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Title: Selection signatures in four lignin genes from switchgrass populations divergently selected for in vitro dry matter digestibility

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. As a result, 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:
ORCiD logo [1] ;  [2] ;  [3] ;  [4] ;  [5]
  1. Univ. of Wisconsin, Madison, WI (United States)
  2. Univ. of Wisconsin, Madison, WI (United States); Dept. of Energy, Great Lakes Bioenergy Research Center, Madison, WI (United States)
  3. USDA-ARS, Lincoln, NE (United States); Univ. of Nebraska, Lincoln, NE (United States)
  4. Dept. of Energy, Great Lakes Bioenergy Research Center, Madison, WI (United States)
  5. Iowa State Univ., Ames, IA (United States)
Publication Date:
Grant/Contract Number:
FC02-07ER64494
Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 11; Journal Issue: 11; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Research Org:
Dept. of Energy, Great Lakes Bioenergy Research Center, Madison, WI (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS
OSTI Identifier:
1363958

Chen, Shiyu, Kaeppler, Shawn M., Vogel, Kenneth P., Casler, Michael D., and Zabotina, Olga A.. Selection signatures in four lignin genes from switchgrass populations divergently selected for in vitro dry matter digestibility. United States: N. p., Web. doi:10.1371/journal.pone.0167005.
Chen, Shiyu, Kaeppler, Shawn M., Vogel, Kenneth P., Casler, Michael D., & Zabotina, Olga A.. Selection signatures in four lignin genes from switchgrass populations divergently selected for in vitro dry matter digestibility. United States. doi:10.1371/journal.pone.0167005.
Chen, Shiyu, Kaeppler, Shawn M., Vogel, Kenneth P., Casler, Michael D., and Zabotina, Olga A.. 2016. "Selection signatures in four lignin genes from switchgrass populations divergently selected for in vitro dry matter digestibility". United States. doi:10.1371/journal.pone.0167005. https://www.osti.gov/servlets/purl/1363958.
@article{osti_1363958,
title = {Selection signatures in four lignin genes from switchgrass populations divergently selected for in vitro dry matter digestibility},
author = {Chen, Shiyu and Kaeppler, Shawn M. and Vogel, Kenneth P. and Casler, Michael D. and Zabotina, Olga A.},
abstractNote = {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. As a result, 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.},
doi = {10.1371/journal.pone.0167005},
journal = {PLoS ONE},
number = 11,
volume = 11,
place = {United States},
year = {2016},
month = {11}
}