Genetic Similarity Analysis Research Articles

Agronomic Performance of Exotic Wheat Lines under Kabul Agro-Ecological Conditions

Agronomic Performance of Exotic Wheat Lines under Kabul Agro-Ecological Conditions Mohammad Wali Salari, Mohammad Bahman Sadeghi, Patrick O. Ongom, Kalimullah Saighani, Ahmad Fahim Samadi, Wakil Ahmad Sarhadi Abstract This research was conducted to assess the agronomic performance of wheat advanced lines developed by Purdue University small grain program under Kabul agro-ecological conditions. Eleven wheat advanced lines from Purdue University and three local check varieties from Kabul were tested for three years under Kabul agro-ecological conditions. Genotypes differed significantly (P < 0.05) for grain yield and the yield components, and a fairly stable performance across years. Spike length and kernel weight were significantly correlated with grain yield, having R2 values of 0.54 and 0.53 respectively. Two Purdue lines: SNOWMASS and IN0762 outperformed the local checks, yielding 2.79 t/ha and 2.62 t/ha respectively. A genetic similarity analysis clustered the studied genotypes into three distinct groups, with some of the local varieties falling in the same category as the exotic lines. The study found exotic lines to be adapted to Kabul conditions, and can be utilized in local breeding programs. Full Text: PDF DOI: 10.15640/jaes.v4n2a15

Detection of Molecular Variation Among Maize Lines and Their Hybrids Using RAPD Markers

A laboratory experiment was carried out at the Biotechnology Research Center – Nahrain University – Baghdad for the year 2013 at the aim of assessing the extent of genetic divergence among seven inbred lines of maize and the twelve single hybrids results from Line X Tester crossing among these lines. Ten of RAPD molecular markers have been used for this purpose (OPA-07, OPA-09, OPA-11, OPA-13, OPC-12, OPD-20, OPI-01,OPO-04, OPN-16 and GB8), just five of these (OPA-09, OPC-12, OPD-20, OPN-16 and GB8) were succeeded in distinguishing among parent lines per se and their F1 hybrids by showing different pattern of DNA fragmentation. The results of genetic similarity analysis and dendrogram tree revealed that the inbred lines T1 and T6 were the most genetic divergent lines as they gained the minimum value of genetic similarity reached 68.6%, which indicates their important role in the future studies and to produce elite hybrids.

Genetic differentiation in Quercus infectoria from northwest of Iran revealed by different nuclear markers

The aim of the present study was to examine the genetic variability of natural populations of Quercus infectoria, based on inter-retrotransposon amplified polymorphism (IRAP), inter-simple sequence repeat (ISSR), and start codon targeted (SCoT) markers, in view of long-term conservation plans. A total of 150 accessions from ten populations of this species were sampled from northwest of Iran. Eighteen ISSR, ten IRAP, and ten SCoT primers generated a total of 466 unambiguous and repeatable bands, from which 448 (96.14 %) were polymorphic for all markers. The polymorphism information content (PIC) values for IRAP, ISSR, and SCoT markers were 0.26, 0.35, and 0.37, respectively. Genetic similarity and distance analyses indicated the existence of high variability among the studied accessions, so that a pairwise Jaccard’s genetic similarity based on combined data ranged from 0.27 to 0.79. Cluster analysis for three different molecular types revealed that the accessions taken for the analysis can be divided into two distinct clusters. Molecular variance analysis revealed that more than 70 % of the variation resided within populations and less than 30 % could be attributed to variation among populations, possibly due to gene flow between populations and life history traits. These data provide valuable information for natural resource conservation.

Genetic diversity of maize germplasm assessed by retrotransposon‐based markers

Maize is one of the most important crops and also a model for grass genome research. Transposable elements comprise over 78% of the maize genome and their ability to generate new copies makes them good potential markers. Interretrotransposon-amplified polymorphism (IRAP) and retrotransposon microsatellite amplified polymorphism (REMAP) protocols were used for the first time in maize to study the genetic variability between maize cultivars. Ten PCR primers were selected based on a systematic analysis of the sequence conservation in the extremities of different high copy number transposable elements, whereas one primer was chosen based on a microsatellite sequence. Of the 16 primer combinations tested, 14 produced polymorphic bands. These markers were used to identify genetic similarity among 20 maize cultivars selected by their different kernel oil content. Genetic similarity analysis was performed based on the polymorphic band profiles and dendrograms were developed by the unweighted pair-group method with arithmetic averages. Clustering technique revealed that samples were grouped into three clusters that differed in their kernel oil content and size, and in their relative embryo size. In the current investigation, there is evidence that IRAP/REMAP may be useful as markers in maize.

