In this study 55 tomato genotypes from different geographical regions were evaluated withISSRmarkers (Inter Simple Sequence Repeats). The seven ISSR primers originated 63 amplified bands, of which 90.48% were polymorphic. The cluster analysis based on the Nei-Li similarity coefficient using the average genetic clustering method (UPGMA) revealed the conformation of five clusters at a level of similarity of 72%. TheISSR technique did not discriminate tomato genotypes according to the species or region of provenance. The structure analysis and the dendrogram did not reveal a genetic structure in the population evaluated. The genotypes ofthe species of S. pimpinellifolium, S. l. cerasiforme, S. lycopersicum and S. peruvianum were found consistently grouped, showing a close genetic relationship among them. A high genetic variation among the individuals within each ofthe groups formed was suggested by the AMOVA. TheISSRmarkers were effective in assessing thegeneticdiversity and structure of populations oftomato genotypes. The high genetic variability found in this study indicates the valuable genetic potential present in tomato germplasm, especially of wild species, which could be used for future breeding programs ofthe species.
anchored primers were used for amplification and (ii) more than half ofthe primers contained four nucle- otide repeats. Nevertheless, a moderate genetic varia- tion at intra- and interspecific levels was determined in Fusarium isolates. Mishra et al. [18,19] reported that there are high levels ofgeneticdiversity using ISSR marker amplification in F. graminearum and F. culmo- rum isolates from different countries. They found 81% ofISSR amplicons to be polymorphic. Similarly, from ISSR analysis among F. poae isolates from England and Argentina, Dinolfo et al.  showed that there was a high level ofgenetic variation. They reported that 89% ofthe produced ISSR bands were polymorphic. Moreover, Li et al.  and Mishra et al.  reported a high level of polymorphic bands (82.3% and 98.3%, respectively) obtained from in their ISSR analysis. Both Mishra et al.  and Dinolfo et al.  used 4 and 25 oligonucleotide primers, respectively, most of which were non-anchored. However, in the current study, 41 primers were examined for ISSR fingerprinting, of which 23 were anchored and 18 non-anchored. Among them, 10 were novel and were developed and used for the first time in this study. Ofthe 24 primers (60%), 7 were novel amplified scorable ISSRmarkers. As a result, variations at the intra- and interspecific level were determined via these primers. Anchored prim- ers have the potential to produce more monomorphic markers. A high number of anchored primers could result with a stable and reproducible but low number of polymorphic bands. The mechanisms accounting for variations in ISSRmarkers are replication slippage, structural rearrangements of chromosomes and inser- tion/deletion SNPs occurring in amplified regions . ISSR analysis is not time consuming and laborious, and it also provides reproducible and reliable results in fungal genetics [19,42-44].
Thegeneticdiversityof 19 Portuguese Opuntia spp. populations and three Italian cultivars was assessed using the 6 SSR markers designed from the Galapagos O. echios [ 13 ] and tested by in another Opuntia species. A unique microsatellite pattern was found for the different species studied, though clearly discriminating at the species level. Among the O. ficus-indica populations, two sub-clusters were identified, one including the white pulp fruits (with cv. Bianca) and the other withthe orange pulp fruits, including the cv. Gialla, the cv. Rossa, and one pale yellow pulp population (OFI-04). However, at the intrapopulation level, the microsatellite pattern over loci was the same, and the individuals could not be distinguished, suggesting that they could be recent vegetative clones. The results revealed a low level ofgeneticdiversity among the Portuguese populations of O. ficus-indica and the Italian cultivars. The spinescent O. ficus-indica f. amyclaea (OFI-01) had the same microsatellite fingerprint as that ofthe O. ficus-indica f. ficus-indica spineless populations, and the clustering did not reflect the spinescence character. Caruso et al. [ 16 ] reached similar conclusions in a previous studyofthe level of intraspecific geneticdiversity among O. ficus-indica cultivated varieties and some related species. These authors obtained results from a cluster analysis that clearly diverge from the current taxonomy, which classifies several Opuntia species based on morphological parameters such as the presence/absence of spines.
