ISSR primers for analysis of genetic variability of Stenocarpella maydis

Fedrigo, Katiane; Giacomin, Renata Mussoi; Faria, Cacilda Márcia Duarte Rios; Silva, Paulo Roberto da

doi:10.1007/s40858-016-0089-1

Cited by 8 publications

(8 citation statements)

References 19 publications

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“…The same comparison above applied to the F. graminearum population evaluated in our study also showed the high polymorphism of this species in the studied region. Polymorphism levels are important information when working with dominant markers because they are one of the parameters that can be used to indicate genetic variability (Fedrigo et al 2016;Rosa et al 2017;Mariano et al 2019). The high polymorphism observed in the populations of F. graminearum, F. meridionale, and F. austroamericanum in southern Brazil implies high genetic variability in these species; thus, presenting a high adaptative potential.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity of Fusarium meridionale, F. austroamericanum, and F. graminearum isolates associated with Fusarium head blight of wheat in Brazil

Arruda

Zchosnki

Silva

et al. 2020

Trop. plant pathol.

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One of the biggest challenges of wheat production worldwide is to overcome fungal diseases, and among these is Fusarium head blight (FHB) caused mainly by the Fusarium graminearum species complex (FGSC). The occurrence of FHB can lead to contamination of grains with mycotoxins, which are harmful to human and animal health. In South America, in addition to F. graminearum sensu stricto (F. graminearum), which is the most common causal agent of FHB worldwide, F. meridionale and F. austroamericanum have also been found in wheat fields. Special attention should be paid to F. meridionale because it produces the trichothecene mycotoxin nivalenol, which has potentially higher levels of toxicity when compared with that of other trichothecene produced by the FGSC. Knowledge of the diversity and genetic structure of populations of pathogens can assist in understanding pathogen survival in the face of host genetic resistance, crop rotation, and management with fungicides. In this study, we used 10 inter-simple sequence repeat (ISSR) primers to estimate the variability, diversity, and genetic structure of populations of F. graminearum, F. meridionale, and F. austroamericanum co-occurring in wheat fields in Paraná State, Brazil. The population of F. graminearum showed the greatest genetic variability according to its polymorphism (P = 86.61%), Nei's genetic diversity (h = 0.28), and Shannon diversity (I = 0.43) indices as compared with that of the populations of F. meridionale (P = 75.89%, h = 0.23, I = 0.36) and F. austroamericanum (P = 67.86%, h = 0.22, I = 0.33). The dendrogram, principal coordinate analysis, Bayesian analysis (K = 4), and the differentiation index (G ST = 0.27) showed very high structure and, consequently, high species differentiation. The overall analysis of our data indicates high variability and genetic structure of the studied populations. This genetic condition guarantees high resilience of these species and could make it difficult to obtain wheat cultivars with good resistance to FHB, as well as may cause chemical control to be less effective.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity of Fusarium meridionale, F. austroamericanum, and F. graminearum isolates associated with Fusarium head blight of wheat in Brazil

Arruda

Zchosnki

Silva

et al. 2020

Trop. plant pathol.

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“…The selection of primers can only be considered effective when the primers selected to differentiate a species show similar results to those obtained using all available primers (Fedrigo et al, 2016). Typically, in a genetic variability study, a high number of primers is used, consequently increasing the costs and time to obtain results.…”

Section: Discussionmentioning

confidence: 99%

“…The use of PIC and RP indexes has been effective in the selection of primers in several species, such as Jathopha curcas (Tatikonda et al, 2009; Grativol et al, 2011), Ipomoea batatas (Camargo et al, 2013), Stenocarpella maydis (Fedrigo et al., 2016), and Achyrocline flaccida (Rosa et al., 2017). Our work shows that the PIC and RP indexes successfully selected ISSR primer in apple, since the average similarity between the genotypes was the same (0.37) when using the nine selected primers and all 26 polymorphic primers.…”

Section: Discussionmentioning

confidence: 99%

“…When working with dominant markers such as ISSR, the percentage of polymorphisms observed can be indicative of genetic variability (Fedrigo et al, 2016). The comparison of our results with those in the literature (Table 4), shows that although we analyzed the largest number of genotypes, the average number of polymorphic fragments per primer and the general percentage of polymorphic fragments is among the smallest.…”

