Determination Of Genetic Relationships Research Articles

Identification of the allelic state of the Rca2 gene for resistance to anthracnose and determination of genetic relatedness in garden strawberry genotypes

The studies were conducted between 2022-2023. The purpose of the work was to analyze the relationship of hybrids and varieties of strawberries resistant and susceptible to anthracnose and to determine the putative allelic status of the anthracnose resistance gene Rca2. Selection of ISSR primers for identifying polymorphism and constructing dendrites of genetic similarity of 19 garden strawberry genotypes from the collection of the Federal State Budgetary Scientific Institution Federal Scientifi c Center for Horticulture. Th e eff ectiveness of ISSR primers was assessed by the ISSR-PCR method, followed by gel electrophoresis of ISSR-PCR products in an agarose gel. To assess the allelic state of the Rca2 gene, the SCAR marker STS-Rca2_240 was used. The genetic distance of the analyzed strawberry samples was determined using the Jaccard coeffi cient. Cluster analysis was carried out using the STATISTICA program (StatSoft ). The putative allelic status of the anthracnose resistance gene Rca2 in the studied varieties and hybrids was established. Diagnostic fragment of the STS-Rca2_240 marker, 240 bp in size. was found in the Alpha variety. Based on an array of genetic similarity coefficients, dendrograms were constructed, during the analysis of which the relationship of the studied variety samples was established. Promising forms were identifi ed that had a high degree of genetic similarity to varieties resistant to anthracnose, and forms that were closely related to susceptible varieties.

A novel approach of kinship determination based on the physical length of genetically shared regions of chromosomes.

Determination of genetic relatedness between individuals plays a crucial role in resolving numerous civil cases involving familial relationships and in forensic investigation concerning missing persons. Short tandem repeats (STRs), known for their high degree of DNA polymorphism, have traditionally been the primary choice of DNA markers in genetic testing, but their application for kinships testing is limited to cases involving close kinship. SNPs have emerged as promising supplementary markers for kinship determination. Nevertheless, the challenging remains in discriminating between third-degree or more distant relatives, such as first cousins, using SNPs. To investigate a kinship analysis method for distant degree of familial relationships using high-density SNP data. A high-density SNP data from 337 individuals of Korean families using Affymetrix Axiom KORV1.0-96 Array was obtained for this study. SNPs were aligned by chromosomal positions, and identity-by-state (IBS) was determined, and then shared regions as consecutive SNPs with IBS of 1 or 2 were investigated. The physical lengths of these IBS segments were measured and summed them to create an Index, as a measure of kinship. The kinship was determined by the physical length of shared chromosomal regions that are distinguished by each kinship. Using this method, the relationship was able be distinguished up to the fourth degree of kinship, and non-relatives were clearly distinguished from true relatives. We also found a potential for this approach to be used universally, regardless of microarray platforms for SNP genotyping and populations. This method has a potential to determine the different degree of kinship between individuals and to distinguish non-relatives from true relatives, which can be of great help for practical applications in kinship determination.

A prospective bacterial whole-genome-sequencing-based surveillance programme for comprehensive early detection of healthcare-associated infection transmission in paediatric oncology patients

Bacterial whole-genome sequencing (WGS) and determination of genetic relatedness is an important tool for investigation of epidemiologically suspected outbreaks. This prospective cohort study evaluated a comprehensive, prospective bacterial WGS-based surveillance programme for early detection of transmission of most bacterial pathogens among patients at a paediatric oncology hospital. Cultured bacterial isolates from clinical diagnostic specimens collected prospectively from both inpatient and outpatient encounters between January 2019 and December 2021 underwent routine WGS and core genome multi-locus sequence typing to determine isolates' relatedness. Previously collected isolates from January to December 2018 were retrospectively analysed for identification of prior or ongoing transmission. Multi-patient clusters were investigated to identify potential transmission events based on temporal and spatial epidemiological links and interventions were introduced. A total of 1497 bacterial isolates from 1025 patients underwent WGS. A total of 259 genetically related clusters were detected, of which 18 (6.9%) multi-patient clusters involving 38 (3.7%) patients were identified. Sixteen clusters involved two patients each, and two clusters involved three patients. Following investigation, epidemiologically plausible transmission links were identified in five (27.8%) multi-patient clusters. None of the multi-patient clusters were suspected by conventional epidemiological surveillance. Bacterial WGS-based surveillance for early detection of hospital transmission detected several limited multi-patient clusters that were unrecognized by conventional epidemiological methods. Genomic surveillance helped efficiently focus interventions while reducing unnecessary investigations.

