Difference between revisions of "Yueqi Zhang"

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'''Summary'''
 
'''Summary'''
The Brassica genus contains many agriculturally important oilseed crops and vegetables. Canola (Brassica napus) is one of the most important oilseed crops worldwide. Canola production in Australia, Europe and North America is threatened by blackleg disease, caused by the fungal pathogen Leptosphaeria maculans. The deployment of qualitative disease resistance genes is the most effective and sustainable approach in controlling the disease. Identification and cloning of qualitative resistance gene candidates is therefore crucial for understanding the gene-for-gene interactions in the pathosystem which will facilitate sustainable management of the disease. Efforts in building multiple genome assemblies of B. napus and its progenitors B. rapa and B. oleracea, coupled with genome-wide prediction of resistance gene analogs in several B. napus assemblies, have greatly facilitated the identification of candidate genes that are associated with disease resistance phenotypes. The aim of this research was to identify and characterise a cluster of qualitative resistance genes, Rlm3-Rlm4-Rlm7-Rlm9, located on B. napus chromosome A07. Firstly, strong candidates for Rlm3, Rlm4 and Rlm7, located within the candidate regions defined by published genetic markers, were identified through sequence comparison of resistance gene analogs between resistant and susceptible cultivars obtained from Nanopore, next generation sequencing and Sanger sequencing approaches. Secondly, the gene relatives for Rlm3, Rlm4, Rlm7 and Rlm9 at syntenic genomic regions in two B. rapa, two B. oleracea and eight B. napus assemblies were identified and compared, to provide insights on the evolution and functions of the genes. Domains and amino acids that are related to the interactions with the corresponding virulence proteins were characterised. Thirdly, PCR screening markers were designed to target unique sequences in the candidate Rlm3, candidate Rlm4, candidate Rlm7 and Rlm9 genes, in order to develop reliable, high-throughput genetic screening markers to complement phenotypic screening. All current and past Australian commercial cultivars were screened with the markers and their blackleg resistance gene complement was identified. Lastly, we aimed to establish a protocol for flow sorting single chromosomes for canola, in order to characterise genetic variations on a specific chromosome of interest in diverse Brassica germplasm and Brassica wild relatives. The highest mitotic index and metaphase index were achieved for the first time in canola. However, persistent issues of metaphase chromosome clumps hindered the flow sorting of single chromosomes, which needs to be overcome as technologies advance.  
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The Brassica genus contains many agriculturally important oilseed crops and vegetables. Canola (''Brassica napus'') is one of the most important oilseed crops worldwide. Canola production in Australia, Europe and North America is threatened by blackleg disease, caused by the fungal pathogen ''Leptosphaeria maculans''. The deployment of qualitative disease resistance genes is the most effective and sustainable approach in controlling the disease. Identification and cloning of qualitative resistance gene candidates is therefore crucial for understanding the gene-for-gene interactions in the pathosystem which will facilitate sustainable management of the disease. Efforts in building multiple genome assemblies of ''B. napus'' and its progenitors ''B. rapa'' and ''B. oleracea'', coupled with genome-wide prediction of resistance gene analogs in several ''B. napus'' assemblies, have greatly facilitated the identification of candidate genes that are associated with disease resistance phenotypes. The aim of this research was to identify and characterise a cluster of qualitative resistance genes, ''Rlm3-Rlm4-Rlm7-Rlm9'', located on ''B. napus'' chromosome A07. Firstly, strong candidates for ''Rlm3, Rlm4'' and ''Rlm7'', located within the candidate regions defined by published genetic markers, were identified through sequence comparison of resistance gene analogs between resistant and susceptible cultivars obtained from Nanopore, next generation sequencing and Sanger sequencing approaches. Secondly, the gene relatives for ''Rlm3, Rlm4, Rlm7'' and ''Rlm9'' at syntenic genomic regions in two ''B. rapa'', two ''B. oleracea'' and eight ''B. napus'' assemblies were identified and compared, to provide insights on the evolution and functions of the genes. Domains and amino acids that are related to the interactions with the corresponding virulence proteins were characterised. Thirdly, PCR screening markers were designed to target unique sequences in the candidate ''Rlm3'', candidate ''Rlm4'', candidate ''Rlm7'' and ''Rlm9'' genes, in order to develop reliable, high-throughput genetic screening markers to complement phenotypic screening. All current and past Australian commercial cultivars were screened with the markers and their blackleg resistance gene complement was identified. Lastly, we aimed to establish a protocol for flow sorting single chromosomes for canola, in order to characterise genetic variations on a specific chromosome of interest in diverse Brassica germplasm and Brassica wild relatives. The highest mitotic index and metaphase index were achieved for the first time in canola. However, persistent issues of metaphase chromosome clumps hindered the flow sorting of single chromosomes, which needs to be overcome as technologies advance.  
  
  
 
'''Why my research is important'''
 
'''Why my research is important'''
 +
 
The identification of the qualitative resistance genes, and molecular and evolutionary characterisation of the gene families, and genetic screening markers have laid the foundation for a revolutionary understanding on the blackleg pathosystem as well as informing more durable management of the precious limited resistance resources worldwide. The first single chromosome isolation protocol in canola paved the way for chromosome genomics in Brassica crops which would facilitate ongoing crop improvements given predicted global population growth and climate change.
 
