to provide a comprehensive analysis. Keywords: SNP, Plink, refinedIBD, Leonberger, companion animals References BROWNING, B.L. and BROWNING, S.R. (2013). Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data. Genetics, 194(2), 459–471. https://doi.org/10.1534/genetics.113.150029 CHANG, C.C., CHOW, C.C., TELLIER, L.C., VATTIKUTI, S., PURCELL, S.M. and LEE, J.J. (2015). Second-Generation PLINK: Rising to the Challenge of Larger and Richer Datasets. GigaScience, (4) 7. https://doi.org/10.1186/s13742-015-0047-8 NASERI, A., LIU, X., TANG, K., ZHANG, S. and ZHI, D. (2019). RaPID: Ultra-Fast, Powerful, and Accurate Detection of Segments Identical by Descent (IBD) in Biobank-Scale Cohorts. Genome Biology, 20(1), 143. https://doi.org/10.1186/s13059-019-1754-8 R CORE TEAM (2019). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/ SPEED, D. and BALDING, D.J. (2015). Relatedness in the Post-Genomic Era: Is It Still Useful? Nature Reviews Genetics, 16(1), 33–44. https://doi.org/10.1038/nrg3821 TAYLOR, A.R., JACOB, P.E., NEAFSEY, D.E. and BUCKEE, C.O. (2019). Estimating Relatedness Between Malaria Parasites. Genetics, 212(4), 1337–1351. https://doi.org/10.1534/genetics.119.302120 WEIR, B.S., ANDERSON, A.D. and HEPLER, A.B. (2006). Genetic Relatedness Analysis: Modern Data and New Challenges. Nature Reviews Genetics, 7(10), 771–780. https://doi.org/10.1038/nrg1960 WRIGHT, S. (1922). Coefficients of Inbreeding and Relationship. The American Naturalist, 56(645), 330–338.

An Analysis of the Genetic Relationships and Inbreeding in Tatra Shepherd Dogs Depending on the Type of Breeding

The aim of the study was the analysis of the structure of the population, relationship coefficients, and inbreeding trends in terms of: sex, breeding system, and inbreeding degree of Tatra Shepherd dogs. The breed's inbreeding rate was 6.34%, and for a standardised 4-generation population was 6.68%. The highest inbreeding rate was found in "non-champion-dogs" and in "Polish dog" groups consisting of males and females. The limit value FX was exceeded for 25.65% of Tatra dogs, and the critical value was exceeded for 11.52%. An increasing ancestor loss coefficient (AVK) was found, which may result in an increased number of inbred animals. In particular, this referred to female dogs in the nCH, PL, and Z groups, whereas a significant increase of AVK was observed in the group of male dogs from foreign kennels. The resulting COR values were 55.58% for males and 55.44% for females.

Admixture Analysis Using Genotyping-by-Sequencing Reveals Genetic Relatedness and Parental Lineage Distribution in Highbush Blueberry Genotypes and Cross Derivatives.

Blueberries (Vaccinium section Cyanococcus) are perennial shrubs widely cultivated for their edible fruits. In this study, we performed admixture and genetic relatedness analysis of northern highbush (NHB, primarily V. corymbosum) and southern highbush (SHB, V. corymbosum introgressed with V. darrowii, V. virgatum, or V. tenellum) blueberry genotypes, and progenies of the BNJ16-5 cross (V. corymbosum × V. darrowii). Using genotyping-by-sequencing (GBS), we generated more than 334 million reads (75 bp). The GBS reads were aligned to the V. corymbosum cv. Draper v1.0 reference genome sequence, and ~2.8 million reads were successfully mapped. From the alignments, we identified 2,244,039 single-nucleotide polymorphisms, which were used for principal component, haplotype, and admixture analysis. Principal component analysis revealed three main groups: (1) NHB cultivars, (2) SHB cultivars, and (3) BNJ16-5 progenies. The overall fixation index (FST) and nucleotide diversity for NHB and SHB cultivars indicated wide genetic differentiation, and haplotype analysis revealed that SHB cultivars are more genetically diverse than NHB cultivars. The admixture analysis identified a mixture of various lineages of parental genomic introgression. This study demonstrated the effectiveness of GBS-derived single-nucleotide polymorphism markers in genetic and admixture analyses to reveal genetic relatedness and to examine parental lineages in blueberry, which may be useful for future breeding plans.

