Bikram S. Gill - US grants

This award supports the participation of ten U.S. scientists in a U.S.-Japan Seminar on Classical and Molecular Cytogenetic Analysis of Cereal Genomes, which will be held in March 8-10, 1994 in Manhattan, Kansas. The co-organizers are Professor Bikram S. Gill, Kansas State University, and Professor Koichiro Tsunewaki, Kyoto University. The major objective of the seminar is to bring together researchers, particularly younger researchers at the Assistant or Associate Professor level, to discuss cereal genome structure and comparative genome mapping. The participants, who are from classical and molecular areas, will discuss problems of common interest such as chromosome structure and function, nucleo-cytoplasmic interactions, and cytoplasmic male sterility. This meeting will stimulate interaction among cereal geneticists, cereal and non-cereal geneticists, and plant and mammalian cytogeneticists. To arrive at common mechanisms underlying the genome structure, evolution, and speciation in polyploid plants, some scientists in polyploid plants are also invited. The proceedings of the seminar will be published as a paperback and widely distributed.

This award provides support for purchase of a phosphor-imager to be placed in the University's Plant Biotechnology Center. There are already several items of genomics-related equipment in the Center, but there is no shared-use imager, a workhorse instrument in modern molecular biology. Among the uses planned are research on the structure and function of expressed genes, functional and comparative genomics, gene mapping, plant cell-cycle studies, investigation of non-host disease resistance mechanisms, and regulation and function of lipid-based signaling. In addition to advancing research, the instrument will broaden the training of students, post-doctoral fellows, and visiting scientists by providing greater access to the latest and most up-to-date equipment. Imagers of this type replace the use of film in many research procedures that require localization of radioactively-labelled proteins and nucleic acids after polyacrylamide gel electrophoresis. Use of the imager speeds up detection and measurement, as well as avoiding the need for chemicals and equipment used in film processing.

Wheat is the most widely grown crop, comprising 17% of all cultivated land, a staple of 40% of the world's population providing 20% of the calories consumed. Wheat also provides approximately 55% of the worlds carbohydrates. To meet human demands in 2050, grain production needs to increase at an annual rate of 1.5+% on an area of land that will not increase much beyond present levels. This implies that significant advances in the understanding of the wheat plant and grain biology must occur in order to increase absolute yield as well as protect the crop from 25% loss due to biotic (pests) and abiotic stress (heat, drought, and salinity). Sequencing of the gene-rich regions of wheat genome is feasible due to the abundance of cytogenetic, molecular, and human resources.

The purpose of the workshop is to establish a plan, utilizing the expertise from other genome sequencing projects, for a possible wheat genome-sequencing project. The workshop will pose broader questions such as: Do we need to sequence the wheat genome? What are the scientific needs for the sequence that cannot be met with existing cereal sequence resources? Is it time to sequence now? What genome should be sequenced (diploid or hexaploid)? What type of sequence should be generated (whole genome shotgun, selected BACs, etc)? What strategies could be used to yield the type of sequence needed? What timetable should be followed for the next steps? How will the broader community be engaged?

A report will be published in hardcopy and posted on pertinent websites before the next Plant and Animal Genome meeting in January 2004.

Planning Grant: I/UCRC for Area Wheat Genetics: Wheat Genetics Resource Center

1238313 Kansas State University; Bikram Gill

Kansas State University (KSU), as the lead institution, will partner with Oklahoma State University to establish an I/UCRC for Wheat Genetics that will feature integrated application of genomics, bioinformatics, high- throughput genotyping, mapping, phenotyping, and cytogenetics to accelerate alien gene introgressions for crop improvement. The proposed I/UCRC will build upon the already existing Wheat Genetics Resource Center (WGRC) at Kansas State University.

Managing bread wheat genetic diversity within domesticated varieties and wild wheat species, as well as workforce training, are critical success factors for the wheat research enterprise. Both will be major functions of the proposed I/UCRC. Adding value to wheat genetic resources will also be a major function of the proposed center. Another focus of the center will be mobilization of genetic diversity to improve crop performance. Finally, a key focus of the center will be the development of new methods for the rapid deployment of useful genetic diversity. Technical innovations will allow rapid transfer of useful traits to elite germplasm
through genotyping by sequencing, marker assisted breeding and doubled haploid and other innovations by center scientists.

The primary research impact of the proposed activity could be, potentially, the characterization (genotypic and phenotypic) of thousands of wild wheat relatives and alien introgression lines, a resource of immense value to the broader wheat improvement community (public and private). The value of this work will be even greater with the proposed I/UCRC investing effort in reducing the segments of alien introgressions carrying genes of interest to wheat improvement programs. WGRC's impressive track record of training and mentorship will be expanded upon in the new I/UCRC by providing additional training and educational activities including industry mentorship and internships, undergraduate research and potential dual degree programs in the plant sciences and various K-State departments.