Ampelographic identification and comparison of some table grape (Vitis vinifera L.) clones

Clonal selection is an important tool for grapevine genetic improvement and high-quality production. Clonal selection has been carried out for 70 yr in Turkey and is being continued with different grape cultivars and rootstocks. In this study, 16 clones belonging to nine grape cultivars were selected by the Atatürk Central Horticultural Research Institute for study over 3 yr. Vines were characterised using standard ampelographic descriptors and the data obtained were transformed into numerical scores for analysis of genetic similarity. Although all the clones studied could be uniquely identified, there was much less variation between clones of a particular cultivar than there was between cultivars.

Analysis of homozygosity and genetic similarity between two succes-sive generations in a meiogynogenetic Japanese flounder family

The artificial induction of gynogenesis is a form of chromosome manipulation that has several applica-tions,including the rapid establishment of inbred lines or strains.The technique offers a high degree of homozy-gosity,sex-control,and accelerated elimination of recessive deleterious genes from a cultured population.We produced two meiotic gynogenetic Japanese flounder(Paralichthys olivaceus) family lines: meio-G1(the first generation) and meio-G2(the second generation).We evaluated the efficacy of artificial meiotic gynogenesis for producing pure inbred lines by quantifying the homozygosity and genetic similarity of meio-G1 and meio-G2 us-ing microsatellite markers The average homozygosity among 15 loci was 0.124 7 for meio-G1 and 0.221 5 for meio-G2,which was higher than that in the natural mating family(0.091 7).The average similarity indices among individuals within meio-G1 and meio-G2 were 0.891 7 and 0.923 8,which were higher than within the natural mating family(0.5603).The average similarity in meio-G2 was slightly higher than in meio-G1.The observed heterozygosity in meio-G1 and meio-G2 was 1 at the Poli9-8tuf,Poli18tuf,Poli107tuf loci,all of which were lo-cated at some distance from the centromere(i.e.,had high recombination frequencies).The loci(Poli33tuf,Po-li24MHFS) closest to the centromere(i.e.,with a low recombination frequency) were homozygous in meio-G1 and meio-G2.Our results suggest that artificially induced meiotic gynogenesis is an efficient method for inbreeding to purify the genome,increase genetic similarity,and fix maternal genetic traits in the Japanese flounder.The mei-ogynogenetic families cultured in our study may be used in further selective breeding research.

SRAP과 SSR 마커를 이용한 국내 육성 팔레놉시스 품종의 유전적 다양성 분석과 품종판별

The aims of this study were to compare genetic distances among 14 Phalaenopsis varieties using simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) marker systems and to determine the discrimination using SSR. A total of 111 SSR primers and 30 SRAP combinations were initially screened. Twelve SSR primers and thirty SRAP combinations showed high polymorphism among the 14 Phalaenopsis varieties including domestic breeding varieties, conserved in National Institute of Horticultural & Herbal Science (NIHHS). The amplified DNA fragments were separated by denaturing acrylamide gels and detected by silver staining method. A total of 474 polymorphic bands, including 55 by SSRs and 419 by SRAPs, were identified and used for genetic diversity analysis. Polymorphic bands were scored for calculating a simple matching coefficient of genetic similarity and cluster analysis with multi-variate statistical package (MVSP) 3.1. Fourteen Phalaenopsis varieties were classified into three major groups at similarity coefficient value of 0.683 and 0.66 using SRAP and SSR, respectively. Also we could discriminate these domestic breeding Palaenopsis varieties using only SSR 20 and SSR 22. The results indicate that SSR analysis is effective for discrimination among Phalaenopsis varieties and SRAP is useful for genetic diversity when there is no sequence information. These studied SSR and SRAP markers will be useful tools for genotype identification, germplasm conservation and genetic relationship study in Phalaenopsis.

The relationship between genetic and chemotypic diversity in American ginseng (Panax quinquefolius L.)

