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

Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne; Gage, Joseph L.; Burdo, Brett; Heckwolf, Sven; Barry, Kerrie; Lipzen, Anna; Ribeiro, Camila Bastos; Kono, Thomas J.  Y.; Kaeppler, Heidi F.; Spalding, Edgar P.; Hirsch, Candice N.; Robin Buell, C.; de Leon, Natalia; Kaeppler, Shawn M.

doi:10.1186/s12870-019-1653-x

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

Journal Article · Thu Jan 31 00:00:00 EST 2019 · BMC Plant Biology

DOI:https://doi.org/10.1186/s12870-019-1653-x· OSTI ID:1571960

Mazaheri, Mona ^[1]; Heckwolf, Marlies ^[1]; Vaillancourt, Brieanne ^[2]; Gage, Joseph L. ^[3]; Burdo, Brett ^[3]; Heckwolf, Sven ^[4]; Barry, Kerrie ^[5]; Lipzen, Anna ^[5]; Ribeiro, Camila Bastos ^[6]; Kono, Thomas J. Y. ^[7]; Kaeppler, Heidi F. ^[1]; Spalding, Edgar P. ^[4]; Hirsch, Candice N. ^[8]; Robin Buell, C. ^[9]; de Leon, Natalia ^[1]; ^[1]

Univ. of Wisconsin, Madison, WI (United States). Dept. of Agronomy; Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center
Michigan State Univ., East Lansing, MI (United States). Dept. of Plant Biology; Michigan State Univ., East Lansing, MI (United States). Great Lakes Bioenergy Research Center
Univ. of Wisconsin, Madison, WI (United States). Dept. of Agronomy
Univ. of Wisconsin, Madison, WI (United States). Dept. of Botany
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Genótika Super Sementes, Sinop (Brazil)
Univ. of Minnesota, St. Paul, MN (United States). Dept. of Agronomy and Plant Genetics; Minnesota Supercomputing Inst., Minneapolis, MN (United States)
Univ. of Minnesota, St. Paul, MN (United States). Dept. of Agronomy and Plant Genetics
Michigan State Univ., East Lansing, MI (United States). Dept. of Plant Biology; Michigan State Univ., East Lansing, MI (United States). Great Lakes Bioenergy Research Center; Michigan State Univ., East Lansing, MI (United States). Plant Resilience Inst.

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). 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. 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. Finally, results of this study provide insights into the genetic control of maize stalk anatomy and biomass.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1571960

Journal Information:: BMC Plant Biology, Journal Name: BMC Plant Biology Journal Issue: 1 Vol. 19; ISSN 1471-2229

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Gateway-compatible vectors for high-throughput gene functional analysis in switchgrass (Panicum virgatum L.) and other monocot species: Gateway-compatible vectors for monocot transformation Mann, David G. J.; LaFayette, Peter R.; Abercrombie, Laura L. Plant Biotechnology Journal, Vol. 10, Issue 2 https://doi.org/10.1111/j.1467-7652.2011.00658.x	journal	September 2011
Zm MADS 69 functions as a flowering activator through the ZmRap2.7‐ ZCN 8 regulatory module and contributes to maize flowering time adaptation Liang, Yameng; Liu, Qiang; Wang, Xufeng New Phytologist, Vol. 221, Issue 4 https://doi.org/10.1111/nph.15512	journal	October 2018
The limited role of differential fractionation in genome content variation and function in maize ( Zea mays L .) inbred lines Brohammer, Alex B.; Kono, Thomas J. Y.; Springer, Nathan M. The Plant Journal, Vol. 93, Issue 1 https://doi.org/10.1111/tpj.13765	journal	December 2017
Diversity of Sea Star-Associated Densoviruses and Transcribed Endogenous Viral Elements of Densovirus Origin Jackson, Elliot W.; Wilhelm, Roland C.; Johnson, Mitchell R. Journal of Virology, Vol. 95, Issue 1 https://doi.org/10.1128/jvi.01594-20	journal	December 2020
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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Kim, Daehwan; Pertea, Geo; Trapnell, Cole Genome Biology, Vol. 14, Issue 4 https://doi.org/10.1186/gb-2013-14-4-r36	journal	January 2013
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Kim, Daehwan; Pertea, Geo; Trapnell, Cole Springer Nature https://doi.org/10.13016/7jyb-2sdy	text	January 2013
Validation of Potential Reference Genes for qPCR in Maize across Abiotic Stresses, Hormone Treatments, and Tissue Types Lin, Yueai; Zhang, Chenlu; Lan, Hai PLoS ONE, Vol. 9, Issue 5 https://doi.org/10.1371/journal.pone.0095445	journal	May 2014
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Identification of pleiotropic loci mediating structural and non-structural carbohydrate accumulation within the sorghum bioenergy association panel using high-throughput markers

Journal Article · Tue Feb 27 19:00:00 EST 2024 · Frontiers in Plant Science · OSTI ID:2580280

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59 BASIC BIOLOGICAL SCIENCES
Zmm22
genome-wide association
maize
plant height
rind
stalk
stover
vascular bundle

Data from: Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.5061/dryad.n0m260p The current record is supplemented by this dataset	dataset	January 2019
Additional file 1: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659596 The current record is supplemented by this dataset	dataset	January 2019
Additional file 1: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659596.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 2: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659602 The current record is supplemented by this audiovisual	audiovisual	January 2019
Additional file 2: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659602.v1 The current record is supplemented by this audiovisual	audiovisual	January 2019
Additional file 3: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659614 The current record is supplemented by this audiovisual	audiovisual	January 2019
Additional file 3: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659614.v1 The current record is supplemented by this audiovisual	audiovisual	January 2019
Additional file 4: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659623 The current record is supplemented by this audiovisual	audiovisual	January 2019
Additional file 4: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659623.v1 The current record is supplemented by this audiovisual	audiovisual	January 2019
Additional file 5: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659635 The current record is supplemented by this dataset	dataset	January 2019
Additional file 5: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659635.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 6: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659638 The current record is supplemented by this audiovisual	audiovisual	January 2019
Additional file 6: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659638.v1 The current record is supplemented by this audiovisual	audiovisual	January 2019
Additional file 7: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659644 The current record is supplemented by this dataset	dataset	January 2019
Additional file 7: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659644.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 8: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659650 The current record is supplemented by this text	text	January 2019
Additional file 8: of Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.7659650.v1 The current record is supplemented by this text	text	January 2019
Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.c.4386014 The current record is supplemented by this collection	collection	January 2019
Genome-wide association analysis of stalk biomass and anatomical traits in maize Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne https://doi.org/10.6084/m9.figshare.c.4386014.v1 The current record is supplemented by this collection	collection	January 2019

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

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