Progress 09/19/13 to 05/21/18
Outputs
Progress Report Objectives (from AD-416): 1: Characterize on a genome wide basis transformation-associated changes in genome sequence/structure to assess the potential for unintended effects during genetic engineering. 1A: Model of early stage product development: transformation 1B: Model of middle stage product development: introgression 1C: Model of late stage product development: evaluation 2: Identify genetic loci that govern selected grain composition traits for maize under target environments. 2A: Estimate the maize grain metabolome. 2B: Estimate the relative impact of genetic versus environmental factors in determining the maize grain metabolome. Approach (from AD-416): We will examine genome-wide responses to plant transformation using next generation DNA sequencing. These changes will be compared with the degree of genetic variation within varieties that occurs due to genetic drift and also with genomic responses to tissue culture. This will help establish how plant genomes change in unexpected ways to transformation, which may contribute to unintended effects to crop composition and quality. We will also test how these genomic responses are mitigated through introgression into elite varieties, through both DNA sequence analysis, compositional analysis via mass spectrometry and agronomic evaluation. In parallel, we will continue our characterization of the genetic and environmental factors that control the maize grain metabolome that was initiated at the end of the previous project cycle. We will use ultra performance liquid chromatography with a range of chemistries to interrogate the grain metabolome more thoroughly. We will also expand the number of varieties, the number of environments, and compare public sector germplasm to that used in the private sector. In addition to the survey-style questions, we will test specific gene/trait associations to potentially identify new traits for maize grain improvement. This is the final progress report for project 8062-21000-040-00D, which terminates on May 21, 2018, and as such is written as a summary of the entire project period. An industry collaboration was formed with an important domestic producer of genetically modified (GMO) crops. An agreement with the Boyce Thompson Institute to secure bioinformatics support was established and runs through the end of the project in September, 2018. A collection of nearly 400 transgenic and control lines including non-transformed, tissue culture and large numbers of T1 siblings segregating for a transgene event was grown by the industry collaborator and tissues for each were delivered to the ARS Holley Center. We performed genome-by-sequencing (GBS) analysis on all lines which provided a low resolution view of genome variation and which suggested no substantive differences among lines. Genome resequencing was performed on a set of eight lines (GMO, non-GMO) and tissue culture control (also non- GMO). The resulting genomes were analyzed first for SNPs, indels and broader structural variation that could be detected within the context of short read resequencing. While all classes of variants were observed, we observed no substantial differences in the transgenic lines as compared to the controls. A number of different assembly programs were tested and deeper sequencing was performed in the last year of the project to better assess structural features and changes (SNPs, indels) in the genome sequence. Prior results suggesting no substantive differences in genomes resulted from the transformation event.
Impacts
(N/A)
Publications
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Progress 10/01/16 to 09/30/17
Outputs
Progress Report Objectives (from AD-416): 1: Characterize on a genome wide basis transformation-associated changes in genome sequence/structure to assess the potential for unintended effects during genetic engineering. 1A: Model of early stage product development: transformation 1B: Model of middle stage product development: introgression 1C: Model of late stage product development: evaluation 2: Identify genetic loci that govern selected grain composition traits for maize under target environments. 2A: Estimate the maize grain metabolome. 2B: Estimate the relative impact of genetic versus environmental factors in determining the maize grain metabolome. Approach (from AD-416): We will examine genome-wide responses to plant transformation using next generation DNA sequencing. These changes will be compared with the degree of genetic variation within varieties that occurs due to genetic drift and also with genomic responses to tissue culture. This will help establish how plant genomes change in unexpected ways to transformation, which may contribute to unintended effects to crop composition and quality. We will also test how these genomic responses are mitigated through introgression into elite varieties, through both DNA sequence analysis, compositional analysis via mass spectrometry and agronomic evaluation. In parallel, we will continue our characterization of the genetic and environmental factors that control the maize grain metabolome that was initiated at the end of the previous project cycle. We will use ultra performance liquid chromatography with a range of chemistries to interrogate the grain metabolome more thoroughly. We will also expand the number of varieties, the number of environments, and compare public sector germplasm to that used in the private sector. In addition to the survey-style questions, we will test specific gene/trait associations to potentially identify new traits for maize grain improvement. An industry collaboration was previously formed with an important domestic producer of genetically modified (GMO) crops. The agreement with the Boyce Thompson Institute to secure bioinformatics support continues. A collection of nearly 400 transgenic and control lines including non- transformed, tissue culture and large numbers of T1 siblings segregating for the transgene event was grown by the industry collaborator and tissues for each were delivered to the Holley Center. We previously performed genome-by-sequencing (GBS) analysis on all lines which provided a low resolution view of genome variation and which suggested no substantive differences among lines. Genome resequencing was performed on a set of eight lines (GMO, non-GMO) and tissue culture control (also non- GMO). The resulting genomes were analyzed in the last year for SNPs, indels and broader structural variation that could be detected within the context of short read resequencing. While all classes of variants were observed, we observed no substantial differences in the transgenic lines as compared to the controls. The data is currently being assembled for publication.
