Transcriptome profiling and validation of gene based single nucleotide polymorphisms (SNPs) in sorghum genotypes with contrasting responses to cold stress

Ratan Chopra, Gloria Burow, Chad Hayes, Yves Emendack, Zhanguo Xin, John Burke

Research output: Contribution to journalArticlepeer-review

29 Scopus citations


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. Conclusion: 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.

Original languageEnglish (US)
Article number1040
JournalBMC Genomics
Issue number1
StatePublished - Dec 9 2015
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2015 Chopra et al.

Copyright 2015 Elsevier B.V., All rights reserved.


  • Cold stress
  • Gene based variants
  • RNAseq
  • Single nucleotide polymorphism
  • Sorghum
  • Transcriptome profiling

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