A survey to determine the Pratylenchus spp. present in South African apple orchards

Pratylenchus spp. are widely known to cause serious damage to apple trees (Colbran, 1963; Bosher and Newton, 1957; Goss, 1961; Palmiter and Braun, 1962). In addition to the direct damage caused to the roots Pratylencus spp. have been associated in some sites where Apple Replant Disease (ARD) is present in South Africa (Tewoldemedhin, 2011). The role of the specific Pratylenchus species in the ARD complex is yet to be determined. Pratylenchus penetrans has been identified as being part of the ARD complex in Washington, USA (Mazzolla, 1998), whereas P. jordanensis was identified in Queensland, Australia (Stirling et al, 1995).

Most of the research and resistance breeding in other countries is focused on Pratylenchus penetrans (Mazzolla, 2012). From the few samples taken from ARD soils, in conjunction with the ARD research group at Plant Pathology, Stellenbosch University, four species were identified. From this very limited survey and the survey in 1984 (Hugo, 1984) it would seem that P. penetrans is not the primary species in South Africa.

In the survey by Hugo (1984), a list of Pratylenchus spp. was compiled, but in more recent projects and samples analysed more species were identified. This shows that the diversity of species could have increased or a shift in the population present has taken place in this area.

The long-term plan with this project was to determine the different species of Pratylenchus in South African apple orchards and subsequently determine which species are the most virulent. The virulence testing and rootstock screening will be done in a new project by dr. Rinus Knoetze.

A survey was conducted of the Pratylenchus spp. present in apple orchards. Samples were initially taken from 50 orchards in 2016/17. The samples were taken in Elgin (2), Grabouw (21), Villiersdorp (2), Vyeboom (5) and the Langkloof (20). The initial plan was to take one sample per 250ha. Only the roots were processed to extract Pratylenchus spp., as the species in the roots will be the infective ones.

During 2017/18 samples were received in the laboratory (Nemlab) and samples with high numbers of Pratylenchus spp. were included in the survey so that more specimens were available for identification purposes. A total of 48 samples were sequenced, 3 individuals per samples, of which 40 (a total of 120 individuals) could be used.

Low numbers of Pratylenchus spp. were initially extracted from root samples collected in the field. From the random samples received by Nemlab from different production areas, Pratylenchus spp. were extracted and sequenced. After a few individuals were sequenced it became clear that an overwhelming percentage of specimens were identified as P. hippeastri. P. hippeastri were identified from 84.17%, P.vulnus from 9.17% and P.penetrans also from 9.17%. More than one species were extracted from some of the samples, thus the percentages were calculated from the total number of samples.

This survey’s value to the industry is the fact that the data collected will be fundamental in ongoing research about Pratylenchus spp in the apple industry. It adds knowledge about the species present and will form a base for future research on rootstocks and virulence trials in new projects to follow.

The initial idea of isolating over 14 different species of Pratylenchus in apple orchards was soon changed when over 80% of sequenced samples came back as P. hippeastri. The only 2 other species found were P. vulnus and P. penetrans both from 9.17% of sequenced samples.

Going forward, the project will not end and samples coming through Nemlab will still be scanned for Pratylenchus. These samples will also be sequenced and added to the database.

Dr. Knoetze will continue with the maintenance of the populations on carrot disks to maintain the pure cultures which will be used in the rootstock screening trial. A follow-up report will be done in Aug 2019 to report on findings in the ongoing sample screening.

An in-depth survey of the apple nurseries is also recommended.