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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Dairy Forage Research » Research » Publications at this Location » Publication #327836
Title: Selection signatures in four lignin genes from switchgrass populations divergently selected for in vitro dry matter digestibility

Author
item CHEN, SHIYU - University Of Wisconsin
item KAEPPLER, SHAWN - University Of Wisconsin
item VOGEL, KENNETH - Retired ARS Employee
item Casler, Michael

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/15/2016
Publication Date: 11/28/2016
Citation: Chen, S., Kaeppler, S., Vogel, K.P., Casler, M.D. 2016. Selection signatures in four lignin genes from switchgrass populations divergently selected for in vitro dry matter digestibility. PLoS One. doi:10.137/journal.pone.0167005.

Interpretive Summary: Switchgrass is undergoing development as a dedicated cellulosic bioenergy crop. However, the biomass of switchgrass is difficult to convert into liquid transportation fuels, because most of its energy is locked in its cell walls. Cell walls are complex structures made up of many sugars locked into a concrete-like matrix called "lignin". Traditional plant breeding and selection for increased fermentability of switchgrass cell walls has been effective to improve the yield of ethanol in a fermentation system. This research aimed to identify individual genes responsible for the improvements in fermentability. Four genes involved in the synthesis of lignin were sequenced using advanced sequencing methods, yielding 183 DNA variants. Of these, 29 DNA variants were found to be strongly associated with the improved fermentation of switchgrass biomass. These DNA variants will be studied further to determine if and how they can be used in a genomics-assisted breeding program by USDA switchgrass breeders.

Technical Abstract: Switchgrass is undergoing development as a dedicated cellulosic bioenergy crop. Fermentation of lignocellulosic biomass to ethanol in a bioenergy system, or to volatile fatty acids in a livestock production system, is strongly and negatively influenced by lignification of cell walls. This study detects specific loci that exhibit selection signatures across switchgrass breeding populations differing in in vitro dry matter digestibility (IVDMD), ethanol yield, and lignin concentration. Allele frequency changes in candidate genes were used to detect loci under selection. Out of the 183 polymorphisms identified in the four candidate genes, twenty-five loci in the intron regions and four loci in coding regions were found to display a selection signature. All loci in the coding regions are synonymous substitutions. Genetic diversity and linkage disequilibrium within the candidate genes were low. Genetic diversity and the number of loci with moderate minor allele frequencies increased after three cycles of selection for high IVDMD. This study provides valuable insight on genetic changes under short-term selection in the polyploid populations, and discovered potential markers for breeding improved biomass quality in switchgrass.