Thegenetic distance between Vasconcellea and Carica has been observed and documented in numerous investigations. Previous studies based on ovary morphology (Badillo 1993) and interspecific hybridization barriers (Manshardt and Wenslaff 1989) indicate that papaya is only distantly related to Vasconcellea. Results of cpDNA analysis of Aradhya et al. (1999) suggest that C. papaya must have diverged from the South American Vasconcellea species early in the evolution and evolved in isolation, probably in Central America. These data supported a recent rehabilitation of Vasconcellea as a genus category (Badillo 2000). On the other hand, Van Droogenbroeck et al. (2004) analyzed thediversityof 18 Vasconcellea species and corroborated the monophyly of Caricaceae in the genera Carica, Jacaratia and Cylicomorpha by RFLP. According to these authors, Caricaceae species are divided into two lineage groups, one with some Vasconcellea spp., including V. monoica and V. goudotiana and the second withthe other
Ofthe 36 markers tested, 13 were polymorphic, which allowed the analysis ofgeneticdiversityofthe introductions from different countries. Kwon et al. (2009) found 54 polymorphic markers in 10 varieties oftomatoof 250 SSRs selected from theSolanum Genomic Network (2011) genomic database. The number of alleles observed in the introductions was between 2 and 8 with an average of 4.92 alleles per locus, the most informative ones being SSR26 and SSR47, with 8 alleles, followed by SSR19; SSR128 and SSR86, with 6 alleles each. The microsatellites withthe lowest value of observed alleles were SSR288 and SSR942, with 3 alleles each (Table 1). Muñoz et al. (2010) reported that a significant number of alleles with microsatellite markers can be related to the origin ofthe material or its genetic nature, either because of its geneticdiversity or geographical distance, so a low number of alleles found can be explained by a narrow geographical collecting area and the analysis ofthe materials. On the other hand, Kwon et al. (2009) evaluated 63 varieties oftomatowith 33 SSR markers, finding 8 SSRs with 2 alleles, 6 with 2 alleles, 8 with 4 alleles, and 11 markers 5 alleles; in total, 132 alleles were identified with an average of 4 alleles versus 64 found in this studywith an average of 4.92 alleles per locus. In this case,
The mean similarity assessed by theISSRmarkers was 62 %, ranging from 30 % (Ventana and Oso Grande) to 88 % (Camino Real and Ventana) (Table 2). These values showed high polymorphism and were consistent with results obtained for other strawberry cultivars (Graham et al., 1996; Arnau et al., 2003; Kuras et al., 2004). The Aromas and Diamante cultivars presented one ofthe greatest similarity values (80 %) probably due to the common parents (‘Cal. 87.112-6’ × ‘Cal. 88.270-1’) (Shaw 1998a; 1998b). Conversely, Tudla cultivar presented less similarity with Oso Grande cultivar, its half-sib, than with all the other cultivars evaluated, showing that the similarity between sibs is greatly affected by the parents’ level of similarity. However, a high degree of similarity was ob- served between the Camino Real and Ventana cultivars (88 %), even though they do not have common parents, but they came from the same breeding program and may share ancestors. Moreover, the selection for important agronomic traits reduces thediversity in crops. The coefficients of similarity among some cultivars in the present study were generally similar with those reported in the literature (Arnau et al., 2003; Kuras et al., 2004; Radmann et al., 2006), indicating great reliability ofthe molecular data.