Ginseng is one of the world's most important herbals used as an adaptogen and a cure for an impressively large range of ailments. Differences in the medicinal properties of ginseng roots have been attributed to variation in ginsenoside composition. In this study, the association between genetic and chemotypic profiles of wild and cultivated American ginseng (Panax quinquefolius L.) roots grown in Maryland was investigated. Ginseng roots were classified into chemotypes based on their relative composition of Re and Rg1. Genetic profiles of these roots were determined from the analysis of 38 polymorphic RAPD markers and used for a cluster analysis of genetic similarities. The close correspondence between chemotype and genetic cluster provides the first DNA-based evidence for the genetic basis of ginsenoside composition. Results of this research are significant for plant breeding and conservation, phytochemical research, and clinical and pharmacological studies. Also, the correlation between RAPD markers and chemotype indicates the potential to use RAPD markers as a reliable and practical method for identification and certification of ginseng roots.

Genetic similarity analysis within Pyropia yezoensis blades developed from both conchospores and blade archeospores using AFLP(1).

Pyropia yezoensis (Ueda) M. S. Hwang et H. G. Choi (previously called Porphyra yezoensis) is an economically important alga. The blades generated from conchospores are genetic chimeras, which are not suitable for genetic similarity analysis. In this study, two types of blades from a single filament of P.yezoensis sporophyte filament were obtained. One type, ConB, consisted of 40 blades that had germinated from conchospores. The other type, ArcB, consisted of 88 blades that had germinated from archeospores released from ConB. Both of them were analyzed by amplified fragment length polymorphism. The low genetic similarity levels for both conchospore-germinated and archeospore-germinated blades demonstrated that the conchcelis we used was cross-fertilized. Furthermore, a higher polymorphic loci ratio (98.6%) was detected in ArcB than in ConB (80.7%), and the average genetic similarity of ArcB (average 0.61) was lower than that of ConB (average 0.71). These differences indicated that genetic analysis using ArcB gives more accurate results.

Wksl3, a New Biocontrol Agent for Salmonella enterica Serovars Enteritidis and Typhimurium in Foods: Characterization, Application, Sequence Analysis, and Oral Acute Toxicity Study

Of the Salmonella enterica serovars, S. Enteritidis and S. Typhimurium are responsible for most of the Salmonella outbreaks implicated in the consumption of contaminated foods in the Republic of Korea. Because of the widespread occurrence of antimicrobial-resistant Salmonella in foods and food processing environments, bacteriophages have recently surfaced as an alternative biocontrol tool. In this study, we isolated a virulent bacteriophage (wksl3) that could specifically infect S. Enteritidis, S. Typhimurium, and several additional serovars. Transmission electron microscopy revealed that phage wksl3 belongs to the family Siphoviridae. Complete genome sequence analysis and bioinformatic analysis revealed that the DNA of phage wksl3 is composed of 42,766 bp with 64 open reading frames. Since it does not encode any phage lysogeny factors, toxins, pathogen-related genes, or food-borne allergens, phage wksl3 may be considered a virulent phage with no side effects. Analysis of genetic similarities between phage wksl3 and four of its relatives (SS3e, vB_SenS-Ent1, SE2, and SETP3) allowed wksl3 to be categorized as a SETP3-like phage. A single-dose test of oral toxicity with BALB/c mice resulted in no abnormal clinical observations. Moreover, phage application to chicken skin at 8°C resulted in an about 2.5-log reduction in the number of Salmonella bacteria during the test period. The strong, stable lytic activity, the significant reduction of the number of S. Enteritidis bacteria after application to food, and the lack of clinical symptoms of this phage suggest that wksl3 may be a useful agent for the protection of foods against S. Enteritidis and S. Typhimurium contamination.

