Optimising Canola Phenology for Australian Growing Environments

Dr Chris Helliwell1, Dr Alec  Zwart1, Alex Boyer1, Andrew Gock1, Dr Bangyou Zheng2, Dr Bill Bovill1, Brett Cocks2, Emmett Leyne1, Dr Ian Greaves1, Dr Jeremy Whish2, Dr Jing Wang1, Dr Julianne Lilley1, Dr Matthew Nelson3, Dr Susie Sprague1, Dr Shannon Dillon1 

1CSIRO Agriculture And Food, Canberra, Australia,

2CSIRO Agriculture and Food, Brisbane, Australia, 3CSIRO Agriculture and Food, Perth, Australia

Increased production and profitability of canola can be achieved by better matching phenology with the growing environment. Improved understanding of the factors determining canola phenology will better enable matching of location-specific growing conditions with variety, and direct breeding strategies for improved high yielding canola varieties that match the optimum flowering window. In this project we are taking the novel approach of combining existing crop modelling and knowledge of flowering processes with large-scale phenomic, ‘omic and environmental data to deliver (1) predictive tools to better inform management of canola genetic resources for optimal productivity across a range of environments, and (2) knowledge of genetic and environmental factors underpinning variation in phenology. The team have assessed phenological traits in a diverse set of ~350 modern Australian and globally important canola genotypes across the range of Australian canola growing environments as well as controlled environments. To complement the phenology data, dense genomic SNP and transcriptome data were generated. Genetic diversity in the panel reflected geographic and crop/maturity type and supports earlier reports of the prominence of Asian germplasm in the pedigrees of Australian cultivars. Genome wide associations of preliminary transcriptome, SNP and phenotype data in these experiments identify known and novel factors underpinning phenology traits. Results from a range of model frameworks to predict phenology and parameter traits using SNP data suggest it is possible to predict these traits based on genome data within sites. The new information and tools generated will better enable management of canola genetic resources for optimal productivity.


Dr Chris Helliwell is the Project Leader – Functional genomics for canola traits.

Characterization of Crr3Tsc clubroot resistance locus in Brassica napus cv. Tosca

Piotr Kopeć1, Katarzyna  Mikolajczyk2, Ewa Jajor3, Agnieszka  Perek3, Joanna  Nowakowska2, Christian  Obermeier4, Harmeet Singh  Chawla4,5, Marek  Korbas3, Iwona  Bartkowiak-Broda2, Wojciech M.  Karlowski1 

1Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Poznan, Poland,
2Department of Genetics and Breeding of Oilseed Crops, Plant Breeding and Acclimatization Institute-National Research Institute, Poznan, Poland,
3Institute of Plant Protection – National Research Institute, Poznan, Poland,
4Department of Plant Breeding, Justus-Liebig-Universitaet Giessen,, Giessen, Germany,
5Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany

The aim of our study was to define and characterize the clubroot resistance locus in the winter oilseed rape cultivar “Tosca”. Following a cross between “Tosca” and a clubroot susceptible line, we have developed a segregating DH population, which was genotyped with Brassica 60k SNP chip, and phenotyped for morphological symptoms, after being challenged with Plasmodiophora brassicae resting spores. We have performed an association analysis, which led to the identification of the ~100 kbp long major-effect resistance locus on the A03 chromosome. Analysis of the genetic and physical evidence showed that the locus corresponds to the Crr3 locus known from the earlier studies on Brassica rapa. Using Oxford Nanopore sequencing we have described the local differences between resistant and susceptible parents. The most striking difference was a tandem duplication of the entire NBS gene. The homologous genes were highly polymorphic between the parents, especially in the pattern-recognizing LRR domain. Leveraging the polymorphisms we have designed homolog-specific markers, which we have tested on a panel of clubroot-resistant Brassica cultivars.


Dr. Katarzyna Mikolajczyk is currently a Head of the Research Division and the Department of Oil Crops of the Plant Breeding and Acclimatization Institute – NRI in Poznan, Poland. She works on the development of DNA markers suitable for marker-assisted breeding of oilseed rape (Brassica napus L.). She was a co-creator and coordinator of the research project which ended last year and resulted in mapping the clubroot resistance locus of the Swedish resynthesis-derived winter-type oilseed rape cultivar “Tosca”. Recently, Dr. Mikolajczyk has co-invented a new qPCR assay for determining the homo- and heterozygous genotypes of B. napus with the ogu-INRA Rfo restorer gene. She is also keen on swing&bluesand bike rides.



