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Title: Transcriptomic analysis of transgressive segregants revealed the central role of photosynthetic capacity and efficiency in biomass accumulation in sugarcane

Abstract

Sugarcane is among the most efficient crops in converting solar energy into chemical energy. However, due to its complex genome structure and inheritance, the genetic and molecular basis of biomass yield in sugarcane is still largely unknown. We created an F2 segregating population by crossing S. officinarum and S. spontaneum and evaluated the biomass yield of the F2 individuals. The F2 individuals exhibited clear transgressive segregation in biomass yield. We sequenced transcriptomes of source and sink tissues from 12 selected extreme segregants to explore the molecular basis of high biomass yield for future breeding of high-yielding energy canes. Among the 103,664 assembled unigenes, 10,115 and 728 showed significant differential expression patterns between the two extreme segregating groups in the top visible dewlap leaf and the 9th culm internode, respectively. The most enriched functional categories were photosynthesis and fermentation in the high-biomass and the low-biomass groups, respectively. Our results revealed that high-biomass yield was mainly determined by assimilation of carbon in source tissues. The high-level expression of fermentative genes in the low-biomass group was likely induced by their low-energy status. Group-specific expression alleles which can be applied in the development of new high-yielding energy cane varieties via molecular breeding were identified.

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [2];  [5]; ORCiD logo [6]
+ Show Author Affiliations
  1. Texas A & M Univ., College Station, TX (United States)
  2. Hawaii Agriculture Research Center, Kunia, HI (United States)
  3. Univ. of Illinois, Urbana-Champaign, IL (United States)
  4. Texas A & M Univ., Weslaco, TX (United States) AgriLife Research Center
  5. Univ. of Illinois, Urbana-Champaign, IL (United States); Fujian Agriculture and Forestry Univ., Fuzhou (China)
  6. Texas A & M Univ., College Station, TX (United States); Fujian Agriculture and Forestry Univ., Fuzhou (China)
Publication Date:
Research Org.:
Univ. of Illinois at Urbana-Champaign, IL (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1500033
Grant/Contract Number:  
SC0010686
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Singh, Ratnesh, Jones, Tyler, Wai, Ching Man, Jifon, John, Nagai, Chifumi, Ming, Ray, and Yu, Qingyi. Transcriptomic analysis of transgressive segregants revealed the central role of photosynthetic capacity and efficiency in biomass accumulation in sugarcane. United States: N. p., 2018. Web. doi:10.1038/s41598-018-22798-5.
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Singh, Ratnesh, Jones, Tyler, Wai, Ching Man, Jifon, John, Nagai, Chifumi, Ming, Ray, & Yu, Qingyi. Transcriptomic analysis of transgressive segregants revealed the central role of photosynthetic capacity and efficiency in biomass accumulation in sugarcane. United States. https://doi.org/10.1038/s41598-018-22798-5
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Singh, Ratnesh, Jones, Tyler, Wai, Ching Man, Jifon, John, Nagai, Chifumi, Ming, Ray, and Yu, Qingyi. Tue . "Transcriptomic analysis of transgressive segregants revealed the central role of photosynthetic capacity and efficiency in biomass accumulation in sugarcane". United States. https://doi.org/10.1038/s41598-018-22798-5. https://www.osti.gov/servlets/purl/1500033.
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@article{osti_1500033,
title = {Transcriptomic analysis of transgressive segregants revealed the central role of photosynthetic capacity and efficiency in biomass accumulation in sugarcane},
author = {Singh, Ratnesh and Jones, Tyler and Wai, Ching Man and Jifon, John and Nagai, Chifumi and Ming, Ray and Yu, Qingyi},
abstractNote = {Sugarcane is among the most efficient crops in converting solar energy into chemical energy. However, due to its complex genome structure and inheritance, the genetic and molecular basis of biomass yield in sugarcane is still largely unknown. We created an F2 segregating population by crossing S. officinarum and S. spontaneum and evaluated the biomass yield of the F2 individuals. The F2 individuals exhibited clear transgressive segregation in biomass yield. We sequenced transcriptomes of source and sink tissues from 12 selected extreme segregants to explore the molecular basis of high biomass yield for future breeding of high-yielding energy canes. Among the 103,664 assembled unigenes, 10,115 and 728 showed significant differential expression patterns between the two extreme segregating groups in the top visible dewlap leaf and the 9th culm internode, respectively. The most enriched functional categories were photosynthesis and fermentation in the high-biomass and the low-biomass groups, respectively. Our results revealed that high-biomass yield was mainly determined by assimilation of carbon in source tissues. The high-level expression of fermentative genes in the low-biomass group was likely induced by their low-energy status. Group-specific expression alleles which can be applied in the development of new high-yielding energy cane varieties via molecular breeding were identified.},
doi = {10.1038/s41598-018-22798-5},
journal = {Scientific Reports},
number = 1,
volume = 8,
place = {United States},
year = {2018},
month = {3}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1038/s41598-018-22798-5
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Figures / Tables:

Figure 1 Figure 1: Distribution of the stalk volumes of the S. officinarum × S. spontaneum F2 clones.
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Works referenced in this record:

BCFtools/csq: haplotype-aware variant consequences
journal, February 2017

Genome remodelling in three modern S. officinarumxS. spontaneum sugarcane cultivars
journal, March 2004

Supply and demand: sink regulation of sugar accumulation in sugarcane
journal, January 2009

