Genomic approaches to increasing resilience in oilseed rape seedling establishment in the Yangtze River basin

Lead Research Organisation: John Innes Centre
Department Name: Crop Genetics


In China poverty is present predominantly in rural regions where annual incomes still depend heavily on returns from crops. A key cause of poverty is financial stress resulting from poor yields, which increasingly are affected by stochastic occurrence of extreme weather, particularly drought and flooding. The Yangtze River Basin is a globally-significant rapeseed growing area, using so-called semi-winter varieties drilled in the hot and seasonally dry month of September and harvested the following year. Around 14 million hectares are under drought stress (20 times the entire UK planting area), and drought during germination and seedling establishment is particularly detrimental to yields. Climate change is threatening rapeseed growing in the Yangtze River Basin because it is both increasing September temperatures, and increasing the frequency and duration of droughts. These conditions are hostile for seed germination and seedling growth, and can even induce dormancy and prevent germination altogether. To continue cultivation it will therefore be important to produce new varieties with enhanced tolerance to heat and drought stress during germination and early seedling growth.
In the modern genomic era the availability of large genotyped populations is greatly accelerating the process of linking traits to individual genes and markers. The principal bottleneck for gene discovery has become our ability to perform smart high throughput phenotyping under relevant conditions for revealing crop properties. This proposal aims to exploit a new phenotyping platform at JIC which automates seed germination, root and shoot growth measurements and increases the frequency of scoring from the traditional once per day to once per hour. We aim to optimise conditions on the platform to mimic the temperature regime and water potential of the Yangtze River catchment in September and screen oilseed rape varieties for germplasm with enhanced ability to germinate and establish effectively under stressful conditions. We will then use statistical tools to identify genes and markers underlying the beneficial traits, and the identity of these genes will be used to form and test hypotheses for the underlying biological mechanisms. We aim to use one European population and one Chinese population derived from a F1 rapeseed variety developed by our partners in the Oilseed Crop Research Institute (OCRI), Wuhan, that will shortly be released onto the Chinese market. This use of elite close-to-market germplasm maximises our chances of translating initial discoveries into new varieties in the shortest possible time window.
In order to understand whether improved material has a chance of mitigating climate change impacts it is also necessary to produce a theoretical framework that links crop establishment performance to weather variation. To do this we will produce hydrothermal time models of rapeseed establishment, modelling existing varieties and our best germplasm under Chinese conditions and test the models in a set of field trials. This will pave the way for a larger study aiming to understand for how long and under what emissions scenarios rapeseed cultivation can continue with current practises in the Yangtze River Basin.

Technical Summary

Rapeseed establishment in the Yangtze River Basin takes place in extremes of heat and dryness that are being exacerbated by climate change. Poor establishment caused by extremes in the September drilling window is the major factor in inter-annual variation in rapeseed yields. The aim of this proposal is to identify alleles and biological mechanisms by which rapeseed establishment in central Chinese climates can be improved, with a focus on elimination of residual dormancy and optimisation of post-germinative shoot growth rates. In preliminary work we have found that dormancy in B. napus is negatively-correlated to flowering time, with spring and Chinese semi-winter varieties more prone to dormancy than winter varieties. This may explain establishment problems in the Yangtze River Basin because such conditions are known to favour dormancy-inducing mechanisms which may slow or prevent early seedling growth. In the genomic era a major bottleneck in linking genes to traits is now the ability to generate high quality phenotypying datasets for large numbers of lines. Our principal method is to exploit a new low cost high throughput seed vigour phenotyping platform developed at JIC to enable gene-trait linkage in two B. napus populations: Dadi-199, a Chinese 280 line double haploid population developed at OCRI with a high density SNP map and the more diverse Diversity Fixed Foundation Set which we have previously used to link trait to gene for seedling establishment under UK conditions. Improvements in throughput mean that we can phenotype both populations in a few months and focus then on understanding the underlying biological mechanisms. Finally, we will use biological modelling to understand the potential of todays' elite germplasm and high-performing lines identified in the screen to germinate under different temperature and water potentials, paving the way to understand how each variety will perform under different climate scenarios.

