Inspiring students on their research journey
I supervise Honours, Masters and PhD student projects in research areas with primary FoR code 3004 – Crop and Pasture Production. Projects focus on understanding and combating root-lesion nematode infestations in important cereal and pulse crops, including wheat, chickpea and mung bean. Below are short project summaries of the current and completed higher degree by research (HDR) student projects that I am the Principal Supervisor or Associate Supervisor.
Current supervisions
QTL mapping of root-lesion nematode resistance in an interspecific chickpea population.
Student: Samara Tarlinton
Program: Honours
Supervisory team: Dr Rebecca Zwart (Principal supervisor)
Commenced: 2024
Cicer arietinum (chickpea) is an agriculturally produced grain legume species that contributes to the food security of many countries. However, increased susceptibility to biotic stressors due to four previous genetic bottlenecks has reduced the genetic diversity of domestic varieties. One of the larger stresses of cultivated chickpeas are nematodes, with root-lesion nematodes causing significant damage. The predominant root-lesion nematode species affecting the chickpea is Pratylenchus thornei. To increase the genetic variation in the crop, wild Cicer species capable of cross breeding with the cultivated varieties (C. echinospermum and C. reticulatum) were collected from the species geographic origin. Phenotypic evaluation of this collection for P. thornei resistance identified several wild Cicer species, including Gunas_100, with superior resistance to P. thornei (Reen et al. 2019). This project will investigate the interspecific cross Kyabra x Gunas_100 to identify QTL associated with P. thornei resistance. This will be completed through a replicated controlled environment glasshouse experiment. The intended outcome of the project is to map the location of QTL influencing P. thornei resistance from the wild Cicer species.
Genetics of root-lesion nematode Pratylenchus thornei resistance in mung bean (Vigna radiata).
Student: Begita Adhikari
Program: PhD
Supervisory Team: Dr Rebecca Zwart (Principal supervisor), Dr Kirsty Owen, Dr Elaine Gough, Dr Noel Knight
Commenced: 2022
Mung bean (Vigna radiata) is a leguminous crop of economic and nutritional importance. Mung bean is a high-value, short-season crop that requires less nitrogen input. Mung bean is a susceptible host of the root-lesion nematode Pratylenchus thornei, which causes population densities to increase in the soil, and which can have an adverse effect on subsequent crops in the rotation. Mung bean yield is also highly dependent on Arbuscular Mycorrhizal Fungi (AMF). Mung bean varieties, selected from the Australian mung bean diversity set and Australian commercial varieties, will be assessed in this project to assess the interaction between P. thornei, AMF, and mung bean genotype. Four hundred and forty-three accessions from the Australian mung bean diversity set, which represent wide phenotypic diversity in many observable traits, will be evaluated in this project for P. thornei resistance through glasshouse phenotyping trials. A genome-wide association study (GWAS) approach will be used to identify single nucleotide polymorphic (SNP) markers linked to quantitative trait loci (QTL) for resistance to P. thornei. The germplasm identified and associated molecular markers will be valuable to breeding programs aiming to improve P. thornei resistance in mung bean.
Investigation into the use of different platforms to phenotype wheat cultivars for tolerance to the root-lesion nematode Pratylenchus thornei.
Student: Neil Robinson
Program: PhD
Supervisory Team: Dr Rebecca Zwart (Principal supervisor), Dr Kirsty Owen, Prof. John Thompson
Commenced: 2021 Part-time
Yield loss of wheat (Triticum aestivum) caused by Pratylenchus thornei are reported worldwide. In the subtropical grain region of eastern Australia, the yield loss of wheat is estimated at A$38 million/year. This value could be much higher, if growers did not include resistant crops in their rotations and select wheat cultivars that are resistant and/or tolerant to P. thornei. Resistant cultivars are those which the inhibit reproduction of P. thornei, while tolerant cultivars can maintain yield when infested by P. thornei. The overarching aim of this study is to reduce the yield losses caused by P. thornei by improving our understanding of the tolerance mechanism(s) and developing novel phenotyping methods to enhance our capabilities for advancing genetic gain. Robinson and colleagues (2019) demonstrated that the normalised difference vegetation index (NDVI) is predictive of grain yield in three field experiments that measured plant growth and yield of wheat cultivars grown on low and high population densities of P. thornei. The current research builds on preliminary studies, by investigating three objectives: (1) Determine if ground-based applications of NDVI and visual assessments of plant growth can predict the tolerance of a wheat cultivar when grown at high population densities of P. thornei, (2) Determine if aerial-based applications of multispectral and thermal imaging, and the water use by a wheat cultivar when grown on high population densities of P. thornei can determine tolerance, (3) Determine if low density sowing of wheat can be used as a platform to select wheat cultivars with tolerance and resistance to P. thornei.
