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Title: The genetic architecture of maize height

item PEIFFER, JASON - North Carolina State University
item ROMAY, MARIA - Cornell University
item GORE, MICHAEL - Cornell University
item Flint-Garcia, Sherry
item ZHANG, ZHIWU - Cornell University
item Millard, Mark
item Gardner, Candice
item McMullen, Michael
item Holland, Jim - Jim
item Bradbury, Peter
item Buckler, Edward - Ed

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2014
Publication Date: 4/1/2014
Publication URL:
Citation: 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.

Interpretive Summary: Plant height is an important complex trait in maize with major implications for agricultural perfomance and yeild protection. Previous studies have identified several genes and pathways that control large differences in plant height; however, the genetic architecture of natural height variation remains largely unexplained. In this study, we measured plant height and related traits in several genetic mapping panels, totaling over 64,500 plots. Our mapping efforts identified several chromosome regions containing genes previously implicated in regulation of plant height, including several genes involved in plant hormone synthesis or regulation. The total genomic variation we identified explained 82% of heritable variation in height across all mapping panels. This finding allows us to develop models to maximize prediction accuracy as two families become more genetically unrelated . Our ability to explain, predict, and discover gene variants responsible for natural height variation will facilitate maize improvement and enhanced yield stability.

Technical Abstract: Height is one of the most heritable and easily measured traits in maize (Zea mays L.). Given a pedigree or estimates of the genomic identity-by-state (IBS) among related plants, height is also accurately predictable. But, mapping alleles explaining natural variation in maize height remains a formidable challenge. To address this challenge, we measured the plant height, ear height, flowering time, and node counts of plants grown in over 64,500 plots across 13 environments. These plots contained over 7,300 inbreds representing most publically available maize inbreds in the U.S.A. as well as families of the maize Nested Association Mapping (NAM) panel. Joint-linkage mapping of quantitative trait loci (QTL), fine mapping in near isogenic lines (NILs), genome wide association studies (GWAS), and genomic best linear unbiased prediction (GBLUP) were performed. The heritability of plant height was estimated to be over 90%. Mapping of NAM family-nested QTL revealed the largest explained about 2% of the height variation. The effects of two tropical alleles at this QTL were independently validated by fine mapping. Several significant associations found by GWAS co-localized with established height loci including brassinosteroid-deficient dwarf1, dwarf plant1, and semi-dwarf2. GBLUP explained over 80% of plant height variation in the observed panels and outperformed bootstrap aggregation of family-nested QTL models in evaluations of prediction accuracy.