The PIC values for all SSR-markers indicated that most ofthemarkers used had high discriminatory power and are useful for geneticdiversity studies (varying from UGSM59 = 0.15 to ESTB60 = 0.93 with mean = 0.57) (Table 3). These results are considered normal according to Pinto, Oliveira, Ulian, Garcia, and Souza (2004), who found a range of 0.28 to 0.90 with a mean of 0.66 by using 30 SSR-markers in 18 cultivars. Singh et al. (2008) evaluated the UGSM29 locus in sugarcane and found a PIC of 0.80 with 13 described alleles. Thestudy conducted by Oliveira et al. (2009) also reported high PIC values (0.92) and a high number of alleles (19 in total) in sugarcane when was used the ESTB60 locus. Duarte Filho et al. (2010) found amplitude of 0.34 to 0.78 with a mean of 0.57 per locus by using 18 SSR primers, whereas Singh et al. (2008) using 168 SSR primers reported a PIC ranging from 0.25 to 0.84 with a mean value of 0.55 per locus. This large PIC variability demonstrated high and low magnitude values because some accessions have divergent geographical distributions, which has been reported by other authors (Cordeiro et al., 2000; Pan, 2006; Singh et al., 2008); in these studies, the following differences should be considered: the number of primers and accessions (which were higher and lower, respectively) as well as the defined markers used to detect the alleles and objectives. The PIC values for SSR markers do not exhibit constant values however merely serve as a reference for the relative ability ofthe marker to detect genetic variability (Singh et al., 2008). In fact, molecular markers have provided a more reliable differentiation of genotypes than phenotypic data and allows establish cultivars into distinct cluster of genotypes based on power marker discrimination and genetic distance. This is valid for the present study because while more than 90% ofthe cultivars belong from the same country of origin, the cultivars used in a particular region ofthe country may not be the same cultivars used in another region.
In this study, some morphological and molecular characterizations were applied, in order to be used as different tools for wheat cultivars and landraces breeding programs and improvement. The morphological analysis of different wheat cultivars recognized that there is a direct relationship between the effect of salinity on plant growth and productivity (Fig. 1-3). The recorded effects ofthe salinity stress on fresh and dry weight, plant length and flowering time ofthe different wheat cultivar plants was in agreement with previous research (Cutler et al., 2010 and Kumar and Wigge, 2010). They recorded that the growth and productivity of plants are greatly affected by environmental factors such as drought, low temperature and soil salinity and they adapt their growth and development in response to perceived stress. To withstand environmental stresses, plants have evolved highly integrated sensing and response signaling pathways that regulate developmental processes, such as growth and flowering. In general, a stress signaling pathway of plants comprises a sensor, signal transduction and a response. The sensor perceives adverse environmental conditions (Cutler et al., 2010). In Arabidopsis thaliana, several perception and signaling pathways have been identified for the response to high salinity in soil, including the salt overly sensitive pathway and the phytohormone abscisic acid (ABA)-dependent and-independent transcriptional regulation pathways (Mahajan et al., 2008). Moreover, they report that floral initiator Shk1 Kinase Binding protein1 (SKB1) and Histone4 arginine3 (H4R3) symmetric dimethylation (H4R3sme2) integrate responses to plant developmental progress and salt stress. SKB1 associates with chromatin and thereby increases the H4R3sme2 level to suppress the transcription of Flowering Locus C (FLC) and a number of stress-responsive genes. During salt stress, the H4R3sme2 level is reduced, as a
Thegenetic distances based on the Jaccard similarity index, using ISSRmarkers, did not correlate with geographic distance between the sampling locations, demonstrating that the accessions did not have distance-related genetic variability. This result could be due to the widespread practice of exchanging accessions between neighboring farmers and relatives, resulting in the same genotype having different names in different localities. Veasey et al. (2008), in a study made with microsatellite markers, also did not find correlations between geographic distances and genetic differences among sweet potato accessions collected in Vale do Ribeira, São Paulo Sate. However, Qiang et al. (2008), who used ISSRmarkers, found an association between genetic and geographic distances working with accessions from various Asian countries, different from thestudyof Veasey et al. (2008) and our study, in which most accessions were from the same geographic region.
