Progress 07/10/13 to 06/30/18
Outputs
Target Audience:Our project aims to provide science-based information to cause a change in knowledge related to the genetics of crop plants. The research is relevant to plant geneticists, plant breeders, seed and biotechnology companies, and federal regulators overseeing biotechnology risk assessment. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project has provided training opportunities for postdoctoral scholars Dr. Li Lei, Dr. Marisa Miller, and Dr. Emily Dittmar. Dr. Maria Fernanda Rodriguez also worked closely with our research group. The project has contributed to the training of one current graduate student and two graduate students who graduated recently. A second-year student, Chaochih Liu has already contributed to five publications that are published or in preprint form. Drs. Ana Poets nee Gonzales and Dr. Thomas Kono (now both working in biocomputing at the University of Minnesota) have completed their PhDs, but continue to contribute to publications in the lab. The project has also trained nine undergraduate students during the reporting period, Abby Proulx, Connor Depies, Corey Carter, Emily Vonderharr, Erica Sun, Malik Samuel, and Skylar Wyant. Seven of the students remain active in the lab. All of the students that have been actively involved in publishable research. For example, Skylar Wyant has contributed to one manuscript in review and is an active contributor to two other projects. How have the results been disseminated to communities of interest?The primary means of dissemination of results has been through publication in professional journals. Multiple members of the lab have also given professional talks. This has included a series of talks. The talks include: Morrell PL (2018) Barley landrace environmental association. Plant & Animal Genome Conference XXVI - Triticeae Genetics and Genomics; Session 3. San Diego, CA. Morrell PL (2018) Deleterious variants and the genetic cost of domestication. Plant & Animal Genome Conference XXVI - Domestication Genomics. San Diego, CA. Morrell PL (2018) New Faculty Forum - speaker and panelist. Genetics Society of America Population, Evolutionary and Quantitative Genetics Conference. Madison, WI. Morrell PL, Stupar RM, Jackson SA, Parrott WA (2018) Comparison of the mutations rates in soybean following transformation, mutagenesis, tissue culture, and conventional breeding. Annual BRAG Project Director's Meeting. Riverdale, MD. Liu C, Lei L, Shao M, Samuels M, Franckowiak J, Steffenson BJ, Morrell PL (2018) Phenotypically wild barley plants show evidence of extensive introgression from cultivated barley. 5th Midwest Population Genetics Meeting. St. Paul, MN. Li L, Poets AM, Liu C, Wyant SR, Hoffman PJ, Carter CK, Trantow RM, Shaw BG, Li X, Muehlbauer GJ, Katagiri F, Morrell PL (2018) Discovery of barley gene candidates for low temperature and drought tolerance via environmental association approaches. 5th Midwest Population Genetics Meeting. St. Paul, MN. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
A paper supporting the BAD_Mutations https://github.com/MorrellLAB/BAD_Mutations deleterious variant annotation tool has been published. The paper reports a set of 2,910 phenotype-changing variants in Arabidopsis thaliana that can be used to train variant annotation tools. Panels of known variants have been widely used to train variant annotation for personalized genomics in humans, but this is the first training panel for plant genomics. We completed analysis of the fate of deleterious variants in a large genomic prediction population in barley. We were able to track the fate of the variants over three breeding cycles or ten generations. As we note below, the number of deleterious variants is closely tied to the productivity of individual inbred lines. This manuscript is available on bioRxiv and in review at Genetics. In collaboration with Dr. Daniel Koenig at University of California, Riverside, we have produce whole genome resequencing data for a species related to cultivated barley, Hordeum murinum ssp. glaucum. The data was aligned to the current barley reference genome so that it could be used as an outgroup taxon to infer the ancestral state of variants identified in barley. Inference of ancestral state has many applications in genomics and population genetics, but is particularly important in determining which nucleotide state is likely deleterious. The genome sequence is included in the manuscript noted above. We used 10X Genomics linked reads to create a whole genome assembly for wild barley, the progenitor of the cultivated species. The genome assembly is being used to identify large structural variants that impact estimates of the distribution of deleterious variants. The assembly will be improved with the addition of Nanopore whole genome sequencing reads and can then be used to improve reference-based read mapping in wild barley. The genome sequence is reported in a manuscript in preparation that examines the mutational load of deleterious variants in wild barley. A manuscript reporting this work is being prepared. We have resequenced the genomes of 126 soybean lines. This included 10X Genomics linked-reads for six lines. We are currently characterized the nature and context of mutations in those lines.
