Population genetic analyses of Phytophthora cinnamomi reveals three lineages and movement between natural vegetation and avocado orchards in South Africa

2022 ◽  
Author(s):  
Juanita Engelbrecht ◽  
Tuan A. Duong ◽  
Trudy Paap ◽  
Joseph Michael Hulbert ◽  
Juanita Joyce Hanneman ◽  
...  
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Phytophthora Cinnamomi ◽  
Resistance Breeding ◽  
Natural Vegetation ◽  
Economic Losses ◽  
Western Cape ◽  
Natural Ecosystems ◽  
Agricultural Industries ◽  
Production Areas

Phytophthora cinnamomi is the causal agent of root rot, canker and dieback of thousands of plant species around the globe. This oomycete not only causes severe economic losses to forestry and agricultural industries, but also threatens the health of various plants in natural ecosystems. In this study, 380 isolates of P. cinnamomi from four avocado production areas and two regions of natural vegetation in South Africa were investigated using 15 microsatellite markers. These populations were found to have a low level of genetic diversity and consisted of isolates from three lineages. Shared genotypes were detected between isolates from avocado orchards and natural vegetation, indicating the movement of isolates between these areas. The population from the Western Cape natural vegetation had the highest genotypic diversity and unique alleles, indicating this could be the point of introduction of P. cinnamomi to South Africa. Index of association analysis suggested that five out of six populations were under linkage disequilibrium suggesting a clonal mode of reproduction whereas genotypes sampled from a recently established avocado orchard in the Western Cape were derived from a randomly recombined population. This study provided novel insights on the genetic diversity and spread of P. cinnamomi in South Africa. It also reported on the predominance of triploidy in natural occurring populations and provided evidence for recombination of P. cinnamomi for the first time. The presence of two dominant genotypes in all avocado production areas in South Africa highlight the importance of considering them in disease management and resistance breeding programmes.

scholarly journals A Survey for ‘Candidatus Liberibacter’ Species in South Africa Confirms the Presence of Only ‘Ca. L. africanus’ in Commercial Citrus

Plant Disease ◽  
2010 ◽  
Vol 94 (2) ◽  
pp. 244-249 ◽  
Author(s):  
G. Pietersen ◽  
E. Arrebola ◽  
J. H. J. Breytenbach ◽  
L. Korsten ◽  
H. F. le Roux ◽  
...  
Keyword(s):  
South Africa ◽  
Western Cape ◽  
Chain Reaction ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Citrus Orchards ◽  
Polymerase Chain ◽  
Serious Disease ◽  
Production Areas ◽  
Representative Samples

Greening disease of citrus is a serious disease known in South Africa since the late 1920s. In South Africa, it is associated with infection by ‘Candidatus Liberibacter africanus’, a heat sensitive, phloem-limited, noncultured alpha-proteobacterium. Huanglongbing (HLB), a similar, but more devastating disease that was described initially from China but which now occurs in several citrus producing countries, is associated with a different Liberibacter species, ‘Ca. L. asiaticus’. A ‘Ca. L. africanus’ subspecies, ‘Ca. L. africanus subsp. capensis’, has been found only in South Africa infecting an indigenous Rutaceous species, Calodendrum capense (Cape Chestnut), in the Western Cape in 1995. The discovery of a new Liberibacter species in Brazil, ‘Ca. L. americanus’, and the spread of ‘Ca. L. asiaticus’ to a number of additional countries over the last few years prompted us to assess whether only ‘Ca. L. africanus’ is present in commercial citrus orchards in South Africa. Samples displaying greening or similar symptoms were collected from 249 citrus trees from 57 orchards distributed throughout the greening affected citrus production areas of South Africa. Multiplex polymerase chain reaction (PCR) was performed on DNA extracts to detect the known citrus Liberibacters. Amplicons were obtained from 197 samples. None of the samples yielded a 1,027-bp amplicon indicative of ‘Ca. L. americanus’ infection. The amplicons of 84 samples were sequenced, and all were identical to the cognate ‘Ca. L. africanus’ Nelspruit sequence in GenBank. No instance of ‘Ca. L. asiaticus’ or ‘Ca. L. africanus subsp. capensis’ sequence was found. Geographically representative samples that tested negative for Liberibacter also tested negative for phytoplasmas based on real-time PCR results. Based on the results of this survey, it is concluded that to date only ‘Ca. L. africanus’ is associated with citrus greening in commercial citrus in South Africa.

