Format

Send to

Choose Destination
BMC Genomics. 2019 May 27;20(1):420. doi: 10.1186/s12864-019-5734-x.

A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism.

Author information

1
Advanced Plant Technology Program, Clemson University, Clemson, SC, USA. lizcooper@uncc.edu.
2
Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA. lizcooper@uncc.edu.
3
Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA. lizcooper@uncc.edu.
4
Advanced Plant Technology Program, Clemson University, Clemson, SC, USA.
5
Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA.
6
HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
7
Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
8
School of Computing, Clemson University, Clemson, SC, USA.
9
School of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.
10
Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
11
Department of Microbiology and Cell Science and UF Genetics Institute, University of Florida, Gainesville, FL, USA.

Abstract

BACKGROUND:

The process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subsequently adapted to more environments and specialized uses. Selective pressure to increase sugar accumulation in certain varieties of the cereal crop Sorghum bicolor is an excellent example of the latter; this has resulted in pronounced phenotypic divergence between sweet and grain-type sorghums, but the genetic mechanisms underlying these differences remain poorly understood.

RESULTS:

Here we present a new reference genome based on an archetypal sweet sorghum line and compare it to the current grain sorghum reference, revealing a high rate of nonsynonymous and potential loss of function mutations, but few changes in gene content or overall genome structure. We also use comparative transcriptomics to highlight changes in gene expression correlated with high stalk sugar content and show that changes in the activity and possibly localization of transporters, along with the timing of sugar metabolism play a critical role in the sweet phenotype.

CONCLUSIONS:

The high level of genomic similarity between sweet and grain sorghum reflects their historical relatedness, rather than their current phenotypic differences, but we find key changes in signaling molecules and transcriptional regulators that represent new candidates for understanding and improving sugar metabolism in this important crop.

KEYWORDS:

Gene expression; Genomics; Sorghum; Sugar metabolism; Sugar transport

PMID:
31133004
PMCID:
PMC6537160
DOI:
10.1186/s12864-019-5734-x
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center