Publications
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Progress 10/01/16 to 09/30/17
Outputs
Target Audience: Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project has provided training opportunities for postdoctoral scholars Dr. Li Lei and Dr. Marisa Miller. Dr. Maria Fernanda Rodriguez also worked closely with our research group. The project has contributed to the training of five graduate students. A first-year student, Chaochih Liu has already contributed to three publications and she is an active contributor on three more manuscripts currently in preparation. Drs. Ana Poets nee Gonzales and Dr. Thomas Kono (now both working in biocomputing at the University of Minnesota) have completed their PhDs, but continue to contribute to publications in the lab. Graduate students Shawn Goggins and Colin Pierce have now completed their programs of study with our group; Mr. Pierce is now a PhD student in biochemistry at the University of Minnesota. The project has also trained nine undergraduate students during the reporting period, Abby Proulx, Connor Depies, Corey Carter, Emily Vonderharr, Erica Sun, Malik Samuel, and Skylar Wyant. Seven of the students remain active in the lab. All of the students that have been actively involved in publishable research. For example, Paul Hoffman (now working in biocomputing at New York Genome Center) contributed to two publications and has a role in two more pending publications. How have the results been disseminated to communities of interest?The primary means of dissemination of results has been through publication in professional journals. In the reporting period this has included the Journal of Heredity and Molecular Biology & Evolution. In the past year, we also contributed to a book chapter on food security in the United States. This chapter is a portion of a multi-national book designed to inform policy makers on food security issues in the Western Hemisphere. The majority of participants in the project have also given oral or poster presentations, including at the annual meeting of the Society for Study of Evolution. Other talks have included two departmental seminars, a talk to federal regulators of biotechnology, and a lightening talk to National Science Foundation awardees regarding software developed in the lab. What do you plan to do during the next reporting period to accomplish the goals?We have funding from multiple sources (NSF, USDA NIFA) that will permit collection of original DNA resequencing data and will fund students and postdocs to contribute to all of the goals outlined. There is ongoing research or manuscripts in draft form that will address Goal 1: Assess the role of deleterious variants, Goal 2: Environmental association, Goal 3: Assess admixture based approaches, and Goal 4: Factors contributing to linkage disequilibrium. Goal 5: Computational biology support, primarily involves interaction with other lab groups and this effort continues on an ongoing and active basis.
Impacts
What was accomplished under these goals?
Five changes in knowledge occurred because of this research. First, related to Goals 1 and 5, we worked with collaborators to identify 2,910 Arabidopsis thaliana phenotype changing amino acid variants. These constitute a validation data set for testing tools and algorithm for deleterious variant annotation in plants. This work will be presented in a manuscript currently in preparation. This is important because variant annotation is a path to accelerate plant breeding through more targeted selection. For Goal 2, we have previously reported environmental association studies in teosinte (the progenitor of maize), wild barley, and wild soybeans. We are extending these same approaches to barley landraces (primitive cultivars) and a manuscript reporting this analysis is near completion. For Goal 3 related to admixture analyses, we are using identity by state-based comparisons to identify genomic regions in wild barley that are subject to introgression from cultivated barley. Because the wild barley accessions maintain wild phenotypes, this analysis has the potential to identify loci that are key to domestication. For Goal 4 on linkage disequilibrium (LD), we are nearing completion of a manuscript reporting the impact of structural variants (inversions, which generate extended LD) on mutational load in wild barley. This work provides a baseline for understanding factors that contribute to mutational load and the cost of domestication in cultigens. For Goal 5, we have continued to refine a DNA sequence handling pipeline (sequence_handling) that greatly accelerates the processing of large amounts of Illumina resequencing and whole genome data. This is available at: https://github.com/MorrellLAB/sequence_handling. In the reporting period, this including an extension of the pipeline to include variant detection (SNP calling) and to incorporate linked reads from the 10X Genomics platform.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Moyers BT, Morrell PL, McKay JK (2017) Genetic costs of domestication and improvement. Journal of Heredity
- Type:
Book Chapters
Status:
Published
Year Published:
2017
Citation:
Allen MF, Morrell PL, Rice CW, Vaux HJ, Dahm CN, Hernandez RR (2017). Food and nutrition security in the United States of America. Challenges and opportunities for this century. InterAmerican Network of Academies of Science (IANAS).
