Assessment of Genetic Variability and Evolutionary Relationships of Rhizoctonia solani Inherent in Legume Crops

Abstract

Rhizoctonia solani is one of the most common soil-borne fungal pathogens of legume crops worldwide. We collected rDNA-ITS sequences from NCBI GenBank, and the aim of this study was to examine the genetic diversity and phylogenetic relationships of various R. solani anastomosis groups (AGs) that are commonly associated with grain legumes (such as soybean, common bean, pea, peanut, cowpea, and chickpea) and forage legumes (including alfalfa and clover). Soybean is recognized as a host for multiple AGs, with AG-1 and AG-2 being extensively investigated. This is evidenced by the higher representation of sequences associated with these AGs in the NCBI GenBank. Other AGs documented in soybean include AG-4, AG-7, AG-11, AG-5, AG-6, and AG-9. Moreover, AG-4 has been extensively studied concerning its occurrence in chickpea, pea, peanut, and alfalfa. Research on the common bean has been primarily focused on AG-2, AG-4, and AG-1. Similarly, AG-1 has been the subject of extensive investigation in clover and cowpea. Collectively, AG-1, AG-2, and AG-4 have consistently been identified and studied across these diverse legume crops. The phylogenetic analysis of R. solani isolates across different legumes indicates that the distinct clades or subclades formed by the isolates correspond to their specific anastomosis groups (AGs) and subgroups, rather than being determined by their host legume crop. Additionally, there is a high degree of sequence similarity among isolates within the same clade or subclade. Principal coordinate analysis (PCoA) further supports this finding, as isolates belonging to the same AGs and/or subgroups cluster together, irrespective of their host legume. Therefore, the observed clustering of R. solani AGs and subgroups without a direct association with the host legume crop provides additional support for the concept of AGs in understanding the genetic relationships and evolution of R. solani.

Keywords: Rhizoctonia solani; anastomosis groups; forage legumes; genetic diversity; grain legumes; phylogeny.

Figure 1

Phylogenetic trees of AG sequences associated with clover, alfalfa, cowpea, and peanut were constructed using the maximum likelihood (ML) method. Only bootstrap values ≥ 70% are shown. Accession number is followed by AGs from the GenBank and isolate name. Different colors show AGs and subgroups. (a,b). Few AG were reported from forage legumes such as alfalfa and clover, (c,d). AGs are associated with cowpea and peanut. Scale bar represents genetic distance for horizontal branch lengths. Athelia rolfsii (strain FSR-052) was used as an outgroup.

Figure 2

Phylogenetic trees of AG sequences associated with chickpea and pea were constructed using the maximum likelihood (ML) method. Only bootstrap values ≥ 70% are shown. Accession number is followed by AGs from the GenBank and isolate name. Different colors show AGs and subgroups. (a) AGs associated with chickpea; (b) AGs associated with pea. Scale bar represents genetic distance for horizontal branch lengths. Athelia rolfsii (strain FSR-052) was used as an outgroup.

Figure 3

Phylogenetic trees of AG sequences associated with soybean and common bean were constructed using the maximum likelihood (ML) method. Only bootstrap values ≥ 70% are shown. Accession number is followed by AGs from the GenBank and isolate name. Different colors show AGs and subgroups and major clades associated with AGs, and these are represented by Roman numerals. (a) Phylogenetic tree of AGs associated with soybean; (b) Phylogenetic tree of AGs associated with the common bean. Scale bar represents genetic distance for horizontal branch lengths. Athelia rolfsii (strain FSR-052) was used as an outgroup.

Figure 4

Phylogenetic trees of sequences associated with all legume crops were constructed using the maximum likelihood (ML) method. Only bootstrap values ≥ 70% have been shown. The common name of the legume crop is followed by reference accession numbers, AGs from the GenBank, and isolate name. Different colors show AGs and clades and/or subclades associated with AGs. The scale bar represents genetic distance for horizontal branch lengths. Athelia rolfsii (strain FSR-052) was used as an outgroup.

Figure 5

Principal coordinate analysis (PCoA) scatter plot based on the percent sequence identity matrix. Different colors of plots represent different AG groups associated with legume: AG-1 (green circle), AG-2 (blue circle), AG-3 (bisque circle), AG-4 (yellow circle), AG-5 (purple circle), AG-7 (antique white circle), AG-11 (aqua circle), AG-10 (brown circle), and FSR-052 (outgroup—red circle).