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Natural Variation in Lignin and Pectin Biosynthesis-Related Genes in Switchgrass (Panicum virgatum L.) and Association of SNP Variants with Dry Matter Traits

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Abstract

Switchgrass (Panicum virgatum), a C4 perennial grass native to North America and developed as a sustainable biofuel feedstock, occurs in two ecotypes, lowland and upland, which vary in their architecture as well as their range of adaptation. In this study, we assessed single nucleotide polymorphism (SNP) variation in 372 switchgrass genotypes for nine genes involved in lignin and pectin biosynthesis. STRUCTURE results at K = 3 differentiated the genotypes into three genetic subpopulations that corresponded largely to the previously characterized upland C1 and lowland C2 and C3 subpopulations. Out of the 146 SNPs identified, 19 SNPs were non-synonymous, including two non-conservative and common SNPs in cinnamyl alcohol dehydrogenase (CAD, Chr01N) and p-coumarate3-hydroxylase (C3H, Chr09N), two genes in the lignin biosynthesis pathway. Allele status at seven of the 19 non-synonymous SNPs, including the non-conservative SNP in C3H, was significantly associated with four dry matter traits within subpopulations. Dry matter traits appeared to be mostly dominant and three of them (acid detergent fiber, non-fiber carbohydrate, water-soluble carbohydrates) were the most frequently differentiated traits. In addition, a heterosis effect was detected at the non-conservative SNP in phenylalanine ammonia-lyase (PAL) for neutral detergent fiber. Association analysis revealed the CAD gene on Chr01N, its homoeolog on Chr01K and cinnamate 4-hydroxylase (C4H, Chr03K) as potential candidates associated with dry matter traits. Further analyses are needed to determine whether these candidate genes play a role in switchgrass lignin content and could be exploited to reduce recalcitrance in this bioenergy crop.

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Funding

This project was achieved with funding provided by The BioEnergy Science Center and The Center for Bioenergy Innovation, U.S. Department of Energy Research Centers supported by the Office of Biological and Environmental Research in the DOE Office of Science.

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Author notes

  1. Bochra A. Bahri

    Present address: Department of Plant Pathology, University of Georgia, Griffin, GA, 30223, USA

  2. Guillaume Daverdin

    Present address: Vinson Edward Ltd, Faversham, ME13 8UP, UK

  3. Xiangyang Xu

    Present address: Wheat, Peanut and Other Field Crops Research Unit, USDA-ARS, Stillwater, OK, 74075, USA

Authors and Affiliations

  1. Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), University of Georgia, Athens, GA, 30602, USA

    Bochra A. Bahri, Guillaume Daverdin, Xiangyang Xu, Ali Missaoui & Katrien M. Devos

  2. Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA

    Bochra A. Bahri, Guillaume Daverdin, Xiangyang Xu & Katrien M. Devos

  3. Laboratory of Bioaggressors and Integrated Protection in Agriculture, The National Agronomic Institute of Tunisia, University of Carthage, 43 Avenue Charles-Nicolle, 1082, Tunis, Tunisia

    Bochra A. Bahri

  4. DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA

    Jan-Fang Cheng & Kerrie W. Barry

  5. Plant Sciences Department, Plant Breeding Center, University of California, Davis, CA, 95616, USA

    E. Charles Brummer

Authors
  1. Bochra A. Bahri
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Bahri, B.A., Daverdin, G., Xu, X. et al. Natural Variation in Lignin and Pectin Biosynthesis-Related Genes in Switchgrass (Panicum virgatum L.) and Association of SNP Variants with Dry Matter Traits. Bioenerg. Res. 13, 79–99 (2020). https://doi.org/10.1007/s12155-020-10090-2

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