Analysis of genetic similarity of Festuca rubra L. and Festuca nigrescens Lam. sub-populations of the south-eastern part of Poland

&lt;p&gt;The investigation of genetic similarity involved &lt;em&gt;Festuca rubra&lt;/em&gt; L. and &lt;em&gt;Festuca nigrescens&lt;/em&gt; Lam. ecotypes. The study plants originated from sub-populations in the south-eastern part of Poland. The analysis of the genetic similarity was performed by the PCR technique with the use of semi-specific primers targeting 12–18 bp long plant gene sequences from the exon targeting (ET) and intron targeting (IT) group. The investigations were carried out using 21 primers. In total, 735 DNA fragments were obtained, out of which the individual primers amplified from 16 (ET 10/18mer) to 56 (ET 11/18mer) fragments. On average, one primer yielded 32.38 polymorphic products from 11 (IT 28/12mer) to 56 (ET 11/18mer). In total, 680 (91.62%) polymorphic products were obtained. The primers used generated PCR products which exhibited high polymorphism. In the case of the 18-nucleotide primers, the number of amplified polymorphic fragments was more than 96%.&lt;/p&gt;&lt;p&gt;Based on the results obtained, it was found that Nei's genetic similarity for the &lt;em&gt;Festuca rubra&lt;/em&gt; and &lt;em&gt;Festuca nigrescens&lt;/em&gt; sub-populations analysed was high enough to correspond to the sub-species status. The genetic similarity between ecotypes of the species is closely related to the site of occurrence of the genotypes studied. The highest similarity was found between ecotypes growing in the immediate vicinity of each other.&lt;/p&gt;.

Genetic divergence among accessions of melon from traditional agriculture of the Brazilian Northeast

The genetic divergence of 38 melon accessions from traditional agriculture of the Brazilian Northeast and three commercial hybrids were evaluated using fruit descriptors and microsatellite markers. The melon germplasm belongs to the botanic varieties cantalupensis (19), momordica (7), conomon (4), and inodorus (3), and to eight genotypes that were identified only at the species level. The fruit descriptors evaluated were: number of fruits per plant (NPF), fruit mass (FM; kg), fruit longitudinal diameter (LD; cm), fruit transversal diameter (TD; cm), shape index based on the LD/TD ratio, flesh pulp thickness, cavity thickness (CT; cm), firmness fruit pulp (N), and soluble solids (SS; °Brix). The results showed high variability for all descriptors, especially for NPF, LD, and FM. The grouping analysis based on fruit descriptors produced eight groups without taxonomic criteria. The LD (22.52%), NPF (19.70%), CT (16.13%), and SS (9.57%) characteristics were the descriptors that contributed the most to genotype dissimilarity. The 17 simple sequence repeat polymorphic markers amplified 41 alleles with an average of 2.41 alleles and three genotypes per locus. Some markers presented a high frequency for the main allele. The genetic diversity ranged from 0.07 to 0.60, the observed heterozygosity had very low values, and the mean polymorphism information content was 0.32. Molecular genetic similarity analyses clustered the accessions in 13 groups, also not following taxonomic ranks. There was no association between morphoagronomic and molecular groupings. In conclusion, there was great variability among the accessions and among and within botanic groups.

Genotyping of Staphylococcus aureus strains among healthcare workers and patients in the tertiary referral Children's Medical Hospital in Tehran, Iran

ABSTRACTNasal carriage among hospital personnel is an important source of nosocomial staphylococcal infection. Therefore, this study aims to evaluate Staphylococcus aureus nasal colonisation among healthcare workers (HCWs) and its association with infection in children through analysis of antibiotic susceptibility profiles and genetic similarity. Nasal swabs were taken from the anterior nares of HCWs and also a total of 130 strains that had been isolated from various clinical samples were examined. Antibiotic susceptibility profiles of the strains were determined using the disc-diffusion technique and genotyping was performed by amplification of the enterobacterial repetitive intergenic consensus sequences (ERIC-PCR). Approximately 48% of clinical strains obtained were methicillin-resistant S. aureus (MRSA), whereas only 24.7% of strains from HCWs were MRSA. Among isolates from HCWs, cephalothin, cefazolin, chloramphenicol, rifampicin and vancomycin were most effective, with susceptibility rates of 100%. In this study, the ERIC-PCR profiles did not reveal any genetic similarity among the S. aureus strains from HCWs and the clinical samples. In contrast, MRSA strains showed clonal dissemination, with clones D and A2 predominant among patients and HCWs, respectively. No association was observed between the MRSA nasal carriers and infections in patients. These findings suggest that MRSA nasal carriage among HCWs may not be the source of related infections in the group studied.