scholarly journals Ethnoveterinary Knowledge and Biological Evaluation of Plants Used for Mitigating Cattle Diseases: A Critical Insight Into the Trends and Patterns in South Africa

2021 ◽  
Vol 8 ◽  
Author(s):  
Mompati V. Chakale ◽  
Mulunda Mwanza ◽  
Adeyemi O. Aremu
Keyword(s):  
South Africa ◽  
Cultural Values ◽  
Rural Areas ◽  
Biological Activities ◽  
Biological Evaluation ◽  
Economic Losses ◽  
Agricultural System ◽  
Western Cape ◽  
Cattle Diseases ◽  
Gastrointestinal Problems

Cattle farming is a traditional agricultural system that contribute to the rural economic, social and cultural values of the communities. Cattle as common with other livestock, are affected by many diseases that cause mortality and economic losses. In many rural households, the use of plants and associated knowledge are popular for managing cattle diseases especially in areas experiencing challenges with conventional veterinary medicine. Evidence on the documentation of indigenous knowledge and biological evaluation of plants used against cattle diseases remain understudied and fragmented. The aim of the review is to collate and analyse the ethnoveterinary knowledge and biological evaluation of plants used against cattle diseases in South Africa. Different scientific databases were systematically explored to extract data from 37 eligible studies. A total of 310 medicinal plants from 81 families used to treat 10 categories of cattle diseases across seven (7) provinces in South Africa. Leguminosae (Fabaceae), Compositae (Astereceae), Asparagaceae, and Xanthorrhoeaceae were the most frequently used plant families. Common plant parts used were leaves and roots. Twenty-seven (27) combination remedies involving 2–6 plants were identified as treatment regimes against cattle diseases. Common preparation methods were infusion and decoction while the administration mode was predominantly unspecified (52%) while oral and topical contributed 26 and 22%, respectively. In terms of diseases, the most treated ones were general systems infection, reproduction disorders and gastrointestinal problems. Currently, an estimated 21% of the 310 plants have been evaluated for diverse biological activities using relevant bioassays related to cattle diseases. Antibacterial activity remained the most studied biological activity. Evidence from the review revealed the significance of ethnoveterinary medicine against cattle diseases especially in rural areas of South Africa. Nevertheless, the use of plants for cattle diseases among other ethnic groups, particularly in the Northern Cape and Western Cape, remain under-studied.

scholarly journals A New Pathotype of Puccinia striiformis f. sp. tritici on Wheat in South Africa

Plant Disease ◽  
1999 ◽  
Vol 83 (6) ◽  
pp. 591-591 ◽  
Author(s):  
W. H. P. Boshoff ◽  
Z. A. Pretorius
Keyword(s):  
South Africa ◽  
Stripe Rust ◽  
Puccinia Striiformis ◽  
Single Step ◽  
Western Cape ◽  
Monogenic Resistance ◽  
Major Resistance Gene ◽  
New Variant ◽  
Production Areas ◽  
Wheat Lines