Planned Impact

A key aim of the project is to identify germplasm and mechanisms which permit enhanced establishment under the stressful conditions. Such conditions of high temperature and low rainfall are increasingly associated with the Yangtze River basin due to climate change. We aim to identify the loci behind the trait we will be able to design molecular markers for breeders. Thus we will be able to provide loci, markers and germplasm directly to breeders that will be useful for breeding new varieties for the Chinese market. In order to make sure our work is as relevant as possible we have taken two steps. Firstly, we have incorporated into the project the analysis of a population constructed at OCRI derived from a leading F1 hybrid soon to be released, Zhongshuang11 x F11. Preliminary analysis in OCRI suggest that there are vigour differences among the lines of the population, and this suggests that if low vigour alleles can be identified they can bred out of the next generation of varieties derived from this material. Using this close-to-market material we have the chance to remove deleterious alleles quickly from Chinese breeding programmes if they can be identified. To ensure relevancy we have included the general manager of Wuhan's leading rapeseed breeding company, Wuhan ZhongyouXiwang, in our steering committee. Benbo Xu will provide advice at key decision points and receive new knowledge at an early stage, enabling him to guide improved establishment in his existing breeding programme. OCRI have an excellent track record in commercialising new varieties in collaboration with Wuhan ZhongyouXiwang, much of this work lead by Prof. Qiong Hu who will also sit on our advisory committee. In total since 2003, over 200 new varieties have been introduced to the Chinese market, with breeders at OCRI a primary source of germplasm. For instance Zhongshuang11 x F11 F1, soon to be introduced by OCRI, has a 10% yield enhancement compared to existing Chinese semi-winter varieties. There is high confidence that this collaborative work between JIC and OCRI-CAAS will deliver impact in a timely manner to Chinese plant breeders.

A further key aim is capacity building at OCRI specifically in the area of high throughput phenotypying. Using expertise at the JIC we will assist Dr Lu in constructing a high throughput seed germination phenotyping facility in Wuhan. This facility will be tested in Objective 3b. Our low-cost approach including timely exploitation of cheap raspberry pi computers is ideally suited to deployment in low and middle income countries. The funding for the facility will come directly from OCRI, but the expertise will come from JIC and our UK partners who will work out in Wuhan in year 2 to help set up the facility. In order to ensure full exploitation of the facility Dr Lu will receive full training in set up, deployment and data analysis during the project at JIC, and will take this expertise home to Wuhan at the end of the project. In this way the project aims to increase capacity in the LMIC country, thus meeting a major objective of the GCRF call.
Finally, the models produced in objective 3 will of general use to plant breeders, predicting the conditions in which existing and improved varieties of oilseed rape will establish in the Yangtze River basin. We aim to follow up this work with a further project that will link the models to future weather simulators and in this way we will be able to understand the limits to rapeseed establishment in the Yangtze River basin under future emissions scenarios. This approach is general, and in principle applicable to any crop whose establishment is highly contingent on environmental variables. In this way we can start to link seed performance to climate variation.


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Description The key aim of the project was to explore the genetic potential of oilseed rape to dapt to sub-optimal soil conditions during drilling. In China oilseed rape is drilled into field in October, and if the soil is dry and the weather too warm then the seed has trouble germinating and the crop fails to establish well. Previous studies have indicated that failing seedling establishment is a major cause of variation in rapeseed yields, and that farm incomes are vulnerable to poor weather in autumn drilling. Notably, most of the poorest 50 million chinese citizens have some reliance of farm incomes, and poor harvests threaten the income of this group especially.

The firsrt outcome is that we have developed a model of rapeseed germination in soils of different temperatures and water potentials. This will be able to be used in the future in combination with gridded climate models to understand how climate change is likely to affect the prospects for successful seedling establishment in China. The model describes the behviour of a range of near-market germplasm. Secondly we have screened large populations for variation in the ability for seeds to germinate and establish in unfavourable conditions. For instance if the soil is too hot or too dry. We have uncovered important genetic variation in the ability of different varieties to germinate and establishment in dry soils especially, variation that has not been discovered in previous studies because they have all used optimal conditions. Using this data we have been able to use tools such as genome wide assocaition to try and locate genetic variation in the oilseed rape genome whose presence is correlated with the more resilient germination traits. This analysis has enabled us to identify at least three new genetic loci which may be important for controlling oilseed rape germination in dry conditions.

DAC relevant findings: we have screened near market Chinese germplasm and identified lines which are suitable for direct seedling in dry conditions. These will be taken forward by local breeders.

DAC Beneficiary country: China
Exploitation Route The cultivation of around 14 million hectares of oilseed rape in China is threatened by high temperatures and dry soils during seed drilling and seedling establishement. This model can now be used by climate scientists to predict future problemss in rapeseed drilling programmes caused by claimte change and to predict and identify suitable mitigating strategy for drillers.