Section: Discussionmentioning

confidence: 99%

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Genetic variability in a Brazilian apple germplasm collection with low chilling requirements

Mariano

Zchonski

Silva

et al. 2019

PeerJ

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The apple (Malus domestica Borkh) originally evolved to require temperatures below 7.2 °C for the induction of budding and flowering. In Brazil, breeders have overcome the climate barrier and developed the cultivars Anabela, Julieta, Carícia, and Eva, with low chilling requirements and good yield characteristics. These cultivars are grown in many warmer climate countries in South America, Africa, and the Middle East. The apple germplasm collection that originated these cultivars has several genotypes with pedigrees for a low chilling requirement. Knowledge of the variability and genetic relationships among these genotypes may be useful in the development of superior new cultivars. In this work, we first selected the best ISSR (inter-simple sequence repeat) primers for genetic studies in apple, and then we used the selected primers to evaluate the genetic variability of the apple germplasm collection at the Instituto Agronômico do Paraná. The evaluation of 42 ISSR primers in 10 apple genotypes allowed us to select the best nine primers based on the polymorphic information content (PIC) and resolving power (RP) indexes. The primer selection step was robust since the dendrogram obtained with the nine selected primers was the same as the one obtained using all 26 polymorphic primers. Primer selection using PIC and RP indexes allowed us to save about 60% of time and costs in the genetic variability study. The nine ISSR primers showed high levels of genetic variability in the 60 apple genotypes evaluated. The relevance of the primer selection step is discussed from the perspective of saving time and money in germplasm characterization. The high genetic variability and the genetic relationships among the genotypes are discussed from the perspective of the development of new apple cultivars, mainly aiming for a low chilling requirement that can better adapt to current climatic conditions or those that may arise with global warming.

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“…flaccida . Additionally, when there is no previous knowledge of microsatellite regions for the genome of the species, ISSR (inter-simple sequence repeat) markers can also be used as an alternative [ 20 – 23 ]. The ISSR markers have the advantage of analyzing multiple loci in a single polymerase chain reaction (PCR); in addition, they are very informative, reliable, and produce a high level of polymorphism [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

Variability and population genetic structure in Achyrocline flaccida (Weinm.) DC., a species with high value in folk medicine in South America

et al. 2017

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Better knowledge of medicinal plant species and their conservation is an urgent need worldwide. Decision making for conservation strategies can be based on the knowledge of the variability and population genetic structure of the species and on the events that may influence these genetic parameters. Achyrocline flaccida (Weinm.) DC. is a native plant from the grassy fields of South America with high value in folk medicine. In spite of its importance, no genetic and conservation studies are available for the species. In this work, microsatellite and ISSR (inter-simple sequence repeat) markers were used to estimate the genetic variability and structure of seven populations of A. flaccida from southern Brazil. The microsatellite markers were inefficient in A. flaccida owing to a high number of null alleles. After the evaluation of 42 ISSR primers on one population, 10 were selected for further analysis of seven A. flaccida populations. The results of ISSR showed that the high number of exclusive absence of loci might contribute to the inter-population differentiation. Genetic variability of the species was high (Nei’s diversity of 0.23 and Shannon diversity of 0.37). AMOVA indicated higher genetic variability within (64.7%) than among (33.96%) populations, and the variability was unevenly distributed (FST 0.33). Gene flow among populations ranged from 1.68 to 5.2 migrants per generation, with an average of 1.39. The results of PCoA and Bayesian analyses corroborated and indicated that the populations are structured. The observed genetic variability and population structure of A. flaccida are discussed in the context of the vegetation formation history in southern Brazil, as well as the possible anthropogenic effects. Additionally, we discuss the implications of the results in the conservation of the species.

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ISSR primers for analysis of genetic variability of Stenocarpella maydis

Cited by 8 publications

References 19 publications

Genetic diversity of Fusarium meridionale, F. austroamericanum, and F. graminearum isolates associated with Fusarium head blight of wheat in Brazil

Genetic diversity of Fusarium meridionale, F. austroamericanum, and F. graminearum isolates associated with Fusarium head blight of wheat in Brazil

Genetic variability in a Brazilian apple germplasm collection with low chilling requirements

Variability and population genetic structure in Achyrocline flaccida (Weinm.) DC., a species with high value in folk medicine in South America

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