N. Bosselut

Multiplex Polymerase Chain Reaction Identification of Single Individuals of the Longidorid Nematodes Xiphinema index, X. diversicaudatum, X. vuittenezi, and X. italiae Using Specific Primers from Ribosomal Genes.

ABSTRACT The species X. index, X. diversicaudatum, X. vuittenezi, and X. italiae are established (E) or putative (P) vectors of Grapevine fanleaf virus (GFLV) (E), Arabis mosaic virus (E), Grapevine chrome mosaic virus (P), and GFLV (P) nepoviruses of grapevine, respectively. All four species are very closely related taxonomically and their low field densities make them difficult to identify from morphological and morphometrical diagnostic characters when only single or few individuals are detected. To improve diagnostic accuracy, a simple method was developed. The internal transcribed spacer 1 (ITS1) region spanning the 18S and 5.8S ribosomal genes was sequenced in one population of each species using two conserved primers from these genes. The ITS1 fragments were 1,132 bp (X. vuittenezi), 1,153 bp (X. index), 1,175 bp (X. diversicaudatum), and 1,190 bp (X. italiae), i.e., a difference of over 5% between the extremes. The sequence variability made it possible to design species-specific internal sense primers that amplified, in combination with the same antisense ITS1 primer, a single signature fragment (340 bp for X. index, 414 bp for X. italiae, 591 bp for X. vuittenezi, and 813 bp for X. diversicaudatum). Tests with DNA from a single adult or juvenile nematode confirmed the specificity of the primers from diverse isolates or populations. The primers were successfully used in a multiplex test for the reliable detection of two to four mixed species, each represented by a single individual. This multiplex-based diagnostic tool will be particularly useful for successful nematode management practices in vineyards.

Validation of the specificity and sensitivity of species-specific primers that provide a reliable molecular diagnostic for Xiphinema diversicaudatum, X. index and X. vuittenezi

Xiphinema diversicaudatum and X. index are vector nematode species of economic importance in viticulture regions as they can transmit Arabis Mosaic, Grapevine Fanleaf and Strawberry Latent Ringspot viruses to grapevine. Wang et al. (2003) designed species-specific diagnostic primers from ribosomal genes for both these vector species as well as a vector and a non-vector species X. italiae and X. vuittenezi, respectively. Our study aimed to confirm the specificity and determine the sensitivity and reliability of the primers for the two vector species, X. diversicaudatumand X. indexwhen challenged with closely related longidorid species and general nematode communities typical of vineyard soil. With one exception, no PCR product was observed when the primers were tested against six Longidorus, one Paralongidorus and one Xiphinema non-target species. Occasionally (three out of eight replicate PCR reactions) a weak PCR product was noted when primers for X. index were tested with L. elongatus. Furthermore, when challenged with a range of non-target nematode species comprising the nematode community typical of viticulture soil, no PCR product was amplified. An experimental dilution series of extracted DNA rigorously demonstrated that DNA from an equivalent single specimen of the target virus-vector species, X. diversicaudatum and/or X. index, could be detected amongst 1000 equivalent non-targetX. vuittenezi. Also, extracted DNA from an equivalent single target specimen was detected when added to DNA extracted from the overall soil nematode community. The primers were assessed further by using serial mixtures of actual nematodes rather than extracted DNA to simulate field soil. Using this method, a single target nematode could be detected amongst 200 non-target specimens. Given their specificity, sensitivity and reliability, it appears that these diagnostic primers will be of great benefit to phytosanitary/quarantine services related to the viticulture industry.

The Ma gene for complete-spectrum resistance to Meloidogyne species in Prunus is a TNL with a huge repeated C-terminal post-LRR region.

Root-knot nematode (RKN) Meloidogyne species are major polyphagous pests of most crops worldwide, and cultivars with durable resistance are urgently needed because of nematicide bans. The Ma gene from the Myrobalan plum (Prunus cerasifera) confers complete-spectrum, heat-stable, and high-level resistance to RKN, which is remarkable in comparison with the Mi-1 gene from tomato (Solanum lycopersicum), the sole RKN resistance gene cloned. We report here the positional cloning and the functional validation of the Ma locus present at the heterozygous state in the P.2175 accession. High-resolution mapping totaling over 3,000 segregants reduced the Ma locus interval to a 32-kb cluster of three Toll/Interleukin1 Receptor-Nucleotide Binding Site-Leucine-Rich Repeat (LRR) genes (TNL1–TNL3), including a pseudogene (TNL2) and a truncated gene (TNL3). The sole complete gene in this interval (TNL1) was validated as Ma, as it conferred the same complete-spectrum and high-level resistance (as in P.2175) using its genomic sequence and native promoter region in Agrobacterium rhizogenes-transformed hairy roots and composite plants. The full-length cDNA (2,048 amino acids) of Ma is the longest of all Resistance genes cloned to date. Its TNL structure is completed by a huge post-LRR (PL) sequence (1,088 amino acids) comprising five repeated carboxyl-terminal PL exons with two conserved motifs. The amino-terminal region (213 amino acids) of the LRR exon is conserved between alleles and contrasts with the high interallelic polymorphisms of its distal region (111 amino acids) and of PL domains. The Ma gene highlights the importance of these uncharacterized PL domains, which may be involved in pathogen recognition through the decoy hypothesis or in nuclear signaling.