Impacts
(N/A)
Publications
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Progress 10/01/15 to 09/30/16
Outputs
Progress Report Objectives (from AD-416): 1: Characterize on a genome wide basis transformation-associated changes in genome sequence/structure to assess the potential for unintended effects during genetic engineering. 1A: Model of early stage product development: transformation 1B: Model of middle stage product development: introgression 1C: Model of late stage product development: evaluation 2: Identify genetic loci that govern selected grain composition traits for maize under target environments. 2A: Estimate the maize grain metabolome. 2B: Estimate the relative impact of genetic versus environmental factors in determining the maize grain metabolome. Approach (from AD-416): We will examine genome-wide responses to plant transformation using next generation DNA sequencing. These changes will be compared with the degree of genetic variation within varieties that occurs due to genetic drift and also with genomic responses to tissue culture. This will help establish how plant genomes change in unexpected ways to transformation, which may contribute to unintended effects to crop composition and quality. We will also test how these genomic responses are mitigated through introgression into elite varieties, through both DNA sequence analysis, compositional analysis via mass spectrometry and agronomic evaluation. In parallel, we will continue our characterization of the genetic and environmental factors that control the maize grain metabolome that was initiated at the end of the previous project cycle. We will use ultra performance liquid chromatography with a range of chemistries to interrogate the grain metabolome more thoroughly. We will also expand the number of varieties, the number of environments, and compare public sector germplasm to that used in the private sector. In addition to the survey-style questions, we will test specific gene/trait associations to potentially identify new traits for maize grain improvement. An industry collaboration was formed with an important domestic producer of genetically modified (GMO) crops. An agreement was set up with the Boyce Thompson Institute to secure bioinformatics support. A collection of nearly 400 transgenic and control lines including non-transformed, tissue culture and large numbers of T1 siblings segregating for the transgene event was grown by the industry collaborator and tissues for each were delivered to the Holley Center. We performed genome-by- sequencing (GBS) analysis on all lines which provided a low resolution view of genome variation and which suggested no substantive differences among lines. We then selected two lines to assess our ability to develop 10X coverage genome sequence data for assessing more finely DNA sequence variation among lines. Protocols were optimized and we then moved to a set of eight lines (GMO, non-GMO) and tissue culture control (also non- GMO) for genome sequencing. The genome sequences were developed for all eight lines and preliminary analysis indicates minimal variation supporting substantial equivalence among transformed and non-transformed genotypes. Assessment of these genome sequences is ongoing. Accomplishments 01 The genome sequences of genetically modified (GMO) and non-GMO maize (corn) lines are substantially equivalent. Transgenic or so-called GMO crops are common in the market place and the public has concern that these modifications designed to optimize plant performance, reduce production costs and minimize pesticide use, may have adverse effects on consumers. ARS researchers in Ithaca, New York assessed multiple GMO, non-GMO and control lines (e.g. plants that had been through the genetic modification process but did not receive the modified DNA) at the level of DNA sequence. These plants were provided by a company that produces GMO plants and thus went through a typical commercial production process used to develop plants currently in the market place. DNA sequencing analysis revealed that only minor DNA sequence differences. Follow-up analysis indicated most were false positives and the degree of remaining variation was consistent with variation among non-GMO siblings. In summary, we found no evidence that transgene integration into maize resulted in any DNA modifications beyond the insertion of the transgene itself, providing DNA sequence that GMO crops are substantially equivalent to their non-GMO counterparts.
