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Antony Kamiri

Candidature

PhD Candidate

Thesis Title

Genomic approaches and metabolite biomarker development for improving Phytophthora root rot (PRR) resistance in chickpea (Cicer sp.)

Research Project

Antony KamiriChickpea (Cicer arietinum L.) ranks as the second most consumed legume globally, grown in over 50 countries and traded in around 140. Australia is a global leader in chickpea exports, contributing over 25% of the market share, second only to India in production. However, climate change has increased the frequency of extreme weather events, exacerbating susceptibility to biotic and abiotic stresses. A major threat to chickpea cultivation in eastern Australia is Phytophthora root rot (PRR), caused by Phytophthora medicaginis. PRR thrives in wet conditions, leading to substantial yield losses and necessitating accelerated breeding strategies to improve resistance and tolerance mechanisms. Traditional breeding has produced over 400 elite chickpea cultivars globally, but the process is time-consuming, requiring 6–8 years. Emerging breeding technologies such as marker-assisted selection, mutation breeding, and gene editing offer faster and more precise approaches, enabling the rapid development of disease-resistant crops. These methods are crucial for enhancing chickpea productivity and adaptability under changing environmental conditions.

A deeper understanding of plant-pathogen interactions at cellular and genomic scales is essential for leveraging these advanced techniques. Chickpea lacks major resistance (R) genes, limiting breeding options. While genome sequences have facilitated studies of host responses to P. medicaginis, efforts in proteomics and transcriptomics have highlighted key signaling pathways like salicylic and jasmonic acid but have not fully explored the role of metabolites in breeding resistance varieties. Metabolites are critical for plant defense, and metabolomic quantitative trait locus (mQTL) mapping holds potential for identifying genetic loci associated with metabolite production. Linking mQTLs to genetic variants can reveal genes that influence metabolite variation and biotic stress tolerance, bridging phenotype and genotype to support the development of resilient chickpea varieties. Recent studies using network analysis have identified small secreted proteins (SSPs) and transcription factors (TFs) involved in regulating host defense mechanisms. While further work is necessary to prove this link, should they control effector regulation, these TFs would be a key mechanism controlling the pathogen entry into biotrophic phase, and exit to the necrotrophic phase hereby referred to us biotrophic to necrotrophic switch (BNS) phase. These preliminary findings therefore, has provided a framework of utilizing metabolites to further our understanding on the disease progression in quantitative pathosystems in non-model pathosystems in P. medicaginis.

My research seeks to identify metabolic PRR resistance biomarkers in chickpea arising from these metabolites, test their stability under extreme environmental conditions, and ultimately guide breeding programs. These biomarkers will enable the identification of mQTLs targeting disease-associated metabolic pathways, paving the way for improved chickpea resistance and sustainable crop production.

Supervisory Panel

A/Prof Jonathan Plett,  A/Prof Michelle Moffitt,  Sean Bithall