Genetic diversity of Alternaria species associated with black point in wheat grains

Abstract

The genus Alternaria is a widely distributed major plant pathogen that can act as a saprophyte in plant debris. Fungi of this genus frequently infect cereal crops and cause such diseases as black point and wheat leaf blight, which decrease the yield and quality of cereal products. A total of 25 Alternaria sp. isolates were collected from germ grains of various wheat cultivars from different geographic regions in Kazakhstan. We investigated the genetic relationships of the main Alternaria species related to black point disease of wheat in Kazakhstan, using the inter-primer binding site (iPBS) DNA profiling technique. We used 25 retrotransposon-based iPBS primers to identify the differences among and within Alternaria species populations, and analyzed the variation using clustering (UPGMA) and statistical approaches (AMOVA). Isolates of Alternaria species clustered into two main genetic groups, with species of A.alternata and A.tennuissima forming one cluster, and isolates of A. infectoria forming another. The genetic diversity found using retrotransposon profiles was strongly correlated with geographic data. Overall, the iPBS fingerprinting technique is highly informative and useful for the evaluation of genetic diversity and relationships of Alternaria species.

DNA profiling and assessment of genetic diversity of relict speciesAllium altaicumPall. on the territory of Altai

“…Retrotransposons enhance the likelihood of mutations and recombination, which allow the organism to exist in extreme conditions ( Galindo-Gonzalez et al, 2017 ). Molecular markers based on interspersed repeats have been efficiently used on rare or endemic plant species whose genomes have not been studied ( Kalendar & Schulman, 2013 ; Kalendar et al, 2019 ; Milovanov et al, 2019 ) and have also been widely used on a wide range of plants (both monocotyledons and dicotyledonous ( Abdollahi Mandoulakani et al, 2015 ; Nie et al, 2019 ; Vuorinen et al, 2018 ; Woodrow et al, 2010 ; Yilmaz et al, 2018 )) and in animals and fungi ( Turzhanova et al, 2020 ).…”

“…The genetic polymorphism research method in rare species using retrotransposons is a simple and accessible method as the RAPD method is used ( Abdollahi Mandoulakani et al, 2015 ; Doungous et al, 2015 , 2019 ; Smykal et al, 2009 ). Variations of these markers have been used in various species of fungi, plants, animals and humans ( Doungous et al, 2015 ; Kalendar & Schulman, 2013 ; Li et al, 2020 ; Turzhanova et al, 2020 ; Vuorinen et al, 2018 ). Due to the fact that many mobile genetic elements “mix” with each other in the process of intra- and intrachromosomal recombination, this leads to convergence of these conserved regions and makes PCR amplification possible.…”

“…Primers complementary to interspersed repeats allow amplification of the region between these repeats if the distance between the repeats does not exceed the processivity of the used DNA polymerases ( Kalendar et al, 2019 ). Therefore, this approach, based on PCR between interspersed repeats and mobile genetic elements, can be easily adapted for any eukaryotic species for the rapid detection of molecular genetic polymorphisms even in an agarose gel ( Doungous et al, 2019 ; Hosid et al, 2012 ; Kalendar, Amenov & Daniyarov, 2018 ; Kalendar & Schulman, 2013 ; Milovanov et al, 2019 ; Turzhanova et al, 2020 ). Thus, application of PCR methods based on the use of conserved sequences of interspersed repeats and mobile genetic elements allows universal and efficient detection of polymorphisms for almost every eukaryotic species ( Kalendar, Amenov & Daniyarov, 2018 ; Smykal et al, 2009 ).…”

Figure 1: Places of collection of samples of rare and endemic species of onions in the territory of Kazakhstani Altai.

“…The genetic polymorphism research method in rare species using retrotransposons is a simple and accessible method as the RAPD method is used (Abdollahi Mandoulakani et al, 2015;Doungous et al, 2015Doungous et al, , 2019Smykal et al, 2009). Variations of these markers have been used in various species of fungi, plants, animals and humans (Doungous et al, 2015;Kalendar & Schulman, 2013;Li et al, 2020;Turzhanova et al, 2020;Vuorinen et al, 2018). Due to the fact that many mobile genetic elements "mix" with each other in the process of intra-and intrachromosomal recombination, this leads to convergence of these conserved regions and makes PCR amplification possible.…”

“…Primers complementary to interspersed repeats allow amplification of the region between these repeats if the distance between the repeats does not exceed the processivity of the used DNA polymerases (Kalendar et al, 2019). Therefore, this approach, based on PCR between interspersed repeats and mobile genetic elements, can be easily adapted for any eukaryotic species for the rapid detection of molecular genetic polymorphisms even in an agarose gel (Doungous et al, 2019;Hosid et al, 2012;Kalendar, Amenov & Daniyarov, 2018;Kalendar & Schulman, 2013;Milovanov et al, 2019;Turzhanova et al, 2020). Thus, application of PCR methods based on the use of conserved sequences of interspersed repeats and mobile genetic elements allows universal and efficient detection of polymorphisms for almost every eukaryotic species (Kalendar, Amenov & Daniyarov, 2018;Smykal et al, 2009).…”