Genetic diversity of Colletotrichum lindemuthianum races based on ITS-rDNA regions

Marcela Coêlho,Rodrigo Chimenez Franzon,Vanusa Silva Ramos Martins,Maria Celeste Gonçalves Vidigal,Pedro Soares Vidigal Filho

doi:10.33158/asb.r112.v6.2020

Marcela Coêlho, Rodrigo Chimenez Franzon + Show 3 more

Open Access

https://doi.org/10.33158/asb.r112.v6.2020

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Abstract

Colletotrichum lindemuthianum is the causal agent of anthracnose in common bean. Favorable conditions for this disease might result in up to 100% yield losses. One of the main challenges for common bean producers and breeders still remains the management disease, since this pathogen exhibits a wide genetic variability probably due to its recombination sexual reproduction. The 5·8S gene and the flanking internal transcribed spacer regions (ITS1 and ITS2) of 40 different isolates of C. lindemuthianum collected in Brazil were amplified by PCR, and sequenced in order to determine genetic variability. The results revealed that 46.88% of SNPs were detected in the ITS1 region, while 53.12% of them were located in the ITS2 region. The genetic distance ranged from 0.000 to 0.169 between races. The greatest distance was observed between the races 10 and 73 with a value of 0.169, indicating a wide genetic variability between them. The phylogenetic tree was composed of three groups. Group I had five subgroups. Similar results were also observed through population structure analysis, which revealed the presence of three clusters. These results suggest that sequence analysis of ITS rDNA regions of C. lindemuthianum may be a valuable tool to identify this pathogen through design of specific primers.

Highlights

Common bean (Phaseolus vulgaris L.) is one of the most important legumes for the human diet in the world, especially in Latin America and Africa (Broughton et al, 2003)
Similar results were obtained by Balardin et al (1999), who performed sequencing studies on Internal Transcribed Spacer (ITS) regions of C. lindemuthianum isolates collected from several parts of the world including Brazil
Considering that the ITS regions can vary intraspecifically in the sequence of bases, they are appropriate to discriminate the possible variations within and among the population of the pathogen. This information is of great relevance since the molecular diversity conferred through the ITS regions in the identification of SNPs can collaborate for a better understanding of the hostpathogen relationship, in the search for the development of new resistant cultivars

Summary

Introduction

Common bean (Phaseolus vulgaris L.) is one of the most important legumes for the human diet in the world, especially in Latin America and Africa (Broughton et al, 2003). The socioeconomic importance of common bean is unquestionable, since this grain legume is in most cases the primary source of proteins, carbohydrates, vitamins and minerals for human diet (Hefni, Öhrvik, Mohamed & Witthoft, 2010). Common bean crop is susceptible to several diseases caused by fungi. Anthracnose caused by Colletotrichum lindemuthianum (Sacc and Magnus) Briosi and Cavara (1889) has a great impact on the grain yield and quality, because of its manifestation during the three growing seasons and severe damage of the crop, which in some cases is estimated 100% losses (Chiorato, Carbonell, Moura, Ito & Colombo, 2006). The severity of the infection depends on both the race and the variety of the common bean (Kimati et al, 1997; Vieira et al, 2006)

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