SNP-based Genetic Diversity and Relationships Analysis of the Korean Native Black Goat and Crossbred Goat

SNP-based Genetic Diversity and Relationships Analysis of the Korean Native Black Goat and Crossbred Goat

Genetic polymorphisms of 44 Y chromosomal genetic markers in the Inner Mongolia Han population and its genetic relationship analysis with other reference populations

Y chromosomal genetic markers in the non-recombining region are commonly used for human evolution research, familial searching, and forensic male differentiation since they strictly follow paternal inheritance. Y chromosomal short tandem repeats (Y-STRs) possess extraordinarily advantages in forensic applications because of their high polymorphisms and special genetic pattern. Here, we assessed the genetic diversities of 41 Y-STRs and three Y chromosomal insertion/deletion (Y-InDels) loci in the Chinese Inner Mongolia Han population; besides, genetic differentiation analyses among the studied Han population and other previously reported populations were conducted based on 27 same Y-STRs. Totally, 425 alleles were observed in 324 Inner Mongolia Han individuals for these Y-markers. Gene diversities of these Y-markers distributed from 0.0306 to 0.9634. The haplotype diversity and discriminatory capacity of these Y-markers in the Inner Mongolia Han population were 0.9999 and 0.98457, respectively. Haplotype resolution comparisons of different Y-marker groups in the studied Han population revealed that higher haplotype resolution could be achieved for these 44 Y-markers. Population genetic analyses of the Inner Mongolia Han population and other reference populations demonstrated that the studied Han population had relatively closer genetic affinities with Northern Han Chinese populations than Southern Han and other minority groups. To sum up, these 44 Y-markers can be utilized as a valuable tool for male differentiation in the Inner Mongolia Han population.

THE STATE OF BROWN CARPATHIAN AND BROWN CAUCASIAN CATTLE BREEDS ON FAO PROJECT TCP/RER/3604 “CONSERVATION AND DEVELOPMENT OF DUAL-PURPOSE CATTLE BREEDS IN EASTERN EUROPE”

