Genome-wide association analysis of stalk biomass and anatomical traits in maize.

BACKGROUND: Maize stover is an important source of crop residues and a promising sustainable energy source in the United States. Stalk is the main component of stover, representing about half of stover dry weight. Characterization of genetic determinants of stalk traits provide a foundation to optimize maize stover as a biofuel feedstock. We investigated maize natural genetic variation in genome-wide association studies (GWAS) to detect candidate genes associated with traits related to stalk biomass (stalk diameter and plant height) and stalk anatomy (rind thickness, vascular bundle density and area). RESULTS: Using a panel of 942 diverse inbred lines, 899,784 RNA-Seq derived single nucleotide polymorphism (SNP) markers were identified. Stalk traits were measured on 800 members of the panel in replicated field trials across years. GWAS revealed 16 candidate genes associated with four stalk traits. Most of the detected candidate genes were involved in fundamental cellular functions, such as regulation of gene expression and cell cycle progression. Two of the regulatory genes (Zmm22 and an ortholog of Fpa) that were associated with plant height were previously shown to be involved in regulating the vegetative to floral transition. The association of Zmm22 with plant height was confirmed using a transgenic approach. Transgenic lines with increased expression of Zmm22 showed a significant decrease in plant height as well as tassel branch number, indicating a pleiotropic effect of Zmm22. CONCLUSION: Substantial heritable variation was observed in the association panel for stalk traits, indicating a large potential for improving useful stalk traits in breeding programs. Genome-wide association analyses detected several candidate genes associated with multiple traits, suggesting common regulatory elements underlie various stalk traits. Results of this study provide insights into the genetic control of maize stalk anatomy and biomass.

Image analysis of anatomical traits in stalk transections of maize and other grasses.

BACKGROUND: Grass stalks architecturally support leaves and reproductive structures, functionally support the transport of water and nutrients, and are harvested for multiple agricultural uses. Research on these basic and applied aspects of grass stalks would benefit from improved capabilities for measuring internal anatomical features. In particular, methods suitable for phenotyping populations of plants are needed. RESULTS: To meet the need for large-scale measurements of stalk anatomy features, we developed custom image processing software that utilized a variety of global thresholding, local filtering, and feature detection methods to measure rind thickness, pith area, vascular bundle counts, and individual vascular bundle size from digital images of hand-cut transections of stalks collected with a flatbed document scanner. The tool determined vascular bundle number with an average accuracy of 90% across maize genotypes that varied five-fold for this trait. The method is demonstrated on maize, sorghum, and Miscanthus stalks. The computer source code is staged for download. CONCLUSIONS: Simplicity of sample preparation and semi-automated analyses enabled by this tool greatly increase measurement throughput relative to standard microscopy-based techniques while maintaining high accuracy. The tool is expected to be useful in genetic and physiological studies of the relationships between stalk anatomy and traits such as biofuel suitability, water use efficiency, or nutrient transport.