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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #318937

Research Project: Genetic Enhancement of Sorghum as a Versatile Crop

Location: Plant Stress and Germplasm Development Research

Title: Translational genomics for abiotic stress in sorghum: transcriptional profiling and validation of SNP markers between germplasm with differential cold tolerance

Author
item Chopra, Ratan
item Burow, Gloria
item Chen, Junping
item Hayes, Chad
item Burke, John
item Xin, Zhanguo
item Emendack, Yves - Orise Fellow

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/29/2015
Publication Date: 9/1/2015
Citation: Chopra, R., Burow, G.B., Chen, J., Hayes, C.M., Burke, J.J., Xin, Z., Emendack, Y. 2015. Translational genomics for abiotic stress in sorghum: transcriptional profiling and validation of SNP markers between germplasm with differential cold tolerance [abstract]. Sorghum Improvement Conference of North America, Setpember 1-3, 2015, Manhattan, Kansas. p. 1.

Interpretive Summary:

Technical Abstract: One focus of the Sorghum Translational Genomics Lab (part of sorghum CRIS, PSGD, CSRL, USDA-ARS, Lubbock TX) 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 molecular and marker assisted breeding. In this report, 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-allelic, single nucleotide polymorphic variants between the susceptible and tolerant lines. Expression analysis showed that in response to cold, a total of 1,903 differentially expressed genes were detected during cold stress treatment in both genotypes. A number of transcription factors were differentially expressed under stress between the sensitive and tolerant genotypes including Dehydration-responsive element-binding factors, C-repeat binding factors, and Ethylene responsive transcription factors. A set of gene transcripts including; 27 Plant Cytochromes, 7 Glutathione S-Transferases, and 20 Heat Shock proteins displayed prominent differential expression under cold stress. A total of 41,603 SNPs were identified between the sensitive and tolerant genotypes with minimum read of 4 using Alpheus pipeline. A total 100 SNP markers between the lines were validated thru endpoint genotyping method. These results provide an insight into the complex mechanisms involved in cold tolerance in sorghum, and provide genomic foundation for future studies on cold tolerance in sorghum and other cereal crops. Here the SNPs identified and validated between the tolerant and sensitive lines demonstrated translation of variation from RNA seq analysis into easily usable DNA marker format for downstream applications of genetic mapping and molecular breeding.