The Flint-Garcia lab investigates several aspects of genetic diversity in maize, including how levels of genetic diversity affects our understanding of genes that control agronomic traits.

Maize was domesticated from teosinte (Zea mays ssp. parviglumis) through a single domestication event in southern Mexico between 6,000 and 9,000 years ago.  Artificial selection affected maize during its domestication from teosinte to landraces as well as  during plant breeding from landraces to modern germplasm (i.e., inbred lines). Large-scale sequencing projects indicate that approximately 2% (or about 1,200 genes) of the approximately 60,000 genes in the maize genome were selected during domestication and/or plant breeding (improvement). Genes that have experienced artificial selection have greatly reduced genetic diversity in the modern germplasm and, therefore, cannot contribute to variation for agronomically important traits. Also of significance, selected genes will not be identified through conventional genetic analyses such as QTL analysis and association mapping. 

Selected Genes

Because selected genes have greatly reduced genetic variation in modern germplasm, they will not be identified in genetic screens and will not be useful in traditional breeding programs.  If selected genes are utilized fully, then we must reintroduce variation from teosinte and/or landraces. 

In order to do this, our lab is creating introgression libraries from ten teosinte and sixteen landrace teosinte accessions in the B73 background, resulting in libraries of small genomic fragments of teosinte in a controlled, temperate background. These libraries will be used to for two purposes:

1. to identify and define the biological functions of domestication and improvement genes and, thereby, identify the traits targeted during domestication and plant breeding
2. to determine if reintroducing genetic variation at these loci affects agronomic traits and, in so doing, enable a novel approach to crop improvement.

In one project, for example, we are using this approach to examine the impact of artificial selection on kernel quality traits, including starch, oil, protein, and amino acid content. This novel approach to crop improvement will lead to a better understanding of the genetic bases of quantitative traits in maize.

Unselected (Neutral) Genes:

For those 98% of maize genes that have not experienced selection, there is ample genetic variation remaining in diverse inbred lines for the identification of QTL and crop improvement by plant breeding. One resource developed as part of our NSF project (www.panzea.org) is the Nested Association Mapping (NAM) population.

NAM combines the strengths of linkage-based QTL Mapping and linkage disequilibrium (LD)-based Association Mapping into a high-resolution, high-powered genome scan for discovery gene-trait associations. NAM was developed by creating twenty-five linkage populations that would capture a large proportion of maize diversity and be useful for both linkage and association mapping. The NAM population is comprised of 5,000 RILs (200 RILs from each cross between the reference parent B73 and twenty-five diverse inbred lines and has been genotyped with 1106 SNPs. NAM has the power to detect twenty QTL per trait, resolved to our LD decay limits (2000 bp).

Our lab is using NAM to identify genes underlying kernel quality traits (e.g., protein, oil, and starch). We are also going to fine map six genes identified by NAM as candidates for the following traits: flowering time, plant development, and kernel quality.

• Strength in Diversity (Spring 2010)

Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nature Genetics 2011;43(2):159-162.

Zhang N, Gur A, Gibon Y, Sulpice R, Flint-Garcia S, McMullen MD, Stitt M and Buckler ES. Genetic analysis of central carbon metabolism unveils an amino acid substitution that alters maize NAD-Dependent isocitrate dehydrogenase activity. PLoS ONE 2010;5(4).

Dubois PG, Olsefski GT, Flint-Garcia S, Setter TL, Hoekenga OA and Brutnell TP. Physiological and genetic characterization of end-of-day far-red light response in maize seedlings. Plant Physiology 2010;154(1):173-186.

Bottoms CA, Flint-Garcia S and McMullen MD. IView: Introgression library visualization and query tool. BMC Bioinformatics 2010;11(SUPPL. 6).

McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, Brown P, Browne C, Eller M, Guill K, Harjes C, Kroon D, Lepak N, Mitchell SE, Peterson B, Pressoir G, Romero S, Rosas MO, Salvo S, Yates H, Hanson M, Jones E, Smith S, Glaubitz JC, Goodman M, Ware D, Holland JB and Buckler ES. Genetic properties of the maize nested association mapping population. Science 2009;325(5941):737-740.

Flint-Garcia SA, Guill KE, Sanchez-Villeda H, Schroeder SG and McMullen MD. Maize amino acid pathways maintain high levels of genetic diversity. Maydica 2009;54(4):375-386.

Flint-Garcia SA, Dashiell KE, Prischmann DA, Bohn MO and Hibbard BE. Conventional screening overlooks resistance sources: Rootworm damage of diverse inbred lines and their R73 hybrids is unrelated. Journal of Economic Entomology 2009;102(3):1317-1324.

Flint-Garcia SA, Buckler ES, Tiffin P, Ersoz E and Springer NM. Heterosis is prevalent for multiple traits in diverse maize germplasm. PLoS ONE 2009;4(10):e7433.

Flint-Garcia SA, Bodnar AL and Scott MP. Wide variability in kernel composition, seed characteristics, and zein profiles among diverse maize inbreds, landraces, and teosinte. Theoretical and Applied Genetics 2009;119(6):1129-1142.

Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, Rosas MO, Rocheford TR, Romay MC, Romero S, Salvo S, Villeda HS, Da Silva HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S and McMullen MD. The genetic architecture of maize flowering time. Science 2009;325(5941):714-718.

Sanchez-Villeda H, Schroeder S, Flint-Garcia S, Guill KE, Yamasaki M and McMullen MD. DNAAlignEditor: DNA alignment editor tool. BMC Bioinformatics 2008;9:art. no. 154.

Flint-Garcia SA, Thuillet AC, Yu J, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman MM and Buckler ES. Maize association population: A high-resolution platform for quantitative trait locus dissection. Plant Journal 2005;44(6):1054-1064.

Flint-Garcia SA, McMullen MD and Darrah LL. Genetic relationship of stalk strength and ear height in maize. Crop Science 2003;43(1):23-31.

Flint-Garcia SA, Jampatong C, Darrah LL and McMullen MD. Quantitative trait locus analysis of stalk strength in four maize populations. Crop Science 2003;43(1):13-22.

Flint-Garcia SA, Darrah LL, McMullen MD and Hibbard BE. Phenotypic versus marker-assisted selection for stalk strength and second-generation European corn borer resistance in maize. Theoretical and Applied Genetics 2003;107(7):1331-1336.

Cocciolone SM, Chopra S, Flint-Garcia SA, McMullen MD and Peterson T. Tissue-specific patterns of a maize Myb transcription factor are epigenetically regulated. Plant Journal 2001;27(5):467-478.