During 2018–2019 Ukraine took part in the project of Food and Agriculture Organization (FAO) «Conservation and development of double-purpose cattle breeds in Eastern Europe» (TCP/RER/3604). The project covered Brown Carpathian and Brown Caucasian breeds of Armenia, Georgia and Ukraine. On the results of the project, experts from the FAO Regional Office for Europe and Central Asia, international experts prepared reports on gender, social and economic characteristics of the studied regions, genomic analysis of samples and provided recommendations for breeding in the regions with the breeds. It was considered expedient to present these results to the general scientific community.
 At each country FAO have chosen service-provider (organization), which should make survey on productive environment of targeted breed (in Ukraine – Brown Carpathian), conclude the general state of the breed, visit at least 100 farms where Caucasian/Carpathian Brown cattle breed was kept, collect information from 300 cows and 20 bulls, and genetic samples from at least 100 cows and 20 bulls kept for breeding. Service-provider in Ukraine was M.V.Zubets Institute of Animal Breeding and Genetics, NAAS.
 Scientists of M.V.Zubets Institute of Animal Breeding and Genetics and other sub-contracting organizations during February-June, 2019 investigated 265 heads of cattle in 31 villages 5 districts of the Transcarpathian region, phenotypically classified as Brown Carpathian breed, including 6 breeding bulls of mating age (1.5–2 years). Each animal was photographed, linearly descriptive features of the exterior were evaluated, the necessary body measurements were taken with the help of appropriate tools, live weight and constitutional features were determined, and samples were taken for genetic testing.
 A total of 554 hair samples were taken from the project (123 – from Armenia, 141 – from Georgia and 290 – from Ukraine).
 The basis for classifying the animals as Brown Carpathian was phenotypic examination and strict compliance with the main characteristics of the breed: uniform grey or brown colour with different shades of it, general conformation typical for the breed, lighter belt along the back, black muzzle with lighter hair around it, black hooves and horn tips, lighter "glasses" around the eyes, thick light hair inside outer ears.
 To form the genetic passport of the population, hair was selected from the tail switch of selected animals using equipment provided by FAO, sent to the laboratories of the International Atomic Energy Agency, Austria. In the laboratory in the district of Siebersdorf, DNA was isolated from the obtained samples, the genetic diversity of populations, the degree of inbreeding and their effective number, kinship between populations were assessed and the genetic structure and level of influence of other breeds were analysed.
 DNA was extracted from each hair follicle using a MasterPure kit (Biozym, Illumina, USA) according to the protocol of the Association of Public Health Laboratories (APHL). The isolated DNA was subjected to a two-step quality control procedure before preparation for wide-genome typing. DNA samples were measured using a Nanodrop spectrophotometer to obtain a concentration with a ratio of 260/280 and 260/230. According to the results obtained using a spectrophotometer, DNA samples were diluted to measure high-quality double-stranded DNA (dsDNA) by PicoGreen Assay. The final working DNA was prepared based on PicoGreen measurements and stored at – 20°C for further processing.
 Sample genotyping was performed using a third-generation 384-cell matrix to assess Bovine individuals on the Affymetrix-Axiom platform (Axiom Bovine Genotyping v3 array). Within the project, 48 individuals of Austrian Simmental and 18 – Ayrshire breeds were also genotyped for comparison. The matrix included 64.000 SNPs, providing a high probability of covering genomic variations of the Bos taurus and Bos indicus breeds.
 Intra-breed genetic diversity was assessed using PLINK v1.09 to calculate actual heterozygosity (H0) and inbreeding coefficient (FIS).
 Analysis of genetic parameters of population diversity evidenced a rather low inbreeding rate of Brown Carpathian breed and a fairly high effective population size compared to European breeds, which can indicate a very limited practice of artificial insemination and lack of selection among bulls.
 Analysis of genetic differentiation and relationship between populations, principal components analysis and determination of admixtures of other breeds proved the uniqueness of the Brown Carpathian breed from a genetic point of view.
 Based on the conducted genomic analysis of populations, consultations with project participants, reports of service providers of each country, an international consultant on animal genetic resources, chairman of the ICAR working group on functional traits, formed a breeding program for the studied populations. The breeding program included proposals for further selection work, calculation of basic selection-genetic parameters, selection effect, number of bulls and heifers for selection nucleus, number of doses to maintain genetic diversity of the population, cost of population restoration, breeding work of breeding centre and work plan by years to implement a breeding program.
 Gender analysis of service providers' reports showed some gender differentiation in livestock care, processing and everyday life of owners of Brown Carpathian cattle.

Domestication of the Emblematic White Cheese-Making Fungus Penicillium camemberti and Its Diversification into Two Varieties

Domestication involves recent adaptation under strong human selection and rapid diversification and therefore constitutes a good model for studies of these processes. We studied the domestication of the emblematic white mold Penicillium camemberti, used for the maturation of soft cheeses, such as Camembert and Brie, about which surprisingly little was known, despite its economic and cultural importance. Whole-genome-based analyses of genetic relationships and diversity revealed that an ancient domestication event led to the emergence of the gray-green P.biforme mold used in cheese making, by divergence from the blue-green wild P.fuscoglaucum fungus. Another much more recent domestication event led to the generation of the P.camemberti clonal lineage as a sister group to P.biforme. Penicillium biforme displayed signs of phenotypic adaptation to cheese making relative to P.fuscoglaucum, in terms of whiter color, faster growth on cheese medium under cave conditions, lower amounts of toxin production, and greater ability to prevent the growth of other fungi. The P.camemberti lineage displayed even stronger signs of domestication for all these phenotypic features. We also identified two differentiated P.camemberti varieties, apparently associated with different kinds of cheeses and with contrasted phenotypic features in terms of color, growth, toxin production, and competitive ability. We have thus identified footprints of domestication in these fungi, with genetic differentiation between cheese and wild populations, bottlenecks, and specific phenotypic traits beneficial for cheese making. This study has not only fundamental implications for our understanding of domestication but can also have important effects on cheese making.

