Transcriptome profiling and validation of gene based single nucleotide polymorphism (SNP) markers in sorghum genotypes with contrasting response to cold stress

Authors: Chopra, Ratan; Burow, Gloria; Hayes, Chad; EMANDACK, YVES - Orise Fellow; Burke, John; Xin, Zhanguo

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/1/2015
Publication Date: 12/9/2015
Citation: Chopra, R., Burow, G.B., Hayes, C.M., Emandack, Y., Burke, J.J., Xin, Z. 2015. Transcriptome profiling and validation of gene based single nucleotide polymorphism (SNP) markers in sorghum genotypes with contrasting response to cold stress. Biomed Central (BMC) Genomics. 16:1-11.

Interpretive Summary: Our goal for translational genomics is to utilize nucleotide variation between sorghum germplasm such as those derived from RNA seq for translation and validation of Single Nucleotide Polymorphism (SNP) into easy access DNA markers for application inmolecular and marker assisted breeding. Here we show that genomic analysis of transcriptome thru RNA seq technology can be utilized simultaneously for identifying differentially expressed genes during cold stress and development of a catalogue validatedof SNP variation. Differentially expressed genes between BTX623(cold sensitive) and HongKeZi (cold tolerant) sorghum germplasm were analyzed under two temperature ( 14C vs 28C). Further, bi-alleic, single nucleotide polymorphic variants between the two germplasm were identified and a subset of 114 SNPs were validated . Expression results showed that in response to cold, a total of 1,903 differentially expressed genes were detected during cold stress in both genotypes. A number of transcription factors were differentially regulated under stress between the sensitive and tolerant genotypes including Dehydration-responsive element-binding factors, C-repeat binding factors, and Ethylene responsive transcription factors. Other genes such as Plant Cytochromes, Glutathione S-Transferases, and Heat Shock proteins were also differentially regulated under stress. A total of 41,603 SNP were found between the sensitive and tolerant genotypes with minimum read of 4 were identified. These results provide an insight into the complex mechanisms involved in chilling tolerance in sorghum, and provide a foundation for future studies on chilling tolerance in sorghum and other cereal crops. The SNPs identified between the tolerant and sensitive lines could be useful in identifying QTLs in the recombinant inbred lines or germplasm for early-season cold tolerance

Technical Abstract: 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 seriously limits stand-establishment and seedling growth. To gain further insight on the molecular mechanism of cold tolerance in sorghum we performed transcriptome profiling between cold sensitive and tolerant sorghum lines using RNA sequencing technology under control and cold stress treatments. We identified differentially expressed genes between contrasting germplasm under each temperature stress and validated bi-alleic, single nucleotide polymorphic variants between the susceptible and tolerant lines. Expression results showed that in response to cold, a total of 1,903 differentially expressed genes were detected during cold stress in both genotypes. A number of transcription factors were differentially regulated under stress between the sensitive and tolerant genotypes including Dehydration-responsive element-binding factors, C-repeat binding factors, and Ethylene responsive transcription factors. Other genes such as Plant Cytochromes, Glutathione S-Transferases, and Heat Shock proteins were also differentially regulated under stress and have been known to be previously involved in stress defense, about 27, 7 and 20 transcripts were differentially expressed respectively. A total of 41,603 SNP were found between the sensitive and tolerant genotypes with minimum read of 4 were identified. These results provide an insight into the complex mechanisms involved in chilling tolerance in sorghum, and provide a foundation for future studies on chilling tolerance in sorghum and other cereal crops. SNPs identified between the tolerant and sensitive lines could be useful in identifying QTLs in the recombinant inbred lines or germplasm for early-season cold tolerance