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Targeted Switchgrass BAC Library Screening and Sequence Analysis Identifies Predicted Biomass and Stress Response-Related Genes

Journal Article · · BioEnergy Research
 [1];  [1];  [2];  [3];  [4];  [4];  [5];  [5];  [4];  [6]
  1. Univ. of California, Davis, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Jawaharlal Nehu Univ., New Delhi (India)
  2. Zhengzhou Tobacco Research Inst. (China)
  3. Univ. of California, Davis, CA (United States)
  4. HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. Samuel Roberts Noble Foundation, Ardmore, OK (United States)
  6. Univ. of California, Davis, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
+ Show Author Affiliations
To identify switchgrass homologs of rice genes, known/predicted to control biomass and stress response-related traits, we screened 96,000 clones from two switchgrass bacterial artificial chromosome (BAC) libraries. Full-length sequencing of 311 BAC clones revealed sequence for ~3.2 % (51.7 Mb) of the switchgrass genome, coding for 3948 genes. A comparison with Arabidopsis and five grass genomes revealed that switchgrass genes share the highest number of homologs with rice (95.5 %) followed by foxtail millet (91.7 %) and Sorghum (91.5 %). One hundred eighteen of the annotated genes are unique to switchgrass. Gene annotation and ontology analysis revealed 695 genes belonging to gene families targeted in the screening. These include 350 kinase, 203 glycosyltransferase (GT), 109 glycoside hydrolase (GH), and 33 ethylene responsive transcription factor (ERF) family genes. Rice homologs of 65 genes, identified here, have demonstrated roles in bioenergy-relevant traits. These include 14 GT2 family genes involved in the synthesis of cellulose and hemicelluloses. Finally, comparative expression analysis in six switchgrass organs revealed a conserved expression pattern for three cellulose synthase (CesA1, CesA2, and CesA9) and five cellulose-synthase-like genes (CslA2, CslA11, CslC1, CslD4, and CslE6). CslF genes that encode mixed linkage glucans are expressed in wider range of tissues in switchgrass compared with rice.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
National Science Foundation (NSF); USDOE Office of Science (SC)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1619073
Journal Information:
BioEnergy Research, Journal Name: BioEnergy Research Journal Issue: 1 Vol. 9; ISSN 1939-1234
Publisher:
SpringerCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (4)

Comparative Transcriptomic Analyses of Differentially Expressed Genes in Transgenic Melatonin Biosynthesis Ovine HIOMT Gene in Switchgrass journal November 2016
Quantitative Trait Loci for Freezing Tolerance in a Lowland x Upland Switchgrass Population journal March 2019
Influence of PGPB Inoculation on HSP70 and HMA3 Gene Expression in Switchgrass under Cadmium Stress journal November 2019
Sweet sorghum as biofuel feedstock: recent advances and available resources journal June 2017

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
BAC library
biofuel
cellulose synthase
glycoside hydrolase
glycosyltransferase
kinase
screening
stress and switchgrass