Identification and characterization of SNPs in released, landrace and wild accessions of mungbean (Vigna radiata (L.) Wilczek) using whole genome re-sequencing

Mungbean [Vigna radiata (L.) R. Wilczek var. radiata] is vital grain legume having nutritional and socio-economic importance, especially in the developing countries. We performed whole-genome re-sequencing of three accessions representing the wild progenitor species, released and landrace of mungbean to identify SNPs with relevance to genetic relationships analysis. Approximately 9.3 million raw reads were obtained using Ion Torrent PGM™ platform and more than 92% of the reads were mapped to the reference mungbean genome. We identified a total of 233,799 single-nucleotide polymorphisms in relation to the reference genome (SNPs: 103,341 in wild, 93,078 in released and 37,380 in landrace accessions) and 9544 insertions and deletions (InDels: 4742 in wild, 3608 in released and 1194 in landrace accessions) in the coding and non-coding regions. In all accessions, genomic variants were unevenly distributed within and across the mungbean chromosomes. Among these 5339, 4739 and 1795 SNPs were non-synonymous in 815, 790 and 317 genes of wild, released and landrace accessions, respectively. These polymorphisms might contribute to the variation in important pathways of genes for abiotic and biotic stress tolerance and important agronomic traits, such as seed dormancy, flowering time and seed size in mungbean. Among the randomly selected SNPs, a selected subset was validated using Sanger sequencing technique. The genomic variations among mungbean wild, released and landrace accessions constitute a powerful tool to support genetic research and molecular breeding of mungbean.

Using spatial genetics to quantify mosquito dispersal for control programs

BackgroundHundreds of millions of people get a mosquito-borne disease every year and nearly one million die. Transmission of these infections is primarily tackled through the control of mosquito vectors. The accurate quantification of mosquito dispersal is critical for the design and optimization of vector control programs, yet the measurement of dispersal using traditional mark-release-recapture (MRR) methods is logistically challenging and often unrepresentative of an insect’s true behavior. Using Aedes aegypti (a major arboviral vector) as a model and two study sites in Singapore, we show how mosquito dispersal can be characterized by the spatial analyses of genetic relatedness among individuals sampled over a short time span without interruption of their natural behaviors.ResultsUsing simple oviposition traps, we captured adult female Ae. aegypti across high-rise apartment blocks and genotyped them using genome-wide SNP markers. We developed a methodology that produces a dispersal kernel for distance which results from one generation of successful breeding (effective dispersal), using the distance separating full siblings and 2nd- and 3rd-degree relatives (close kin). The estimated dispersal distance kernel was exponential (Laplacian), with a mean dispersal distance (and dispersal kernel spread σ) of 45.2 m (95% CI 39.7–51.3 m), and 10% probability of a dispersal > 100 m (95% CI 92–117 m). Our genetically derived estimates matched the parametrized dispersal kernels from previous MRR experiments. If few close kin are captured, a conventional genetic isolation-by-distance analysis can be used, as it can produce σ estimates congruent with the close-kin method if effective population density is accurately estimated. Genetic patch size, estimated by spatial autocorrelation analysis, reflects the spatial extent of the dispersal kernel “tail” that influences, for example, the critical radii of release zones and the speed of Wolbachia spread in mosquito replacement programs.ConclusionsWe demonstrate that spatial genetics can provide a robust characterization of mosquito dispersal. With the decreasing cost of next-generation sequencing, the production of spatial genetic data is increasingly accessible. Given the challenges of conventional MRR methods, and the importance of quantified dispersal in operational vector control decisions, we recommend genetic-based dispersal characterization as the more desirable means of parameterization.

Analysis of genetic relationships of genotypes of the genus Rosa L. from the collection of Nikita Botanical Gardens using ISSR and IRAP DNA markers