Completed supervisions
Resistance of wild relatives (Cicer reticulatum and C. echinospermum) of chickpea (C. arietinum) to the root-lesion nematode Pratylenchus neglectus.
Student: Hannah Rostad
Program: Masters of Research
Supervisory Team Dr Rebecca Zwart (Principal supervisor), Prof. John Thompson
Completed: 2022
Chickpea (Cicer arietinum L.) is a major legume crop consumed worldwide. Its nutritional value as a pulse and its ability to fix atmospheric nitrogen denote its global importance in the cereal-pulse cropping systems. Australia is the largest exporter and second largest producer of chickpea after India. Pratylenchus neglectus (Rensch) Filipjev & Schuurmans-Stekhoven is a root-lesion nematode that invades, feeds, and reproduces in the roots of grain crops including chickpea and wheat (Triticum aestivum L.). In Australia, chickpea and wheat are commonly grown in rotation and damage by P. neglectus accounts for a large annual economic loss in production of both crops. Cultivated chickpea has little genetic diversity limiting the potential for improvement to abiotic and biotic resistance through plant breeding. However, the chickpea genepool may be expanded through introgression of favourable genes present in wild related species. New germplasm collections from southeast Turkey of two wild species, C. reticulatum Ladizinsky and C. echinospermum P.H. Davis, have substantially increased the previously limited world collection of these species. This research assessed 243 C. reticulatum and 86 C. echinospermum accessions from the 2013 and 2014 collection missions that spanned 32 collection sites within Turkey. The accessions were assessed in replicated pot experiments under controlled glasshouse conditions. Multi-experiment analyses to determine genetic rankings of accessions showed improved resistance in wild Cicer accessions compared to Australia’s elite moderately resistant breeding cultivar PBA HatTrick. This study is unique, evaluating P. neglectus resistance of this collection and providing important information on P. neglectus-chickpea interactions which is lacking worldwide. This study has revealed new sources of P. neglectus resistance that can be introgressed into commercial chickpea cultivars to improve the diversity and level of resistance that chickpea has to this nematode species. Results from this study will contribute to a genome wide association study to identify markers and candidate genes for P. neglectus resistance. Chickpea cultivars with improved resistance provide growers with more flexible crop rotations, a reduction of P. neglectus population densities in infested fields and more profitable yields.
Identification of candidate resistance genes in chickpea (Cicer arietinum) against root-lesion nematode Pratylenchus thornei.
Student: Sonal Channale
Program: PhD
Supervisory Team: Dr Rebecca Zwart (Principal supervisor), Prof. John Thompson, Dr Mandendar Thudi
Completed: 2022
Chickpea, a versatile legume crucial for nutritional security in semi-arid regions, faces significant biotic stress, including from the root-lesion nematode (RLN) Pratylenchus thornei. Due to its polyphagous nature, P. thornei restricts crop rotation options, and control measures like nematicides and soil solarization are either environmentally harmful or ineffective. To address this, the study applied a two-pronged strategy: elucidating the resistance mechanism in chickpea using comparative transcriptomics and identifying genomic regions and candidate genes for resistance through genome-wide association studies (GWAS). RNA-seq analysis using three chickpea genotypes (resistant, moderately resistant and susceptible to P. thornei), revealed 962 differentially expressed genes (DEGs) related to defense, stress response, growth, and secondary metabolism. Further, GWAS on 278 chickpea genotypes from the ICRISAT chickpea reference collection identified significant SNPs and candidate genes associated with P. thornei resistance. These findings suggest a polygenic resistance mechanism, providing a durable solution for breeding P. thornei-resistant chickpea cultivars. Molecular markers derived from these genes can enhance breeding programs through marker-assisted selection.
The interaction between arbuscular mycorrhizal fungi, rhizobia and root-lesion nematodes (Pratylenchus thornei) in mung bean (Vigna radiata).
