skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data

Authors:
ORCiD logo [1];  [2];  [3];  [3];  [3];  [3];  [4];  [5];  [6];  [7];  [1]
  1. US Dairy Forage Research Center, USDA-ARS, 1925 Linden Dr. W Madison WI 53706 USA
  2. DuPont Pioneer, Johnston IA 50131 USA, Department of Plant Biology, Michigan State University, East Lansing MI 48824 USA, DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing MI 48824 USA
  3. DOE Joint Genome Institute, Walnut Creek CA 94598 USA
  4. Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr Madison WI 53706 USA
  5. Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr Madison WI 53706 USA, DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave Madison WI 53726 USA
  6. Department of Plant Biology, Michigan State University, East Lansing MI 48824 USA, DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing MI 48824 USA
  7. Department of Agronomy, Purdue University, 915 West State Street West Lafayette IN 47907 USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1401223
Grant/Contract Number:
FC02-07ER64494; AC02-05CH11231; SC0010631; SC0008180
Resource Type:
Journal Article: Publisher's Accepted Manuscript
Journal Name:
New Phytologist
Additional Journal Information:
Journal Volume: 213; Journal Issue: 1; Related Information: CHORUS Timestamp: 2017-10-20 16:54:35; Journal ID: ISSN 0028-646X
Publisher:
Wiley-Blackwell
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Grabowski, Paul P., Evans, Joseph, Daum, Chris, Deshpande, Shweta, Barry, Kerrie W., Kennedy, Megan, Ramstein, Guillaume, Kaeppler, Shawn M., Buell, C. Robin, Jiang, Yiwei, and Casler, Michael D. Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data. United Kingdom: N. p., 2016. Web. doi:10.1111/nph.14101.
Grabowski, Paul P., Evans, Joseph, Daum, Chris, Deshpande, Shweta, Barry, Kerrie W., Kennedy, Megan, Ramstein, Guillaume, Kaeppler, Shawn M., Buell, C. Robin, Jiang, Yiwei, & Casler, Michael D. Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data. United Kingdom. doi:10.1111/nph.14101.
Grabowski, Paul P., Evans, Joseph, Daum, Chris, Deshpande, Shweta, Barry, Kerrie W., Kennedy, Megan, Ramstein, Guillaume, Kaeppler, Shawn M., Buell, C. Robin, Jiang, Yiwei, and Casler, Michael D. Fri . "Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data". United Kingdom. doi:10.1111/nph.14101.
@article{osti_1401223,
title = {Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data},
author = {Grabowski, Paul P. and Evans, Joseph and Daum, Chris and Deshpande, Shweta and Barry, Kerrie W. and Kennedy, Megan and Ramstein, Guillaume and Kaeppler, Shawn M. and Buell, C. Robin and Jiang, Yiwei and Casler, Michael D.},
abstractNote = {},
doi = {10.1111/nph.14101},
journal = {New Phytologist},
number = 1,
volume = 213,
place = {United Kingdom},
year = {Fri Jul 22 00:00:00 EDT 2016},
month = {Fri Jul 22 00:00:00 EDT 2016}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1111/nph.14101

Citation Metrics:
Cited by: 4works
Citation information provided by
Web of Science