The identification of the qualitative resistance genes, and molecular and evolutionary characterisation of the gene families, and genetic screening markers have laid the foundation for a revolutionary understanding on the blackleg pathosystem as well as informing more durable management of the precious limited resistance resources worldwide. The first single chromosome isolation protocol in canola paved the way for chromosome genomics in Brassica crops which would facilitate ongoing crop improvements given predicted global population growth and climate change.
  
 
==Publications==
 
==Publications==
  
'''Yueqi Zhang''', David Edwards & Jacqueline Batley. 2020. Comparison and evolutionary analysis Brassica Nucleotide Binding Site Leucine Rich Repeat (NLR) genes and importance for disease resistance breeding. The Plant Genome, pp. e20060-e20060. https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/tpg2.20060
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'''Yueqi Zhang''', David Edwards & Jacqueline Batley. 2020. Comparison and evolutionary analysis ''Brassica'' Nucleotide Binding Site Leucine Rich Repeat (NLR) genes and importance for disease resistance breeding. The Plant Genome, pp. e20060-e20060. https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/tpg2.20060
  
'''Yueqi Zhang''', Ting Xiang Neik, Junrey Amas, Aldrin Cantila, Nur Shuhadah Mohd Saad, Tingting Wu & Jacqueline Batley. 2020. DNA-based screening of Brassica germplasms. In: Dulloo E (ed) Plant genetic resources: A review of current research and future needs, Burleigh Dodds Science Publishing, Sawston, Cambridge, UK. https://www.amazon.com.au/Plant-Genetic-Resources-Current-Research/dp/1786764512
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'''Yueqi Zhang''', Ting Xiang Neik, Junrey Amas, Aldrin Cantila, Nur Shuhadah Mohd Saad, Tingting Wu & Jacqueline Batley. 2020. DNA-based screening of ''Brassica'' germplasms. In: Dulloo E (ed) Plant genetic resources: A review of current research and future needs, Burleigh Dodds Science Publishing, Sawston, Cambridge, UK. https://www.amazon.com.au/Plant-Genetic-Resources-Current-Research/dp/1786764512
  
'''Yueqi Zhang''', William Thomas, David Edwards & Jacqueline Batley. 2020. Frontiers in dissecting and managing Brassica diseases: from SNP based genome wide association with RGA gene repertoires to building pan-RGAomes, The International Journal of Molecular Sciences, , vol 21, no. 23, pp.8964. https://www.mdpi.com/1422-0067/21/23/8964
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'''Yueqi Zhang''', William Thomas, David Edwards & Jacqueline Batley. 2020. Frontiers in dissecting and managing ''Brassica'' diseases: from SNP based genome wide association with RGA gene repertoires to building pan-RGAomes, The International Journal of Molecular Sciences, , vol 21, no. 23, pp.8964. https://www.mdpi.com/1422-0067/21/23/8964
  
 
Soodeh Tirnaz, '''Yueqi Zhang''' & Jacqueline Batley. 2020. Genome-wide mining of disease resistance gene analogs using conserved domains. In: Jain M., Garg R. (eds) Legume Genomics. Methods in Molecular Biology, vol 2107, pp 365-375, Humana, New York, NY. https://link.springer.com/protocol/10.1007/978-1-0716-0235-5_20
 
Soodeh Tirnaz, '''Yueqi Zhang''' & Jacqueline Batley. 2020. Genome-wide mining of disease resistance gene analogs using conserved domains. In: Jain M., Garg R. (eds) Legume Genomics. Methods in Molecular Biology, vol 2107, pp 365-375, Humana, New York, NY. https://link.springer.com/protocol/10.1007/978-1-0716-0235-5_20

Latest revision as of 08:40, 3 March 2021

Biography

Yueqi obtained her Bachelor of Biotechnology with first class Honours degree at the Australian National University. She joined the multi-national biotechnology company Epoch Life Science (USA) subsidiary Taihe Biotech (Beijing) Corp. Ltd and made contributions to international endeavours on crop improvement, medical research and environmentally friendly chemical productions. She has been a PhD student in the Batley lab since October 2017 researching the identification and characterisation of resistance genes in canola against blackleg disease using a wide range of genetic, transcriptomic, genomic, flow cytometry and microscopy technologies.