Following the detection of Puccinia striiformis f. sp. tritici for the first time on wheat (Triticum aestivum) in the Western Cape in August 1996, stripe rust has spread to all the important wheat production areas in South Africa. Only the introduced pathotype (pt. 6E16) was detected in surveys of these areas during 1996 and 1997. In 1998, a severe stripe rust epidemic occurred in the eastern Free State on the extensively grown cultivars Hugenoot and Carina, both which are resistant to pt. 6E16. Stripe rust severities of 100% were common on flag and lower leaves, and widespread applications of fungicides were necessary. Avirulence/virulence characteristics of P. striifomis f. sp. tritici isolates collected from Hugenoot and Carina were determined on 17 standard stripe rust differential wheat lines and 11 supplementary testers. The latter testers included the wheat lines TP981 and TP1295 (supplied by R. Johnson, Cambridge, UK), both of which have a major resistance gene in common with the differentials Heines Peko, Reichersberg 42, Strubes Dickkopf, Clement, and Heines VII (1). Isolates obtained from Hugenoot and Carina differed from pt. 6E16 based on virulence to Reichersberg 42 (Yr7,25), Heines Peko (Yr2,6,25), TP981 (Yr25), and TP1295 (Yr25). The new variant, designated as 6E22, was also identified in collections from the province KwaZulu-Natal. Seedling tests with 6E16 and 6E22 have shown that Hugenoot, Carina, and Tugela-DN are the only local cultivars affected by the new pathotype. The occurrence of pt. 6E22, which appears to be a single-step adaptation from 6E16 adding virulence to Yr25, emphasizes the vulnerability of monogenic resistance to this disease. Reference: (1) R. A. McIntosh et al. Wheat Inform. Serv. 85:56, 1997.

scholarly journals Genetic diversity of Ehrlichia ruminantium field strains from selected farms in South Africa

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Helena C. Steyn ◽  
Alri Pretorius
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Vaccine Development ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Region ◽  
Economic Losses ◽  
Ehrlichia Ruminantium ◽  
Field Samples ◽  
Endemic Areas

Heartwater is a tick-borne disease caused by the intracellular rickettsial parasite Ehrlichia ruminantium and transmitted by Amblyomma hebraeum ticks. Heartwater is problematic in endemic areas because it causes high mortality in ruminants and leads to economic losses that threaten productivity and food security. This may indicate that there is augmented genetic diversity in the field, which may result in isolates that are more virulent than the Ball3 and Welgevonden isolates. The genetic diversity of E. ruminantium was investigated in this study, focussing on the pCS20 gene region and four polymorphic open reading frames (ORFs) identified by subtractive hybridisation. The 16S ribosomal ribonucleic acid gene confirmed E. ruminantium in brain, blood and tick genomic deoxyribonucleic acid samples (n = 3792) collected from 122 farms that were randomly selected from seven provinces of South Africa where heartwater is endemic. The conserved E. ruminantium pCS20 quantitative polymerase chain reaction (qPCR) assay was used to scan all collected field samples. A total of 433 samples tested positive with the qPCR using the pCS20 gene region, of which 167 were sequenced. The known stocks and field samples were analysed, and phylogenetic trees were generated from consensus sequences. A total of 25 new clades were identified; of these, nine isolates from infected blood could be propagated in cell cultures. These clades were not geographically confined to a certain area but were distributed amongst heartwater-endemic areas in South Africa. Thus, the knowledge of strain diversity of E. ruminantium is essential for control of heartwater and provides a basis for further vaccine development.

scholarly journals Genetic diversity of ‘Candidatus Liberibacter africanus’ in South Africa based on microsatellite markers

2021 ◽  
Author(s):  
Ronel Roberts ◽  
Hong Lin ◽  
Gerhard Pietersen
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Western Cape ◽  
African Continent ◽  
High Genetic Diversity ◽  
North West ◽  
Citrus Greening Disease ◽  
Genetic Groups ◽  
Candidatus Liberibacter ◽  
Fastidious Bacterium

AbstractCitrus Greening disease (CG) in South Africa (SA) is associated with the fastidious bacterium ‘Candidatus Liberibacter africanus’ (Laf). It has been observed that Laf isolates obtained from different geographic localities in SA differed in the rate of transmission during grafting experiments leading to the hypothesis that genetic variation of Laf may exist in this country. To determine this, 167 Laf isolates obtained from Limpopo, North West, Mpumalanga and the Western Cape were subjected to microsatellite analyses, using four polymorphic markers. From UPGMA and STRUCTURE analysis, it was shown that most sources belong to one of two major genetic groups of Laf and these comprise 25 distinct haplotypes. Four samples included within this study did not group with these two major groups, suggesting a potential third and fourth genetic group of Laf being present, which can be validated by further sampling. Results further indicate that Laf populations in SA are formed by geographic locality. The high genetic diversity observed for Laf within this study is consistent with the hypothesis that Laf originated on the African continent, warranting further genetic analysis of Laf populations from Africa. This is the first study to unveil the genetic diversity of Laf.

