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ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » Research » Research Project #424655

Research Project: Genetics and Genomics of Complex Traits in Grain Crops

Location: Plant Genetics Research

2014 Annual Report


Objectives
Objective 1: Create novel genetic resources for complex trait dissection in diverse maize germplasm. • Sub-objective 1.1: Create, genotype, and phenotype doubled haploid (DH) lines from a synthetic population containing diverse germplasm, including teosinte alleles. • Sub-objective 1.2: Create, genotype and phenotype novel quantitative trait loci (QTL) populations derived from a (teosinte x B73) x B73 population. Objective 2: Characterize the genetic basis of important agronomic traits (heterosis, drought tolerance, yield components, DIMBOA synthesis, and kernel composition) in maize. • Sub-objective 2.1: Determine the genetic basis of heterosis and its relationship to recombination and the Hill-Robertson effect. • Sub-objective 2.2: Fine-map the regulatory site for the major QTL of DIMBOA synthesis for chromosome 4 from CI31A. • Sub-objective 2.3: Fine map the genes responsible for a KRN QTL on chromosome 2 and a KWT QTL (specific QTL to be chosen based on 2012 data) in a teosinte x maize population. • Sub-objective 2.4: Determine the genetic basis of kernel composition in maize x teosinte introgression libraries, and compare the QTL and effects to those observed in maize. Objective 3: Determine molecular and biochemical mechanisms of drought tolerance in maize and model species. • Sub-objective 3.1: Determine the expression patterns of transcription factor (TF) genes in the drought response of maize. • Sub-objective 3.2: To fully characterize the molecular genetic basis of the conserved interplay between reactive oxygen species (ROS) and amino acid metabolism, linked through gamma-glutamyl amino acids (GGAA) metabolism and transport, and the role of GGAA metabolism in dehydration tolerance. Objective 4: Identify and curate key datasets that will serve to benchmark genomic discovery tools for key agronomic traits, especially response to biotic and abiotic environmental stressors. • Sub-objective 4.1: Bring into The Maize Genome Database (MaizeGDB) the phenotypic data generated by critically important research endeavors including the Maize Diversity Project. • Sub-objective 4.2: Curate maize metabolism and pathways data for release as a BioCyc database and as GO annotation files. Objective 5: Characterize the relationship between root biology and drought tolerance in wheat and related species. • Sub-objective 5.1: Elucidate the physiological basis of root growth responses in wheat (hard and soft red winter) and the “wheat model” Brachypodium distachyon, to imposed water deficits.


Approach
Create and fully describe double haploid lines and QTL populations for complex trait dissection. Map and characterize yield QTLs to interrogate the genetic basis of heterosis in maize. Use QTL fine mapping protocols to define the genetic regulation of DIMBOA synthesis in maize. Develop targeted metabolomic profiles to define the role of nitrogen metabolism in establishing dehydration tolerance in the C4 grasses, including maize. Combine field experiments and transgenic maize lines to determine the role of selected transcription factors in the response of roots to water deficits and their possible role in drought tolerance. Use modern curation tools to improve the phenotype to gene utility of the MaizeGDB and improve linkages to other community database efforts.