that long distances between regions would affect habitat conditions, and that natural spatial barriers would cause the greatest genotypic di- versity among the research material. In addition, three cultivars (including two ofthe oldest Polish cultivars of P. pratensis) were included in our research and subjected to the same anal- yses. All the plant material was evaluated for geneticdiversity using two systems ofmarkers based on DNA amplification (RAPD and ISSR). In the present study, the effectiveness ofthe methods in assessing thegeneticdiversityofthe selected forms of P. pratensis was com- pared. Furthermore, we investigated whether these methods could be useful in establishing a link between the geographical origin of a given population and their assessed genetic variability. Primers withthe greatest differentiating powers correlating with geographical distance were selected for ISSR, the more effective method in that respect. Principal Compo- nent Analysis (PCA) was used for this procedure, which was performed on the chosen values of DNA amplification products obtained in the presence of those selected ISSRmarkerswiththe highest genetic differentiating power with respect to the studied forms of P. pratensis.
In the dendrogram constructed ofthe subpopulations ofthe breeds studied (Fig. 2), the S and T subpopulations per breed were grouped in the same cluster. In fact, theISSRmarkers used in this study showed a low potential for separating the S and T subpopulations as different clusters. TheISSRmarkers amplify intergenic and non-coding regions ofthe genome, and these regions may not have any effect on the number of kids (twining trait). It seems that a study on major genes known for the twining trait can distinguish S subpopulations from T subpopulations. For example, Rasouli et al. (2016) reported that the twinning rate in Markhoz goats was sig- nificantly influenced by the IGF-I and IGFBP-3 genotypes; also, the association of two single nucleotide polymorphisms (SNPs) in the growth hormone (GH) gene withthe litter size and superovulation response in goat breeds has been studied, and the results have shown that the two loci ofthe GH gene are highly associated with abundant prolificacy and a super- ovulation response in goat breeds (Zhang et al., 2011).
The objective of this study was to compare methods of multivariate analysis on the evaluation ofgeneticdiversityof mini tomato and to identify promising genotypes with resistance to pests. The experiment was conducted at the Vegetable Experiment Station ofthe Universidade Federal de Uberlândia, Monte Carmelo campus, from April 2013 to November 2016. The experimental design was a randomized complete block design with 16 treatments and four replications totaling 64 plots, and each plot represented by five plants. Sixteen genotypes were characterized, 12 from the F 2 RC 1 generation, obtained through the interspecific crossing between the wild access LA-716 (Solanum pennellii) and pre-commercial lines of mini tomato (UFU-73 and UFU-2) (Solanum lycopersicum) and the UFU-2 lines. The content of acyl sugar, the amount of glandular trichomes (types I, IV, VI and VII), twospotted spider mite and whitefly resistance were evaluated. We concluded that there exist genetic variability between the genotypes. The number of groups formed by the canonical variated analysis was higher (four groups) than that obtained by the Tocher method (three groups) and UPGMA (three groups), demonstrating a greater discrimination power. The Tocher and UPGMA methods were consistent in the analysis ofthegenetic divergence in pest resistant germplasm oftomato, withthe acyl sugar content being the most important variable. Genotype UFU-73-F 2 RC 1 # 11 is resistant to pest attack, while the other studied lines have intermediate resistance.
ABSTRACT. Distinct genetic structure in populations of Chrysoperla externa (Hagen) (Neuroptera, Chrysopidae) shown by geneticmarkersISSR and COI gene. Green lacewings are generalist predators, and the species Chrysoperla externa presents a great potential for use in biological control of agricultural pests due to its high predation and reproduction capacities, as well as its easy mass rearing in the laboratory. The adaptive success of a species is related to genetic variability, so that population genetic studies are extremely important in order to maximize success ofthe biological control. Thus, the present study used nuclear (Inter Simple Sequence Repeat – ISSR) and mitochondrial (Cytochrome Oxidase I – COI) molecular markers to estimate thegenetic variability of 12 populations in the São Paulo State, Brazil, as well as thegenetic relationships between populations. High levels ofgeneticdiversity were observed for both markers, and the highest values ofgeneticdiversity appear associated with municipalities that have the greatest areas of native vegetation. There was high haplotype sharing, and there was no corre- lation between themarkers and the geographic distribution ofthe populations. The AMOVA indicated absence ofgenetic structure for the COI gene, suggesting that the sampled areas formed a single population unit. However, the great genetic differentiation among populations showed by ISSR demonstrates that these have been under differentiation after their expansion or may also reflect distinct dispersal behavior between males and females.
