Data from: 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.