Raising the ceiling on UK wheat yields / introgression and assessment of novel 'large-ear' CIMMYT germplasm into UK pre-breeding lines

Lead Research Organisation: University of Nottingham
Department Name: Sch of Biosciences

Abstract

Most major changes in UK wheats, such as the introduction of dwarfing genes (which reduced plant height, but increased the yield) have been introduced from wide crosses. Wide crosses can still be used to introduce new genes which allow further major changes to be made in UK wheats. The proposal presented here will introduce new genes conferring longer ear rachis (= axis of the ear) associated with improved ear fertility from Mexican wheats (from CIMMYT) which could facilitate a quantum leap in overall yield in UK wheats. The material to test this has already been produced. Specifically, we have created a population of lines from a cross between the Mexican 'big-ear' line and a productive (highly efficient at turning sunlight into sugar) UK adapted wheat, Rialto. In a preliminary study, we have shown rachis length to be positively correlated with ear fertility (and grain number per unit land area). This proposal asks for funds to look at why the Mexican wheat produces more grain for each ear than UK wheat and whether we can use the same genes to improve UK wheat yields. The programme works with UK plant breeders from CPB-Twyford Ltd to produce wheat pre-breeding lines containing these new genes from the Mexican material. For breeders to introduce novel traits into elite UK varieties, they must first know which genes are responsible for controlling the traits and how they work to cause differences between varieties. So, we will map the genes controlling ear fertility and in doing so develop genetic markers to facilitate their selection in breeding programmes. The weather and environmental conditions can vary considerably between different countries and genes that may be useful in some countries may not be in others. We plan to carry out physiological experiments which would identify why the Mexican wheat has more grains in each ear and how this might help improve wheat yield in the UK varieties. We will also carry out experiments to examine whether these genes influence other important determinants of yield at the crop level, such as ear number and grain weight. Crucially, there should be added benefits due to the high photosynthetic ability of Rialto combined with more fertile ears in the 'big-ear' line. We already have seed from the crosses which are needed to do this work, but need funding to understand how wheat controls the number of grains produced per ear. Our industrial partner will use their breeding expertise to make new lines suited to UK breeding, and we will help develop these lines and also use these lines to help us understand the genetics of how many grains are produced per ear. Using this combined approach we will then identify a pool of candidate genes which may directly influence this trait.

Technical Summary

Under good management conditions in the UK, winter wheat is generally sink limited, with more photoassimilates produced during crop development than can be stored in the grain. This is largely due to limited grain number per ear. The International Center for Maize and Wheat Improvement (CIMMYT) has identified novel material with long ear rachis which has far higher potential grain number per ear than UK wheats. We have generated a doubled-haploid (DH) population (140 lines) of a cross between this CIMMYT novel ear material and the productive (high radiation-use efficiency, ratio of DM production to radiation interception) UK adapted wheat, Rialto. Crucially, there should be synergies between the high photosynthetic capacity in Rialto and improved ear fertility in the novel CIMMYT line. This research proposal presents an integrated approach using developmental, physiological and molecular genetic evaluation of lines from this cross to begin to understand the basis of this trait at all three levels. This will be coupled with the introgression of the 'long ear' phenotype into the CPB-Twyford UK wheat breeding programme and analysis of individual back-cross lines of a DH in each of an elite winter wheat and spring wheat UK background. We have shown that grains per square metre has had the highest phenotypic correlation with grain yield and contributed most to its genetic gain in modern UK wheat varieties in recent years. In a preliminary study, we have shown a positive correlation between both rachis length and spikelets/ear; and spikelets/ear and grains per square metre, in the DH lines. The developmental and physiological aspects of this proposal focus on understanding the biological processes determining fertile florets/ear at anthesis, concentrating on the biology of the plant during spikelet primordia production up to terminal spikelet and fertile floret survival up to anthesis. Specific objectives are to: (1) develop a detailed genetic map for the DH population and perform QTL analysis on trait data, (2) introduce the 'long ear' phenotype into UK pre-breeding and breeding lines through a back-crossing programme to each of an elite winter wheat and spring wheat variety (CPB-Twyford Ltd). We will then (3) use the DH population to identify the developmental and physiological basis of the novel ear fertility trait and (4) use specific DH lines to identify candidate genes for the novel ear phenotype using wheat microarrays. Finally we will (5) investigate the relationship between ear fertility and grain yield in the DH population. These objectives will be pursued through the combined expertise of the research team and CBP-Tywford Ltd, who will provide significant financial assistance through the back-crossing programme to evaluate and introgress these genes into UK varieties. Material from this backcrossing programme will be made available to the research team to pursue initial results obtained in the DH population and the research team will be directly involved in the back-crossing programme through marker-assisted selection in later generations. This integration between the research and plant breeding teams represents a powerful linkage from fundamental science to the generation of pre-breeding lines, facilitating the elucidation of this trait. The research proposed is novel in that it will improve understanding of the basic biological processes underpinning ear fertility in cereal plants and extend this to examine the generic effects within the unique ecological context of the most important UK cereal crop wheat.
 
