Genetic diversity and yield stability for increased resilience against climate change in the UK

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


There are major opportunities to increase crop resilience to climate change by increasing diversity. In the UK, weather patterns are likely to become more variable; with increased frequency of droughts, floods and short spells of high temperature stress (11). These changes will render UK agriculture highly vulnerable, with sudden temperature changes, rather than the mean rise, likely to have major effects on agricultural productivity (11; 24). The most economically important crop in the UK is wheat. The interaction between crop development and temperature is complex, but it has been demonstrated that the most vulnerable stage is at flowering (anthesis) (e.g. 6). The intensity and the duration of an extreme weather event affects the period of grain filling and yield reduction is directly linked to maximum temperature stress (2). These sudden, extreme events are distinct from the mean changes in global temperature; gradual increase enables selection of characteristics that improve genetic adaptation to an environment (16) whereas sudden events are considered to be largely beyond the threshold of cellular function. Plant communities with high species diversity have a greater resilience to environmental variations, in terms of (i) resource use (22); and (ii) the stability of biomass production (10). In applying these ecological principles to arable systems, the risk of crop failure can be reduced by increasing crop diversity by harnessing the complementation between different genotypes. At anthesis, an extension of this vulnerable growth stage will increase the chance that a number of individuals will escape the extreme event by flowering before, or after it. In winter wheat, the genetic mechanisms controlling ear emergence and anthesis are categorised according to their environmental interaction. Twenty eight to 56 days of cold treatment (vernalization) induces ear emergence. Genes shown to control vernalization requirement include Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3 (14; 15). Varieties can also be categorised according to daylight (photoperiod) requirement. In bread wheat this difference is largely controlled by Ppd-D1 and Ppd-B1 (17), dominant alleles which confer early ear emergence through photoperiod insensitivity. These genes have profound effects on mega-environment adaptation but a third set, earliness per se (eps) genes, can mediate developmental rate independent of specific environmental signals (19). The vernalization and photoperiod genes confer environmental adaptation; but the eps effects facilitate more subtle manipulation of the life cycle for regional adaptation. The advent of whole genome genotyping and Quantitative Trait Locus (QTL) analysis has allowed the identification a number of important eps effects segregating in Western European elite germplasm; a large proportion of the genetic variation in ear emergence can now be accounted for (8). The eps genes describe the mean flowering time point, but variation in genotype can result from: (1) Time of first anthesis; (2) Duration of anthesis within a single ear; (3) Duration across tillers; and (4) Time of day for peak anthesis. Further genotypic effects involve absolute temperature tolerance at seed set. This proposed research aims to test the hypothesis that: greater genotypic heterogeneity increases crop resilience under increasing climatic stress. The single character of flowering has been selected to test the proof of concept. The proposed research will develop new genetic markers for heading date. NILs for the UK eps QTLs and two CCPs, one heterogeneous for eps genes alone, and the other with a wide genetic background, will be dissected genetically and physiologically. The performance of the different genotypes to specific timed heat stress events will determine the contribution of flowering diversity to crop resilience.

Technical Summary

Targeted marker development for 8 major eps QTL Bulked material from doubled haploid populations in which eps effects were identified will be screened with genetic markers derived from the collinear regions of rice and Brachypodium. Marker assays will be based on single strand conformation polymorphism protocols (SSCP) developed in BBSRC Tools and Resources BBE023568. The use of bulked segregant analysis (BSA) will ensure that any polymorphism identified will be targeted to the region of interest. Polymorphic markers will be sequenced and used to construct a haplotype for the eps QTL. Genotyping CCPs The parents of the CCPs will be genotyped using the markers developed. A sub set of markers will be chosen that provide maximum discrimination of the parental origin of the chromosomal regions of interest. Up to 20 markers at each eps locus (160 total) will be used to genotype the epsCCP and YQCCP populations. This data will be complemented by SSR data from Defra SA LINK project LK0999. Characterisation of NILs NILs for 8 eps QTL have been developed in the Defra WGIN project. The NILs will be subjected to the same stresses as the CCPs and their relative performance assessed in terms of fertility, above ground biomass, and yield components. Each line will be dissected to identify the timing of key growth stages- terminal spikelet, tiller number (primary and secondary), onset of stem extension, ear emergence (GS55), anthesis, and grain filling. Stresses NILs and CCPs in replicate sets will be subjected to timed heat stress events at 36C within the period of anthesis. Treatments will be in cabinets for the NILs, and tunnels for the CCPs. The two CCPs will additionally be subjected to the combined effect of heat and drought stress. The interaction of the two stresses will be used to quantify the stability of yield performance in the CCP heterogeneous for the eps genes (the epsCCP) compared to a diverse population including a range of eps genes (YQCCP).

Planned Impact

The output from the proposed research have implications for: (1) Food security: The dissection of anthesis and evaluation of the crop performance relative to specific timed extreme temperature events will contribute to how crop resilience to climate change can be achieved. (2) Economics: Increased food security has major implications for economic stability, at the local farm-scale and at the national level. (3) Biodiversity: Increased on-farm diversity may contribute to environmental goods and services by supporting a greater level of biodiversity. (4) Cereal breeding: Dissection of anthesis will provide new markers for the control of flowering in wheat. Non-academic beneficiaries are: (1) The general public: Increased food security has obvious benefits to the general public, but will also assist in the maintaining stable, and relatively low prices for food. The increased crop diversity, if populations were developed (through ORC), may provide a number of environmental goods and services. These would include increased biodiversity, and adaptation to local conditions (which a consequently influence on the level of agrochemical inputs). (2) The agricultural community: The increased resilience of crops to fluctuations in climate will stabilise yields, from year to year. More predictable returns from cereal crops will not only ensure farm businesses remain viable but will also have implications for animal feed production, and the export market. (3) Cereal breeders: Breeders will gain additional markers for the development of novel cereal varieties. This is of particular relevance since there has been increased observation of sterility in ears (Foot, pers. comm). New successful varieties have major economic implications for the breeding industry, with potential market development in the UK and for other countries in Europe. Dissemination of Information: The general public will receive information relating to the project outputs through timely, relevant press releases coordinated by the PR departments at the John Innes Centre and at the University of Reading. The agricultural community will benefit from the research through improved varieties, but will also hear about the research through timely, agreed articles in the popular press, and at workshops and open days (at JIC). Cereal breeders will obtain frequent updates relating to project developments through the attendance of Limagrain UK Ltd representatives at consortium meetings. Further information transfer will be achieved through the WGIN and Monogram meetings.


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Description We have shown what genetic markers can be used to achieve predictive breeding for flowering time in bread wheat. These markers are available to our partners and breeders to select for genotypes that avoid heat stress. We have shown that EPS-D1 interacts with ambient temperature, explaining important elements of GxE. Follow on work has shown the important effects of these genes on fertiity and yield.
Exploitation Route New molecular markers can be used by breeders.
Sectors Agriculture, Food and Drink

Description Molecular markers for breeding with validated beneficial effects for grain yield or yield neutral adaptive benefit.
First Year Of Impact 2017
Sector Agriculture, Food and Drink
Impact Types Cultural,Economic,Policy & public services

Description Invited speaker at PlantGen2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation on genetics of adaptation in bread wheat
Year(s) Of Engagement Activity 2017