scholarly journals Honeybush (Cyclopia spp.) phenology and associated arthropod diversity in the Overberg region, South Africa

Bothalia ◽  
2019 ◽  
Vol 49 (1) ◽  
Author(s):  
Eleonore L. Slabbert ◽  
Rhoda R. Malgas ◽  
Ruan Veldtman ◽  
Pia Addison
Keyword(s):  
South Africa ◽  
Management Practices ◽  
Cape Floristic Region ◽  
Arthropod Community ◽  
Western Cape ◽  
Baseline Knowledge ◽  
Medicinal Properties ◽  
High Level ◽  
Production Areas ◽  
Suction Sampling

Background: Cyclopia is endemic to regions of the Cape Floristic Region across the Eastern and Western Cape provinces of South Africa and is commonly known as honeybush. Honeybush has historically been used as an herbal tea, and has proven medicinal properties. Honeybush biomass and extracts are used in the functional foods and cosmetics sectors, both locally and overseas. The growing demand for honeybush calls for increased agricultural production and a shift away from the predominantly wild harvested supply.Objectives: The current study aimed to address the lack of baseline knowledge on honeybush phenology and its associated arthropod community to advance sustainable production of commercially valued plants in the genus.Method: The study was conducted on wild and cultivated Cyclopia species (Cyclopia maculata and Cyclopia genistoides) at respective sites in the Overberg region. Sampling took place from April 2014 to April 2015 using qualitative methods for recording seasonal honeybush phenology and suction sampling for aboveground arthropods. Focal insect taxa (Coleoptera, Hemiptera, Thysanoptera, Lepidoptera and Hymenoptera) were sorted and identified to family level and classified into functional feeding guilds.Results: Qualitative phenology observations of wild C. maculata and cultivated C. genistoides indicated a high level of congruency in seasonality of phenophase stages. Associated arthropod assemblages contained a diversity of families per functional feeding group, namely phytophagous, zoophagous and omnivorous taxa, with high seasonal variability.Conclusion: Findings highlight the complexity of ecological elements to be taken into consideration for ecologically sound honeybush cultivation. Outcomes can be applied to land management practices and governance policies promoting sustainable agroecosystems in honeybush production areas.

scholarly journals First Report of Virulence in Puccinia graminis f. sp. tritici to Wheat Stem Rust Resistance Genes Sr8b and Sr38 in South Africa

Plant Disease ◽  
2002 ◽  
Vol 86 (8) ◽  
pp. 922-922 ◽  
Author(s):  
W. H. P. Boshoff ◽  
Z. A. Pretorius ◽  
B. D. van Niekerk ◽  
J. S. Komen
Keyword(s):  
South Africa ◽  
South African ◽  
Stem Rust ◽  
Resistance Breeding ◽  
Wheat Breeding ◽  
Similar Reaction ◽  
Western Cape ◽  
Wheat Stem Rust ◽  
Breeding Lines ◽  
Plant Soil

