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United States Department of Agriculture

Agricultural Research Service

Research Project: DISSECTING COMPLEX TRAITS IN MAIZE AND BIOFUEL GRASSES BY APPLYING GENOMICS, BIOINFORMATICS, AND GENETIC RESOURCES

Location: Plant, Soil and Nutrition Research

2011 Annual Report


1a.Objectives (from AD-416)
This project will develop a genetic platform to identify useful variation in a high throughput fashion, and then use this platform to identify those genes and alleles that control kernel quality and tolerance to abiotic stresses. Bioinformatic tools will be developed in conjunction with the above to allow for the rapid analysis of plant germplasm diversity. Although the direct application of these approaches will be in maize and biofuel grasses, many of these genetic, statistical, and bioinformatic approaches could have broad implications for both the plant and animal genetics community at large. Objective 1: Develop statistical, genetic, and genomic approaches for dissecting complex traits in crop plants. Objective 2: Identify key genes and natural allelic variation for improving abiotic stress tolerance, nitrogen use efficiency, nutritional quality, and biofuel potential for maize and related grasses. Objective 3: Development of bioinformatic tools to mine and present functional allelic variation.


1b.Approach (from AD-416)
This project will use the natural variation inherent in the maize and biofuel grass genomes for the dissection of complex traits and for the identification of superior alleles. Such discovery is important to the development of improved breeding strategies for maize, the number one production crop in the world. First, this project will develop genetic resources that allow for the rapid dissection of any complex trait to the gene level. These resources will involve the creation of germplasm, the genotyping of this germplasm, and the development of statistical analyses. Using this platform, the project will then dissect the quantitative traits of nutritional quality, nitrogen use, biofuel productivity, and aluminum tolerance. The identification of advantageous alleles could allow for marker-assisted improvement of maize’s nutrition profile for humans and animals, increased processing efficiency, lower fertilizer requirements, and better adaptation to acidic soils. Finally, this project will improve access to diversity data and analysis tools for plant breeders and geneticists. We will facilitate the use of these materials by creating analysis tools, user friendly websites, and breeder decision making tools.


3.Progress Report
Progress was made on three objectives, all of which fall under National Program 301. In support of component 1, Plant and Microbial Genetic Resource Management, we developed approaches to reduce the cost of genotyping by more than 10-fold. We have been successful at using next generation sequencers to accomplish this, which will radically change how we genotype the USDA-ARS germplasm collections and breeding populations. In the past year, we have genotyped nearly 10,000 maize lines. This includes all maize NAM and all maize inbreds lines at North Central Plant Introduction Center in Ames, Iowa. This directly addresses the national problem to Assess the Systematic Relationships and Genetic Diversity of Crop Genetic Resources.

In support of component 2, Crop Informatics, Genomics, and Genetic Analyses, the main problem is Genetic Analyses and Mapping of Important Traits. We have made progress in three areas:

In collaboration with ARS researchers at Cold Spring Harbor, NY and Columbia, MO, we have been developing the approaches to fully sequence the maize genome. This is especially complicated as nearly 70% of the genome in one maize variety is entirely different from another variety. Bioinformatic, genetic, and molecular approaches are being combined to solve this problem and increase our knowledge to 10 to 30-fold more regions of the maize genome. Overall, we have identified 55 million variants across maize and its wild relatives.

With the latest next generation sequencing technology, we currently have knowledge of 55 million variable regions in the maize genome. Relating this molecular variation to trait variation is a substantial challenge. We have been successful at combining powerful genetic designs, statistical models, and high throughput biochemical assays (with collaborators) to dissect aspect of nitrogen, carbon, and tocopherol metabolism. We have identified a key set of genes controlling leaf central carbon and nitrogen metabolism in the adult leaf. Additionally, we have identified dozens of genes involved in tocopherol content in contrast to previous studies that have identified just a couple.

In collaboration with ARS researchers in Ames, IA, Columbia, MO, and Raleigh, NC, and university researchers at Purdue and the University of Nebraska, we are evaluating basic growth traits and yield for the nearly 3,000 maize lines and hybrids in the USDA Plant Introduction Station and Stock Center. Together these studies will help pinpoint the genes controlling basic developmental traits, and provide a perspective on the useful genetic variation in the germplasm collection. Additionally, we will make progress in evaluating how a broad spectrum of maize diversity contributes to yield with yield trials in six locations across the US. This will allow specific hypothesis on hybrid vigor to be tested.