Save / Share:
  • Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between themore » populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.« less
  • Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, providemore » better treatment options for patients. It may also provide information for development of assays that can rapidly identify Cipro-resistant isolates of this pathogen. In this study, we then selected a large number of F. tularensis live vaccine strain (LVS) isolates that survived in progressively higher Ciprofloxacin concentrations, screened the isolates using a whole genome F. tularensis LVS tiling microarray and Illumina sequencing, and identified both known and novel mutations associated with resistance. For genes containing mutations encode DNA gyrase subunit A, a hypothetical protein, an asparagine synthase, a sugar transamine/perosamine synthetase and others. Finally, structural modeling performed on these proteins provides insights into the potential function of these proteins and how they might contribute to Cipro resistance mechanisms.« less
  • Over the past two decades, switchgrass (Panicum virgatum) has emerged as a priority biofuel feedstock. The bulk of switchgrass biomass is in the vegetative portion of the plant; therefore, increasing the length of vegetative growth will lead to an increase in overall biomass yield. The goal of this study was to gain insight into the control of flowering time in switchgrass that would assist in development of cultivars with longer vegetative phases through delayed flowering. RNA sequencing was used to assess genome-wide expression profiles across a developmental series between switchgrass genotypes belonging to the two main ecotypes: upland, typically earlymore » flowering, and lowland, typically late flowering. Leaf blades and tissues enriched for the shoot apical meristem (SAM) were collected in a developmental series from emergence through anthesis for RNA extraction. RNA from samples that flanked the SAM transition stage was sequenced for expression analyses. The analyses revealed differential expression patterns between early- and late-flowering genotypes for known flowering time orthologs. Namely, genes shown to play roles in photoperiod response and the circadian clock in other species were identified as potential candidates for regulating flowering time in the switchgrass genotypes analyzed. Based on their expression patterns, many of the differentially expressed genes could also be classified as putative promoters or repressors of flowering. The candidate genes presented here may be used to guide switchgrass improvement through marker-assisted breeding and/or transgenic or gene editing approaches.Over the past two decades, switchgrass (Panicum virgatum) has emerged as a priority biofuel feedstock. The bulk of switchgrass biomass is in the vegetative portion of the plant; therefore, increasing the length of vegetative growth will lead to an increase in overall biomass yield. The goal of this study was to gain insight into the control of flowering time in switchgrass that would assist in development of cultivars with longer vegetative phases through delayed flowering. RNA sequencing was used to assess genome-wide expression profiles across a developmental series between switchgrass genotypes belonging to the two main ecotypes: upland, typically early flowering, and lowland, typically late flowering. Leaf blades and tissues enriched for the shoot apical meristem (SAM) were collected in a developmental series from emergence through anthesis for RNA extraction. RNA from samples that flanked the SAM transition stage was sequenced for expression analyses. The analyses revealed differential expression patterns between early- and late-flowering genotypes for known flowering time orthologs. Namely, genes shown to play roles in photoperiod response and the circadian clock in other species were identified as potential candidates for regulating flowering time in the switchgrass genotypes analyzed. Based on their expression patterns, many of the differentially expressed genes could also be classified as putative promoters or repressors of flowering. The candidate genes presented here may then be used to guide switchgrass improvement through marker-assisted breeding and/or transgenic or gene editing approaches.« less
  • Over the past two decades, switchgrass (Panicum virgatum) has emerged as a priority biofuel feedstock. The bulk of switchgrass biomass is in the vegetative portion of the plant; therefore, increasing the length of vegetative growth will lead to an increase in overall biomass yield. The goal of this study was to gain insight into the control of flowering time in switchgrass that would assist in development of cultivars with longer vegetative phases through delayed flowering. RNA sequencing was used to assess genome-wide expression profiles across a developmental series between switchgrass genotypes belonging to the two main ecotypes: upland, typically earlymore » flowering, and lowland, typically late flowering. Leaf blades and tissues enriched for the shoot apical meristem (SAM) were collected in a developmental series from emergence through anthesis for RNA extraction. RNA from samples that flanked the SAM transition stage was sequenced for expression analyses. The analyses revealed differential expression patterns between early- and late-flowering genotypes for known flowering time orthologs. Namely, genes shown to play roles in photoperiod response and the circadian clock in other species were identified as potential candidates for regulating flowering time in the switchgrass genotypes analyzed. Based on their expression patterns, many of the differentially expressed genes could also be classified as putative promoters or repressors of flowering. The candidate genes presented here may be used to guide switchgrass improvement through marker-assisted breeding and/or transgenic or gene editing approaches.Over the past two decades, switchgrass (Panicum virgatum) has emerged as a priority biofuel feedstock. The bulk of switchgrass biomass is in the vegetative portion of the plant; therefore, increasing the length of vegetative growth will lead to an increase in overall biomass yield. The goal of this study was to gain insight into the control of flowering time in switchgrass that would assist in development of cultivars with longer vegetative phases through delayed flowering. RNA sequencing was used to assess genome-wide expression profiles across a developmental series between switchgrass genotypes belonging to the two main ecotypes: upland, typically early flowering, and lowland, typically late flowering. Leaf blades and tissues enriched for the shoot apical meristem (SAM) were collected in a developmental series from emergence through anthesis for RNA extraction. RNA from samples that flanked the SAM transition stage was sequenced for expression analyses. The analyses revealed differential expression patterns between early- and late-flowering genotypes for known flowering time orthologs. Namely, genes shown to play roles in photoperiod response and the circadian clock in other species were identified as potential candidates for regulating flowering time in the switchgrass genotypes analyzed. Based on their expression patterns, many of the differentially expressed genes could also be classified as putative promoters or repressors of flowering. The candidate genes presented here may then be used to guide switchgrass improvement through marker-assisted breeding and/or transgenic or gene editing approaches.« less