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INVESTIGATOR: Dubcovsky, J.; Akhunov, ED, D.

PERFORMING INSTITUTION:
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS, CALIFORNIA 95616-8671

NIFA CAP: LEVERAGING HIGH-THROUGHPUT GENOTYPING AND PHENOTYPING TECHNOLOGIES TO ACCELERATE WHEAT IMPROVEMENT AND MITIGATE THE IMPACTS OF CLIMATE CHANGE

NON-TECHNICAL SUMMARY: Urgent action is needed for sustainableincreases in wheat productivity to feed a growing human population in rapidly changing growing environments. Wheat varieties developed by public wheat breeding programs account for ~60% of the US wheat acreage and contribute >$4 billion in annual production value. Further increases in productivity are required to maintain competitiveness of US wheat. This project will establish a nationally coordinated consortium of public wheat breeders and researchers to accelerate rates of improvement in grain yield. Breeding cycles will be shortened by implementing high-throughput genotyping and phenotyping technologies integrated with a centralized data storage and informatics analysis platform. To address national needs for more plant breeders, this project will provide multidisciplinary training in modern plant breeding to a cohort of 20 PhD students placed in active breeding programs. The specific objectives of the project are to i) implement genomic selection (GS) in public wheat breeding programs, ii) implement an Unmanned Aircraft System (UAS) high-throughput phenotyping (HTP) centralized data analysis pipeline, iii) develop decision support tools within BreedBase to enable GS implementation in the breeding programs, iv) characterize natural and induced regulatory variants affecting gene expression in wheat and integrate them into our GS platforms, v) train a new cohort of 20 plant breeders. This project addresses the integrated education and research priorities in the following focus areas: i) integration between genotyping and high-throughput phenotyping for source- and sink- related traits, ii) implementation of genomic selection approaches into active public breeding programs and cultivar production, and iii) functional genomic studies to identify pathways affecting plant productivity and deployment of this information into genomic selection.

OBJECTIVES: Overall goal: The overall goals of this project are to accelerate breeding cycles to mitigate the impact of climate change on wheat productivity and to train a new generation of plant breeders.The specific objectives of the project are to: 1) Develop cost-effective, medium-density, single nucleotide polymorphism (SNP) assays incorporating both functional and haplotype-tagging SNPs for effective genome-wide imputation and link these assays with practical haplotype graphs (PHG) to establish a centralized automated platform for genomic selection (GS) in public wheat breeding programs.2) Implement a centralized high-throughput phenotyping platform based on unmanned aerial systems (UAS-HTP). This centralized BRAPI-compliant platform will support data processing, analysis and management and is aimed at accelerating the adoption of UAS-HTP in public wheat breeding programs. Phenotypic data will be deposited into the public T3/BreedBase database.3) Develop improved breeding decision support tools based on T3/BreedBase capable of maintaining centralized upload and processing of genotypic and agronomic data from public breeding programs. Promote the exchange of data and analyses tools with equivalent public wheat breeding databases used by CIMMYT and the UK.4) Develop a publicly accessible genomic catalogue of natural and induced genetic variants that regulate gene expression in wheat, assess the role of regulatory diversity in controlling pathways underlying variation in growth and grain yield, and integrate information about regulatory variants into the T3/BreedBase database.5) Train a new cohort of 20 plant breeders within an active Community of Practice in plant breeding, by integrating them into active wheat breeding programs that combine field research, UAS-HTP, and GS to accelerate the development of improved wheat varieties.In rapidly changing environments, a species' chance of survival depends on two factors: levels of genetic variation and efficiency of selection for beneficial variants. Our project plans to use strategies affecting both factors to mitigate the impact of climate change on wheat productivity.Increasing genetic diversity: The ability to develop varieties adapted to changing climatic conditions will strongly depend on the availability of novel climate-adaptive diversity. Several teams in this project will explore wild relatives of wheat selected from diverse geographic regions with distinct and extreme climatic conditions as a source of climate-adaptive diversity for future wheat breeding. This introgressed diversity will be systematically evaluated in multiple environments for adaptive potential by collecting image data using the UAS-based sensory technologies.In addition to natural variation, this project will also incorporate novel induced diversity generated by chemical mutagenesis and CRISPR. Mutants that increase grain size and weight (e.g. gw2) and grain number (e.g. ful2, vrt2, and svp1) identified in our previous grant will be incorporated into elite lines in the public breeding programs.Accelerating breeding cycles: The second strategy for mitigating the negative effects of climate change on wheat productivity is based on accelerating breeding cycles. Shortening of breeding cycles allows for effective selection of superior allelic complexes better adapted to the climatic conditions. The GS pipelines proposed in this project can reduce the time from crosses to released varieties by facilitating selection in off season nurseries or in "rapid breeding" greenhouses and by identifying valuable parental lines combining multiple favorable alleles for inclusion in crossing blocks at earlier generations.