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

Abstract

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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