During the 2000 to 2001 season, 27 stem rust samples were collected from wheat (Triticum aestivum), barley (Hordeum vulgare), and triticale (× Triticosecale) cultivars and lines in the Western Cape, South Africa. Following inoculation and multiplication on McNair 701 seedlings, 40 single pustule isolates of P. graminis f. sp. tritici were established. Twenty-six isolates obtained from wheat, barley, or triticale that produced a similar reaction pattern on a set of differentiating host lines, were designated as pathotype Pgt-2SA55. Pgt-2SA55 is avirulent to Sr5, -6, -7b, -8b, -9b, -9e, -9g, -23, -24, -27, -30, -38, and -Gt, and virulent to Sr11, and -Agi. The remaining 14 isolates, all from wheat and designated as pathotype Pgt-2SA88, were avirulent to Sr24, -27, and -Agi, and virulent to Sr5, -6, -7b, -8b, -9b, -9e, -9g, -11, -23, -30, -38, and -Gt. On an expanded differential set, representative isolates of each pathotype were all avirulent to Sr13, -15, -21, -22, -25, -26, -29, -31, -32, -33, -35, -39, -43, and -Em, and virulent to Sr7a, -8a, -9a, -9d, -9f, -10, -12, -14, -16, -19, -20, -34, and Lc. Pgt-2SA55 was avirulent on cv. Renown (Sr2, -7b, -9d, and -17), whereas Pgt-2SA88 was virulent on this cultivar and Line R Sel carrying only Sr17. Both pathotypes differ from those identified previously in South Africa (1) and to our knowledge, Pgt-2SA88 is the first local isolate to have virulence towards Sr8b and the T. ventricosum-derived gene Sr38. Virulence to Sr38 has been reported in a P. graminis f. sp. tritici isolate collected in Uganda (2). Pathotype Pgt-2SA88 is virulent to seedlings of the previously resistant South African cvs. SST 57 (heterogeneous), Tugela, Tugela DN, and PAN 3377. Furthermore, 20% of the elite breeding lines in the spring and winter wheat breeding program of the Small Grain Institute expressed susceptible seedling reactions to Pgt-2SA88. Triticale cvs. Rex and Kiewiet were heterogeneous in their seedling reaction towards Pgt-2SA55. Seedling and field reactions recorded for the barley cvs. Sterling and SSG 532 and the experimental varieties Puma and Jaguar, showed an increase in stem rust susceptibility to Pgt-2SA55 when compared with existing South African pathotypes. The higher incidence of stem rust in commercial fields and experimental plots of wheat and barley in the Western Cape may be attributed to a recent increase in the cultivation of stem rust-susceptible cultivars in the region. The detection of two new pathotypes of P. graminis f. sp. tritici is of concern to the local small grain industry and requires continued resistance breeding. References: (1) W. H. P. Boshoff et al. S. Afr. J Plant Soil 17:60, 2000. (2) Z. A. Pretorius et al. Plant Dis. 84:203, 2000.

scholarly journals Trunk Disease Fungi Associated With Diospyros kaki in South Africa

Plant Disease ◽  
2016 ◽  
Vol 100 (12) ◽  
pp. 2383-2393 ◽  
Author(s):  
P. Moyo ◽  
L. Mostert ◽  
M. Bester ◽  
F. Halleen
Keyword(s):  
South Africa ◽  
Morphological Characteristics ◽  
Diospyros Kaki ◽  
Western Cape ◽  
Eutypa Lata ◽  
Trunk Disease ◽  
Pathogenicity Tests ◽  
Production Areas ◽  
The Impact ◽  
First Time

Persimmon trees with dieback symptoms and cankers were observed in three production areas in Western Cape Province in South Africa. Isolations were made from diseased branches, cankers, and pruning wounds as well as fungal fruiting bodies on dead branches and old pruning wounds. Several trunk disease pathogens were identified based on morphological characteristics and by molecular methods, including Diaporthe eres, D. infecunda, Eutypella citricola, E. microtheca, Phaeoacremonium parasiticum, P. scolyti, P. australiense, P. minimum, Fomitiporia capensis, Fomitiporia sp., Fomitiporella sp., and Inocutis sp., which were isolated from persimmon for the first time in the world. Other first reports from persimmon in South Africa include D. foeniculina, D. ambigua, D. mutila, Diaporthe sp., Neofusicoccum australe, N. parvum, Diplodia seriata, and Eutypa lata. Pathogenicity tests conducted with all species, except the basidiomycetes, confirmed their status as possible persimmon pathogens. This is the first study to determine and identify fungi associated with diseased persimmon in South Africa. The knowledge gained in this study forms the basis for further research to determine the impact of these fungi on persimmon productivity.

Gasteria langebergensis, a new status for a Gasteria from the Western Cape, South Africa

Bradleya ◽  
2019 ◽  
Vol 2019 (37) ◽  
pp. 167
Author(s):  
E.J. Van Jaarsveld ◽  
B.J.M. Zonneveld ◽  
D.V. Tribble
Keyword(s):  
South Africa ◽  
Western Cape
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