Progress 09/01/08 to 08/31/12
Outputs
OUTPUTS: Identify deletion mutants with increased biomass. Over 12,000 chemical (EMS AND DEB) and irradiation (gamma ray)-induced mutants of IR64 were screened at IRRI and 13 lines with increased biomass relative to IR64 were identified and genotyped to confirm genetic purity. One of these mutants that has reproducibly shown a two-fold increase in biomass under both field and greenhouse conditions also shows increased height, tiller number, tiller length, seed weight, girth and photosynthetic rate relative to IR64. To identify the deletions in DEB 1612-6-1, we performed a comparative genomic hybridization experiment using a custom Nimblegen O. sativa whole genome array with 2.1 million features tiled across the genome. We identified 14 deletions in the mutant, ranging in size from 90 to 5,721 bps that were confirmed with PCR. DEB 1612-6-1 has been backcrossed to IR64 and F2 seeds generated. Segregation of confirmed deletions with the high biomass phenotype in the F2 is in progress. Short read whole genome sequencing of segregants of both high and normal biomass will be used to identify the gene responsible for the yield increase. A similar strategy will be used to identify candidate genes from the remaining 12 mutants. Comprehensive information, including phenotypic data, QTL mapping data (generated in this and past projects), genome SNP variation, and transcript and metabolite profiles, are being used to identify candidate genes or pathways contributing to biomass accumulation. The power of the SNP comparisons across varieties is increasing as new SNP data becomes available for more rice varieties. Furthermore, metabolome data has been generated for the 20 OryzaSNPset lines. These data are being integrated into our analysis to select candidate genes that govern biomass traits. Our first candidate genes were selected by compiling and combining a number of diverse datasets. Currently, 8 candidate genes are in our transformation pipeline to determine their impact on biomass and we expect several more candidates for validation derived from mutants described above. Phenotypic data are still being collected for the transgenic and mutant lines to assess the impact of the candidate genes on biomass-related traits. Integrate expression and mapping data into gene browser/database to allow easy navigation and use of the data. A preliminary web based genome browser (GBrowse) platform was developed for in-house use to allow visualization and scalable integration of gene, QTL, metabolite, SNP, probe sequence (Nimblegen arrays for deletion discovery), and mapping data into an easily navigated format (http://csu-bir.colostate.edu/), similar to http://qtaro.abr.affrc.go.jp/cgi-bin/gbrowse/Oryza_sativa/. PARTICIPANTS: Training: Paul Tanger, PhD student, variation in cell wall composition; Courtney Jahn, PostDoctoral Fellow, physiological and morphological variation & gene discovery in rice; Bettina Broeckling, PostDoctoral Fellow, mutant analysis; gene discovery; Amanda Broz, PostDoctoral Fellow, gene validation in rice; Leah DeRose-Wilson, PostDoctoral Fellow, biomass QTL analysis; Rene Corral, Undergraduate, phenotyping; Sasha Broadstone (Undergraduate), phenotyping; Jacqueline Johnson (Undergraduate), phenotyping TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
We have used rice as a model grass to identify novel biomass genes and determine natural variation in cell-wall composition because of the wide array of rice genomic tools and the ease of genetic manipulation relative to emerging grass bioenergy crops. In rice, we established an efficient pipeline to identify loci for biomass production and composition. With this funding, we have made significant progress towards identifying key biomass genes and provided key information to expedite improvement of bioenergy grass crops. We have: (1) Identified key morphological and physiological parameters and developmental stages important for biomass accumulation in diverse rice varieties. These data are informing selection of traits for systematically improving biomass. (2) Identified candidate genes/genic regions governing biomass accumulation using diverse strategies. (3) Begun validation of key gene candidates by silencing and overexpression. Furthermore, we have generated some important materials for future analysis of biomass traits: (1) Large recombinant inbred populations (more than 1700 RIL for some populations) of rice segregating for biomass traits. (2) Mutants in rice that are larger (more biomass) and that produce more grain (higher yielding) than the wildtype parent. These mutants are key to understanding the genetic and biological processes involved in biomass productivity. (3) We contributed to the draft sequence of IR64, with 70X genome sequence coverage, and have begun sequencing and assembly of Aswina and Azucena, two parents of biomass interest. Each of these varieties has been used in genetic population development relevant to biomass productivity.
Publications
- Ainsworth EA and Bush DR. 2011. Carbohydrate export from the leaf - A highly regulated process and target to enhance photosynthesis and productivity. Plant Physiol 155: 64-69
- Feuillet, C, JE Leach, J Rogers, PS Schnable, K Eversole. 2011. Crop genome sequencing: lessons and rationales. Trends Plant Sci 16:77-88. doi:10.1016/j.tplants.2010.10.005.
|
Progress 09/01/09 to 08/31/10
Outputs
OUTPUTS: Developing a sustainable cellulosic biofuels feedstock will require maximizing plant biomass, and, thus, it is critical to identify the genes that can lead to increases in biomass to meet bioenergy needs. We use rice as a model system to understand the functional and genetic basis of biomass accumulation in grasses. This functional understanding can be applied to bioenergy crops. We focused on 20 diverse rice cultivars (OryzaSNP set) because they were recently resequenced and are part of an effort of recombinant inbred line development. We characterized variation in morphological and physiological traits relevant to biomass at different developmental stages. Significant findings are: (1) Rice exhibits tremendous variation for biomass accumulation. Quantification of this variation among the OryzaSNP varieties provides a framework to identify and target traits for improvement. (2) Dry biomass was between 26-57% of the wet biomass. Selection for high levels of dry matter content at harvest would increase net energy density, and decrease harvest, transport and drying costs. (3) Stems make up the largest proportion of the dry biomass; selection for more stems would increase biomass. (4) Biomass is positively correlated to tiller number, girth, leaf length, cell wall polymers, etc; any of these traits can be measured as early and easy biomass predictors. (6) Biomass is negatively correlated to photosynthesis, suggesting a possible trade-off between photosynthetic capacity and other traits that need to be considered for increase of biomass. (7) Although heritability estimates were significant for all traits, heritabilities were higher in traits relating to plant size and architecture than for physiological traits. (8) Variation was largely explained by variety and varietal class (advanced vs landrace), but not by varietal groupings (indica, japonica, and aus). (9) Traits that covaried at maturity also covaried at early time points, suggesting assays on young plants reliably predict adult plant phenotype. PARTICIPANTS: Dr. Courtney Jahn, post doctoral fellow Dr. Leah Derose-Wilson, post doctoral fellow Dr. Betina Brockling, post doctoral fellow Dr. Amanda Broz, post doctoral fellow TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
We characterized variation in morphological and physiological traits relevant to biomass at several different developmental stages, providing the first comprehensive analysis of physiological and morphological traits in a system that can be linked to genetic variation in rice (Jahn et al. 2011. Plant Physiol). This is the first step in the identification of genes governing biomass traits. We have developed the genetic populations that are needed to identify the QTL governing biomass traits. The data derived is critical to understanding the genetic processes involved in biomass accumulation and for crop improvement for food (e.g., understanding genes controlling tiller number).
Publications
- Jahn, C, J McKay, R Mauleon, J Stephens, K McNally, D Bush, H Leung, J Leach. 2011. Genetic variation in biomass traits among 20 diverse rice varieties. Plant Physiol 155(1):157-68.
- Jahn, C.E., I. Ona, J. Stephens, C. Vera Cruz, D. Bush, H. Leung, J. McKay, J.E. Leach. 2010. Screening a diverse set of rice varieties for variation in biomass and resistance to plant disease. Poster presentation at the 10th Japan-US Seminar: Genome-Enabled Integration of Research in Plant Pathogen Systems. January 24-28, Corvallis, OR.
- Leach, J.E., Jahn, C.E., A. Bordeos, M. Baroidan, J.Stephens, E. Peachey, D. R. Bush, H. Leung, J. K. Mckay. 2010. Genetic Variation In Biomass Traits Among 20 Diverse Rice Varieties. Plant and Animal Genome XVIII. SanDiego, CA January 9-13. http://www.intl-pag.org/18/abstracts/P05b_PAGXVIII_241.html
|
Progress 09/01/08 to 08/31/09
Outputs
OUTPUTS: Biofuels provide a potential means to produce energy while reducing reliance on petroleum. Developing a sustainable cellulosic biofuels feedstock will require maximizing plant biomass, and, thus, it is critical to identify the genes and genetic pathways that can lead to increases in biomass to meet bioenergy needs. We are using rice as a model system to understand the functional and genetic basis of biomass accumulation in grasses. This functional understanding can then be applied to emerging bioenergy crops (e.g., switchgrass, Miscanthus). Twenty diverse rice cultivars were recently resequenced to determine the degree and distribution of polymorphism in the genome. We analyzed this set of cultivars for variation in biomass traits including plant size and architecture, and physiological traits of leaf gas exchange at several different developmental stages. We found significant genetic variation among the 20 lines in all morphological and physiological traits. Although heritability estimates were significant for all traits, heritabilities were higher in traits relating to plant size and architecture than for physiological traits. Rice varietal groupings (indica, japonica, and aus) account for a significant portion of the genetic variation. Traits found to significantly covary at maturity also covary at early time points. Examining these data in an evolutionary context reveals that cultivars have achieved high biomass production via independent developmental and physiological pathways. Using a comprehensive phenotype/genotype mapping approach, we are linking these data and phenotypic data from experimental genetic populations to determine loci, pathways and trait combinations required for optimum biomass production in grasses. To identify quantitative trait loci governing biomass traits, we have advanced two types of genetic populations. We are using an existing F4 Moroberekan X IR64 population to generate near-isogenic lines with contrasting biomass characteristics. Of the 123 F4 families analyzed, six showed clear segregation within the line for high and low vegetative dry weight (vdw). Two F4 lines where the high biomass segregants have vdw ~80% higher than the two parents (Moroberekan and IR64) are being used to develop near isogenic lines. A second cross (Moroberekan x IR64-21), developed from the OryzaSNP set, has the advantage of a large population size and provides the appropriate materials for fine-scale mapping. Over 2000 F2 plants have been assessed for phenotypic variation in biomass-related traits. Leaf tissues from individual plants were sampled for DNA extraction for bulk segregant analysis. PARTICIPANTS: Dr. Courtney Jahn, post doctoral fellow; Dr. Leah Derose-Wilson, post doctoral fellow; Dr. Betina Brockling, post doctoral fellow; Marietta Baroidan, Assistant Scientist, International Rice Research Institute; Alicia Bordeos, Assistant Scientist, International Rice Research Institute; Dr. Ken McNally, Institute Scientist, International Rice Research Institute. TARGET AUDIENCES: Biofuel industry, biomass research scientists, rice geneticists PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
We have identified cultivars that exhibit genetic variation in diverse biomass traits. Genetic populations of these cultivars are in development and will be used to identify the quantitative trait loci for biomass traits. Screening of the populations is underway. The data derived is not only useful for understanding the genetic processes involved in biomass accumulation. It is also relevant to crop improvement for food (e.g., understanding genes controlling tiller number).
Publications
- No publications reported this period
|
|