- Type:
Journal Articles
Status:
Under Review
Year Published:
2017
Citation:
Kono TJY, Lei L, Shih C, Hoffman PJ, Morrell PL, Fay JC (preprint). Comparative genomics approaches accurately predict deleterious variants in plants. BioRxiv.
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Plant genetics and genomics researchers, geneticists and breeders; weed scientists, evolutionary biologists, population geneticists. Users and producers of barley, maize, wheat, and soybeans. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project has provided training opportunities for a postdoctoral scholar, Dr. Li Lei and for four graduate students. Two of the graduate students produced published work within the reporting period. This includes Dr. Ana Poets nee Gonzales and Dr. Thomas Kono (now postdocs at the University of Minnesota), Shawn Goggins, and Colin Pierce. The project has also trained six undergraduate students, Connor Depies, Corey Carter, Paul Hoffman, Richard Trantow, Erica Sun, and Skylar Wyant. All of the students that have been actively involved in publishable research, with students Paul Hoffman and former undergraduate Chaochih Liu contributing to multiple publications. How have the results been disseminated to communities of interest?The primary means of dissemination of results has been through publication in professional journals. Most of the publications are in journals with a primary focus on genetics and genomics, specifically G3: Genes Genomes Genetics, Genetics, Molecular Biology & Evolution, and Nature Plants. The majority of participants in the project have also given oral or poster presentations, including at the International Barley Genetics Symposium in Minneapolis in 2016. What do you plan to do during the next reporting period to accomplish the goals?We have secured funding from multiple sources (NSF, USDA NIFA) that will permit collection of original DNA resequencing data and will fund students and postdocs to contribute to all of the goals outlined. There is ongoing research or manuscripts in draft form that will address Goal 1: Assess the role of deleterious variants, Goal 2: Environment association, Goal 3: Assess admixture based approaches, and Goal 4: Factors contributing to linkage disequilibrium. Goal 5: Computational biology support, primarily involves interaction with other lab groups and this effort continues on an ongoing and active basis.
Impacts
What was accomplished under these goals?
Five changes in knowledge occurred because of this research. First, related to Goal 1 and 5, we have tested the software we developed for annotation of deleterious variants against a set of known phenotype-changing variants and found it to be more accurate for methods of annotation of variants in plants. This work will be presented in a manuscript currently in preparation. Accurate annotation provides the potential to change plant breeding to incorporate selection against deleterious variants. For Goal 2, we are identifying the genomic position of both previously published genes and associations in our analysis. This should result in one of the first studies to integrate genomic physical position information with trait data. For Goal 3 related to admixture analyses, we published a detailed paper on barley breeding history in the journal G3. For Goal 4, we are working on two manuscript related to historical recombination and the impact of structural variants on linkage disequilibrium. For Goal 5, we created a DNA sequence handling pipeline (sequence_handling) that greatly accelerates the processing of large amounts of data. This is available at: https://github.com/MorrellLAB/sequence_handling.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Poets, A. M., Mohammadi, M., Seth, K., Wang, H., Kono, T. J., Fang, Z. et al. (2015). The effects of both recent and long-term selection and genetic drift are readily evident in North American barley breeding populations. G3, 6(3), 609-622.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Durvasula, A., Kent, T. V., Hoffman, P. J., Liu, C., Kono, T. J. Y., Morrell, P. L. et al. (2016). ANGSD-wrapper: utilities for analyzing next generation sequencing data. Molecular Ecology Resources, 16(6), 1449-1454.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Fang, Z., & Morrell, P. L. (2016). Domestication: Polyploidy boosts domestication. Nature Plants, 2, 16116.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Anderson, J. E., Kono, T. J., Stupar, R. M., Kantar, M. B., & Morrell, P. L. (2016). Environmental association analyses identify candidates for abiotic stress tolerance in Glycine soja, the wild progenitor of cultivated soybeans. G3, 6(4), 835-843.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Kono, T. J. Y., Fu, F., Mohammadi, M., Hoffman, P. J., Liu, C., Stupar, R. M. et al. (2016). The role of deleterious substitutions in crop genomes. Molecular Biology and Evolution, 33(9), 2307-2317.