4.Accomplishments
1. Identified genes controlling leaf architecture. Maize field increases in the last half century in the US have largely been the product of breeding maize lines that maintain high yield at very high plant densities. The angle and size of leaves are key aspect of this adaptation to high density, but little was known about what genes control the natural variation. In the first maize genome wide association study using the diverse germplasm from around the world, ARS researchers at the Robert W. Holley Center at Ithaca, NY, identified a number of key genes controlling leaf architecture by combing novel germplasm, statistics, genomics, and field trials. The current goal of maize breeding is to develop models that can predict key field traits using molecular markers, so that all breeding can be accelerated and useful genetic diversity can be combined. This study helps accurately predict the leaf architecture, which is required to combine maize diversity from the tropics with good environmental and disease resistance and high-density varieties in the US.

2. Unraveled the pedigree of the world’s grape varieties. The USDA National Plant Germplasm System holds the diversity of thousands of critical species to global agriculture. In this study, ARS researchers at the Robert W. Holley Center at Ithaca, NY, characterized the entire USDA grape collection using the latest genomic tools, which provided 100-fold more detailed view than ever before for this important fruit crop. This study showed that our elite grape varieties have tremendous diversity, but there have been almost no new varieties or cross made among the wine grape in the last several centuries. The consequences of this lack of breeding of wine grapes is that the wine grape is currently susceptible to numerous pathogens and now requires tremendous chemical inputs to keep pathogens at bay. This study suggests a genomics enabled grape breeding program would likely be extremely successful in creating sustainable grapes given all the untapped diversity.


Review Publications
Kump, K., Bradbury, P., Buckler IV, E.S., Belcher, A., Oropeza-Rosas, M., Wisser, R., Zwonitzer, J., Kresovich, S., McMullen, M.D., Ware, D., Balint Kurti, P.J., Holland, J.B. 2011. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nature Genetics. 43:163-168.

Li, H., Bradbury, P., Buckler IV, E.S., Ersoz, E., Wang, J. 2011. Joint QTL linkage mapping for multiple-cross mating design sharing one common parent. PLoS One. 6:e17573.

Glover, J.D., Reganold, J.P., Bell, L.W., Borevitz, J., Brummer, E.C., Buckler IV, E.S., Cox, C.M., Cox, T., Crews, T.E., Culman, S.W., Dehann, L.R., Eriksson, D., Gill, B., Holland, J.B., Hu, F.Y., Hulke, B.S., Ibrahim, A., Jackson, W., Jones, S., Murray, S., Paterson, A.H., Ploschuk, E., Sacks, E.J., Snapp, S., Tao, D.Y., Van Tassel, D., Wade, L., Wyse, D., Xu, Y. 2010. Increasing Food and Ecosystem Security through Perennial Grain Breeding. Science. 328:1638-1639

Setter, T.L., Yan, J., Warburton, M.L., Ribaut, J., Xu, Y., Sawkins, M., Buckler, E.S., Zhang, Z., Gore, M.A. 2010. Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought. Journal of Experimental Botany. 62:701-716. doi:10.1093/jxb/erq308.

Yan, J., Kandianis, C.B., Haries, C.E., Bai, L., Kim, E., Yang, X., Skinner, D., Fu, Z., Mitchell, S., Li, Q., Fernandez, M., Zaharieva, M., Babu, R., Fu, Y., Palacios, N., Li, J., DellaPenna, D., Brutnell, T., Buckler, E.S., Warburton, M.L., Rocheford, T. 2010. Rare Genetic Variation at Zea mays crtRB1 Increases B-carotene in Maize Grain. Nature Genetics. 42:322-329.

Flint Garcia, S.A., Buckler IV, E.S., Tiffin, P., Ersoz, E., Springer, N.M. 2009. Heterosis is Prevalent for Multiple Traits in Diverse Maize Germplasm. PLoS One. 4:e7433.

Poland, J.A., Bradbury, P., Buckler IV, E.S., Nelson, R. 2011. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proceedings of the National Academy of Sciences. 108:6893-6898.

Elshire, R.J., Glaubitz, J.C., Sun, Q., Poland, J.A., Kawamoto, K., Buckler IV, E.S., Mitchell, S.E. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 123:307-326.

Myles, S., Boyko, A., Owens, C.L., Brown, P., Fabrizio, G., Aradhya, M.K., Prins, B.H., Reynolds, A., Chia, J., Ware, D., Bustamante, C., Buckler IV, E.S. 2011. Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences. 10.1073/pnas.1009363108.

Last Modified: 7/24/2014
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