Country-Wide qPCR Based Assessment of Plasmodiophora brassicae Spread in Agricultural Soils and Recommendations for the Cultivation of Brassicaceae Crops in Poland

Clubroot is a damaging disease of oilseed rape and vegetable brassicas worldwide, caused by the soil-borne protist Plasmodiophora brassicae Wor. Due to the long life of resting spores, the assessment of the pathogen abundance in agricultural fields can serve as a guideline for disease control at the country-wide level or the regional scale. Between 2013 and 2019, we collected 431 soil samples from fields cultivated with Brassicaceae crops throughout 16 provinces of Poland. The samples were subjected to qPCR based analysis of P. brassicae DNA concentration. From these data, the spore loads and gene copies g−1 soil were calculated and used to produce an assessment of the current clubroot risk potential at a country-wide and regional scale. The country-wide map, showing the spread of the pathogen in agricultural soils, was made using ArcGis software package implementing the interpolation with the Inverse Distance Weight method. The calculation of gene copies specific to P. brassicae helped to formulate the recommendations for farmers in respect to the cultivation guidelines. It showed a high risk of yield losses in defined regions of north, south-west and central Poland and an urgent need to undertake intensive preventative measures.

Characterization of the Brazilian vegetable brassicas production chain

ABSTRACT Brassica crops worldwide provide the greatest diversity of products used by man derived from a single genus. Collectively, leafy, flower and root vegetables can be eaten fresh, cooked and processed. The production of these vegetables in Brazil has been growing exponentially in the last decades, due to its economic importance, with major production volumes in several states and a quick monetary return for growers in areas considered of small acreage. With expansion, a number of aspects, including demands for quality and safety of these foods introduce themselves, strictly attached to the forms of production, logistics and their appearance. To meet the challenges and list the trends within the activities of different agents, a multiple case study was held in the states of Amazon, Minas Gerais, Paraná and Rio de Janeiro. Altogether, 55 stakeholders were interviewed, along with the compilation of different sources of data to characterize this productive chain. Changes in the scenario are imperative in order to maintain the activity of overcoming years, being related to cultivars adaptation, plant health, productions costs and difficulties during the establishment of crops. To overcome these adversities, a collective effort in terms of organization, technology transfer and R&D from official and private agents, technical assistance, and regional sanitary inspection is imperative, aiming, especially, in actions regarding themes like protected cultivation, mechanization/automation and adding value to products by processing and packaging, listed by stakeholders as priority.

The detection of Plasmodiophora brassicae using loop-mediated isothermal DNA amplification

<em>Plasmodiophora brassicae</em>, the cause of clubroot, is a very serious problem preventing from successful and profitable cultivation of oilseed rape in Poland. The pathogen was found in all main growing areas of oilseed rape; it also causes considerable problems in growing of vegetable brassicas. The aim of this work was to elaborate fast, cheap and reliable screening method to detect <em>P. brassicae</em>. To achieve this aim the Loop-mediated isothermal DNA amplification (LAMP) technique has been elaborated. The set of three primer pairs was designed using LAMP software. The detection was performed with the GspSSD polymerase, isolated from bacteria <em>Geobacillus</em> sp., with strand displacement activity. DNA extraction from clubbed roots obtained from farmers’ fields of oilseed rape infected by <em>P. brassicae</em> was done using a modified CTAB method. The reaction was performed for 60 min at 62^oC. The visual detection was done using CFX96 Real Time PCR Detection System (BioRad) or Gerie II Amplicatior (Optigen). The detection with LAMP proved its usefulness; it was easy, fast and accurate and independent of plant age. The detection limit was 5 spores per 1 µl of the spore suspension, so LAMP was less sensitive than quantitative PCR tests reported in the literature. However, the method is cheap and simple, so it is a good alternative, when it comes to practical use and the assessment of numerous samples.