Description The project produced an extensive genetic map of the CIMMYT CMH79A.955 x Rialto DH mapping population and
provided stocks of this important population for use in other projects. The project required refinement of field phenotyping
methodologies for assessment of ear fertility traits which included advanced protocols for scoring progression of floret
development and protocols for determination of stem, leaf, and ear assimilate partitioning. These high throughput and low
cost screens allowed very large scale field screens. The output of this was the identification of DH lines with improved ear
fertility compared to the UK parental cultivar Rialto. Within the project some of these novel lines with improved ear fertility
were shown to confer a yield advantage in field experiments at two sites.
A major output of this project is the production of a set of high resolution backcross substitution lines which has been
developed in one winter wheat (Humber) and one spring wheat (Ashby) background at KWS UK Ltd. In year 1 (2006//7),
each of 80 DH lines was crossed with each of Humber (winter wheat) and Ashby (spring wheat) and F1s were
backcrossed to respective recurrent parents to produce BC1S1. In years 2 and 3, these were then selfed for 2
generations. Material in the BC1S2 generation was selected for 'large-ear' phenotype. The BC3 heterozygotes (for the
tiller inhibition Tin1A locus) have been selfed (June 2010) to produce BC3S1 lines. 16 pairs of BC3 lines for Tin1A have
been developed. Marker-selected BC3 heterozygotes will also be backcrossed to respective recurrent parents to produce
BC4 and BC5 with marker selection at each generation to develop full NIL pairs, allowing multiplication for full NIL
assessment in 2012/13.
In addition, this DH material has so far been backcrossed according to phenotype (tillers/plant, spikelets/ear, grains/ear
and ear fertility index) to BC3. The number of original DH lines that carry the novel Mexican parental QTLs of interest on
1B, 2A, 3A and 7B is 5, 5, 7 and 5, respectively, in the Humber background and 3, 6, 6 and 5, respectively, in the Ashby
background. Full NILs (BC5) will also be developed based on marker-based selection in 2012/13.
Exploitation Route Genetic maps and QTL
Through QTL analysis of the phenotypic data from the DH population we have identified novel QTL for prioritised traits
controlling ear fertility and yield potential. These QTL cannot be explained by adaptive (Ppd-D1 - on chr 2D; Vrn-A1- on
chr 5A, Rht-B1 - on chr 4B) genes. They increase grain number through increasing spikelet number (potentially earlinessper se), partitioning of assimilate to the ear and efficiency of converting ear DM into grains (grains per g ear DM at anthesis, ear fertility index; EFI) contributing to more grains per unit land area and grain yield. In field plot (6 x 2 m)
experiments (132 lines) the range in grains/ear (23-77) was significantly above Rialto (54), associated with the tiller
inhibitionTin1A gene (Ribas-Vargas et al., 2008) and modified by novel QTLs on: (i) Chr 1B, modifying grain weight
without an obvious effect on sink size (ii) Chr 2A; combining both trials in 2007-8, this locus increased fertility, grains/ear,
grains/m2, EFI and yield without a negative effect on grain weight in the absence of Tin1A, (iii) Chr 3A, increasing spikelet
number, grains/ear, grains/m2 and yield across most plot trials in 2007-09 and iv) Chr 7B modifying grains/ear. The QTL
data (132 lines) show the Tin-1A locus makes a significant contribution to spikelets/ear and floret fertility, boosting sink
size (15%-23% of total trait variation) and feeding through into grains/ear (11%-22% of total trait variation), without having
a deleterious effect on either EFI or grain weight. Removal of Tin-1A carrying lines from the QTL analysis (n = 30,
remainder = 102) does not eliminate QTL effects observed on Chr 1B, 2A, 3A and 7B, arguing these are novel loci
independent of Tin-1A for their action. Knowledge of these QTL effects will allow for their selection in wheat breeding
programmes using the genetic markers developed in this project.

