Progress 01/01/10 to 09/30/14
Outputs
Target Audience: Work on this project has resulted in a number of formal collaborations including public breeders (Rita Mumm, formerly at Illinois) and industry (Dupont Pioneer). We have given more than 35 invited seminars discussing the research resulting from this project over the course of this project, including talks to industry (Seminis, Dupont, BASF), public breeders (Illinois corn breeders school, USDA, North Central Regional Corn Breeding Research Meeting), and international audiences (National Maize Improvement Center in Beijing, conferences in France and Canada, invited research seminars in Canada and Mexico). These invitations speak to the broad interest in both public and private sector in applying population genetic methods to increasingly large genomic datasets to identify loci of interest in breeding populations. We have also reached other researchers in genetics/genomics via publications, presentations, social media, and providing data and software available online. A number of the software tools developed during this time period have been used (and cited) by other labs. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Nine postdoctoral scholars have worked on various aspects of this project. Of these, 4 are currently a postdoc and the other 5 have successful careers as professors (3), in non-governmental organizations focusing on agriculture (1) or in the agriculture industry (1). Seventeen undergraduate students have worked on aspects of this project, including several from under-represented groups. At least five of them are now in graduate school and two more have successful technical careers. How have the results been disseminated to communities of interest? In addition to our presentations at research universities and companies, I have begun in this last year a twitter presence to disseminate information about our work more broadly. This has already had tremendous impact both on our research (two new students, new research collaborations), but also an impact on the reach of our research output. For example, statistics from sumall.com suggest this twitter account has had a mention reach (number of users who have had the opportunity to see the account mentioned) of more than 500,000 users, and a retweet reach (number of users who have had the opportunity to see our messages resent by others) of more than 2 million users. Finally, we have begun to make our presentations publicly availably via slideshare (http://www.slideshare.net/jrossibarra/presentations), and these presentations have been viewed, to date, approximately than 4,000 times. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
We have characterized the adaptation of maize to highland environments, discovering that maize has used multiple molecular routes to achieve adaptation to colder temperatures and that most of this came from standing genetic variation. This suggests that the wider pool of maize landraces likely contains substantial variation which breeders could use to adapt maize to future climate changes. We identified important candidate loci selected during maize domestication and modern breeding. Not only has this lead to an improved understanding of the genetic architecture and process of maize breeding, but identifying these loci provides useful information to breeders in terms of prediction. We have shown that deleterious variants are important determinants of heterosis, and ongoing work suggests understanding that evolutionary history of different sites in the genome provides predictive power for maize yield. We have used genetic data to uncover histories of maize movement and gene flow between maize and teosinte, helping identify the origin of maize in the SW US and the genetic center of maize domestication. We have shown the role of transposable elements in generating novel diversity via impacts on gene expression, genome rearrangement, and novel functional alleles.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Pyhajarvi T, Hufford MB, Mezmouk S, Ross-Ibarra J (2013) Complex patterns of local adaptation in teosinte. Genome Biology and Evolution 5:1594-1609
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Wills DM, Whipple C, Takuno S, Kursela LE, Shannon LM, Ross-Ibarra J, Doebley JF (2013) From many, one: genetic control of prolificacy during maize domestication. PLoS Genetics 9(6): e1003604.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Hufford MB, Lubinsky P, Pyhajarvi T, Devengenzo MT, Ellstrand NC, Ross-Ibarra J (2013) The genomic signature of crop-wild introgression in maize. PLoS Genetics 9(5): e1003477
- Type:
Journal Articles
Status:
Under Review
Year Published:
2014
Citation:
Gerke JP, Edwards JW, Guill KE, Ross-Ibarra J, McMullen MD. The genomic response to 50 years of selection in maize.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2015
Citation:
Takuno S, Ralph P, Mezmouk S, Swarts K, Elshire RJ, Glaubitz JC, Buckler ES, Hufford MB, and Ross-Ibarra J. The molecular basis of parallel adaptation to highland climate in domesticated maize.
