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.
Highlights
Root-knot nematodes (Meloidogyne) are polyphagous, obligate pests that are distributed worldwide and parasitize almost all the higher plant species, resulting in great economic losses[1]
Several studies have been conducted to elucidate the genetic diversity of Meloidogyne populations by using different molecular techniques, e.g. random amplified polymorphic DNA (RAPD), restriction fragment length polymorphisms (RFLP), PCR based on sequences of rDNA, mtDNA, ITS and IGS, or satellite DNA probe markers[18,19,20,21,22,23,24,25,26]
This study aimed to investigate the genetic diversity of three different Meloidogyne species viz. M. enterolobii, M. incognita and M. javanica using Genotyping by sequencing (GBS) in order to highlight relationships among these species and loci putatively involved in virulence
Summary
Root-knot nematodes (Meloidogyne) are polyphagous, obligate pests that are distributed worldwide and parasitize almost all the higher plant species, resulting in great economic losses[1]. Its established occurrence in South Africa fits the hypothesis of the late Dr Kent Kleynhans and Mr Piet Willers that the occurrence and host range is wider than the initial localities and hosts around Mbombela, Mpumalanga (personal communication, Dr Kent Keynhans, Agricultural Research Council-Plant Protection Research Institute, Pretoria, 1998) It has been reported from other crop production areas, infecting green pepper (Capsicum annuum); potato (Solanum tuberosum) and tomato (Solanum lycopersicum)[16,17]. This scenario justified a more detailed genetic study of South African Meloidogyne populations to determine if genomic differences linked with virulence exhibited by M. enterolobii could be found between M. incognita and M. javanica. When using a sufficiently big pool size, Pool-Seq even showed to be more appropriate for estimating allele frequencies and is more cost effective than sequencing the DNA of individuals[36]
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