Transcriptomic Identification of Drought-Related Genes and SSR Markers in Sudan Grass Based on RNA-Seq

Frontiers in Plant Science
Yongqun ZhuDandan Peng

Abstract

Sudan grass (Sorghum sudanense) is an annual warm-season gramineous forage grass that is widely used as pasture, hay, and silage. However, drought stress severely impacts its yield, and there is limited information about the mechanisms of drought tolerance in Sudan grass. In this study, we used next-generation sequencing to identify differentially expressed genes (DEGs) in the Sudan grass variety Wulate No.1, and we developed simple sequence repeat (SSR) markers associated with drought stress. From 852,543,826 raw reads, nearly 816,854,366 clean reads were identified and used for analysis. A total of 80,686 unigenes were obtained via de novo assembly of the clean reads including 45,065 unigenes (55.9%) that were identified as coding sequences (CDSs). According to Gene Ontology analysis, 31,444 unigenes were annotated, 11,778 unigenes were identified to 25 categories in the clusters of orthologous groups of proteins (KOG) classification, and 11,223 unigenes were assigned to 280 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Additionally, there were 2,329 DEGs under a short-term of 25% polyethylene glycol (PEG) treatment, while 5,101 DEGs were identified under the long-term of 25% PEG treatment. DEGs were enriched in pa...Continue Reading

References

Sep 30, 1975·Annals of the New York Academy of Sciences·C R DawsonK G Krul
Apr 19, 2002·Genome Génome / Conseil National De Recherches Canada·Ying WangAlbert G Abbott
May 10, 2002·Plant Molecular Biology·A C SanchezH T Nguyen
Dec 14, 2002·Plant Physiology·Joel A KrepsJeff F Harper
Sep 15, 2005·Plant Molecular Biology·Christina D BuchananJohn E Mullet
Nov 1, 2006·Journal of Experimental Botany·Kazuo Shinozaki, Kazuko Yamaguchi-Shinozaki
Jun 5, 2007·Genome Génome / Conseil National De Recherches Canada·Y Q Wu, Yinghua Huang
Dec 14, 2007·Nucleic Acids Research·Minoru KanehisaYoshihiro Yamanishi
Jan 10, 2008·Archives of Environmental Contamination and Toxicology·Lan WeiZhenguo Shen
May 1, 2008·Nucleic Acids Research·Stefan GötzAna Conesa
Jun 12, 2009·BMC Plant Biology·Shunxue TangSteven J Knapp
Nov 17, 2009·Biotechnology Advances·M Ashraf
Feb 6, 2010·Genome Biology·Matthew D YoungAlicia Oshlack
Aug 10, 2010·Genome Research·Yann Surget-Groba, Juan I Montoya-Burgos
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Jan 31, 2012·Plant Physiology and Biochemistry : PPB·Farah DeebaVivek Pandey
Jan 11, 2014·Functional & Integrative Genomics·Arun K ShankerB Venkateswarlu
Feb 14, 2014·PloS One·Claudio Benicio Cardoso-SilvaRenato Vicentini
Mar 25, 2014·Frontiers in Plant Science·Yuriko OsakabeLam-Son P Tran
Mar 1, 2013·Applications in Plant Sciences·Samuel E FoxPankaj Jaiswal
May 6, 2016·Frontiers in Plant Science·Xiu HuangYan-Hong Yan

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRP095822

Methods Mentioned

BETA
RNA-Seq
transgenic
electrophoresis
PCR
protein folding
genotyping

Software Mentioned

blast
DESeq R
blastx
PFAM
MISA
Trinity
house Perl scripts
HMMER
DESeq
GOseq R package

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.