Progress Report
Over the lifetime of the project this research addresses the application of genetics and genomics in the study of complex traits in grain crops and all of the objectives are relevant to NP 301 Action Plan, Component 1 – Crop Genetic Improvement, Problem Statement 1B: Innovative approaches to crop genetic improvement and trait analysis. In objective 1, we obtained over 3000 doubled haploid (DH) lines from the Zea Synthetic, a population containing teosinte at approximately 12% teosinte and 88% maize, representing inbred lines from around the world. A trial of 1000 DH was planted in Ames, IA, Aurora, NY, Clayton, NC and Columbia, MO for evaluation of agronomic (maturity, plant/ear height, number of ears, kernel weight) and fitness (total kernel number) traits. We created 1000 self-pollinated families from the Teosinte Synthetic, which contains 25% teosinte and 75% B73 (maize genome inbred line). We planted two replicates of these 1000 families in Columbia, MO, and collected data for several agronomic and domestication traits (maturity, plant/ear height, tillering and branching habits, kernel row number, and kernel weight). In objective 2, we continued evaluation of teosinte near isogenic lines (NILs) for agronomic traits including leaf length, width, and angle. We focused on kernel row number (KRN) and kernel composition (KCOMP) for future studies. We identified a strong-effect QTL for KRN on chromosome 2, where one of the teosinte alleles is predicted to decrease row number by 4 rows. We completed the first round of fine mapping for this QTL and submitted a manuscript discussing this result. We also completed our near infrared (NIR) calibration for kernel composition traits, and have nearly completed NIR scans of 6 replicates of the teosinte NILs. We collected field data for the heterosis field trials and stored it in a local database for further study. In objective 3, we completed one rain-out shelter experiment for transcription factor expression analysis with maize seedlings but because of issues related to soil conditions we had to repeat the experiment in a new system that allows for rapid soil drainage. We completed analysis of the transcription factor expression data from the lab-based studies and developed the artificial miRNA constructs to perform selective drought functional assays using a knock-down or knock-out strategy. We made use of existing transposon tag collections within the maize germplasm collections that allowed us to target six transcription factors for functional assessment without the need for transgenic approaches. We fully established the N15 protocols for nitrogen mobilization studies and analyzed data from our first dehydration experiments aimed at establishing a baseline for nitrogen redistribution under drought. We completed non-targeted metabolite profiles for both roots and shoots of model species, Sporobolus stapfianus, and leaf tissue for maize. We obtained the necessary root tissues to complete the maize root aspect of this analysis. We maximized the likelihood that we can isolate the appropriate and desired S. stapfianus sequences for cloning by completing a full genome sequence (rough draft). The specific genes needed to control and regulate the biosynthesis and catabolism of the targeted nitrogenous compounds in both S. stapfianus and maize can now be isolated in toto from both species. The full bioinformatics analysis of the S. stapfianus shoot and root transcriptomes have been completed and manuscripts are in preparation. In objective 4, using a phenotyping pipeline we developed, data from recent papers that include the nested associated mapping (NAM) and IBM lines were used to prepare an annotated phenotype scoring for over 50 traits, with links to the species neutral terms that are being used for computing in comparative phenomics. The pipeline includes custom Oracle tables linked to a local copy of MaizeGDB provided by the MaizeGDB team at Ames, IA. We also contributed to an effort to define standards for describing traits and phenotypes (collaboration with Corvallis OR, USDA scientists at Albany CA and Ames IA). The goal was to make phenotypes more accessible to tools for not just maize but other crops and model plants. The emphasis was on traits studied by the US Maize Diversity Project, related work by US public corn breeding researchers at Madison WI, Ames IA, and ARS scientists at Ithaca NY, Columbia MO, and Raleigh NC. In collaboration with scientists at Stanford, CA and Ames IA, experimental evidence for several metabolism pathways were integrated into a computed genome-to-metabolism database for maize, and which is closely associated with species-neutral metabolism databases accessed by major functional genomics repositories. The pathways that were updated focused on key regulatory pathways and include: biosynthesis of plant hormones and degradations of cytokinins. In addition, other work included updating evidence for biosynthesis of B vitamins, and carotenoid. The goal was to have much of the available evidence for maize imported by the end of the project cycle. In connection to this kind of curation, standard vocabularies are also being used in collaboration with Ames, IA scientists in the UniProt project.


Accomplishments
1. Zea synthetic doubled haploids. There are a nearly infinite number of rare maize gene variants that may play a significant role in important quantitative agronomic traits and many strongly harmful genetic variants have been purged during the inbreeding of maize over the last century. Teosinte, the non-inbred wild ancestor of maize, contains many beneficial and agronomically useful gene variants but still contains some that are harmful and that are masked. It is the goal of plant breeding to increase the frequency of beneficial variants, in this case by obtaining them from the wild ancestor (teosinte), and to decrease the frequency of harmful variants in breeding maize lines. ARS scientists in Columbia MO created a population of 3,330 maize lines that have identical genetic variants on each chromosome (double haploids or DH lines) which can be used to precisely identify new beneficial gene variants that contribute to desirable agronomic traits. A trial of the first 1000 DH has been planted in four locations for evaluation of agronomic (maturity, plant/ear height, number of ears, kernel weight) and fitness (total kernel number) traits. The data we collect will be used to identify genetic regions that are underrepresented in modern inbred parents that are used to make commercial hybrid corn. These studies will reintroduce genetic variation from teosinte into modern maize germplasm which will enhance the ability of maize breeders to improve yields and performance to address critical food security issues.

