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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 #321047

Research Project: Genetic Enhancement of Sorghum as a Versatile Crop

Location: Plant Stress and Germplasm Development Research

Title: Transcriptome analysis and SNP validation in sorghum using RNA seq data from germplasm with differential response to cold tolerance.

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

Submitted to: Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 9/15/2015
Publication Date: 9/15/2015
Citation: urow, G.B., Chopra, R., Burke, J.J., Xin, Z., Emendack, Y., Chen, J., Hayes, C.M. 2015. Transcriptome analysis and SNP validation in sorghum using RNA seq data from germplasm with differential response to cold tolerance. p.1.

Interpretive Summary:

Technical Abstract: Currently there is a critical need for breeder friendly, easy access and high troughput single nucleotide polymorphic (SNP) markers in implementation of molecular breeding for sorghum improvement. To address this need 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.