- Type:
Journal Articles
Status:
Published
Year Published:
2011
Citation:
Hufford MB, Gepts P, Ross-Ibarra J (2011) Influence of cryptic population structure on observed mating patterns in the wild progenitor of maize (Zea mays ssp. parviglumis). Molecular Ecology 20: 46-55
- Type:
Journal Articles
Status:
Published
Year Published:
2012
Citation:
Hufford MB, Xun X, van Heerwaarden J, Pyhajarvi T, Chia J-M, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler S, Lai J, Morrell PL, Shannon LM, Song C, Spinger NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J (2012) Comparative population genomics of maize domestication and improvement. Nature Genetics 44:808-811
- Type:
Journal Articles
Status:
Published
Year Published:
2012
Citation:
van Heerwaarden J, Hufford MB, Ross-Ibarra J (2012) Historical genomics of North American maize. PNAS 109: 12420-12425
- Type:
Journal Articles
Status:
Published
Year Published:
2012
Citation:
Cook JP, McMullen MD, Holland JB, Tian F, Bradbury P, Ross-Ibarra J, Buckler ES, Flint-Garcia SA (2012) Genetic architecture of maize kernel composition in the Nested Association Mapping and Inbred Association panels. Plant Physiology 158: 824-834
- Type:
Journal Articles
Status:
Published
Year Published:
2012
Citation:
Chia J-M, Song C, Bradbury P, Costich D, de Leon N, Doebley JC, Elshire RJ, Gaut BS, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna BM, Pyh�j�rvi T, Rong T, Sekhon RS, Sun Q, Tenaillon M, Tian F, Wang J, Xu X, Zhang Z, Kaeppler S, Ross-Ibarra J, McMullen M, Buckler ES, Zhang G, Xu Y, Ware, D (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics 44:803-807
- Type:
Journal Articles
Status:
Published
Year Published:
2012
Citation:
Morrell PL, Buckler ES, Ross-Ibarra J (2012) Crop genomics: advances and applications. Nature Reviews Genetics 13:85-96
- Type:
Journal Articles
Status:
Published
Year Published:
2011
Citation:
van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, Sanchez Gonzalez JJ, Ross-Ibarra J (2011) Genetic signals of origin, spread and introgression in a large sample of maize landraces. PNAS 108: 1088-1092
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Mezmouk S, Ross-Ibarra J (2014) The pattern and distribution of deleterious mutations in maize. G3 4:163-171
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Makarevitch I, Waters M, West P, Stitzer M, Ross-Ibarra J, Springer NM (2015) Mobile elements contribute to activation of genes in response to abiotic stress. PLoS Genetics 11(1): e1004915
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Waters AJ, Bilinski P, Eichten SR, Vaugh MW, Ross-Ibarra J, Gehring M, Springer NM (2013) Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species. PNAS 110:19639-19644
- Type:
Journal Articles
Status:
Published
Year Published:
2012
Citation:
Hufford MB, Bilinski P, Pyhajarvi T, Ross-Ibarra J (2012) Teosinte as a model system for population and ecological genomics. Trends in Genetics 12: 606-615
- Type:
Journal Articles
Status:
Published
Year Published:
2012
Citation:
Fang Z, Pyhajarvi T, Weber AL, Dawe RK, Glaubitz JC, Sianchez Gonzalez J, Ross-Ibarra C, Doebley J, Morrell PL, Ross-Ibarra J (2012) Megabase-scale inversion polymorphism in the wild ancestor of maize. Genetics 191:883-894
- Type:
Journal Articles
Status:
Published
Year Published:
2011
Citation:
Studer A, Zhao Q, Ross-Ibarra J, Doebley J (2011) Identification of a functional transposon insertion in the maize domestication gene tb1. Nature Genetics 43:1160-1163
- Type:
Journal Articles
Status:
Published
Year Published:
2010
Citation:
van Heerwaarden J, van Eeuwijk FA, Ross-Ibarra J (2010) Genetic diversity in a crop metapopulation. Heredity 104: 28-39
|
Progress 01/01/13 to 09/30/13
Outputs
Target Audience: Continued work on this project has resulted in a collaboration with a retired breeder from Dupont Pioneer to develop pedigree methods for assessing selection during maize breeding. We are working on developing a formal collaboration with researchers at Dupont Pioneer on this project as well. We gave more than 10 presentations on maize diversity and genomic approaches to understanding diversity, including organizing and speaking at the opening Major Symposium of the American Society of Plant Biologists, and as a plenary speaker to the Canadian Plant Genomics meeting. These invitations speak to the broad interest in both public and private sector in applying population genetic methods to increasingly large genomic datasets to identify loci of interest in breeding populations. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? As part of continued work exploring maize diversity, we now have 7 undergraduate students (including 1 female and 4 minority students) working on projects related to understanding maize diversity. In particular, I have put together a team of 4 undergraduate students to work on understanding the role of centromeres in patterning diversity across the USDA maize germplasm collection. In addition to undergraduate students, 1 new graduate student (in addition to 3 current students and 1 postdoc) will be working on this project. During this time period, former postdoc Shohei Takuno was offered and began an Assistant Professorship in his home institution in Japan, and current postdoc Sofiane Mezmouk was offered (and accepted) a research geneticist position at a prominent seed company, strongly suggesting that the training postdoctoral scholars have received has had a beneficial impact on their careers. How have the results been disseminated to communities of interest? In addition to our presentations at research universities and companies, I have begun in this last year a twitter presence to disseminate information about our work more broadly. This has already had tremendous impact both on our research (two new students, new research collaborations), but also an impact on the reach of our research output. For example, statistics from sumall.com suggest this twitter account has had a mention reach (number of users who have had the opportunity to see the account mentioned) of 485,000 users, and a retweet reach (number of users who have had the opportunity to see our messages resent by others) of more than 2.2 million users. Finally, we have begun to make our presentations publicly availably via slideshare (http://www.slideshare.net/jrossibarra/presentations), and these presentations have been viewed, to date, more than 1,200 times. What do you plan to do during the next reporting period to accomplish the goals? We are revisiting our earlier analysis of maize inbred diversity, now with increased genetic resolution and, thanks to partnership with current and former researchers in industry, information on pedigree. We will also finish our initial investigation of the genetic basis of highland adaptation, and being our in-depth look of genome-scale data from across the Americas.
Impacts
What was accomplished under these goals?
We have characterized adaptive diversity in the wild ancestors of maize (Pyhajarvi et al. 2013) and their contribution to maize adaptation to new environments thorugh gene flow (Hufford et al. 2013). These findings have led to a new research direction investigating whether landrace populations of maize have used similar genetic architectures to adapt to similar environmental challenges. We are submitting two grants this year as a result of this work, to investigate the genetic architecture of maize adaptation to high altitude, and to understand the broader role of teosinte introgression in maize evolution.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Pyhajarvi T, Hufford MB, Mezmouk S, Ross-Ibarra J (2013) Complex patterns of local adaptation in teosinte. Genome Biology and Evolution 5:1594-1609
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Wills DM, Whipple C, Takuno S, Kursela LE, Shannon LM, Ross-Ibarra J, Doebley JF (2013) From many, one: genetic control of prolificacy during maize domestication]. PLoS Genetics 9(6): e1003604.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Hufford MB, Lubinsky P, Pyh�j�rvi T, Devengenzo MT, Ellstrand NC, Ross-Ibarra J (2013) The genomic signature of crop-wild introgression in maize. PLoS Genetics 9(5): e1003477
- Type:
Journal Articles
Status:
Under Review
Year Published:
2014
Citation:
Gerke JP, Edwards JW, Guill KE, {\bf Ross-Ibarra J}, McMullen MD. The genomic response to 50 years of selection in maize. In Review
|
Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: We have genotyped a chronological sample of 400 North American corn belt lines for 46,000 single nucleotide polymorphisms. We have used these data to identify genomic regions that have changed in frequency due to likely selection. We have also detailed ancestry relationships along the maize genome. These data result in a list of candidate loci that appear to have been of agronomic importance (but are still polymorphic in modern inbred breeding lines), as well as the ability to assign a genotypic breeding value to individual lines based on their genotype. In collaboration with Monsanto, we have performed a yield trial of a subset of these lines and are in the process of testing whether loci identified via population genetic processes are enriched in associations for yield. We have arranged a collaboration with Dr. Rita Mumm at the University of Illinois, which will allow us to test our candidate loci using an association analysis approach. Her data consist of hybrid yield trials of 12 inbred lines that we have genotyped. Additionally, we can make use of hybrid data from a large number of crosses performed using a maize association panel, for which we have genotype data for all lines. We are working with this data and another association panel to assess the role of deleterious alleles in hybrid vigor. Results have been disseminated via publications (see below) as well as oral presentations: Oral/ Poster Presentations (only 2012 shown): Maize Genetics Conference (8 posters, 1 oral presentation) (OR) 2012 Crop Wild Relative Genomics meeting (CA) 2012