Rosewood, Aniba rosaeodora is an endangered species in Amazon forests and its natural stands have been heavily depleted due to over-exploitation for the cosmetic industry. This study aimed to investigate thegeneticdiversity and population structure of 90 rosewood accessions from eight localities in the Peruvian Amazon through 11 Inter Simple Sequence Repeats (ISSR) primers. TheISSR primers produced a sum of 378 bands, of which 375 (99.2%) were polymorphic, with an average polymorphism information content (PIC) value of 0.774. The mean effective number of alleles (Ne), Shannon informative index (I), gene diversity (He) and total gene diversity (Ht) were 1.485, 0.294, 0.453 and 0.252, respectively. Analysis of molecular variance (AMOVA) showed the presence of maximum variability within populations (88%). The Structure algorithm, neighbor joining and principal coordinate analysis (PCoA) grouped the 90 rosewood accessions into three main populations (A, B and C). Diversity indices at the inter-population level revealed a greater geneticdiversity in population A, due to higher gene flow. The neighbor-joining analysis grouped populations A and B, while population C was found to be divergent at the inter population level. We concluded that population A reflects higher geneticdiversity and should be prioritized for future management and conservation plans.
ABSTRACT. Eucalyptus cladocalyx F. Muell is a tree endemic to southern Australia and is distributed across four isolated regions: Kangaroo Island, southern Flinders Ranges, and two geographical zones in Eyre Peninsula. E. cladocalyx is capable of growing under extreme environmental conditions, including dry and saline soils. The objective of this study was to analyze geneticdiversity in 45 half-sib families planted in northern Chile that are distributed across five different zones (provenances). Genetic variability was assessed using ISSR (Inter Simple Sequence Repeat) molecular markers. The results showed low levels ofgeneticdiversity within populations (He = 0.113 to 0.268) in contrast with other Eucalyptus species. In addition, there was a significant genetic differentiation among provenances (Φst = 0.14); populations from the Kangaroo Island provenance showed more differentiation than any other population. These results are in agreement with previous studies ofthe species. Our study revealed that Chilean resources are a representative sample of Australian populations; therefore, the germplasm planted in northern Chile would be sufficient for the development of improvement programs. ISSR-Marker technology could be an alternative to identify genotypes of interest in material selection.
ABSTRACT - Elaeagnus is a Eurasian tree with 77 species worldwide. In this study, ISSRmarkers were used to establish the level ofgenetic relationships and polymorphism across nine genotypes of Elaeagnus angustifolia collected from 9 different regions of West Azarbaijan province. TheISSR analysis with 11 anchored primers also generated 116 scorable loci, of which 92 were polymorphic (79.3%). The estimated Jaccard similarity coefficient ranged from 0.44 to 0.76 for theISSRmarkers. Cluster analysis was carried out, based on the Unweighted Pair Group Method with Arithmetic Averages (UPGMA) and the dendrogram drawn withthe help ofthe NTSYSpc 2.02 software. The analysis revealed 5 main clusters for theISSR data. According to our results, there is a relatively high genetic distance across E. angustifolia genotypes in the West Azarbaijan province of Iran. Furthermore, it could be inferred that ISSRmarkers are suitable tools for the evaluation ofgeneticdiversity and relationships within the Elaeagnus genus.