Program Director's Recommendation
1338897 Kansas State University; Bikram Gill
1338906 Colorado State University; Patrick Byrne

Kansas State University (KSU), as the lead institution, will partner with Colorado State University to establish an I/UCRC for Wheat Genetics that will build upon the already existing Wheat Genetics Resource Center (WGRC) at Kansas State University. The Center proposes to overcome challenges facing the wheat industry partners, and that will strategically and efficiently derive value from the wealth of genetic diversity in the Wheat Genetics Resource Center (WGRC).

The proposed Center will focus on developing new methods for using wheat genetic diversity, both natural and induced, to solve problems for farmers and end users of wheat. Industry members will provide market awareness, ensuring delivery of traits important to end-users. WGRC's goal will be to significantly reduce the market-ready time by providing novel traits in elite genotypes. WGRC will develop and apply innovative methods to incorporate novel, high-value traits in wheat breeding programs for sustainable and profitable crop production. WGRC houses one of the worlds premier collections of wheat germplasm and genetic tools, routinely capitalized in applied breeding programs worldwide.

The project will have significant broader impacts in a number of areas. Wheat is a critical source of protein, and world health depends upon production which has been impacted by climate change. A doctoral program in seed and wheat breeding will be an element of the program and is clearly needed. Over the last few years, the researchers involved in the center have had significant impact through providing industrially relevant education to a large number of students, including many from underrepresented groups.

Wheat (Triticum aestivum L.) is one of the world's most important food crops and a staple for billions throughout the world. Hidden within loaves of bread is one of largest and most complex genomes of important plant species. The size and complexity of the bread wheat genome, which is more than five times larger than the human genome, have hindered development of a reference framework that can serve as a resource for genetic studies and breeding applications. A better understanding of the wheat genome will also give insight into the structure, function and evolution of complex, polyploid plant genomes. Advancement of population-based sequencing methods for assembling plant genomes will have broad implications throughout the plant genomics community, particularly for species with limited genomic resources and large, intractable genomes. User-friendly tools for population sequencing developed through this project will enable applications of this approach in the broader plant genome community. Through integrated education and outreach activities, this project will recruit and train new generations of computational biologists to address complex and challenging genomics questions. In partnership with the Kansas Foundation for Ag in the Classroom (KFAC), multi-tiered educational materials on plant genomes and domestication will be developed and implemented in middle and high school classrooms across the state. Through KFAC, students will be given access to advanced material targeting Next Generation Science Standards, including resource materials on careers in plant science. At the undergraduate level, internships will be developed to attract non-biology students from computationally-intensive fields. Interns with diverse social and academic backgrounds will be challenged with cutting-edge bioinformatics through coursework and research in U.S. labs followed by summer internships working with European project collaborators. At the postdoctoral level, scholars working on this project will gain skills in cutting-edge genomics along with mentoring and international research experience. To disseminate bioinformatics approaches developed through this project, annual workshops for bioinformatics training in population sequencing and genotyping-by-sequencing will be held for graduate and postdoctoral training.

As an approach for developing sequence resources for crop plants with large genomes, next-generation sequencing (NGS) can be applied to rapidly generate a whole genome sequence that is readily assembled into short contigs. These contigs primarily contain the gene-rich, non-repetitive portions of complex genomes. However, WGS assemblies have limited utility because these gene-rich contigs remain unanchored and unordered on the chromosomes. Novel, cost-effective approaches are needed for anchoring and ordering large, complex genomes. Through this project, new methods for assembling and ordering complex plant genomes will be developed and applied to understanding the genomes of wheat and its wild relatives. NGS will be applied to segregating populations of diploid, tetraploid and hexaploid wheat species, leveraging linkage information to develop an ordered whole-genome assembly for each species. This approach (POPSEQ) uses millions of genetic markers to order the assembled gene space onto a physical framework. The project will target 1x whole-genome sequence coverage across multiple diploid (AA and DD genomes), tetraploid (AABB) and hexaploid (AABBDD) populations to develop high-density genetic maps. These high-density genetic maps can then be used to anchor sequence contigs and scaffolds, giving physical context to genome assemblies. Ordered assemblies will be iteratively improved and made available to the wheat community through MIPS (http://mips.helmholtz-muenchen.de/plant/genomes.jsp), T3 (http://triticeaetoolbox.org/) and GrainGenes (http://wheat.pw.usda.gov/) databases. Genetic stocks will be made available through the KSU Wheat Genetics Resource Center and the USDA-ARS National Small Grains Collection.