Intra and between population genetic relationships among wild cherries [Prunus avium (L.) L.] based on molecular markers

Wild cherries [Prunus avium (L.) L.] are considered typical trees of the Slovenian landscape and often form vigorous natural populations. The determination of genetic relationships among cultivated and wild cherry tree genotypes is important for scientific and economic reasons. Both old trees and young plants were included in our genetic analysis. Sampling took place at two different locations near Maribor, NE Slovenia. The aim of the study was to determine the genetic relationships and variability among plants belonging to the studied populations. We focused on young trees and seedlings growing around old trees, which could be their hypothetical parents. We also analysed genetic uniformity within populations and identified genetically distant plants that had likely migrated as seeds from other populations. Three microsatellite loci were taken into account, 38 genotypes were examined, and 19 polymorphic alleles were detected, corresponding to an average of 6.3 per locus. Genetic distances between the studied genotypes were calculated using the Jaccard’s coefficient and a dendrogram was constructed. Genetic structure was analysed using both Principal Coordinate Analysis (PCoA) and Bayesian model-based analysis. Our study showed that there were differences between the two populations, however, there was some “communication” between them. We observed genetic relatedness as well as a relatively high level of uniformity within each of the wild cherry populations.

Assessment of phylogenetic diversity and relationships among <i>Grewia tenax</i> population in Sudan using RAPD and ISSR molecular markers

<abstract> <p>This research is conducted to study the genetic diversity of the genus <italic>Grewia tenax</italic> in Sudan. This plant has a common vernacular Sudanese Arabic name: “Gudeim”. It is mainly cultivated in North Darfur and Western Sudan. Common uses of <italic>Grewia</italic> species were overviewed in areas of nutrition, folk medicine and famine food. The genetic variation and genetic relationships among <italic>Grewia spp</italic> populations from different regions were efficiently determined using RAPD and ISSR markers.</p> <p>The results of genetic analysis were statistically analyzed by STATISTCA and GenALEx 6.5 software. The results of molecular variance revealed that 74% of total genetic diversity was due to within populations variations as opposed to 26% due to variations between populations unweighted pair- group method with arithmetic average (UPGMA) were constructed for and RAPD + ISSR. The UPGMA results showed variability of <italic>Grewia</italic> genotypes.</p> <p>It was concluded that both the marker systems RAPD and ISSR combination can be effectively used in determination of genetic relationships among <italic>Grewia tenax</italic> genotypes.</p> </abstract>

Determination of genetic relationships among Salvia species by RAPD and ISSR analyses

Determination of genetic relationships among Salvia species by RAPD and ISSR analyses

Using ISSR markers in determination of genetic relationship between 2n = 54 and 2n = 60 cytotypes of Nannospalax xanthodon (Nordmann, 1840) (Mammalia, Rodentia) from Central Anatolia

Using ISSR markers in determination of genetic relationship between 2n = 54 and 2n = 60 cytotypes of Nannospalax xanthodon (Nordmann, 1840) (Mammalia, Rodentia) from Central Anatolia

Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations.

We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate and the presence of contamination from present-day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present-day contamination and sequencing error. The model is validated by a simulation study as well as the analysis of aligned sequences from present-day human genomes. We then apply the method to the recently published genome sequences of ancient Europeans, developing a statistical treatment to determine confidence in assigned relatedness that is, in some cases, more precise than previously reported. As the majority of ancient specimens are from animals, this method would be applicable to investigate kinship in nonhuman remains. The developed software grups (Genetic Relatedness Using Pedigree Simulations) is implemented in Python and freely available.

RAPD-PCR analysis of Staphylococcus aureus strains isolated from different sources

Determination of genetic relationship among Staphylococcus aureus isolates is important for epidemiological surveillance and control of infections caused by this bacterium. The present study was conducted to determine the molecular diversity of S. aureus strains isolated from human, bovine, and food samples using random amplified polymorphic DNA (RAPD)-PCR method. A total of 208 S. aureus strains including 60 human (patients and healthy carriers), 83 bovine milk, and 65 food (pastry and cheese) isolates were assessed. The isolates were confirmed to be methicillin-resistance/susceptible S. aureus (MRSA or MSSA) using common biochemical tests and a species-specific PCR, and finally, they were genetically typed using RAPD-PCR method. Forty-seven RAPD profiles (13, 21, and 15 profiles for isolates from human, bovine, and food samples, respectively) were identified in the examined isolates. Based on these profiles and the constructed dendrogram, all of 208 S. aureus strains were divided into nine major clusters from A to I, at 80% similarity. Some clusters (A, B, C, E, and H) contained S. aureus strains isolated from only one source, while the others (D, F, G, and I) contained isolates from more than one source. The results revealed that although most of S. aureus strains of the same source were placed in certain clusters, there were also some strains of different sources which shared the same RAPD profiles indicating possible transmission of S. aureus strains (especially MRSA ones) among different hosts. Thus, effective hygiene measures should be considered to break transmission chains.

