Candidate Variants for Additive and Interactive Effects on Bioenergy Traits in Switchgrass ( Panicum virgatum L.) Identified by Genome‐Wide Association Analyses

Ramstein, Guillaume P.; Evans, Joseph; Nandety, Aruna; Saha, Malay C.; Brummer, E. Charles; Kaeppler, Shawn M.; Buell, C. Robin; Casler, Michael D.

doi:10.3835/plantgenome2018.01.0002

Candidate Variants for Additive and Interactive Effects on Bioenergy Traits in Switchgrass ( Panicum virgatum L.) Identified by Genome‐Wide Association Analyses

Journal Article · Thu Nov 01 00:00:00 EDT 2018 · The Plant Genome

DOI:https://doi.org/10.3835/plantgenome2018.01.0002· OSTI ID:1630198

Ramstein, Guillaume P. ^[1]; Evans, Joseph ^[2]; Nandety, Aruna ^[3]; Saha, Malay C. ^[4]; Brummer, E. Charles ^[5]; Kaeppler, Shawn M. ^[6]; Buell, C. Robin ^[7]; Casler, Michael D. ^[8]

Dep. of Agronomy Univ. of Wisconsin‐Madison 1575 Linden Dr. Madison WI 53706, Institute of Biotechnology, Cornell Univ. 130 Biotechnology Bldg. Ithaca NY 14853
US Dep. of Energy Great Lakes Bioenergy Research Center, Dep. of Plant Biology Michigan State Univ. 325 East Grand River, Suite 350 East Lansing MI 48824
Forage Improvement Division Samuel Roberts Noble Foundation 2510 Sam Noble Parkway Ardmore OK 73401
Forage Improvement Division Samuel Roberts Noble Foundation 2510 Sam Noble Parkway Ardmore OK 73401, BioEnergy Science Center, Oak Ridge National Lab. 1 Bethel Valley Rd. Oak Ridge TN 37831
BioEnergy Science Center, Oak Ridge National Lab. 1 Bethel Valley Rd. Oak Ridge TN 37831, Dep. of Plant Sciences, Plant and Environmental Sciences Bldg. Univ. of California Davis CA 95616
Dep. of Agronomy Univ. of Wisconsin‐Madison 1575 Linden Dr. Madison WI 53706, US Dep. of Energy Great Lakes Bioenergy Research Center
US Dep. of Energy Great Lakes Bioenergy Research Center, DuPont Pioneer 7000 NW 62nd Ave. Johnston IA 50131, Dep. of Plant Biology Michigan State Univ. 325 East Grand River, Suite 350 East Lansing MI 48824
Dep. of Agronomy Univ. of Wisconsin‐Madison 1575 Linden Dr. Madison WI 53706, USDA‐ARS 1925 Linden Dr. Madison WI 53706

Switchgrass ( Panicum virgatum L.) is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving simple additive marker effects and also interactions with genetic backgrounds (e.g., ecotypes) or synergies with other markers. We analyzed plant height, C content, N content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotypes. We performed association analyses based on exome capture sequencing and tested 439,170 markers for marginal effects, 83,290 markers for marker × ecotype interactions, and up to 311,445 marker pairs for pairwise interactions. Analyses of pairwise interactions focused on subsets of marker pairs preselected on the basis of marginal marker effects, gene ontology annotation, and pairwise marker associations. Our tests identified 12 significant effects. Homology and gene expression information corroborated seven effects and indicated plausible causal pathways: flowering time and lignin synthesis for plant height; plant growth and senescence for C content and mineral concentration. Four pairwise interactions were detected, including three interactions preselected on the basis of pairwise marker correlations. Furthermore, a marker × ecotype interaction and a pairwise interaction were confirmed in an independent switchgrass panel. Our analyses identified reliable candidate variants for important bioenergy traits. Moreover, they exemplified the importance of interactive effects for depicting genetic bases and illustrated the usefulness of preselecting marker pairs for identifying pairwise marker interactions in association studies.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: FC02-07ER64494; AC02-05CH11231

OSTI ID:: 1630198

Alternate ID(s):: OSTI ID: 1787375

Journal Information:: The Plant Genome, Journal Name: The Plant Genome Journal Issue: 3 Vol. 11; ISSN 1940-3372

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: United States

Language:: English

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