Genetic Variation and Aggressiveness of Phytophthora capsici, Foot Rot Pathogen of Pepper (Piper nigrum L.) in Sarawak

Kavitha, Vijeandran (2024) Genetic Variation and Aggressiveness of Phytophthora capsici, Foot Rot Pathogen of Pepper (Piper nigrum L.) in Sarawak. Masters thesis, Faculty of Resource Science and Technology.

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Abstract

Phytophthora capsici is the causal agent of Phytophthora foot rot disease in black pepper (Piper nigrum L.) and given its devastating impact on black pepper's growth stages, leading to significant yield reductions, an in-depth understanding of its diversity is crucial. Hence, this study aims (i) to isolate P. capsici from infected black pepper plants in Sarawak and characterise the isolates based on their morphology; (ii) to examine the aggressiveness of P. capsici isolates on common black pepper cultivars planted in Sarawak; (iii) and to investigate the genetic variation of P. capsici isolated from infected black pepper plants in Sarawak. Firstly, sampling was conducted in four major black pepper-growing divisions in Sarawak: Sarikei, Betong, Serian, and Kuching. Samples were collected from black pepper vines displaying clear symptoms of the disease. In total, 153 samples were gathered from 28 farms. For isolation, two techniques were utilised: tissue plating and leaf-baiting. Overall, 52 isolates were retrieved across 10 farms originating from Sarikei, Betong and Serian. Through the sequence of Internal Transcribed Spacers region, 30 selected isolates were confirmed asP. capsici. The isolates exhibited distinct colony growth patterns, sporangia morphologies, and radial growth rates on different media (Corn Meal Agar, V8 Juice Agar, and Potato Dextrose Agar). All isolates consistently exhibited torulose hyphae structure, and the presence of oogonia when pairing isolates amongst one another revealed the existence of opposite mating types. Black pepper cuttings from Kuching and Semenggok Aman varieties were inoculated with P. capsici to assess their aggressiveness. The time taken for the vines to die post-inoculation was recorded and analysed using the Kaplan–Meier estimator to determine disease severity and plot survival curves. Across both sets of aggressiveness tests, IJ1 stood out as the most virulent isolate while EBK1 was the least virulent isolate overall. To assess the population's genetic diversity, 52 isolates retrieved from this study were iii genotyped using three Random Amplified Microsatellites (RAMS) and five Inter Simple Sequence Repeats (ISSR) primers. The UPGMA tree based on the RAMS and ISSR combined fingerprint revealed a close relationship between populations, displaying apparent clustering based on geographical locations. The mean value of the percentage of polymorphic loci, Shannon’s Information Index and Nei’s genetic diversity were 59.52%, 0.294, and 0.193, respectively. Analysis of molecular variance revealed a higher diversity within populations (73%) than among populations (27%), indicating high gene flow between populations and the possibility of shared origin. This study provides the first baseline information on the genetic diversity and aggressiveness of P. capsici in Sarawak, highlighting the potential risk for further genetic diversity if left uncontrolled. As black pepper production in Sarawak faces challenges, this study offers insights into the regional black pepper industry.

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