 Germplasm Enhancement of Maize, ASTA Conference (IA) 2012 Pioneer Hi-Bred (CA) 2012
 Plenary Speaker, Coastwide Salmonid Genomics Conference (CA) 2012 
BASF Plant Science (NC) 2012 
Pioneer Hi-Bred (IA) 2012
 Illinois Corn Breeders School (IL) 2012
 Keynote Speaker, North Central Regional Corn Breeding Research Meeting (IL) 2012 
Plant and Animal Genome Conference, symposium on ecological genomics (CA) 2012 PARTICIPANTS: Dr. Shohei Takuno has started work on this project, investigating the role of parallel adaptation to high-elevation environments in Mexico and S. America to understand climate-related adaptation in maize. Dr. Sofiane Mezmouk has begun work on this project, using statistical and quantitative genomic approaches to identify deleterious mutations in the maize genome and predict their effect on phenotype. Matthew Hufford is a postdoctoral scholar who has developed the pipeline for germination, germplasm management, and DNA preparation. He has trained two undergraduates in laboratory methods, and has been learning computational methods for SNP analysis. He has led the analysis of 103 genomes of domesticated and wild maize to understand changes in selection during domestication and subsequent improvement (Hufford et al. 2012). As a result of his work on this grant, he has recently been offered a faculty position to continue his work on maize genetics at Iowa State University. Joost van Heerwaarden was a postdoctoral scholar who developed statistical approaches to correct for linkage (van Heerwaarden et al. 2010) and introgression (van Heewaarden et al 2011), and analyzed the chronological sampling of corn belt lines using a novel application of environmental association analysis (van Heerwaarden et al, 2012). Joost has left the laboratory for a research position at the University of Wageningen . Tanja Pyhajarvi is a postdoctoral scholar, funded on an independent fellowship, who has been working on several projects related to the grant, including analysis of candidate genes (Hufford et al. 2012) and association analysis of maize and teosinte genotypes with environmental variables and phenotypes (Pyhajarvi et al. submitted). She now has a research position at her home University in Oulu. Monsanto Corporation has graciously provided field space and labor to perform yield trials in order to ground truth our statistical analyses. A subset of the lines genotyped will be used in an association mapping study in collaboration with Sherry Flint-Garcia (USDA, Missouri) and Mike McMullen (USDA, Missouri). This collaboration has also enabled us to access additional samples beyond those initially planned for genotyping. We have been working to develop methods for analysis of large SNP datasets in collaboration with several labs, including John Doebley (U. Wisconsin), Ed Buckler (USDA, Cornell), and Doreen Ware (USDA, Cold Spring Harbor). TARGET AUDIENCES: s a result of presentations at the maize genetics conference in March, we were invited to participate in the Illinois Corn Breeders' school in March of 2012. Further work on the grant has led to presentations to the private-public collaborative GEM project at the ASTA meeting in Chicago, DuPont Pioneer at their headquarters in Iowa and their drought station in California, BASF Plant Sciences in North Carolina, the Plant and Animal Genome Conference symposium on translational genomics, and as the keynote speaker at the North Central Regional Corn Breeding Research Meeting in Illinois, the private-public UC Davis Seed Central group, and the Coastwide Salmonid Genomics Conference. These invitations speak to the broad interest in both public and private sector in applying population genetic methods to increasingly large genomic datasets to identify loci of interest in breeding populations. Of special note is the request from the Salmonid Genomics group, which highlights the broad appeal of these approaches to workers in other systems. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Publications describing the outcomes of this work are currently in preparation or have been published. We have identified lists of candidate agronomic loci, and projects are underway to evaluate these loci using association methods. We have used - for the first time to our knowledge - multiple probabilistic prediction methods to identify deleterious alleles and track their frequencies in breeding populations. Our work so far has led to the development of several novel statistical approaches, including use of environmental association methods to correct for population structure and estimate allele frequency change over time in a breeding program and an approach for evaluating potential agronomic value of a line based on genotypic data.