In connection with the development of breeding and the creation of new plant varieties, the problem of their genotyping and identification is becoming increasingly important, therefore the use of molecular methods to identify genetic originality and assess plant genetic diversity appears to be relevant. As part of the work performed, informative ISSR and IRAP DNA markers promising for the study of genetic diversity of the Rosa L. genus were sought and applied to analysis of genetic relationships among 26 accessions of the genus Rosa L. from the gene pool collection of Nikita Botanical Gardens. They included 18 cultivated varieties and 8 accessions of wild species. The species sample included representatives of two subgenera, Rosa and Platyrhodon. The subgenus Platyrhodon was represented by one accession of the species R. roxburghii Tratt. Cultivated roses were represented by varieties of garden groups hybrid tea, floribunda, and grandiflora. The tested markers included 32 ISSRs and 13 IRAPs. Five ISSR markers (UBC 824, ASSR29, 3A21, UBC 864, and UBC 843) and three IRAPs (TDK 2R, Сass1, and Сass2) were chosen as the most promising. They were used for genotyping the studied sample of genotypes. In general, they appeared to be suitable for further use in studying the genetic diversity of the genus Rosa L. The numbers of polymorphic fragments ranged from 12 to 31, averaging 19.25 fragments per marker. For markers UBC 864 and UBC 843, unique fingerprints were identified in each accession studied. The genetic relationships of the studied species and varieties of roses analyzed by the UPGMA, PCoA, and Bayesian methods performed on the basis of IRAP and ISSR genotyping are consistent with their taxonomic positions. The genotype of the species R. roxburghii of the subgenus Platyrhodon was determined genetically as the most distant. According to clustering methods, the representative of the species R. bengalensis did not stand out from the group of cultivated varieties. When assessing the level of genetic similarity among the cultivated varieties of garden roses, the most genetically isolated varieties were ‘Flamingo’, ‘Queen Elizabeth’, and ‘Kordes Sondermeldung’; for most of the other varieties, groups of the greatest genetic similarity were identified. This assessment reflects general trends in phylogenetic relationships, both among the studied species of the genus and among cultivated varieties.

Genetic analysis of twenty two selected genotypes of Jatropha curcas L. (physic nut) from Africa, Asia and America, using SSR and AFLP markers

Twenty two genotypes of J. curcas L. from Africa (Senegal, Burkina Faso, Mali, Congo and Madagascar Island), Asia (Cambodia, China and India) and America (Ecuador, Dominican Republic and Brazil) selected for their vigor and their productivity were analyzed with ten SSR primer pairs and six AFLP primer combinations. The two marker approaches showed their ability to effectively reveal polymorphism among the selected genotypes: 94.02 and 56% of polymorphism for AFLPs and SSRs respectively. Among the three groups of selected genotypes, the Asian group was the least diverse while the genetic diversities found in African and American groups were slightly comparable. The Nei’s genetic diversity (He) of all twenty-two selected genotypes was 0.2029 based on combined SSR+AFLP data. The Gst value and the AMOVA analysis indicated that more than 80% of the genetic diversity resided within the groups. The analysis of the genetic relationships between the genotypes using the Nei’s standard dissimilarity matrix gave dissimilarity coefficients ranging from 0.14397 to 0.73943 with an average of 0.3540. The most distant genotypes were found between a genotype from Africa (Congo) and one from America (Ecuador). The clustering of genotypes obtained with the neighbor-joining dendrogram and the PCoA analysis revealed the existence of a certain level of diversity that can be used by breeders. Key words: Biodiesel, genetic diversity, jatropha, molecular markers, AFLP, SSR, plant breeding.

Use of a whole genome sequencing-based approach for Mycobacterium tuberculosis surveillance in Europe in 2017-2019: an ECDC pilot study.

Whole genome sequencing (WGS) can be used for molecular typing and characterisation of Mycobacterium tuberculosis complex (MTBC) strains. We evaluated the systematic use of a WGS-based approach for MTBC surveillance involving all European Union/European Economic Area (EU/EEA) countries and highlight the challenges and lessons learnt to be considered for the future development of a WGS-based surveillance system.WGS and epidemiological data of patients with rifampicin-resistant (RR) and multidrug-resistant (MDR) tuberculosis (TB) were collected from EU/EEA countries between January 2017 and December 2019. WGS-based genetic relatedness analysis was performed using a standardised approach including both core genome multilocus sequence typing (cgMLST) and single nucleotide polymorphism (SNP)-based calculation of distances on all WGS data that fulfilled minimum quality criteria to ensure data comparability.A total of 2218 RR/MDR-MTBC isolates were collected from 25 countries. Among these, 56 cross-border clusters with increased likelihood of recent transmission (≤5 SNPs distance) comprising 316 RR/MDR-MTBC isolates were identified. The cross-border clusters included between two and 30 resistant isolates from two to six countries, demonstrating different RR/MDR-TB transmission patterns in Western and Eastern EU countries.This pilot study shows that a WGS-based surveillance system is not only feasible but can efficiently elucidate the dynamics of in-country and cross-border RR/MDR-TB transmission across EU/EEA countries. Lessons learnt from this study highlight that the establishment of an EU/EEA centralised WGS-based surveillance system for TB will require strengthening of national integrated systems performing prospective WGS surveillance and the development of clear procedures to facilitate international collaboration for the investigation of cross-border clusters.