The new genes we have discovered can be used to develop markers which can be used by breeders to deliver resilient gemrination traits to elite chinese rapeseed varieties, We are working with China's most important oilseed rape breeders at the Oilseed Crop Research Institute in Wuhan, and they will be able to use these markers on their own germplasm collections to develop varieties with superior germination performance. Although the work is most relevant to ODA country China, it could also have implications for UK breeders and fgor those in other ODA countries with significant rapeseed cultivation such as India and Bangladesh.
Sectors Agriculture, Food and Drink

Description DAC beneficiary country: China We have undertaken a capacity building programme and installed a new state of the art seed vigour phenotyping platform in Wuhan China. The first in the world was developed at the John Innes centre, and we have now a functioning copycat system in china whiuch has been used to analyse seed vigour in a large rapeseed population containing close to market chinese germplasm. We have seconded a researcher from the oilseed crops research institute in Wuhan China to the John Innes Centre and trained them in seed vigour analysis, computer vision and automated seed phenotyping. They will be able to take this knowledge back to the ODA country China to improve the efficiency of seedf germination phenotyping in Wuhan. We have held a project meeting in Norwich in September 2018 which was attended by senior research staff from the oilseed crop research institute in Wuhan, and by their senior rapeseed breeder QH. Using the automated platform we have been able to help QH phenotype their breeding material in China. QH is female and thus the project here has impact for people of female gender. We did not perceive or monitor any risks in this regard. The impact addresses the sustainable development goal 9: industry, innovation and infrastructure by installing new technology for high throughput phenotyping in Wuhan, China.It has the potential to address goal 1, No Poverty, by stabilising farm incomes from year to year.
First Year Of Impact 2018
Sector Agriculture, Food and Drink
Impact Types Economic

Description BBSRC international partnership award
Amount £24,200 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 05/2017 
End 04/2019
Description CEPAMs funding at the John Innes cENTRE
Amount £99,752 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2018 
End 08/2019
Description Collaboration with University of York in rapeseed genomics 
Organisation University of York
Country United Kingdom 
Sector Academic/University 
PI Contribution We provided large phenotyping datasets as part of the project, on variation in oilseed rape germination.
Collaborator Contribution Our partners performed genome wide assocation so that we could find genetic markers associated with our traits oif interest. Thios collaboration is essential for the project.
Impact We have identified new genes in oilseed rape associated with seed germination performance.
Start Year 2018
Description OCRI-CAAS partnership 
Organisation Chinese Academy of Agricultural Sciences
Country China 
Sector Academic/University 
PI Contribution We formed a collaborative partnership for this porposal seconding a researcher from the oilseeds crop research institute in Wuhan China to the UK. We are capacity building in China by installing a state of the art automated seed vigour phenotyping platform in Wuhan which has been used to investigate seed vigour in near market chinese oilseed rape germplasm. We also provide training of researchers and access to our genetics pipelines.
Collaborator Contribution They ahve brough skill and expertise in rapeseed cultivation in China plus access to Chinese state and private sector breeding programmes. OCRI-CAAS have facilitated the transfer of their improved crop transformation protocols to the UK.
Impact Project meeting between JIC researchers and OCRI-CAAS, September 2017. Installation of the automated phenoytping platform, December 2017. The collaboration is multidisciplnary, requiring our expertise in computer vision and machine learning. Miniconference in May 2019 in Wuhan, China. Researchers from JIC networked with scientists from the chinese academcy of agribultural science and Huazhong agricultural university in Wuhan. The Chinese partners placed a postdoc on secondment to facotlitate the learning by JIXC staff of the brassica transformation protocol used in Wuhan.
Start Year 2017
Title Installation of automated seed vigour phenotyping at OCRI-CAAS in Wuhan, China 
Description We have developed a new platform for automated analysis of seed vigour at JIC. As part of the capacity building in the patwhasy to impact objective we oversaw installation of a similar platform in Wuhan, transferring our capability to a new location. 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2017 
Impact The teamn in OCRI-CAAS analysed a collection of 180 near market lines in Wuhan for germination performance and selected lines with useful traits for future breeding programmes. 
Description Proeject management meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We held a meeting with senior staff from the Oilseed Crop Research institute in Wuhan, China and with their leading oilseed rape breeder to discuss project progress and inform decision making. We raised awareness that there was substantial variation in rapeseed for germination under water stress conditions. One outcome is that breeders in Wuhan have been able to look for similar variation in their own germplam.
Year(s) Of Engagement Activity 2018