Publications
- Hufford M.B., Bilinski P., Pyhajarvi T., Ross-Ibarra J. 2012. Teosinte as a model system for population and ecological genomics. Trends in Genetics 12:606-615
- Fang, Z., T. Pyhajarvi, A.L. Weber, R.K. Dawe, J.C. Glaubitz, J. Sanchez Gonzalez, C. Ross-Ibarra, J. Doebley J, P.L. Morrell, J. Ross-Ibarra. 2012. Megabase-scale inversion polymorphism in the wild ancestor of maize. Genetics 191:883-894
- Hufford, M.B., X. Xun*, J. van Heerwaarden, T. Pyhajarvi, J-M. Chia, R.A. Cartwright, R.J. Elshire, J.C. Glaubitz, K.E. Guill, S. Kaeppler, J. Lai, P.L. Morrell, L.M. Shannon, C. Song, N.M. Springer, R.A. Swanson-Wagner, P. Tiffin, J. Wang, G. Zhang, J. Doebley, M.D. McMullen, D. Ware, E.S. Buckler, S. Yang, J. Ross-Ibarra. 2012. Comparative population genomics of maize domestication and improvement. Nature Genetics 44:808-811
- Chia, J-M, C. Song, P. Bradbury, D. Costich, N. de Leon, J.C. Doebley, R.J. Elshire, B.S. Gaut, L. Geller, J.C. Glaubitz, M. Gore, K.E. Guill, J. Holland, M.B. Hufford, J. Lai, M. Li, X. Liu, Y. Lu, R. McCombie, R. Nelson, J. Poland, B.M. Prasanna, T. Pyhajarvi , T. Rong, R.S. Sekhon, Q. Sun, M. Tenaillon, F. Tian, J. Wang, X. Xu, Z. Zhang, S. Kaeppler, J. Ross-Ibarra, M. McMullen, E.S. Buckler, G. Zhang, Y. Xu, D. Ware. 2012.
- Gerke JP, Edwards JW, Guill KE, (\bf Ross-Ibarra J), McMullen MD. 2012. The genomic response to 50 years of selection in maize. In Prep
- Swanson-Wagner R, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J, Myers CL, Tiffin P, Springer NM. Reshaping of the maize transcriptome by domestication. (2012) PNAS 109: 11878-11883
- van Heerwaarden, J., M.B. Hufford, J. Ross-Ibarra. 2012. Historical genomics of North American maize. PNAS 109: 12420-12425
|
Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: We have genotyped a chronological sample of 400 North American corn belt lines for 46,000 single nucleotide polymorphisms. We have used these data to identify genomic regions that have changed in frequency due to likely selection. We have also detailed ancestry relationships along the maize genome. These data result in a list of candidate loci that appear to have been of agronomic importance (but are still polymorphic in modern inbred breeding lines), as well as the ability to assign a genotypic breeding value to individual lines based on their genotype. We have arranged a collaboration with Dr. Rita Mumm at the University of Illinois, which will allow us to test our candidate loci using an association analysis approach. Her data consist of hybrid yield trials of 12 inbred lines that we have genotyped. Additionally, we can make use of hybrid data from a large number of crosses performed using a maize association panel, for which we have genotype data for all lines. Results have been disseminated via publications (see below) as well as oral presentations: Oral/ Poster Presentations (only 2011 shown): Hufford, M.B., ..22 authors ... Ross-Ibarra, J. Genome-wide effects of domestication and improvement in landraces and modern maize. Oral presentation at the Maize Genetics Conference, Chicago, 2011. Chia, J., ..10 authors.. Ross-Ibarra, J., McMullen, M.D., Buckler, E.S., and Ware, D. Maize HapMapV2 - Capturing variation in a genome in flux. Oral presentation at the Maize Genetics Conference, Chicago, 2011. Pyhajarvi, T., Hufford, M.B., and Ross-Ibarra, J. Genomic effects of local adapation in Zea mays ssp. parviglumis populations. Poster presentation at the Maize Genetics Conference, Chicago, 2011. van Heerwaarden, J, Hufford, M.B., and Ross-Ibarra, J. A genome-wide view of breeding history and selection in North American maize lines. Poster presentation at the Maize Genetics Conference, Chicago, 2011 Ross-Ibarra J. The domestication of maize: the where, the what, and the huh Oral presentation at the ASA/CSSA/SSSA Convention, symposium on maize biology, San Antonio, 2011 Ross-Ibarra J. The population genomics of maize domestication and improvement. Oral presentation to the Dept. of Plant & Microbial Biology, UC Berkeley, 2011 