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2017
Citation:
Liu, Q., Zhou, Y., Morrell, P. L., & Gaut, B. S. (2017). Deleterious variants in Asian rice and the potential cost of domestication. Molecular Biology & Evolution.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Nice, L. M., Steffenson, B. J., Brown-Guedira, G. L., Akhunov, E. D., Liu, C., Kono, T. J. et al. (2016). Development and genetic characterization of an advanced backcross-nested association mapping (AB-NAM) population of wild � cultivated barley. Genetics, 203(3), 1453-1467.
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Progress 10/01/14 to 09/30/15
Outputs
Target Audience:Plant genetics and genomics researchers, geneticists and breeders; weed scientists, evolutionary biologists, population geneticists. Users and producers of barley, maize, wheat, and soybeans. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project has provided training opportunities for three graduate students, all of whom have published work within the reporting period. This includes Dr. Ana Poets nee Gonzales (now and postdoc at the University of Minnesota, Thomas Kono, and Shawn Goggins. The project has also trained four undergraduate students, Ashley Rozmarin, Chaochih Liu, Paul Hoffman, and Skylar Wyant. All of the students that have been in the have also presented their work at professional meetings in the form of posters or oral presentations. How have the results been disseminated to communities of interest?The primary means of dissemination of results has been through publication in professional journals. Most of the publications are in journals with a primary focus on genetics and genomics, specifically G3: Genes Genomes Genetics, Trends in Genetics, and Genome Biology. All participants in the project have also given oral or poster presentations. What do you plan to do during the next reporting period to accomplish the goals?We have secured funding from multiple sources (NSF, USDA NIFA) that will permit collection of original DNA resequencing data and will fund students and postdocs to contribute to all of the goals outlined. There is ongoing research or manuscripts in draft form that will address Goal 1: Assess the role of deleterious variants, Goal 2: Environment association, Goal 3: Assess admixture based approaches, and Goal 4: Factors contributing to linkage disequilibrium. Goal 5: Computational biology support, primarily involves interaction with other lab groups and this effort continues on an ongoing and active basis.
Impacts
What was accomplished under these goals?
Three real changes in knowledge occurred because of this research. First, related to Goal 1, we found that every inbred line of crop we surveyed contains many deleterious mutations, on the order of 1,000 to 1,500 per barley inbred line. This provides the potential to change plant breeding to incorporate selection against deleterious mutations. Second, with regard to Goals 2 and 4, we found that environmental association approaches being applied by evolutionary biologist are quite useful for identifying variants associated with precipitation and temperature variables in crop relatives. However, we note that in accord with previous theory, the most significant variants associated with climatic adaptation are associated with chromosomal structural variation, particularly chromosomal inversions. This relates to Goal 4 because it results in large domains of linkage disequilibrium where recombination is limited. Finally, with regard to Goal 3, assessing admixture, we found that cultivated barley appears to have mosaic ancestry with genetic contributions evident from proximate wild populations, consistent with adaptive contributions from wild populations. All of this work is either published or to be reported in forthcoming manuscripts and all of these areas will be explored in greater detail by our ongoing research.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Poets AM, Fang Z, Clegg MT, Morrell PL 2015. Barley landraces are characterized by geographically heterogeneous genomic origins. Genome Biol 16: 173.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
He SL, Yang Y, Morrell PL, Yi TS 2015. Nucleotide sequence diversity and linkage disequilibrium of four nuclear loci in foxtail millet (Setaria italica). PLoS One 10: e0137088.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Gaut BS, Diez CM, Morrell PL (2015) Genomics and the contrasting dynamics of annual and perennial domestication. Trends in Genetics 31:709-719.