The genetic architecture of canola flowering time

Dr Bai Zetao1, Dr Harsh Raman1, Dr Rosy Raman2, Mr Brett McVittie2, Dr Xie Meili1, Dr Yuanyuan  Zhang1, Dr Shengyi Liu1 

1Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China,
2NSW Department of Primary Industries, WAGGA WAGGA, Australia

Flowering time is a complex trait that determines plant fitness and agronomic performance (productivity) of canola to its local growing environment.  Understanding the genetic architecture of flowering time is therefore important for improving canola yield as well as understanding the evolution of divergent ecotypes (spring, semi-winter and winter types). To reveal the genetic architecture of flowering time trait, a genome wide association study (GWAS) was performed using two diversity panels representing Australian Brassica napus homozygous diversity lines (n = 326) and Chinese diversity lines (n = 324). Each GWAS panel was assessed for flowering time in separate experiments (Australia: 4 environments, China: 3 environments). To identify causal variants for flowering time, both GWAS panels of 650 lines were genotyped using Illumina sequencing (~7 to 90× coverage), and over two million high quality SNP markers were used for genome-wide association analysis (GWA). We found extensive variation in flowering time among accessions, ranging from 30 to 140 days. Accounting both population structure and kinship matrices, GWA identified 1,312 and 1,175 SNP marker loci that show significant association with flowering time, estimated in Australian and Chinese environments, respectively. At least, 10 consistent loci were identified on A02, A05, A07, A10, C01, C02, C03, and C04 chromosomes across multiple environments and countries. We identified several orthologues of Arabidopsis thaliana flowering genes, including FLOWERING LOCUS C and FLOWERING LOCUS T on the B. napus cv. Darmor-bzh genome. Data on structural and functional variants underlying flowering time genes will be presented.


Dr Harsh Raman is a Senior Principal Research Scientist at the Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga. He joined the NSW DPI in 1996 and led plant genetics and pre-breeding research in wheat, barley and canola. He has published over 120 peer-refereed papers in national and international journals.



Characterization of Histone H3 Lysine 4 and 36 Tri-methylation in Brassica rapa L.

Mr Hasan Mehraj1, Dr Satoshi Takahashi2, Dr Yutaka  Suzuki3, Dr Motoaki Seki2,4,5, Dr Elizabeth S.  Dennis6,7, Dr Ryo  Fujimoto1 

1Kobe University, Nada-Ku, Kobe, Japan,
2RIKEN Center for Sustainable Resource Science, Yokohama, Japan,
3Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan, 4RIKEN Cluster for Pioneering Research, Saitama, Japan,
5Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan,
6CSIRO Agriculture and Food, Canberra, Australia,
7School of Life Sciences, Faculty of Science, University of Technology, Sydney, Australia

Brassica rapa L. is an important agricultural crop that includes many important vegetables such as Chinese cabbage, pak choi, turnip etc. B. rapa has experienced whole-genome triplication that generates three subgenomes (LF, MF1, and MF2). Covalent modifications of histone proteins act as epigenetic regulators of gene expression. We report the distribution of two active histone marks (H3K4me3 and H3K36me3) in 14-day leaves in two lines of B. rapa by chromatin immunoprecipitation sequencing. Both lines were enriched with H3K4me3 and H3K36me3 marks at the transcription start site, and the transcription level of a gene was associated with the level of H3K4me3 and H3K36me3. The expression of H3K4me3- and H3K36me3-marked genes had a low level of tissue specificity. Genes with both H3K4me3 and H3K36me3 had a high level of expression and were constitutively expressed. Bivalent active and repressive histone modifications such as H3K4me3 and H3K27me3 marks or antagonistic coexistence of H3K36me3 and H3K27me3 marks were observed in some genes. Expression may be influenced by abiotic and biotic stresses in genes having both H3K4me3 and H3K27me3 marks. The presence of H3K36me3 marks but not H3K4me3 marks was associated with different levels of gene expression or tissue specificity between paralogous pairs of genes, suggesting that H3K36me3 might be involved in subfunctionalization of the subgenomes.

Keywords: histone H3 lysine 4 tri-methylation, histone H3 lysine 36 tri-methylation, epigenetics, subfunctionalization, Brassica

Correspondence: Ryo Fujimoto [leo@people.kobe-u.ac.jp]


To come



Multiple genes control physiological and agronomic water use efficiency in canola

Dr Harsh Raman1, Dr Rosy Raman1, Mr Brett  McVittie1, Dr Ramethaa  Pirathiban2, Dr Niharika  Sharma3, Dr Yuanyuan  Zhang4, Prof Shengyi Liu4, Prof Graham  Farquhar5, Prof Brian Cullis2, Dr David Tabah6, Mr Andrew  Easton6

 1NSW Department Of Primary Industries, WAGGA WAGGA, Australia,
2Centre for Bioinformatics and Biometrics, National Institute for Applied Statistics Research Australia, University of Wollongong , Wollongong, Australia,
3NSW Department of Primary Industries, Orange Agricultural Institute, Orange, Australia,
4Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China,
5Research School of Biology, Australian National University, Canberra, Australia,
6Advanta Seeds Pty Ltd, 268 Anzac Avenue, Toowoomba,  Australia