Physiological data sets and analyses
The DH population has been phenotyped for prioritised ear fertility traits and grain yield through crop development and in
multiple locations. The 132 DH lines were grown both at Univ. Nottingham and KWS UK Ltd (Thriplow, Hertfordshire) in
each of 2006-7, 2007-8 and 2008-9 in field plots at a normal planting density (300 seeds/m2). Detailed physiological
analysis for ear fertility traits and yield and yield components at harvest was carried out in the two environments. The data
sets will be made available on personal web pages and submitted to the appropriate database upon publication of the
corresponding paper (est. 3-6 months).

The project has provided a new framework for the deployment of novel ear fertility traits from CIMMYT large-ear
phenotype lines into UK wheats. In summary, in the pre-anthesis period grains/m2 may be determined by the product of :
i) days from sowing to flowering, ii) crop growth rate (g/m2/d), iii) ear DM partitioning index (ear DM / above-ground DM)
at anthesis and iv) ear fertility index (grains per gram ear DM at anthesis; grains/g). In the DH population, grains/m2 was
positively and closely associated with EFI, which, in turn, was associated with improved spikelet number and floret fertility
at anthesis. EFI was also associated with the amount of chaff per ear, with high EFI associated with decreased allocation
of assimilate to the lemma bract and a lower rachis specific weight (DM per unit rachis length). The data collected give a
new clear picture of the physiological components of ear fertility and yield potential and the genotype x environment
interactions of these traits in wheat. This data informed the trait prioritisation, trait ontology, and data collection
methodologies for the analysis of the backcross lines in the development of the near-isogenic lines. The NILs will allow to
us to test more precisely the benefit of the novel alleles for increased grain number and yield and to fine map the genes
regulating these traits to facilitate their deployment in UK breeding programs.
Sectors Agriculture, Food and Drink,Environment

 
Description A major output of this project is the production of a set of high resolution backcross substitution lines which has been developed in one winter wheat (Humber) and one spring wheat (Ashby) background at KWS UK Ltd. In year 1 (2006//7), each of 80 DH lines was crossed with each of Humber (winter wheat) and Ashby (spring wheat) and F1s were backcrossed to respective recurrent parents to produce BC1S1. In years 2 and 3, these were then selfed for 2 generations. Material in the BC1S2 generation was selected for 'large-ear' phenotype. The BC3 heterozygotes (for the tiller inhibition Tin1A locus) have been selfed (June 2010) to produce BC3S1 lines. 16 pairs of BC3 lines for Tin1A have been developed. Marker-selected BC3 heterozygotes will also be backcrossed to respective recurrent parents to produce BC4 and BC5 with marker selection at each generation to develop full NIL pairs, allowing multiplication for full NIL assessment in 2012/13. In addition, this DH material has so far been backcrossed according to phenotype (tillers/plant, spikelets/ear, grains/ear and ear fertility index) to BC3. The number of original DH lines that carry the novel Mexican parental QTLs of interest on 1B, 2A, 3A and 7B is 5, 5, 7 and 5, respectively, in the Humber background and 3, 6, 6 and 5, respectively, in the Ashby background. Full NILs (BC5) will also be developed based on marker-based selection in 2012/13. Exploitation and application: All the germplasm developed will be available free of IP restrictions to public sector researchers but covered by appropriate MTAs. In addition, the raw QTL data will been made available on personal web pages and submitted to the appropriate database upon publication of the corresponding paper (est. 3-6 months). This complies with BBSRC's desire that research results be fully available to the public and research community. The proposed research has provided a route by which the UK wheat breeding industry may directly exploit novel traits and markers for ear fertility generated from publicly funded research. KWS UK Ltd has already begun to generate SNP marker data for this cross, which will further enhance the genetic map and link directly into the developing genome sequence. The DH population is also being widely used in other research at Nottingham and beyond. In particular, the DH lines and associated map are being used to test for variation in straw lignin content and digestibility as part of the BSBEC LACE programme and for components of Fusarium head-blight tolerance. Both projects will draw on resources developed in this programme. Coordination of data collection, phenotyping methodologies, and standardised trait naming (trait ontology) required the development of common standard operating procedures for University of Nottingham and KWS UK Ltd. Data were collated at University of Nottingham in a relational database. This resulted in a high level of quality assurance for statistical analysis and QTL discovery. These bioanalytical resources have generic value for any large data set genetics project.
First Year Of Impact 2010
Sector Agriculture, Food and Drink,Energy,Environment
Impact Types Societal,Economic,Policy & public services