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Progress 10/01/13 to 09/30/14
Outputs
Target Audience: Plant genetics and genomics researchers, geneticists and breeders; weed scientists, evolutionary biologists, population geneticists. Users and producers of barley, maize, wheat, and soybeans. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? The project has provided training opportunities for three graduate students, all of whom have published work within the reporting period. This includes Dr. Zhou Fang (now a postdoctoral scholar at North Carolina State University), Ana Poets nee Gonzales, and Thomas Kono. The project has also trained three undergraduate students, Ashley Rozmarin, Chaochih Liu, and Yancy Ribbens. All of the graduate students have also presented their work at professional meetings in the form of posters or oral presentations. How have the results been disseminated to communities of interest? The primary means of dissemination of results has been through publication in professional journals. Most of the publications are in journals with a primary focus on genetics, specifically G3: Genes Genomes Genetics and Journal of Heredity. All participants in the project have also given oral or poster presentations. What do you plan to do during the next reporting period to accomplish the goals? We have secured funding from multiple sources (NSF, USDA NIFA, Minnesota Agricultural Experiment Station etc.) that will permit collection of original DNA resequencing data and will fund students and postdocs to contribute to all of the goals outlined. There is ongoing research or manuscripts in draft form that will address Goal 1: Assess the role of deleterious variants, Goal 2: Environment association, Goal 3: Assess admixture based approaches, and Goal 4: Factors contributing to linkage disequilibrium. Goal 5: Computational biology support, primarily involves interaction with other lab groups and this effort continues on an ongoing and active basis.
Impacts
What was accomplished under these goals?
Three real changes in knowledge occurred because of this research. First, related to Goal 1, we found that every inbred line of crop we surveyed contains many deleterious mutations, on the order of 2,000 per barley inbred line. This provides the potential to change plant breeding to incorporate selection against deleterious mutations. Second, with regard to Goals 2 and 4, we found that environmental association approaches being applied by evolutionary biologist are quite useful for identifying variants associated with precipitation and temperature variables in crop relatives. However, we note that in accord with previous theory, the most significant variants associated with climatic adaptation are associated with chromosomal structural variation, particularly chromosomal inversions. This relates to Goal 4 because it results in large domains of linkage disequilibrium where recombination is limited. Finally, with regard to Goal 3, assessing admixture, we found that cultivated barley appears to have mosaic ancestry with genetic contributions evident from proximate wild populations, consistent with adaptive contributions from wild populations. All of this work is either published or to be reported in forthcoming manuscripts and all of these areas will be explored in greater detail by our ongoing research.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Fang Z, Gonzales AM, Clegg MT, Muehlbauer GJ, Smith KP, Steffenson BJ, Morrell PL (2014) Two genomic regions contribute disproportionately to geographic differentiation in wild barley. G3 4: 1193-1203.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Morrell PL, Gonzales AM, Meyer KK, Clegg MT (2014) Resequencing data indicate a modest effect of domestication on diversity in barley: a cultigen with multiple origins. J Hered 105: 253-264.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
McCoy AM, Schaefer R, Petersen JL, Morrell PL, Slamka MA, Mickelson JR, Valberg SJ, McCue ME (2014) Evidence of positive selection for a glycogen synthase (GYS1) mutation in domestic horse populations. J Hered 105: 163-172.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Kono TJ, Seth K, Poland JA, Morrell PL (2014) SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Mol Ecol Resour 14: 419-425.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Kantar MB, Betts K, Michno J-MS, Luby JJ, Morrell PL, Hulke BS, Stupar RM, Wyse DL (2014) Evaluating an interspecific Helianthus annuus x Helianthus tuberosus population for use in a perennial sunflower breeding program. Field Crops Research 155: 254-264.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Fang Z, Eule-Nashoba A, Powers C, Kono TY, Morrell PL, Smith KP (2013) Comparative analyses identify the contributions of exotic donors to disease resistance in a barley experimental population. G3 3: 1945-1953.
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Progress 07/10/13 to 09/30/13
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
This is a new project.
Publications
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