Marker-assisted selection for the wide-spectrum resistance to root-knot nematodes conferred by the Ma gene from Myrobalan plum (Prunus cerasifera) in interspecific Prunus material

Prunus species express a more or less wide spectrum of resistance to root-knot nematodes (RKN) of the genus Meloidogyne. Among them, sources from Myrobalan plum (P. cerasifera) control all major and minor RKN species tested. In this outbreeding species, the clones P.2175 and P.2980 are heterozygous for the Ma single dominant gene and carry the alleles Ma1 and Ma3, respectively. Each allele confers a high-level resistance to the predominant RKN, M. arenaria, M. incognita and M. javanica and to the Florida isolate of an unknown Meloidogyne sp. which overcomes the resistance from peach and almond sources. The polymorphism of two coupling-phase SCAR markers tightly linked to Ma, SCAL19690 and SCAFLP2202, was evaluated within diverse diploid Prunus accessions. This material belongs to the subgenera Prunophora (Myrobalan and apricot) or Amygdalus (peach, almond and almond-peach) and includes the RKN resistance sources ‘Nemared’, ‘Alnem 1’ and ‘GF.557’. The alleles SCAL19690 and SCAFLP2202 were not present in three apricot cultivars (‘Moniqui’, ‘Luizet’ and ‘Stark Early Orange’) representative of the genetic diversity of this species and they segregated in an interspecific cross between P.2980 and apricot. These results suggest that apricot, reported as resistant to M. arenaria, M. incognita and M. javanica, and the Myrobalan plum might possess two different resistance systems. SCAL19690 and SCAFLP2202 were also absent from all tested Amygdalus material, whatever its resistance to RKN. Eight Myrobalan×Amygdalus segregating progenies including bispecific (P.2175 or P.2980×peach or almond) and trispecific (P.2175 or P.2980×almond-peach) hybrids were tested with the Florida isolate to identify individuals carrying the Ma resistance alleles. Both SCARs were then evaluated for segregation in these progenies to develop marker-assisted selection of Prunus interspecific rootstocks. SCAL19690 and SCAFLP2202 could be clearly detected and their tight linkage to Ma1 and Ma3 was confirmed. Consequently these SCARs appear to be powerful tools to screen for RKN resistance conferred by the Ma gene. They should also facilitate marker-assisted pyramiding of Ma with other resistance genes from the Amygdalus subgenus or from the botanically-related Armeniaca section.

Genetic dissection of resistance to root-knot nematodes Meloidogyne spp. in plum, peach, almond, and apricot from various segregating interspecific Prunus progenies

Sources of resistance in Prunus spp. exhibit different spectra to the root-knot nematodes (RKN) Meloidogyne incognita, Meloidogyne javanica and Meloidogyne floridensis. In this Prunus genus, two dominant genes, Ma with a complete spectrum from the heterozygous Myrobalan plums P.2175 and P.2980 (section Euprunus; subgenus Prunophora) and RMia with a more restricted spectrum from the peaches Nemared and Shalil (subgenus Amygdalus), have been identified. This study characterizes the resistance spectra of interspecific crosses involving (1) previous Myrobalan and peach sources, (2) two Alnem almonds (subgenus Amygdalus) resistant to M. javanica, and (3) the apricot A.3923, representing a species considered RKN-resistant (section Armeniaca; Prunophora). For both latter species, genetic data could be obtained through F1 crosses with genetically characterized Myrobalans that conferred their rooting ability for clonal multiplication of the hybrids and permitted their simultaneous evaluation to the three RKN. Crosses involving either Ma or RMia or both generated the expected resistance spectra. Nemared confirmed the species-specific resistance to M. incognita conferred by RMia. This rootstock, also previously considered resistant to M. javanica, was susceptible to the M. javanica isolate used, what illustrates an isolate-specific resistance to this species. Alnem accessions were shown homozygous resistant to M. javanica. In the progeny P.2980 × A.3923, Ma markers allowed to distinguish resistant individuals carrying that gene from resistant individuals lacking it. Distribution of non-Ma individuals in this cross suggested, in the apricot parent, (1) the absence of a major gene allelic to Ma and (2) the presence of a non RKN specific polygenic resistance.