Hufford, M, Lubinsky, P., Pyhajarvi, T., Ellstrand, N, and Ross-Ibarra J. Dueling genomes: Reciprocal gene flow in hybrid swarms of maize and its wild relative, Zea mays ssp. mexicana. Oral presentation at the Society for the Study of Evolution conference, Oklahoma City, 2011 Pyhajarvi, T., Hufford, M, and Ross-Ibarra J. Genomic effects of local adaptation in the wild relatives of maize. Oral presentation at the Society for the Study of Evolution conference, Oklahoma City, 2011 PARTICIPANTS: As a result of presentations at the maize genetics conference in March, we have been invited to participate in the Illinois Corn Breeders' school in March of 2012 and as the plenary speaker of the public Corn Breeder's research conference a few weeks later. This will allow us to present our results and methods to a wider audience including both public and private breeders. TARGET AUDIENCES: Three postdoctoral scholars and one undergraduate technician worked on this project during this reporting period. Dr. Mathew Hufford oversaw the design and implementation of the sample preparation pipeline, training the undergraduate intern Lauren Sagara in the process. Together, they processed and genotyped >400 samples that will be used for the project. Dr. Joost van Heerwaarden worked on developing statistical tools for the analysis of SNP data and oversaw the selection of samples for the analysis. Lauren Sagara was an undergraduate student who has been trained in a number of laboratory techniques including germination, DNA extraction and quantification and PCR. She has performed the majority of the DNA preparation for genotyping of the lines used for the grant. She has since graduated and is now working full time as lab manager in our laboratory. Matthew Hufford is a postdoctoral scholar who has developed the pipeline for germination, germplasm management, and DNA preparation. He has trained two undergraduates in laboratory methods, and has been learning computational methods for SNP analysis. He has led the analysis of 103 genomes of domesticated and wild maize to understand changes in selection during domestication and subsequent improvement (Hufford et al. Submitted). Joost van Heerwaarden was a postdoctoral scholar who developed statistical approaches to correct for linkage (van Heerwaarden et al. 2010) and introgression (van Heewaarden et al 2011), and analyzed the chronological sampling of corn belt lines using a novel application of environmental association analysis (van Heerwaarden et al, Submitted). Joost has left the laboratory for a position at the University of Wageningen . Tanja Pyhajarvi is a postdoctoral scholar, funded on an independent fellowship, who has been working on several projects related to the grant, including analysis of candidate genes (Hufford et al. Submitted) and association analysis of maize and teosinte genotypes with environmental variables and phenotypes (Pyhajarvi et al. In prep). A subset of the lines genotyped will be used in an association mapping study in collaboration with Sherry Flint-Garcia (USDA, Missouri) and Mike McMullen (USDA, Missouri). This collaboration has also enabled us to access additional samples beyond those initially planned for genotyping. We have been working to develop methods for analysis of large SNP datasets in collaboration with several labs, including John Doebley (U. Wisconsin), Ed Buckler (USDA, Cornell), and Doreen Ware (USDA, Cold Spring Harbor). PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Several publications describing the outcomes of this work are currently in preparation or have been submitted. We have identified lists of candidate agronomic loci, and projects are underway to evaluate these loci using association methods. Our work so far has led to the development of several novel statistical approaches, including use of environmental association methods to correct for population structure and estimate allele frequency change over time in a breeding program and an approach for evaluating potential agronomic value of a line based on genotypic data.