Determination of genetic relatedness among Turkish apple germplasm based on ISSR markers

Apple ( Malus domestica Borkh) is the most economically important pome fruits worldwide and Turkey is within origin center of apple. In this research, inter-simple sequence repeat (ISSR) markers were used to determine relationships among the Turkish apple accessions and some selected foreign cultivars and species. Fourteen ISSR primers produced a total of 111 fragments and 76 of them were polymorphic. The number of average polymorphic fragments per primer was 5.4. The mean polymorphism information content (PIC) was 0.37. The unweighted pair group method arithmetic average (UPGMA) analysis demonstrated that the accessions had a similarity range from 0.79 to 0.98. All accessions studied were discriminated and many subgroups were determined in the dendrogram based on the UPGMA analysis. High level of variation among the Turkish apples existed. Foreign cultivars, M.baccata , M. prunifolia and M. sylvestris accessions studied mix-clustered among the Turkish accessions. For sub-structuring Bayesian analysis, 71 loosely or uncorrelated markers with less than 10% missing data were used. This indicated absence of subpopulations, meaning well and equal introgression of genetic backgrounds or species available among the accessions. It can be concluded that Turkey was rich in apple genetic diversity, which may provide opportunity for apple breedind programs.

High frequency of virulence genes among Escherichia coli with the blaCTX-M genotype from diarrheic piglets in China

The purpose of this study was to characterize the virulence potential and determine the molecular epidemiology of extended-spectrum β-lactamases (ESBLs) in CTX-M-producing Escherichia coli isolated from piglets with diarrhea in China. A total of 62 E. coli isolates were obtained among which 49 and 13 were collected from diarrheic and healthy piglets, respectively. Cefotaxime resistant strains were screened for the presence of ESBL, adhesin and exotoxin genes as well as for their biofilm-forming ability. Characterization of blaCTX-M plasmids was determined by conjugation along with the determination of genetic relatedness and plasmid replicon type. CTX-M producers were found in 36 isolates with 6 different subtypes: blaCTX-M-14,27,65 from CTX-M-9G (n=27) and blaCTX-M-55, 15,79 from CTX-M-1G (n=22). This also included 13 isolates that carried two different CTX-M genes. Thirty of 36 CTX-M producers and 12 of 13 multiple CTX-M alleles were confirmed from diarrheic piglets. The presence of the iron regulatory gene irp2 as well as EAST1 was found in 83.3% (25/30) of CTX-M-producing isolates from diarrheic piglets and these were significantly better biofilm formers. PFGE profiles of CTX-M-positive isolates indicated the spread of multidrug resistance was primarily horizontal and spread via transferable plasmids. Most blaCTX-M-9G genes (10/17) were located on the IncFIB type plasmid with sizes of 40–145kb, while the blaCTX-M-1G (11/16) genes were located on the ∼100kb IncN-type plasmid. Together, our findings demonstrate that CTX-M ESBL-producing E. coli from diarrheic piglets were associated with serious multidrug resistance, increased biofilm-forming ability and the irp2 gene of HPI. Our findings highlight the need to urgent control the spread of resistant strains through food chain.

Molecular profiling and genetic diversity of mungbean (Vigna radiataL.) genotypes using ISSR and SSR markers

Five lines of four mungbean genotypes were analyzed for polymorphism using a total of five Inter Simple Sequence Repeat (ISSR) and two Simple Sequence Repeat (SSR) markers. Unique alleles differentiating the genotypes could be identified. Amplification of genomic DNA of most popular four Indian mungbean genotypes with these ISSR and SSR primers yielded 162 fragments that could be scored, of which 56 were polymorphic, with an average of 8.0 polymorphic fragments per primer. Number of amplified bands with ISSR and SSR primers ranged from 7 to 37. Percentage polymorphism ranged from 28.56 (UBC 836) to 57.14 (SSR 2). Polymorphic Information Content ranged from 0.584 (SSR 2) to 0.907 (UBC 809). The results indicated that both of the markers ISSR and SSR individually can be effectively used in determination of genetic relationship among Vigna species. It could be concluded that, the information of genetic similarities and diversity among Vigna genotypes can easily be identified using molecular techniques.