  • McCormick, A. J.; Watt, D. A.; Cramer, M. D.
  • Journal of Experimental Botany, Vol. 60, Issue 2
  • DOI: 10.1093/jxb/ern310

Diurnal Changes in Maize Leaf Photosynthesis: I. Carbon Exchange Rate, Assimilate Export Rate, and Enzyme Activities
journal, February 1987

  • Kalt-Torres, Willy; Kerr, Phillip S.; Usuda, Hideaki
  • Plant Physiology, Vol. 83, Issue 2
  • DOI: 10.1104/pp.83.2.283

mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
journal, March 2004

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
journal, November 2009

RNAmmer: consistent and rapid annotation of ribosomal RNA genes
journal, April 2007

  • Lagesen, Karin; Hallin, Peter; Rødland, Einar Andreas
  • Nucleic Acids Research, Vol. 35, Issue 9
  • DOI: 10.1093/nar/gkm160

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
journal, July 2013

  • Haas, Brian J.; Papanicolaou, Alexie; Yassour, Moran
  • Nature Protocols, Vol. 8, Issue 8
  • DOI: 10.1038/nprot.2013.084

Sink strength regulates photosynthesis in sugarcane
journal, September 2006

Fast gapped-read alignment with Bowtie 2
journal, March 2012

  • Langmead, Ben; Salzberg, Steven L.
  • Nature Methods, Vol. 9, Issue 4
  • DOI: 10.1038/nmeth.1923

Regulation of Respiration and Fermentation to Control the Plant Internal Oxygen Concentration
journal, December 2008

  • Zabalza, Ana; van Dongen, Joost T.; Froehlich, Anja
  • Plant Physiology, Vol. 149, Issue 2
  • DOI: 10.1104/pp.108.129288

The Brazilian biofuels industry
journal, January 2008

Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen
journal, January 2001

  • Krogh, Anders; Larsson, Björn; von Heijne, Gunnar
  • Journal of Molecular Biology, Vol. 305, Issue 3
  • DOI: 10.1006/jmbi.2000.4315

Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers
journal, July 2001

  • Hoarau, J. -Y.; Offmann, B.; D’Hont, A.
  • Theoretical and Applied Genetics, Vol. 103, Issue 1
  • DOI: 10.1007/s001220000390

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011

  • Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
  • Nature Methods, Vol. 8, Issue 10
  • DOI: 10.1038/nmeth.1701

Characterisation of the double genome structure of modern sugarcane cultivars (
journal, January 1996

  • D’Hont, Angélique; Grivet, Laurent; Feldmann, Philippe
  • MGG Molecular & General Genetics, Vol. 250, Issue 4
  • DOI: 10.1007/s004380050092

QTL Analysis in a Complex Autopolyploid: Genetic Control of Sugar Content in Sugarcane
journal, November 2001

Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes
journal, April 1998

  • D'Hont, Angélique; Ison, David; Alix, Karine
  • Genome, Vol. 41, Issue 2
  • DOI: 10.1139/g98-023

Carbon Partitioning during Sucrose Accumulation in Sugarcane Internodal Tissue
journal, December 1997

Extensive Allelic Variation in Gene Expression in Populus F 1 Hybrids
journal, December 2007

Full-length transcriptome assembly from RNA-Seq data without a reference genome
journal, May 2011

  • Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran
  • Nature Biotechnology, Vol. 29, Issue 7
  • DOI: 10.1038/nbt.1883

Pfam: the protein families database
journal, November 2013

  • Finn, Robert D.; Bateman, Alex; Clements, Jody
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1223

What is the maximum efficiency with which photosynthesis can convert solar energy into biomass?
journal, April 2008

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
journal, August 2011

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data: Mercator: sequence functional annotation server
journal, December 2013

  • Lohse, Marc; Nagel, Axel; Herter, Thomas
  • Plant, Cell & Environment, Vol. 37, Issue 5
  • DOI: 10.1111/pce.12231

Coordination of carbon supply and plant growth
journal, September 2007

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
journal, April 2013

  • Mistry, Jaina; Finn, Robert D.; Eddy, Sean R.
  • Nucleic Acids Research, Vol. 41, Issue 12
  • DOI: 10.1093/nar/gkt263

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes
journal, January 2010

Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants
journal, April 2015

A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar
journal, February 2005

  • Aitken, K. S.; Jackson, P. A.; McIntyre, C. L.
  • Theoretical and Applied Genetics, Vol. 110, Issue 5
  • DOI: 10.1007/s00122-004-1813-7

Plants to power: bioenergy to fuel the future
journal, August 2008

Taxonomy and Evolution
journal, June 1933

Transcriptional profiling of two contrasting genotypes uncovers molecular mechanisms underlying salt tolerance in alfalfa
journal, March 2021

Diurnal Changes in Maize Leaf Photosynthesis: II. Levels of Metabolic Intermediates of Sucrose Synthesis and the Regulatory Metabolite Fructose 2,6-Bisphosphate
journal, February 1987

  • Usuda, Hideaki; Kalt-Torres, Willy; Kerr, Phillip S.
  • Plant Physiology, Vol. 83, Issue 2
  • DOI: 10.1104/pp.83.2.289

Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission
journal, February 2021

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    Works referencing / citing this record:

    Suberin and hemicellulose in sugarcane cell wall architecture and crop digestibility: A biotechnological perspective
    journal, February 2019

    • Figueiredo, Raquel; Araújo, Pedro; Llerena, Juan Pablo P.
    • Food and Energy Security, Vol. 8, Issue 3
    • DOI: 10.1002/fes3.163
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