Genetic similarity in a hybrid population of 'Montenegrina' and 'King' mandarins

The objective of this work was to confirm the hybrids obtained in plants originated from the crossing between the mandarins Citrus deliciosa 'Montenegrina' and C. nobilis 'King', and to estimate the genetic similarity among hybrids, and between each hybrid and its parents. Twenty‑three pairs of microsatellite primers were tested. Fourteen of these pairs showed polymorphic bands between parents. Primers CCSM 129 and CCSME 52 were sufficient to identify the 12 nucellar clones observed in the studied population. Genetic similarity analysis of the population (hybrids and parents) showed 0.56 average similarity. Besides the 12 clones of 'Montenegrina' identified, 25 hybrids were found of which D18, C32, D06, C05 and D09 are the more similar to 'Montenegrina'.

Disentangling invasion processes in a dynamic shipping–boating network

The relative importance of multiple vectors to the initial establishment, spread and population dynamics of invasive species remains poorly understood. This study used molecular methods to clarify the roles of commercial shipping and recreational boating in the invasion by the cosmopolitan tunicate, Botryllus schlosseri. We evaluated (i) single vs. multiple introduction scenarios, (ii) the relative importance of shipping and boating to primary introductions, (iii) the interaction between these vectors for spread (i.e. the presence of a shipping-boating network) and (iv) the role of boating in determining population similarity. Tunicates were sampled from 26 populations along the Nova Scotia, Canada, coast that were exposed to either shipping (i.e. ports) or boating (i.e. marinas) activities. A total of 874 individuals (c. 30 per population) from five ports and 21 marinas was collected and analysed using both mitochondrial cytochrome c oxidase subunit I gene (COI) and 10 nuclear microsatellite markers. The geographical location of multiple hotspot populations indicates that multiple invasions have occurred in Nova Scotia. A loss of genetic diversity from port to marina populations suggests a stronger influence of ships than recreational boats on primary coastal introductions. Population genetic similarity analysis reveals a dependence of marina populations on those that had been previously established in ports. Empirical data on marina connectivity because of boating better explains patterns in population similarities than does natural spread. We conclude that frequent primary introductions arise by ships and that secondary spread occurs gradually thereafter around individual ports, facilitated by recreational boating.

DNA fingerprinting of eucalyptus clones using microsatellite markers

Microsatellite marker was used to verify eucalyptus clones. Thirty nine primer pairs were selected. Twenty eight primer pairs could amplify DNA in which 18 of them showed polymorphic band pattern among 25 eucalyptus clones. One hundred and fifty-two distinct DNA bands were scored and calculated for the genetic similarity and cluster analysis using simple matching and unweighed pair group method using arithmetic average (UPGMA). From the phylogenetic tree, these eucalyptus clones were divided into four clusters. Two sets of primer pairs, namely EMBRA 2 and EMBRA 22, EMBRA 2 and EMBRA 63, EMBRA 22 and EMBRA 69 or EMBRA 63 and EMBRA 69 were combined and able to simultaneously amplify DNA in a duplex PCR reaction which made fingerprinting of eucalyptus clones easier and less expensive.

Selection and application of SSR markers for variety discrimination, genetic similarity and relation analysis in gerbera (Gerbera hybrida)

Gerbera is one of the most important floricultural crops worldwide, yet few robust and informative molecular markers were available for use in gerbera breeding and genetic studies. Previously we reported the first set of 99 EST-SSR markers. This study further characterized these markers using a much larger group of gerbera accessions and selected 53 robust, informative markers. The selected markers each amplified two to seven alleles, their PIC value ranged from 0.207 to 0.771, observed heterozygosity from 0.100 to 0.775, and expected heterozygosity from 0.224 to 0.801. Observed heterozygosity varied considerably among gerberas, ranging from 0.245 to 0.615. Similar levels of genetic diversity (observed and expected heterozygosity and Shannon's index) were observed among groups of gerberas for different uses (breeding lines, cut flower, seed-propagated pot-type, and tissue culture-propagated pot-type). The selected markers unequivocally differentiated all gerberas in the study, including six pairs of highly similar varieties that were indistinguishable morphologically. The great majority of the 861 pairwise comparisons among the 40 gerbera accessions showed a Jaccard similarity coefficient between 0.290 and 0.700 and a few pairs between 0.800 and 0.970. The UPGMA dendrogram based on similarity coefficients and population inference analysis with STRUCTURE separated the gerbera accessions into two major clusters that largely correspond to breeding approaches and/or propagation methods. These results showed that the selected markers were very powerful for discriminating gerberas and revealed genetic structures in cultivated gerberas. Application of these markers may also facilitate assessment of clonal fidelity and future DUS tests in gerberas.

