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BMC Plant Biol. 2019 Jan 31;19(1):45. doi: 10.1186/s12870-019-1653-x.

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

Author information

1
Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA.
2
Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, 53706, USA.
3
Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
4
Department of Energy, Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.
5
Department of Botany, University of Wisconsin, Madison, WI, 53706, USA.
6
Department of Energy, Joint Genome Institute, Walnut Creek, California, 94598, USA.
7
Genótika Super Sementes. Colonizador Ênio Pipino - St. Industrial Sul, Sinop, MT, 78550-098, Brazil.
8
Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN, 55108, USA.
9
Present address: Minnesota Supercomputing Institute, 117 Pleasant Street SE, Minneapolis, MN, 55455, USA.
10
Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
11
Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA. smkaeppl@wisc.edu.
12
Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, 53706, USA. smkaeppl@wisc.edu.

Abstract

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.

KEYWORDS:

Genome-wide association; Maize; Plant height; Rind; Stalk; Stover; Vascular bundle; Zmm22

PMID:
30704393
PMCID:
PMC6357476
DOI:
10.1186/s12870-019-1653-x
[Indexed for MEDLINE]
Free PMC Article

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