Td-DAMD-PCR assays for fingerprinting of commercial carnations

Dianthus L. is one of the highly valued plant species in the family Caryophyllaceae. More than 30,000 cultivars of commercial carnations have been recorded and there is a need for an effective and cheap method to reveal their genetic diversity and identify the cultivars. To the best of our knowledge this is the first report of implementation of the touchdown direct amplification of minisatellite-region DNA polymerase chain reaction (Td-DAMD-PCR) technique in the genus Dianthus. A total of 12 core minisatellite primers empirically selected from 22 primers were used in fingerprinting and phylogenetic studies of some commercial carnation cultivars. Analysis revealed that commercial carnations have a wide genetic base and they were probably obtained using inter-crosses between and among different species of the genus Dianthus. A total of 17 DNA markers were variety specific and most of the remaining markers obtained in the present study were useful in fingerprinting of the commercial varieties studied. Commercial varieties were differentiated in spray and standard carnation groups in a principal coordinate analysis and a Bayesian 50% majority-rule consensus tree. Td-DAMD-PCR markers reported in this study could be very useful in species identification, determination of genetic relationships, and phylogenetic studies of species of Dianthus.

Comments on: frequency of alleles and haplotypes of the human leukocyte antigen system in Bauru, São Paulo.

Despitethe use of various DNA markers, e.g., mitochondrial DNA,Y-chromosome, and microsatellites, HLA loci continue to beregarded as useful genetic markers in the determination ofgenetic relatedness and degree of admixture between differ-entpopulations.Itisalsousedtodetermineaprobablegeneticrelationship between populations.

Determination of Genetic Relationships among Eight Cymbidium Species on The Basis of Internal Transcribed Spacer Region of rRNA gene

Nuclear ribosomal DNA (rDNA) was analyzed to identify inter-specific genetic relationships among 8 Cymbidium species (Cymbidium insigne, C. ensifolium, C. marginatum, C. faberi, C. gyokuchin, C. kanran, C. forrestii, and C. goeringii). Nuclear rDNA including 2 internal transcribed spacer (ITS) regions and 5.8S, was amplified using polymerase chain reaction and sequenced. The sequences were compared via pair-wise multiple alignment to determine the genetic relationships among the studied species. The lengths of the ITS1, ITS2, and 5.8S regions were 235 bp, from 255 bp to 257 bp, and from 153 bp to 165 bp, respectively. Sequence similarities in the ITS region ranged from 78.7% between C. gyokuchin and C. kanran to 96.8% between C. ensifolium and C. kanran. A phylogenetic tree was constructed from nuclear rDNA nucleotide sequence data of the 8 cymbidiums and 1 outgroup species to estimate genetic relationships. The tree revealed that cymbidiums could be classified by their ecological traits, such as their temperature preference or inflorescence pattern. The phylogenetic data is applicable for identification, classification, and breeding of cymbidiums.

Allele frequencies of 15 STR loci in Azerbaijan population

The biological basis of contemporary forensic DNA profiling is linked to the processes of cell and human reproduction. From the many variations that subsequently exist on the human genome, short tandem repeats (STRs) have emerged as the most suitable markers for current forensic identification. The variation of short tandem repeats or microsatellites dispersed through the whole human genome, is actively investigated in forensic labs for personal identification and determination of genetic relationships between individuals.

Determination of genetic relationships between evergreen azalea cultivars in China using AFLP markers

Evergreen azaleas are among the most important ornamental shrubs in China. Today, there are probably over 300 cultivars preserved in different nurseries, but with little information available on the cultivar itself or relationships between cultivars. Amplified fragment length polymorphism (AFLP) markers were employed to determine the genetic relationships between evergreen azalea cultivars in China. One hundred and thirty genotypes collected from gardens and nurseries, including cultivars classified in the groups East, West, Hairy, and Summer, unknown cultivars, and close species, were analyzed using three primer pairs. A total of 408 polymorphic fragments were generated by AFLP reactions with an average of 136 fragments per primer pair. The average values of expected heterozygosity and Shannon's information index were 0.3395 and 0.5153, respectively. Genetic similarities were generated based on Dice coefficients, used to construct a neighbor joining tree, and bootstrapped for 100 replicates in Treecon V1.3b. Principal coordinate analysis (PCO) was performed based on Dice distances using NTSYS-pc software. The AFLP technique was useful for analyzing genetic diversity in evergreen azaleas. Cluster analysis revealed that cultivars in the West and Summer groups were quite distinct from other groups in the four-group classification system and that the East and Hairy groups should be redefined.