Impacts
(N/A)
Publications
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Progress 10/01/14 to 09/30/15
Outputs
Progress Report Objectives (from AD-416): 1: Characterize on a genome wide basis transformation-associated changes in genome sequence/structure to assess the potential for unintended effects during genetic engineering. 1A: Model of early stage product development: transformation 1B: Model of middle stage product development: introgression 1C: Model of late stage product development: evaluation 2: Identify genetic loci that govern selected grain composition traits for maize under target environments. 2A: Estimate the maize grain metabolome. 2B: Estimate the relative impact of genetic versus environmental factors in determining the maize grain metabolome. Approach (from AD-416): We will examine genome-wide responses to plant transformation using next generation DNA sequencing. These changes will be compared with the degree of genetic variation within varieties that occurs due to genetic drift and also with genomic responses to tissue culture. This will help establish how plant genomes change in unexpected ways to transformation, which may contribute to unintended effects to crop composition and quality. We will also test how these genomic responses are mitigated through introgression into elite varieties, through both DNA sequence analysis, compositional analysis via mass spectrometry and agronomic evaluation. In parallel, we will continue our characterization of the genetic and environmental factors that control the maize grain metabolome that was initiated at the end of the previous project cycle. We will use ultra performance liquid chromatography with a range of chemistries to interrogate the grain metabolome more thoroughly. We will also expand the number of varieties, the number of environments, and compare public sector germplasm to that used in the private sector. In addition to the survey-style questions, we will test specific gene/trait associations to potentially identify new traits for maize grain improvement. Lead scientist is no longer employed by ARS as of January 3, 2014. No research was conducted as the new research project had recently started when sead scientist left ARS and the position has not yet been refilled. Therefore, there is nothing to report.
Impacts
(N/A)
Publications
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Progress 10/01/13 to 09/30/14
Outputs
Progress Report Objectives (from AD-416): 1: Characterize on a genome wide basis transformation-associated changes in genome sequence/structure to assess the potential for unintended effects during genetic engineering. 1A: Model of early stage product development: transformation 1B: Model of middle stage product development: introgression 1C: Model of late stage product development: evaluation 2: Identify genetic loci that govern selected grain composition traits for maize under target environments. 2A: Estimate the maize grain metabolome. 2B: Estimate the relative impact of genetic versus environmental factors in determining the maize grain metabolome. Approach (from AD-416): We will examine genome-wide responses to plant transformation using next generation DNA sequencing. These changes will be compared with the degree of genetic variation within varieties that occurs due to genetic drift and also with genomic responses to tissue culture. This will help establish how plant genomes change in unexpected ways to transformation, which may contribute to unintended effects to crop composition and quality. We will also test how these genomic responses are mitigated through introgression into elite varieties, through both DNA sequence analysis, compositional analysis via mass spectrometry and agronomic evaluation. In parallel, we will continue our characterization of the genetic and environmental factors that control the maize grain metabolome that was initiated at the end of the previous project cycle. We will use ultra performance liquid chromatography with a range of chemistries to interrogate the grain metabolome more thoroughly. We will also expand the number of varieties, the number of environments, and compare public sector germplasm to that used in the private sector. In addition to the survey-style questions, we will test specific gene/trait associations to potentially identify new traits for maize grain improvement. Lead Scientist is no longer employed by ARS as of January 3, 2014. No research was conducted as the new project had recently started when Lead Scientist left ARS and the position has not yet been refilled.
Impacts
(N/A)
Publications
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