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ARS Home » Plains Area » El Reno, Oklahoma » Oklahoma and Central Plains Agricultural Research Center » Peanut and Small Grains Research Unit » Research » Publications at this Location » Publication #356690
Research Project: Genetic Mechanisms and Improvement of Insect Resistance in Wheat, Barley, and Sorghum

Location: Peanut and Small Grains Research Unit

Title: Natural variation in lignin and pectin biosynthesis-related genes associated with switchgrass (Panicum virgatum L.) ecotype differentiation

Author
item BAHRI, BOCHRA - University Of Georgia
item DAVERDIN, GUILLAUME - University Of Georgia
item Xu, Xiangyang
item CHENG, JAN-FANG - Joint Genome Institute
item BARRY, KERRIE - Joint Genome Institute
item BRUMMER, E. CHARLES - University Of California, Davis
item DEVOS, KATRIEN - University Of Georgia
item MISSAOUI, ALI - University Of Georgia

Submitted to: BioEnergy Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/3/2019
Publication Date: 2/11/2020
Citation: Bahri, B.A., Daverdin, G., Xu, X., Cheng, J., Barry, K.W., Brummer, E., Devos, K., Missaoui, A. 2020. Natural variation in lignin and pectin biosynthesis-related genes associated with switchgrass (Panicum virgatum L.) ecotype differentiation. BioEnergy Research. 13:79-99. https://doi.org/10.1007/s12155-020-10090-2.
DOI: https://doi.org/10.1007/s12155-020-10090-2

Interpretive Summary: 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 range of adaptation. In this study, we assessed SNP variation in 372 switchgrass genotypes for nine genes involved in lignin and pectin biosynthesis, and 146 SNPs were identified. Of these, two SNPs identified in cinnamyl alcohol dehydrogenase and p-coumarate 3-hydroxylase, two genes in the lignin biosynthesis pathway, were associated with plant height and stem diameter. Because a higher lignin content has been suggested to correlate with higher biomass traits in other plant systems, further analyses are needed to determine whether these two SNPs play a role in switchgrass lignin content and could be exploited to reduce recalcitrance in this bioenergy crop.

Technical 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-coumarate 3-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.