Comparative genetic structure within single-origin pairs of rice (Oryza sativa L.) landraces from in situ and ex situ conservation programs in Yunnan of China using microsatellite markers

The genetic structure and diversity of eight pairs of rice landraces from in situ (collected in 2007) and ex situ (collected in 1980) conservation programs were studied using 20 pairs of microsatellite markers with high polymorphism. Each pair of rice landraces shares a name and origin and has similar seed and plant traits. The number of alleles detected in the populations from in situ conservation ranged from 43 to 88 with the mean number of alleles per locus ranging from 2.15 to 4.40, while the number of alleles detected in the populations from ex situ conservation ranged from 33 to 65, and the mean of alleles per locus ranged from 1.65 to 3.25. Compared to the ex situ populations, the number of alleles, the number of specific alleles and the genetic diversity index showed a significant increase in the in situ populations. Further, the numbers of specific alleles from in situ populations were 2.1–5.0 times greater than in ex situ populations except for rice landrace ‘Qitougu’. An AMOVA showed that the within-landrace genetic structure differed significantly between in situ and ex situ conservation treatments with differences exceeding 20%. The analysis of genetic similarity reached similar conclusions to those of the AMOVA. Compared with ex situ conservation programs, the rice landraces under in situ conservation programs had more alleles and higher genetic diversity in Yunnan of China.

Evaluation of Genetic Similarity and Agronomic Traits of Castor Bean Populations Naturally Grown in the Eastern Mediterranean Region of Turkey

ABSTRACTGenetic characterization of wild castor bean genotypes collected from the eastern Mediterranean region of Turkey was evaluated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) of seed storage proteins. Five distinct groups were identified from the cluster analysis of the castor bean genotypes studied at 0.80 coefficient level. Cluster analysis showed that some of the genotypes from the same location were grouped separately. Genetic similarity coefficients ranged from 0.36 to 0.95 among genotypes. The highest similarity (95%) was obtained between Iskenderun-1 and Iskenderun-2; Adana-4 and Iskenderun-2; Iskenderun-4 and Mersin-1. In addition to genetic diversity, plant characteristics such as stem color, seed color, days to maturity, plant height, main spike length, 100-seed weight and seed yield per plant were recorded. The results of both genetic similarity and agronomic analysis of castor bean genotypes would help in planning breeding programs for improving high yielding cultivars.

Genetic diversity analysis of rice cultivars (Oryza sativa L.) differing in salinity tolerance based on RAPD and SSR markers

Thirty rice cultivars were evaluated for salinity tolerance during the seedling stage and were divided into five tolerance groups including tolerant (T), moderately tolerant (MT), moderately susceptible (MS), susceptible (S) and highly susceptible (HS) which comprised 5, 10, 9, 4 and 2 cultivars respectively. Genetic diversity of all rice cultivars was evaluated using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) markers. The cultivars were evaluated for polymorphisms after amplification with 20 random decamer primers and 20 SSR primer pairs. A total of 161 RAPD markers and 190 SSR alleles were produced which revealed 68.94% and 89.47% polymorphism respectively. Mean genetic similarity coefficient was 0.82 for RAPD and 0.70 for SSR. Cluster analysis based on RAPD markers was effective in grouping cultivars based on their salt tolerance ability. Group IA 1 , IB and IV contained three T, three S and two HS rice cultivars respectively. The MT and MS cultivars which showed similar physiological responses to salinity were resolved into two groups: Group IA 2 and Group II comprising ten and eight MT/MS cultivars respectively. Cluster analysis based on SSR markers separated rice cultivars into groups based on genetic relatedness which did not correspond to salinity tolerance level. The results from this study provided some useful implications for salt tolerance breeding programs. The evaluation of genetic similarity and cluster analysis together with salt tolerance ability provides some useful guides for assisting plant breeders in selecting suitable genetically diverse parents for the crossing program.