2. Resurrection grass genome. Droughts occurring in the U.S. and across the globe threaten food security and contribute to the growing problem of malnutrition and hunger. Understanding how plants respond to soil water deficits at the genetic and genomic level is critical to our ability to develop drought tolerant crops. ARS scientists in Columbia, MO are studying the response of a desiccation-tolerant resurrection forage grass to dehydration as a way to develop genetic insights into mechanisms by which plants protect their tissues from dehydration damage and how they quickly repair such damage when it occurs. In a major step forward, the ARS scientists have completed a draft genome of the resurrection grass that provides a complete record of the gene complement of this plant. The analysis of which genes respond to both dehydration and re-watering provides us with a map of the mechanisms and processes involved in the dehydration tolerance of this grass. The draft genome is an important step in our understanding of what specific processes and gene regulatory mechanisms we can target for drought tolerance in grain crops, such as maize, wheat and rice. The knowledge we gain will enable breeders to develop novel genetic strategies for improving drought tolerance in grain crops to improve food security and address yield stability in a changing climate.

3. Phenotyping pipeline. One of the major issues facing plant researchers and breeders is the need to quickly and efficiently access data and information that has been amassed and published by the scientific community. This is particularly critical for maize geneticists and breeders when it comes to the descriptions of the phenotypes (detailed descriptions and images of a plant) and phenotypic evaluations of the U.S. germplasm accessions that represent the diversity of maize. This is made more difficult as much of the current phenotype scoring data for key agronomic traits are scattered in supplemental data files attached to publications, or are only available by request from the authors. ARS scientists in Columbia have developed a web-based “pipeline” that integrates recently published phenotypic evaluations for over 7000 public germplasm accessions. The pipeline enables researchers to find the phenotype scores for these lines, all of which have been characterized for diversity at the DNA sequence level (genotyped). The pipeline is flexible and can be readily modified to suit requirements by MaizeGDB (the main maize database), other informatics tools, and the research community that desires customized spreadsheets. An immediate result of products of the pipeline is the access to all data in a central and publicly accessible location (MaizeGDB). The long-term benefits will be the enhanced prediction of gene functions in maize, as well as other important crops. The pipeline facilitates the selection of germplasm by breeders and geneticists working to improve agronomic traits in maize and other grain crops.


Review Publications
Peiffer, J.A., Romay, M.C., Gore, M.A., Flint Garcia, S.A., Zhang, Z., Millard, M.J., Gardner, C.A., McMullen, M.D., Holland, J.B., Bradbury, P., Buckler IV, E.S. 2014. The genetic architecture of maize height. Genetics. 196:1337-1356.
Williams, M., Oliver, M.J., Pallardy, S.G. 2014. Plant water relations I: uptake and transport. The Plant Cell. 26:1.
Flint Garcia, S.A. 2013. Genetics and consequences of crop domestication. Journal of Agricultural and Food Chemistry. 61:8267-8276.
Romay, M.C., Millard, M.J., Glaubitz, J.C., Peiffer, J.A., Swarts, K.L., Casstevens, T.M., Elshire, R.J., Acharya, C.B., Mitchell, S.E., Flint Garcia, S.A., McMullen, M.D., Holland, J.B., Buckler IV, E.S., Gardner, C.A. 2013. Comprehensive genotyping of the US national maize inbred seed bank. Genome Biology. 14(6):1-18.
Gaff, D., Oliver, M.J. 2013. The evolution of desiccation-tolerance in angiosperm plants, a rare yet common phenomenon! Functional Plant Biology. 40:315-328.
Stark, L., Greenwood, J., Brinda, J., Oliver, M.J. 2013. The desert moss Pterygoneurum lamellatum (Pottiaceae) exhibits an inducible ecological strategy of desiccation tolerance: effects of rate of drying on shoot damage and regeneration. American Journal of Botany. 100(8):1522-1531.
Williams, M., Oliver, M.J., Pallardy, S.G. 2014. Plant water relations II: how plants manage water deficit and why it matters. The Plant Cell. 26(4):1-15.