title: Selection Signatures in Four Lignin Genes from Switchgrass Populations Divergently Selected for In Vitro Dry Matter Digestibility.
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 that differ 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. Selection in both directions were observed on polymorphisms that appeared to be under selection. Genetic diversity and linkage disequilibrium within the candidate genes were low. The recurrent divergent selection caused excessive moderate allele frequencies in the cycle 3 reduced lignin population as compared to the base population. This study provides valuable insight on genetic changes occurring in short-term selection in the polyploid populations, and discovered potential markers for breeding switchgrass with improved biomass quality.
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Shiyu
authors.identifier: http://orcid.org/0000-0003-0102-8112
authors.initials: S
authors.lastname: Chen
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.|Department of Energy, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America.
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Kaeppler
authors.affiliation: USDA-ARS, Grain, Forage, and Bioenergy Research Unit, Lincoln, Nebraska, United States of America.|Department of Agronomy & Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America.
authors.forename: Kenneth P
authors.initials: KP
authors.lastname: Vogel
authors.affiliation: Department of Energy, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America.|USDA-ARS, U.S. Dairy Forage Research Center, Madison, Wisconsin, United States of America.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Casler
mesh_terms: D018533:Biomass; D002473:Cell Wall; D004063:Digestion; D014644:Genetic Variation / Q000235:genetics*; D008031:Lignin / Q000235:genetics* / Q000378:metabolism; D008897:Panicum / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics*; D030821:Plants, Genetically Modified / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D012641:Selection, Genetic / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D008031:Lignin