 
Description BBSRC Industrial Case Studentship Advancing Harvest Index through Genomics Enabled Breeding
Amount £70,000 (GBP)
Funding ID 2102620 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 09/2021
 
Description CONACYT PhD Studentship Genetic analysis of physiological traits to increase grain partitioning in high biomass cultivars in wheat
Amount £95,000 (GBP)
Organisation National Council on Science and Technology (CONACYT) 
Sector Public
Country Mexico
Start 10/2015 
End 09/2018
 
Description National Council on Science and Technology (CONACYT) PhD studentship Identifying canopy architecture traits to increase radiation-use efficiency and grain yield in wheat
Amount £90,000 (GBP)
Organisation Government of Mexico 
Sector Public
Country Mexico
Start 10/2017 
End 08/2021
 
Description USDA National Institute Food Agency - International Wheat Yield Partnership Program
Amount $163,000 (USD)
Organisation U.S. Department of Agriculture USDA 
Sector Public
Country United States
Start 11/2016 
End 10/2019
 
Title High resolution backcross substitution wheat lines 
Description A major output of this project is the production of a set of high resolution backcross substitution lines which has been developed in one winter wheat (Humber) and one spring wheat (Ashby) background at KWS UK Ltd. In year 1 (2006//7), each of 80 DH lines was crossed with each of Humber (winter wheat) and Ashby (spring wheat) and F1s were backcrossed to respective recurrent parents to produce BC1S1. 
Type Of Material Biological samples 
Provided To Others? No  
Impact Inclusion of advanced genotypes with high spike fertility in the wheat breeding programme of KWS UK Ltd 
 
Description Partnerhsip with Dr Ali Babar at University of florida 
Organisation University of Florida
Country United States 
Sector Academic/University 
PI Contribution As a result of the research carried out in this BBSRC project, I have following discussions with Dr Ali Babar University of Florida successfully jointly applied for a NIFA-IWYP grant "Advancing harvest index through genomics enabled breeding." in which I am the PI at Nottingham University,
Collaborator Contribution Sharing of SNP mapping array data sets and wheat germplasm for genetic analysis for grain partitioning traits in wheat
Impact Multidisciplinary: genomics, physiology, breeding. Outputs include marker-trait association for grain partitioning traits for application in wheat breeding.
Start Year 2017
 
Description Partnership in International Wheat Yield Consortium 
Organisation International Centre for Maize and Wheat Improvement (CIMMYT)
Country Mexico 
Sector Charity/Non Profit 
PI Contribution As a result of the research carried out in this BBSRC project, I have following discussions with CIMMYT joined the Internatioal Wheat Yield Consortium led by CIMMYT. In this Consortium I lead sub-project 2.1 on "Enhancing ear fertility and grain number while maintaining lodging resistance". Two PhD students (Carolina Rivera and Eliseo Trujillo) are worklng in the area of optimizing DM partitioning to improve grain number with CONACYT Studentships secured from the Mexican government and registered at Nottingham on 1 October 2011. In addition a grant of $50,000 from CIMMYT has been awarded by CIMMYT to Nottingham for research activities on this sub-project.
Collaborator Contribution Prof Matthew Reynolds Head of Physiology in CIMMYT Wheat Program is co-supervisor of the PhD Studentships of Carolina Rivera and Eliseo Trujillo. The field experiments of the two PhD studentships was based at the CIMMYT Research station at Ciudad Obregon, Sonora, Mexico and co-supervised by Matthew Reynolds. CIMMYT also provide a financial contribution to the PhD living stipends of the students when they are based at at Nottingham for 6 months of each calendar year.
Impact PhD studentships and papers presented at 1st - 3rd International Wheat Yield Consortium meetings at C. Obregon Mexico 2012-2014
Start Year 2011
 
Description Partnership with KWS UK Ltd Dr Ed Byrne and Dr Jacob Lage Wheat Ear Fertility 
Organisation KWS UK
Country United Kingdom 
Sector Private 
PI Contribution Through results on project "Raising the ceiling on UK wheat yields / introgression and assessment of novel 'large-ear' CIMMYT germplasm into UK pre-breeding lines" and "Enhancing diversity in UK wheat through a public sector prebreeding programme" discussion of future genetic analysis of ear fertility traits had resulted a new iCase PhD studentship on " grain partitioning in high biomass backgrounds in wheat"
Collaborator Contribution In kind genomics analysis of wheat mapping populations and provision of wheat field plots
Impact ICASE Phd Multidisciplinary: genomics, physiology, pre-breeding.
Start Year 2015