Research Interests

Crop genetics and genomics, Disease resistance genes, Plant-pathogen interactions, Chromosomal flow cytometry and Microscopy

Current Projects

Identification of qualitative disease resistance genes in canola against blackleg

Evolutionary and comparative analysis on gene relatives of qualitative disease resistance genes

Development of genetic markers for the identified qualitative disease resistance gene for durable management

Development of protocol for isolating single chromosomes in canola for sequencing


Summary

The Brassica genus contains many agriculturally important oilseed crops and vegetables. Canola (Brassica napus) is one of the most important oilseed crops worldwide. Canola production in Australia, Europe and North America is threatened by blackleg disease, caused by the fungal pathogen Leptosphaeria maculans. The deployment of qualitative disease resistance genes is the most effective and sustainable approach in controlling the disease. Identification and cloning of qualitative resistance gene candidates is therefore crucial for understanding the gene-for-gene interactions in the pathosystem which will facilitate sustainable management of the disease. Efforts in building multiple genome assemblies of B. napus and its progenitors B. rapa and B. oleracea, coupled with genome-wide prediction of resistance gene analogs in several B. napus assemblies, have greatly facilitated the identification of candidate genes that are associated with disease resistance phenotypes. The aim of this research was to identify and characterise a cluster of qualitative resistance genes, Rlm3-Rlm4-Rlm7-Rlm9, located on B. napus chromosome A07. Firstly, strong candidates for Rlm3, Rlm4 and Rlm7, located within the candidate regions defined by published genetic markers, were identified through sequence comparison of resistance gene analogs between resistant and susceptible cultivars obtained from Nanopore, next generation sequencing and Sanger sequencing approaches. Secondly, the gene relatives for Rlm3, Rlm4, Rlm7 and Rlm9 at syntenic genomic regions in two B. rapa, two B. oleracea and eight B. napus assemblies were identified and compared, to provide insights on the evolution and functions of the genes. Domains and amino acids that are related to the interactions with the corresponding virulence proteins were characterised. Thirdly, PCR screening markers were designed to target unique sequences in the candidate Rlm3, candidate Rlm4, candidate Rlm7 and Rlm9 genes, in order to develop reliable, high-throughput genetic screening markers to complement phenotypic screening. All current and past Australian commercial cultivars were screened with the markers and their blackleg resistance gene complement was identified. Lastly, we aimed to establish a protocol for flow sorting single chromosomes for canola, in order to characterise genetic variations on a specific chromosome of interest in diverse Brassica germplasm and Brassica wild relatives. The highest mitotic index and metaphase index were achieved for the first time in canola. However, persistent issues of metaphase chromosome clumps hindered the flow sorting of single chromosomes, which needs to be overcome as technologies advance.


Why my research is important

The identification of the qualitative resistance genes, and molecular and evolutionary characterisation of the gene families, and genetic screening markers have laid the foundation for a revolutionary understanding on the blackleg pathosystem as well as informing more durable management of the precious limited resistance resources worldwide. The first single chromosome isolation protocol in canola paved the way for chromosome genomics in Brassica crops which would facilitate ongoing crop improvements given predicted global population growth and climate change.

Publications

Yueqi Zhang, David Edwards & Jacqueline Batley. 2020. Comparison and evolutionary analysis Brassica Nucleotide Binding Site Leucine Rich Repeat (NLR) genes and importance for disease resistance breeding. The Plant Genome, pp. e20060-e20060. https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/tpg2.20060

Yueqi Zhang, Ting Xiang Neik, Junrey Amas, Aldrin Cantila, Nur Shuhadah Mohd Saad, Tingting Wu & Jacqueline Batley. 2020. DNA-based screening of Brassica germplasms. In: Dulloo E (ed) Plant genetic resources: A review of current research and future needs, Burleigh Dodds Science Publishing, Sawston, Cambridge, UK. https://www.amazon.com.au/Plant-Genetic-Resources-Current-Research/dp/1786764512

Yueqi Zhang, William Thomas, David Edwards & Jacqueline Batley. 2020. Frontiers in dissecting and managing Brassica diseases: from SNP based genome wide association with RGA gene repertoires to building pan-RGAomes, The International Journal of Molecular Sciences, , vol 21, no. 23, pp.8964. https://www.mdpi.com/1422-0067/21/23/8964

Soodeh Tirnaz, Yueqi Zhang & Jacqueline Batley. 2020. Genome-wide mining of disease resistance gene analogs using conserved domains. In: Jain M., Garg R. (eds) Legume Genomics. Methods in Molecular Biology, vol 2107, pp 365-375, Humana, New York, NY. https://link.springer.com/protocol/10.1007/978-1-0716-0235-5_20

Anna Nowicka, Martin Kovacik, Barbara Tokarz, Jan Vrana, Yueqi Zhang, Dorota Weigt, Jaroslav Doležel & Ales Pecinka. 2020. Dynamics of endoreduplication in developing barley seeds. Journal of Experimental Botany, vol 72, pp 268-282. https://academic.oup.com/jxb/article-abstract/72/2/268/5917133

Funding

•Scholarship for International Research Fees (SIRF) and an International Living Allowance Scholarship (Ad Hoc Postgraduate Scholarship) to undertake a PhD in Plant Biology, The University of Western Australia

•Mike Carroll Travelling Award 2018 AU$3,500

•Postgraduate Research Travel Awards (PGRTA) 2018 AU$3,000

Contact Details

Yueqi Zhang

Room 1.122, School of Biological Sciences, Faculty of Science

The University of Western Australia

Crawley, WA 6009, Perth, Australia

Email: 22078946@student.uwa.edu.au