title: Transcriptome profiling and validation of gene based single nucleotide polymorphisms (SNPs) in sorghum genotypes with contrasting responses to cold stress.
abstract: BACKGROUND
  Sorghum is a versatile cereal crop, with excellent heat and drought tolerance. However, it is susceptible to early-season cold stress (12-15 °C) which limits stand-establishment and seedling growth. To gain further insights on the molecular mechanism of cold tolerance in sorghum we performed transcriptome profiling between known cold sensitive and tolerant sorghum lines using RNA sequencing technology under control and cold stress treatments.
  
  
  RESULTS
  Here we report on the identification of differentially expressed genes (DEGs) between contrasting sorghum genotypes, HongkeZi (cold tolerant) and BTx623 (cold sensitive) under cool and control temperatures using RNAseq approach to elucidate the molecular basis of sorghum response to cold stress. Furthermore, we validated bi-allelic variants in the form of single nucleotide polymorphism (SNPs) between the cold susceptible and tolerant lines of sorghum. An analysis of transcriptome profile showed that in response to cold, a total of 1910 DEGs were detected under cold and control temperatures in both genotypes. We identified a subset of genes under cold stress for downstream analysis, including transcription factors that exhibit differential abundance between the sensitive and tolerant genotypes. We identified transcription factors including Dehydration-responsive element-binding factors, C-repeat binding factors, and Ethylene responsive transcription factors as significantly upregulated during cold stress in cold tolerant HKZ. Additionally, specific genes such as plant cytochromes, glutathione s-transferases, and heat shock proteins were found differentially regulated under cold stress between cold tolerant and susceptible genotype of sorghum. A total of 41,603 SNP were identified between the cold sensitive and tolerant genotypes with minimum read of four. Approximately 89 % of the 114 SNP sites selected for evaluation were validated using endpoint genotyping technology.
  
  
  CONCLUSIONS
  A new strategy which involved an integrated analysis of differential gene expression and identification of bi-allelic single nucleotide polymorphism (SNP) was conducted to determine and analyze differentially expressed genes and variation involved in cold stress response of sorghum. The results gathered provide an insight into the complex mechanisms associated with cold response in sorghum, which involve an array of transcription factors and genes which were previously related to abiotic stress response. This study also offers resource for gene based SNP that can be applied towards targeted genomic studies of cold tolerance in sorghum and other cereal crops.
authors.affiliation: Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA.
authors.forename: Ratan
authors.initials: R
authors.lastname: Chopra
authors.affiliation: Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA. Gloria.burow@ars.usda.gov.
authors.forename: Gloria
authors.initials: G
authors.lastname: Burow
authors.affiliation: Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA.
authors.forename: Chad
authors.initials: C
authors.lastname: Hayes
authors.affiliation: Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA.
authors.forename: Yves
authors.initials: Y
authors.lastname: Emendack
authors.affiliation: Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA.
authors.forename: Zhanguo
authors.initials: Z
authors.lastname: Xin
authors.affiliation: Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, 79415, USA.
authors.forename: John
authors.initials: J
authors.lastname: Burke
mesh_terms: D002874:Chromosome Mapping; D016000:Cluster Analysis; D003080:Cold Temperature; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005838:Genotype; D058977:Molecular Sequence Annotation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D045868:Sorghum / Q000235:genetics*; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome