Common use of Background and Rationale Clause in Contracts

Background and Rationale. Scientists at TAES have been developed a sorghum genome technology platform consisting of integrated genetic, cytogenetic and comparative genome maps since 1998. The TAES sorghum genetic map contains over 3,000 DNA markers based on data collected from 137 RIL lines derived from BTx623 X IS3620C. A physical map that is aligned to the sorghum genetic map has been constructed from ~16X deep BAC libraries, HICF fingerprinting, 6D BAC pooling, and ~5,000 EST-STS linkers. BACs from this map have been end-sequences and sequence scanned providing information for aligning DOE sequence assemblies to the map. The sorghum genome sequence assemblies produced by DOE based on 8X shotgun coverage of the genome are large (up to 14 Mbp). Test alignment of DOE sequence assemblies to SBI03 is promising revealing 6 miss-assemblies in the euchromatic region (~47Mbp) that were easily corrected. Funding is requested to accelerate the next set of sorghum genome map platform improvements including aligning the DOE [***] to the TAES [***] and [***] followed by [***] and resolution of issues related to [***] [***]/[***]. In addition, [***] of the [***] will be done in a targeted manner ([***], [***]/[***]) at different levels depending on need (automated [***] and by [***] analysis, [***] models, [***], etc.). For example, DOE funding will allow implementation of [***] of sorghum [***] matching [***] in [***] in 20[***] in collaboration with ▇▇▇▇▇▇ ▇▇▇▇/▇▇▇▇▇▇▇ ▇▇▇▇▇ (Cold Spring Harbor). We will focus [***] efforts on [***] relevant to [***] with funding from DOE. We also plan to bring in [***] of [***] (from prior [***], RT-PCR data, plus [***]/[***] data when it becomes available). Comparative genetic maps and the comparative aligned genome sequences focused on sorghum, rice, maize, and switchgrass will be updated on a regular basis. The TAES sorghum genome map platform is a key resource for all future QTL mapping, annotation, and gene discovery projects done at TAES and those carried out in collaboration with CERES. As such, the genome map/sequence platform provides our group an advantage in terms of gene discovery/IP capture. For QTL mapping and gene discovery research it would be ideal if TAES and CERES were operating with a common genome sequence/genetic map framework. If CERES provides funding to help TAES to continue development of the TAES genome map/sequence platform, then TAES will make the genome map/sequence platform available to CERES with regular quality and annotation updates. CERES will be free to do their own in house annotation of the aligned sorghum genome map/sequence provided by TAES and to use the information provided by TAES for commercial purposes.

Background and Rationale. Scientists at TAES have been developed a sorghum genome technology platform consisting of integrated genetic, cytogenetic and comparative genome maps since 1998. The TAES sorghum genetic map contains over 3,000 DNA markers based on data collected from 137 RIL lines derived from BTx623 X IS3620C. A physical map that is aligned to the sorghum genetic map has been constructed from ~16X deep BAC libraries, HICF fingerprinting, 6D BAC pooling, and ~5,000 EST-STS linkers. BACs from this map have been end-sequences and sequence scanned providing information for aligning DOE sequence assemblies to the map. The sorghum genome sequence assemblies produced by DOE based on 8X shotgun coverage of the genome are large (up to 14 Mbp). Test alignment of DOE sequence assemblies to SBI03 is promising revealing 6 miss-assemblies in the euchromatic region (~47Mbp) that were easily corrected. Funding is requested to accelerate the next set of sorghum genome map platform improvements including aligning the DOE [***] sequence scaffolds to the TAES [***] genetic and [***] physical map followed by [***] and resolution of issues related to [***] [***]sequence order/[***]quality. In addition, [***] of the [***] sequence will be done in a targeted manner ([***]QTL, [***]specific genes/[***]pathways) at different levels depending on need (automated [***] prediction and by [***] analysis, [***] metabolic pathway models, [***]gene expression, etc.). For example, DOE funding will allow implementation of [***] MetaCyc Annotation of sorghum [***] genes matching [***] known proteins in [***] metabolic pathways in 20[***] in collaboration with ▇▇▇▇▇▇ ▇▇▇▇/▇▇▇▇▇▇▇ ▇▇▇▇▇ (Cold Spring Harbor). We will focus [***] manual annotation efforts on [***] pathways relevant to [***] with funding from DOE. We also plan to bring in [***] annotation of [***] gene expression (from prior [***]microarray, RT-PCR data, plus [***]Solexa/[***] SAGE data when it becomes available). Comparative genetic maps and the comparative aligned genome sequences focused on sorghum, rice, maize, and switchgrass will be updated on a regular basis. The TAES sorghum genome map platform is a key resource for all future QTL mapping, annotation, and gene discovery projects done at TAES and those carried out in collaboration with CERES. As such, the genome map/sequence platform provides our group an advantage in terms of gene discovery/IP capture. For QTL mapping and gene discovery research it would be ideal if TAES and CERES were operating with a common genome sequence/genetic map framework. If CERES provides funding to help TAES to continue development of the TAES genome map/sequence platform, then TAES will make the genome map/sequence platform available to CERES with regular quality and annotation updates. CERES will be free to do their own in house annotation of the aligned sorghum genome map/sequence provided by TAES and to use the information provided by TAES for commercial purposes.