Genetic structure of Tunisian sheep breeds as inferred from genome-wide SNP markers

Abstract Assessing the status of genetic variability of native sheep breeds could provide important clues for research and policy makers to devise better strategies for the conservation and management of genetic resources. In this study, a genetic investigation of Tunisian sheep breeds using a genome-wide scan of approximately 50,000 SNPs was performed. To reconstruct genetic structure and relationships among four sheep breeds, 40 samples belonging to fat-tailed Barbarine, Queue Fine de l’Ouest, Noire de Thibar and D’Man breeds were genotyped using Illumina Ovine SNP50 BeadChip. Tunisian breeds averaged 96 % polymorphic loci with an expected heterozygosity (He = 0.36). Genetic analysis of relationship between breeds using Bayesian clustering, MDS and Neighbor-Network analysis, and estimation of FST genetic structure, highlighted the genetic differentiation of Noire de Thibar breed from the other local breeds, reflecting the effect of past events of introgression of European gene pool. The Queue Fine de l’Ouest breed showed a genetic heterogeneity and was close to Barbarine and D'Man breeds, as evidenced by MDS and the lowest level of differentiation with Barbarine breed (FST = 1.8 %). The D'Man breed shared a considerable gene flow with the thin-tailed Queue Fine de l'Ouest breed. Possible factors explaining the genetic patterns observed, such as considerable gene flow probably due to anthropogenic activities in the light of population management and conservation programs.

Short Communication: Identification and phylogenetic analysis of Corynebacterium diphtheriae isolates from Jakarta, Indonesia based on partial rpoB gene

Abstract. Yasmon A, Rosana Y, Usman D, Prilandari LI, Hartono TS. 2020. Short Communication: Identification and phylogenetic analysis of Corynebacterium diphtheriae isolates from Jakarta, Indonesia based on partial rpoB gene. Biodiversitas 21: 3070-3075. Indonesia is a developing country with the greatest potential of diphtheria, so accurate identification is needed to detect C. diphtheriae. The genetic relationship analysis is important to be determined so that this transmittable disease can be prevented. In this study, we reported the identification and phylogenetic analysis of C. diphtheriae based on partial rpoB gene. Twelve samples from throat swabs of diphtheria suspected patients from 2018 to 2019 were used in this study. The result of VITEK 2 ANC-Automated Testing identified that all isolates were C. diphtheriae. However, the identification based on partial rpoB gene analysis showed that only 10 out of 12 isolates were C. diphtheriae, while 2 other isolates were C. argentoratense. Of 10 C. diphtheriae strains/isolates, 2 strains were unique for Indonesia. Thus, it is needed to evaluate the accuracy of VITEK 2 ANC-Automated Testing and to conduct further comprehensive studies on the genetic relationships of C. diphtheriae strains based on multiple virulence genes, multilocus sequence typing and/or whole-genome analysis.

Research of Mating System in Tupaia belangeri by Microsatellite DNA Markers

Mating system of a population refers to the general behavioral strategies which employed in obtaining mates. In order to investigate the genetic parentage of 151 individuals in Tupaia belangeri from Haikou Forest Farm, 8 microsatellite loci with higher polymorphic characters were used for genetic relationship analysis. The results showed that the number of alleles per polymorphic locus in 151 individuals ranged from 2 to 9. The average observed and expected heterozygosities per locus ranged from 0.2476 to 0.8367 and from 0.2789 to 0.7773, respectively. While the polymorphic information content ranged from 0.2469 to 0.7773. Except the locus (TBC1) deviated from Hardy–Weinberg equilibrium, the others 7 microsatellite loci were employed to research the mating system in T. belangeri, which found that non-strictly monogamous in T. belangeri, but exhibited evidence of multiple paternity. All of the results suggested that characteristics of 8 microsatellite loci provide an excellent tool for the research of mating systems and fine-scaled population structuring of tree shrew, which was the first molecular evidence for mating system in T. belangeri.