ABSTRACT. Analysis ofthegeneticdiversity in Metopolophium dirhodum (Walker) (Hemiptera, Aphididae). The emergence of host-races within aphids may constitute an obstacle to pest management by means of plant resistance. There are examples of host-races within cereals aphids, but their occurrence in Rose Grain Aphid, Metopolophium dirhodum (Walker, 1849), has not been reported yet. In this work, RAPD markers were used to assess effects ofthe hosts and geographic distance on thegeneticdiversityof M. dirhodum lineages. Twenty-three clones were collected on oats and wheat in twelve localitites of southern Brazil. From twenty-seven primers tested, only four primers showed polymorphisms. Fourteen different genotypes were revealed by cluster analysis. Five genotypes were collected only on wheat; seven only on oats and two were collected in both hosts. Genetic and geographical distances among all clonal lineages were not correlated. Analysis of molecular variance showed that some molecular markers are not randomly distributed among clonal lineages collected on oats and on wheat. These results suggest the existence of host-races within M. dirhodum, which should be further investigated using a combination of ecological and genetic data.
Tomato samples were collected from June through November of 1999 in fields located around the cities of Igarapé, Mateus Leme, and Bicas (the green belt of Belo Horizonte, MG), Várzea Alegre (ES), São Fidélis (Northern RJ) and Paty do Alferes (Southern RJ) (Table 1). Young leaves from 15 plants showing typical symptoms of begomovirus infection (yellow mosaic, leaf curling, and stunting) were collected from each field, except in Paty do Alferes, where 20, 24 and 25 samples were collected in each ofthe three fields sampled (Table 1). A number of weed samples were also collected. Samples were placed in plastic bags and taken to the laboratory, where they were wrapped in aluminum foil, labeled and stored at -80 o C.
RESUMO - A grande diversidade de plantas do Semiárido representa um recurso natural vital para as populações humanas dessa região. Muitas dessas plantas são exploradas de forma extrativista e entre elas, as espécies do gênero Stylosanthes, que são nativas tem grande potencial, porém, os trabalhos realizados têm sido modestos e pouco se conhece a respeito da variabilidade existente nessas plantas. Por isso, esforços devem ser priorizados no sentido de estudá-las, o que certamente poderá ajudar a criar formas para o desenvolvimento de cultivares e, assim, amenizar a escassez de forragem nessa região. Entretanto, para iniciar trabalhos de melhoramento, primeiro deve-se buscar variabilidade genética. Assim, este trabalho avaliou 25 acessos de Stylosanthes spp., a fim de identificar os melhores para serem genitores no programa de melhoramento genético para o Semiárido baiano. Para isso, foram conduzidos dois experimentos em diferentes locais no delineamento blocos casualizados completos com quatro repetições num espaçamento 3,0 × 0,8 m. Foi constatada grande diversidade genética entre os acessos, sendo que os genótipos BGF 08-007, BGF 08-016, BGF 08-015 e BGF 08-021, mostraram-se como os mais divergentes na avaliação geral. Para a formação de populações segregantes, recomenda-se combinar os genótipos BGF 08-016, BGF 08-015, BGF 08-007 e BGF 08-006, e para cruzamentos interespecíficos recomenda-se hibridar o acesso BGF-024 com os acessos BGF 08-016 e BGF 08-015, possibilitando o surgimento de indivíduos superiores para os descritores de massa, os mais importantes para o melhoramento visando alimentação animal.
The obtained LC–MS/MS data were matched withthe L. esculentum database (with a total of 34,824 sequences) concatenated with reverse decoy database. A total of 347 lysine succinylation peptides with peptide score >40 (S1 Table) were identified in tomato. These peptides with varying abundance depending on their length occurred on 202 succinylated proteins with dif- ferent numbers of succinylated sites ranging from 1 to 9. Out ofthe 202 identified succinylated proteins, 60.4% (122/202) had a single succinylated site, 24.6% (49/202) had two, and 8.4% (17/202) contained three; the average degree of succinylation was 1.7 (347/202). Notably, most ofthe proteins with multiple succinylations were chloroplast and mitochondrial proteins involved in diverse metabolic pathways (S1 Table). Moreover, the most extensively succiny- lated protein with up to nine independent lysine residues was dihydrolipoyl dehydrogenase, which is a mitochondrial enzyme and plays a vital role in energy metabolism (S1 Table).