Assessment of genetic variations among highly endangered medicinal plant Bacopa monnieri (L.) from Central India using RAPD and ISSR analysis

Genetic variations of 15 Brahmi (Bacopa monnieri L.) accessions were evaluated using random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) markers. During RAPD analysis, amplification of genomic DNA of the 15 accessions by 22 primers generated 197 fragments, of which 187 were polymorphic with an average of 8.95 bands per primer. The amplified products varied in size from 2,200 to 250 bp. Twenty-five selected ISSR primers produced 284 bands across 15 accessions, of which 270 were polymorphic with an average of 10.80 bands per primer. The PIC value ranges from 0.363 to 0.908 for RAPD primers, while 0.419 to 0.836 in case of ISSR. The size of amplified bands ranged from 2,800 to 240 bp. Similarity index values ranged from 0.16 to 0.95 (RAPD), 0.18 to 0.98 (ISSR) and 0.179 to 0.945 for pooled ISSR and RAPD markers data. Mantel test revealed the similar distribution pattern of the polymorphism between RAPD and ISSR markers and the correlation co-efficient (r) was 0.71384. The results indicated that both of the marker systems RAPD and ISSR, individually or combined can be effectively used in determination of genetic relationship among B. Monnieri accessions collected from different parts of Central India. It could be concluded that the information of genetic similarities and diversity among Brahmi accessions is necessary for their conservation and breeding programs.

Development of novel microsatellites in Lagerstroemia indica and DNA fingerprinting in Chinese Lagerstroemia cultivars

Lagerstroemia spp. (crape myrtles) are popular woody ornamental flowering shrubs and trees distributed throughout temperate regions worldwide. In China, crape myrtles, especially the species L. indica, have been cultivated for nearly 1700 years, and germplasm resources are extensive. Therefore, investigating crape myrtle germplasm and their genetic diversity would assist international cultivar identification and breeding programs. Analysis of SSRs (Simple Sequence Repeats, also known as microsatellites) is currently the preferred method for the identification and determination of genetic relationships. The aim of this study was to develop and evaluate SSRs in crape myrtles as well as to evaluate genetic diversity and to perform fingerprinting analysis. Thirty-nine SSRs were isolated from enriched genomic libraries of L. indica. Primers were designed for 33 loci, 12 of which were polymorphic among 50 crape myrtle cultivars. In addition, we evaluated 14 SSRs from Lagerstroemia caudata. A total of 151 alleles were detected, and the average number of alleles per locus was 5.8. The observed heterozygosity ranged from 0.10 to 0.84, with a mean of 0.42 per locus. The average polymorphic information content (PIC) value and genetic similarity coefficient were 0.48 and 0.39, respectively, indicating wide genetic variation among all crape myrtle cultivars. Using the 26 SSRs above, all cultivars can be unambiguously identified and separated into two distinct groups. These newly developed SSRs can be efficiently used for crape myrtle genetic diversity assessment, DNA fingerprinting, and molecular breeding.

Determination of genetic relationships among elite thermosensitive genic male sterile lines (TGMS) of rice (Oryza sativa L.) employing morphological and simple sequence repeat (SSR) markers

A set of morphological traits and SSR markers were used to determine the genetic relationship among 12 elite thermosensitive genic male sterile (TGMS) lines developed at three different research institutions of India. Agro-morphological data recorded on 20 morphological traits revealed a wide base of genetic variation and a set of four morphological traits could distinguish most of the TGMS lines. Analysis with 30 SSR markers (20 EST-SSRs and 10 genomic SSRs) revealed 27 markers to be polymorphic, amplifying a total of 83 alleles. Each SSR marker amplified 2-6 alleles with an average of 2.76 alleles per marker and a PIC value varying from 0.54 to 0.96. Cluster analysis based on SSR and morphological data clearly differentiated the lines according to their source of origin. Correlation analysis between morphological and molecular data revealed a very poor association (r = 0.06), which could be attributed to selection pressure, genetic drift, sampling error and unknown relationship among related lines. The SSR markers discriminated the genotypes distinctly and quantified the genetic diversity precisely among the TGMS lines. Data on the yield per plant indicated that the genotypes grouping under a similar cluster showed same heterotic behaviour as compared to the genotypes from different clusters when crossed to similar pollinators.