Publications
- Morrell PL, Buckler ES, Ross-Ibarra J. (2012) Crop genomics: advances and applications. Nature Reviews Genetics 13:85-96
- Cook, JP, McMullen JD, Holland JB, Tian F, Bradbury P, Ross-Ibarra J, Buckler ES, Flint-Garcia SA.(2011) Genetic architecture of maize kernel composition in the Nested Association Mapping and Inbred Association panels. Plant Physiology 158: 824-834
- Studer, A., Q. Zhao, J. Ross-Ibarra, J. Doebley. (2011). Identification of a functional transposon insertion in the maize domestication gene tb1. Nature Genetics 43:1160-1163
- Tenaillon, M.I., M.B. Hufford, B.S. Gaut, J. Ross-Ibarra. (2011). Genome size and TE content as determined by high-throughput sequencing in maize and Zea luxurians. Genome Biology and Evolution 3: 29-229
|
Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: We have identified candidate genes that show evidence of selection during maize domestication and during subsequent improvement. The statistical data resulting from our selection-mapping data is already being used to refine previous QTL analyses. Further work on these genes may validate many that could be of use to breeding. We have developed novel statistical methods that can be applied to SNP data in other plant taxa for performing selection mapping or analysis of population structure. Finally, we have completed genotyping more than 800 maize and teosinte lines for diversity analyses using the Illumina 55,000 SNP chip. Results have been disseminated via the following oral presentations: Ross-Ibarra, J. Population genetic approaches to studying maize: a haplotype map and a second look at maize origins. Invited seminar, USDA Agricultural Research Service, Ames, Iowa. 2010 Ross-Ibarra, J. Genome scans and transposable element evolution in maize. Invited seminar, Microbial and Plant Genomics Institute, U. Minnesota 2010 Ross-Ibarra, J. Evolutionary genomics of teosinte and maize. Invited seminar, Society for Molecular Biology and Evolution, "Plant Ecological Genomics" Symposium, Lyon, France 2010 Van Heerwaarden, J. A second look at the geographic origin of maize. Maize Genetics Conference, Riva del Garda, Italy 2010 PARTICIPANTS: Three postdoctoral scholars are being trained on using genomic and statistical tools to identify candidate genes: Matthew Hufford, Tanja Pyhajarvi, Joost van Heerwaarden One undergraduate technician has been trained in laboratory methods: Lauren Sagara, undergraduate technician In collaboration with Monsanto, Inc. we have developed a mapping population to test our candidate loci. The first yield trial of the population is being grown out this year. A subset of the lines genotyped will be used in an association mapping study in collaboration with Sherry Flint-Garcia (USDA, Missouri) and Mike McMullen (USDA, Missouri). This collaboration has also enabled us to access additional samples beyond those initially planned for genotyping. Additionally, we have developed methods for selection mapping and candidate gene identification using large SNP datasets in collaboration with several labs, including John Doebley (U. Wisconsin), Ed Buckler (USDA, Cornell), and Doreen Ware (USDA, Cold Spring Harbor). TARGET AUDIENCES: Presented a seminar on our work identifying candidate genes using selection-mapping methods to National Program leaders and others at NIFA headquarters in Washington, DC. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
We continue working on statistical methods, and publications describing the outcomes of this work are currently in preparation. Publications highlighting the novel findings regarding selection during domestication and improvement are also underway. Our initial focus statistically was on the description of population structure, as reflected in the publications that describe evidence of cryptic population structure and present methods to identify and correct for unknown population structure in populations. We have additionally shown how it is possible to make use of linked marker data from multiple genes to estimate population structure, correcting for the effects of linkage among markers. This latter development will be of use with EST or exome-sequencing approaches to study population structure in wild or cultivated populations.
Publications
- van Heerwaarden, J., J. Doebley, W.H. Briggs, J.C. Glaubitz, M.M. Goodman, J.J. Sanchez Gonzalez, and J. Ross-Ibarra. 2011. Genetic signals of origin, spread and introgression in a large sample of maize landraces. PNAS 108: 1088-1092
- Hufford, M.B., P. Gepts, and J. Ross-Ibarra. 2011. Influence of cryptic population structure on observed mating patterns in the wild progenitor of maize (Zea mays ssp. parviglumis). Molecular Ecology 20: 46-55
- van Heerwaarden, J., J. Ross-Ibarra, J. Doebley, J.C. Glaubitz, J. Sanchez Gonzalez, B.S. Gaut, and L.E. Eguiarte. 2010. Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis). Molecular Ecology 19: 1162-1173
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