Drought stress (water deficit) is a major limitation of canola production in Australia and elsewhere.  In this study, we assessed genetic variation for key exemplar traits involved in adaptation strategies under water deficit conditions (drought escape, and drought avoidance) in a 11-5101 DH population. Genetic analyses identified multiple QTL that contribute to variation in flowering time (drought escape); Δ13C and fractional ground cover (drought avoidance) and agronomic WUE (seed yield). Both parental lines contributed favourable alleles for trait variation. Candidate genes that underlie QTL regions for drought resistance traits were identified. Our multi-environment data showed that early flowering is negatively related to seed yield, while high shoot biomass, early ground cover, plant height and high Δ13C are positively related to seed yield. To understand physiological basis of water use efficiency, we made gas exchange measurements and showed that leaf intrinsic water use efficiency is negatively related with Δ13C, but the latter had positive relationship with seed yield. To uncover functional genes and gene networks that contribute to effective water use, we performed mRNA sequencing of parental lines of 11-5101 population that showed significant variation in iWUE, Δ13C signatures and seed yield. Transcriptome analysis revealed that 906 genes are differentially expressed in response to water deficit, including those which were located within QTL regions associated with adaptive traits. In summary, our research identified the useful variation in drought related traits and molecular tools  that would accelerate the development of improved canola varieties for cultivation under water deficit conditions.


Dr Harsh Raman is a Senior Principal Research Scientist at the Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga. He joined the NSW DPI in 1996 and led plant genetics and pre-breeding research in wheat, barley and canola. He has published over 120 peer-refereed papers in national and international journals.

Genetic improvement of canola field establishment

Dr Matthew Nelson1,2, Dr Ian Greaves3, Dr  Jose Barrero3, Mrs Trijntje Hughes3, Mr Mark Cmiel3, Mrs Karen Treble1, Dr Andrew Fletcher1, Dr John Kirkegaard3, Dr Greg Rebetzke3

1CSIRO Agriculture & Food, Perth, Australia,
2The University of Western Australia, Perth, Australia,
3CSIRO Agriculture & Food, Canberra, Australia

Canola (Brassica napus L.) is Australia’s most important oilseed crop but it suffers from unreliable field establishment. On average only 50-60% viable sown seeds germinate, emerge and reach establishment (four-leaf stage). Poor establishment is costly to growers due to reduced yield potential, more complex weed management issues and in extreme cases the need to resow paddocks. The causes of poor establishment are complex in nature with genetic, environment and management components. This project addresses the genetic component. We aim to deliver to canola breeders the genetic tools and knowledge required to develop varieties with greater establishment potential. To this end, we have developed robust and simple phenotyping methods for early development traits that contribute to establishment potential at seed germination, pre-emergent and post-emergent growth stages. These methods are highly repeatable with heritabilities ranging from 0.71 (biomass at 294 ºCd) to 0.96 (germination vigour) in both an international diversity panel (n=100) and in current Australian canola varieties (n=28). We will discuss plans for the next phase of the project where we will determine the genetic factors controlling these traits and identify molecular markers that can be used in genomic selection for improved establishment potential. We will also present initial findings of field trials aimed at ground-truthing our predictions of establishment potential of diverse canola accessions.


Dr Nelson leads the Crop Adaptation team and is the Impact Lead for ‘Future Crops’ at CSIRO. Having gained his PhD in crop genetics at the John Innes Centre (UK) in 2000, he worked as a molecular breeder in commercial crop breeding programs in The Netherlands and Australia, and as a crop geneticist and pre-breeder at the University of Western Australia and Royal Botanic Garden, Kew (UK). He joined CSIRO in 2018 to lead a national program of canola improvement. His research interests include canola adaptation (phenology and establishment), legume domestication and the effective use of wild germplasm in crop improvement.



Genome wide association study (GWAS) of early vigour and flowering time in canola (Brassica napus)

Mr Kianoush Nikoumanesh1, Dr Harsh Raman2, Professor Wallace Cowling3, Dr  Li Li1

1Animal Genetics and Breeding Unit (a joint venture of NSW Department of Primary Industries and the University of New England), University of New England, Armidale, Australia,
2NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, Australia,
3School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia

Canola is one of the most agronomically important members of the Brassicaceae family with an approximately 1 billion USD export value for the Australian agriculture industry. However, this crop requires more efficient plant breeding strategies to satisfy its market dynamics and problems resulted from its limited genetic diversity. Therefore, accurate identification of genomic regions (QTLs) controlling the genetic architecture of important traits (e.g. early vigour and flowering time) and the estimation of their effects are of crucial priorities for a sustainable plant breeding program in canola. In this study we have used genome wide association study (GWAS) to find statistically significant associations between early vigour and flowering time and more than 13,000 Illumina Infinium™ Single Nucleotide Polymorphisms (SNPs) in a canola germplasm. For days to 50% flowering, we found significant associations in genomic regions, particularly chromosomes A02 and A03, that seem to be associated in controlling the flowering time. We compared the results from three different methods for our analysis: 1) general linear model, 2) mixed model using kinship matrix (K), and 3) a unified Mixed Model that incorporates both K and population structure (Q). Consistent QTLs were located in similar chromosome regions in the three different methods across three trial locations. Similar methods were employed to assess QTLs for early vigour in the glasshouse and field. Potential epistatic interactions between genes controlling early vigour and flowering time were explored. The study will also identify SNP molecular markers for these traits for use in the Australian canola breeding industry.


My ultimate career goal is to help Australian growers gain a competitive edge in this world’s turbulent economy.



Genetic analysis of phi thickening development in Brassica roots

Dr David Collings1, Ms Maketalena Aleamotu’a1, Dr Harsh Raman2, Dr David McCurdy1

1The University of Newcastle, Callaghan, Australia,
2NSW Department of Primary Industries, Wagga Wagga, Australia\

Phi thickenings are single bands of secondary cell wall formed within the apex of the developing root in many species, particularly in Brassica. While their function(s) remain unknown, we speculate that they stiffen the root tip, aiding in soil penetration, thus representing a potentially important agricultural trait. Our aims are to determine the molecular pathways leading to thickening development, and subsequently to determine their functions. We have previously demonstrated that different Brassica cultivars vary in their ability to form phi thickening in response to salt and the stress hormone jasmonic acid (JA). In this project, we use this variability to characterise the molecular development of thickenings.

We initiated a genome wide association study (GWAS) using more than 200 lines from the BnAssyst diversity panel by phenotyping phi thickening induction in response to salt or JA. Strong variability was detected: some lines induced strongly with both stimuli while some formed no thickenings, and others responded to only one stimulus. We have also assessed several Brassica breeding populations, identifying crosses in which parental lines showed different phi thickening induction responses. In one Brassica rapa cross, for example, the segregtation of two separate phenotypes in the F2 progeny is consistent with the presence of multiple genetic differences in both JA signalling and late in the phi thickening developmental pathway. Data from both analyses are currently being processed to determine genetic loci associated with phi thickening induction, an outcome directly applicable to crop breeding strategies in Brassica and other crops where phi thickenings occur.


A plant cell and molecular biologist interested in root growth and development, from the biophysical through to the cellular level.



A genome wide association study (GWAS) in canola identifies multiple loci for the natural variation in Al3+ resistance.

Dr Hanmei Du1,4, Geetha Perera1, Dr Akitomo Kawasaki1,2, Dr Harsh Raman3, Gilbert Permaloo1, Dr Peter R Ryan1

1CSIRO Agriculture And Food, Canberra, Australia,
2Elizabeth Macarthur Agricultural Institute, NSW DPI, Menangle, Australia,
3Graham Centre for Agricultural Innovation, NSW DPI, Wagga Wagga, Australia,
4Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China, Sichuan Agricultural University, Chengdu, China

Acid soils limit the yields of most grain crops including many cereals and canola. Aluminium (Al3+) is the main cause of this limitation because the toxic Al3+ cations prevalent in acid soils inhibit root growth. Lime application is the most effective way of reversing soil acidification but it is a long-term strategy that requires years to ameliorate the subsoil. The use of better-adapted germplasm is a complementary strategy that maintains yields while liming takes effect. Significant genotypic variation for Al3+ resistance has been reported for wheat, barley and many legume crops but few studies have investigated canola. As a consequence, breeding programs do not target acid soil-tolerance in canola because genetic variation and convincing QTL have not been reported. To investigate this further, we conducted a genome-wide associated study (GWAS) using the BnASSYST canola diversity panel. We screened 350 lines in hydroponics with and without a toxic concentration of AlCl3 (pH 4.4) and measured shoot biomass, root biomass and root length. Significant variation for Al3+ resistance traits (relative root length, relative shoot weight and relative root weight) was observed. BnASSYST panel was genotyped with ~15000 high-quality genotyping-by-sequencing based markers. By accounting both population structure and kinship matrices, we identified several genome-wide QTL for different measures of Al3+ resistance. The GWAS suggests that multiple genes are responsible for natural variation in Al3+ resistance in canola. Our results provide new genetic resources and QTL/markers for improving Al3+ resistance in canola via genomic and marker-assisted selection.


Post-docs in Univ Tasmania and in the USA (USDA and Cornell University)

Worked most of his career at CSIRO, Canberra

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