Student: Elaine Gough
Program: PhD
Supervisory Team: Dr Kirsty Owen (Principal Supervisor), Prof. John Thompson, Dr Rebecca Zwart
Completed: 2021
There are a limited number of reports on interactions between the beneficial microsymbionts arbuscular mycorrhizal fungi (AMF) and rhizobia which co-occur with the root-lesion nematode Pratylenchus sp. within the roots of legumes. Mung bean (Vigna radiata) is an important summer legume in the sub-tropical grain region of eastern Australia. It is a host of AMF, Pratylenchus thornei and nitrogen (N) fixing Bradyrhizobium bacteria. These microorganisms are dependent on mung bean for photosynthates and their interactions influence host production and nutrition. Nodulation failure in mung bean reduces plant production, nutrition and N budgets in soils and could be explained by a lack of mycorrhizal inoculum in the soil and/or by infestation with P. thornei. Furthermore, AMF colonisation of the roots may alter the population densities of P. thornei in mung bean. A systematic review was carried out to clarify the effect of interactions between AMF and Pratylenchus spp., which showed that their interactions depended on the taxonomic order and genus of AMF, along with host plant functional groupings. With this specificity in mind, the interaction of AMF, rhizobia and P. thornei was investigated for mung bean cv. Jade-AU grown in a vertisol with a full factorial of these biological treatments in glasshouse experiments. The conservation of AMF within farming systems is strongly advocated to promote and protect their valuable role in increasing biological nodulation and N fixation efficiency by rhizobia, and in improved crop nutrition and yield, while reducing fertiliser inputs. However, it is also crucial to understand that AMF may increase population densities of P. thornei. Agronomic practices and plant breeding to promote the synergism between AMF and rhizobia for mung bean yield, while limiting population densities of P. thornei will benefit mung bean production and subsequent crops in long-term sustainable farming systems.
Elucidation of biochemical defence mechanisms in wheat (Triticum aestivum) against root-lesion nematode (Pratylenchus thornei)
Student: Md. Motiur Rahaman
Program: PhD
Supervisory Team: Dr Rebecca Zwart (Principal Supervisor), Prof. John Thompson, Dr Kirsty Owen, Prof. Saman Seneweera
Completed: 2021
In this PhD project, histopathology, comparative enzyme profiling and metabolomics studies were conducted to elucidate the potential defence mechanisms in wheat against P. thornei infestation. Mainly, two sources of resistance against P. thornei were used in this study for different experiments (i) GS50a and its derived lines (ii) synthetic hexaploid CPI133872 and its derived lines. These were compared with susceptible wheat genotypes that were parents of the resistant derivatives. The results have suggested both higher levels of total phenol and phenol oxidases could be responsible for superior resistance in the synthetic hexaploid CPI133872. Metabolomic profiling was performed with resistant (QT16528; an advanced breeding lines derived from the synthetic hexaploid CPI133872) and susceptible wheat genotypes (including Janz) to understand the role of wheat metabolites in resistance and susceptibility to P. thornei. The majority of metabolites potentially responsible for resistance in QT16258 were found to be constitutively expressed. Understanding the biochemical defence mechanisms in wheat against P. thornei could lead to novel nematode management tools to minimise plant damage and consequent loss in wheat yield from this nematode species.
Assessing the resistance to root-lesion nematode (Pratylenchus thornei) in a new collection of wild chickpea (Cicer reticulatum and C. echinospermum) from Turkey.
Student: Roslyn Reen
Program: Research Masters
Supervisory Team: Prof. John Thompson (Principal Supervisor), Dr Rebecca Zwart, Dr Kirsty Owen
Completed: 2020
Chickpea (Cicer arietinum L.) is an ancient grain legume first domesticated some 10,000 years ago and is now the second major pulse produced worldwide. The root-lesion nematode Pratylenchus thornei is a microscopic eelworm, and is the foremost nematode species affecting chickpea production worldwide with yield losses of intolerant Australian cultivars estimated to be up to 25% of annual crop yields. Crop improvement has been challenged by the narrow genetic diversity within cultivated chickpea and a previous limited world collection of wild chickpea. Crop wild relatives are a rich source of genetic diversity from which to source new allelic variation including disease resistance, and thereby play a major role in meeting challenges for 21st century agriculture. Recent collection missions in south-eastern Turkey have boosted accession numbers of wild chickpea, namely C. reticulatum Ladizinsky and C. echinospermum P. H. Davis, the only wild species crossable with the cultigen C. arietinum. This study evaluated 174 accessions (133 C. reticulatum and 41 C. echinospermum) under controlled-environment conditions to identify levels of P. thornei resistance within the collection.
