10.5061/DRYAD.N0M260P
Mazaheri, Mona
University of Wisconsin-Madison
Heckwolf, Marlies
University of Wisconsin-Madison
Vaillancourt, Brieanne
Department of Plant Biology
Gage, Joseph L.
University of Wisconsin-Madison
Burdo, Brett
University of Wisconsin-Madison
Heckwolf, Sven
University of Wisconsin-Madison
Barry, Kerrie
Joint Genome Institute
Lipzen, Anna
Joint Genome Institute
Ribeiro, Camila Bastos
Genótika Super Sementes. Colonizador Ênio Pipino - St. Industrial Sul,
Sinop, Brazil
Kono, Thomas J. Y.
University of Minnesota
Kaeppler, Heidi F.
University of Wisconsin-Madison
Spalding, Edgar P.
University of Wisconsin-Madison
Hirsch, Candice N.
University of Minnesota
Buell, C. Robin
Department of Plant Biology
de Leon, Natalia
University of Wisconsin-Madison
Kaeppler, Shawn M.
University of Wisconsin-Madison
Data from: Genome-wide association analysis of stalk biomass and
anatomical traits in maize
Dryad
dataset
2019
genome-wide association
Vascular bundle
Stalk
Maize
Rind
Zmm22
plant height
2019-02-05T19:42:33Z
2019-02-05T19:42:33Z
en
https://doi.org/10.1186/s12870-019-1653-x
2110241242 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
widiv_942g_899784SNPs_imputed_filteredGenos_noRTA_AGPv4.hmp.txtImputed
data of 899,784 SNPs generated from RNA-Seq reads of 942 inbred lines.
SNPs were called from mapping to the version 4 maize B73 (AGPv4) reference
sequence. Imputation was done using fastPHASE v1.4.0 (Scheet and Stephens,
2006).62biomAP_v_B73_SNPMatrix.txt.gzSNP calls generated from high quality
whole genome resequencing of 56 inbreds (Brohammer et al., 2018). This
dataset was used to validate imputation results of 899,784 SNPs detected
in this study.