Genetic diversity and phylogeny of South African Meloidogyne populations using genotyping by sequencing

Abstract

Meloidogyne species cause great crop losses worldwide. Although genetic host plant resistance is an effective control strategy to minimize damage caused by Meloidogyne, some resistant genes are ineffective against virulent species such as Meloidogyne enterolobii. Detailed knowledge about the genetic composition of Meloidogyne species is thus essential. This study focused on genotyping-by-sequencing (GBS) and Pool-Seq to elucidate the genetic relation between South African M. enterolobii, M. incognita and M. javanica populations. Hence, 653 common single nucleotide polymorphisms (SNPs) were identified and used to compare these species at genetic level. Allele frequencies of 34 SNPs consistently differed between the three Meloidogyne species studied. Principal component and phylogenetic analyses grouped the M. enterolobii populations in one clade, showing a distant relation to the M. javanica populations. These two species also shared genetic links with the M. incognita populations studied. GBS has been used successfully in this study to identify SNPs that discriminated among the three Meloidogyne species investigated. Alleles, only occurring in the genome of M. enterolobii and located in genes involved in virulence in other animal species (e.g. a serine/threonine phosphatase and zinc finger) have also been identified, accentuating the value of GBS in future studies of this nature.

Further observations on Meloidogyne enterolobii (Nematoda: Meloidogynidae) infecting guava (Psidium guajava) in India

“…4B ). In this line, use of molecular markers, viz., ribosomal D2D3 expansion segment, ITS rDNA, IGS rDNA, mitochondrial COI, viable region between COII and 16S rDNA, mitochondrial NADH5 and SCAR marker has been found to be more robust for specific confirmation of the species ( Tigano et al, 2010 ; Onkendi and Moleleki, 2013 ; Rashidifard et al, 2018 ); and SCAR marker proved best in the situation of occurrence of mixed populations consisting of M. enterolobii, M. incognita, M. javanica , and M. hapla Chitwood, 1949 ( Rashidifard et al, 2018 ).…”

Genetic intraspecific diversity of Meloidogyne javanica parasitizing vegetables in southern Iran

“…Accurate distinction of M. enterolobii , M. javanica , and M. incognita was still challenging using various molecular techniques, except for SCAR-PCR ( Zijlstra et al, 2000 ) and genotyping by sequencing method for identifying diagnostic single nucleotide polymorphisms ( Rashidifard et al, 2018 ). In our study, SCAR markers were used successfully for distinguishing populations of M. javanica from M. incognita , so 37 populations produced specific band of M. javanica and four populations produced the band typical for M. incognita .…”

“…RAPD markers revealed a low intraspecific genetic diversity (14%) among 17 isolates of this species parasitizing potato in Brazil (Medina et al, 2017). Principal component and phylogenetic analyses revealed distant relationship between M. javanica and M. enterolobii Yang and Eisenback, 1983 populations from South Africa (Rashidifard et al, 2018).…”

Meloidogyne enterolobii, a Major Threat to Tomato Production: Current Status and Future Prospects for Its Management

“…Analysis of single nucleotide polymorphisms (SNPs) could be a beneficial low cost and high-throughput tool for M. enterolobii diagnosis ( Davis et al, 2005 ; Holterman et al, 2012 ). Genotyping-by-sequencing (GBS) technique discovers SNPs to whole-genome profiling of association panels ( Elshire et al, 2011 ) and has been used successfully to investigate the phylogenetic genetic relationships of M. enterolobii , M. incognita , and M. javanica populations in South Africa and identify 34 SNPs that were useful to discriminate between the three Meloidogyne species investigated ( Rashidifard et al, 2018 ). The complete genomes of the root-knot species M. incognita , M. hapla , and M. enterolobii have been sequenced and reported ( Abad et al, 2008 ; Opperman et al, 2008 ; Koutsovoulos et al, 2019 ).…”