Location: Sugarcane ResearchTitle: Identification of cold-responsive genes in energycane for their use in genetic diversity analysis and future functional marker development Author
Submitted to: Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/3/2013
Publication Date: 7/18/2013
Publication URL: http://handle.nal.usda.gov/10113/63057
Citation: Khan, N.A., Bedre, R., Parco, A., Bernaola, L., Hale, A.L., Kimbeng, C., Pontif, M., Baisakh, N. 2013. Identification of cold-responsive genes in energycane for their use in genetic diversity analysis and future functional marker development. Plant Science. 211:122-131. Interpretive Summary: Sugarcane is a tropical crop that has not traditionally performed well in cold environments. Because of the crop’s ability to rapidly accumulate biomass, it is of interest as dedicated crop for bioenergy production in temperate environments. Molecular markers have the potential to hasten the process of breeding for cold-adapted sugarcane varieties and energycane selected strictly for use as a biofuel feedstock. The objective of this study was to identify sections of DNA that are highly related to cold tolerance in sugarcane. One cold tolerant energycane variety, Ho 02-144, and one sensitive one, L 79-1002, were subjected to cold temperatures in a growth chamber. Gene products were measured that indicated which genes were differentially expressed between the two varieties. Two hundred sixty genes related to cold response were identified. Research is ongoing to determine which of these genes are directly correlated with cold tolerance.
Technical Abstract: Breeding for cold tolerance in sugarcane will allow its cultivation as a dedicated biomass crop in cold environments. Development of functional markers to facilitate marker-assisted breeding requires identification of cold stress tolerance genes. Using suppression subtractive hybridization, 465 cold-responsive genes were isolated from the cold-tolerant energycane Ho02-144. Predicted gene interactions network indicated several associated pathways that may coordinately regulate cold tolerance responses in energycane. Expression analysis of a select set of genes, representing signaling and transcription factors, genes involved in polyamine and antioxidant biosynthesis, protein degradation and in the repair of damaged proteins in the cytosol, showed their time-dependent regulation under cold-stress. Comparative expression profiles of these genes between Ho02-144 and a cold-sensitive clone (L79-1002) showed that almost all genes were induced immediately upon imposition of cold stress and maintained their expression in Ho02-144 whereas they were either downregulated or their upregulation was very low in L79-1002. Simple sequence repeat markers derived from 260 cold-responsive genes showed allelic diversity among the cold-sensitive commercial hybrids that were distinct from the Saccharum spontaneum clones. Future efforts will target sequence polymorphism information of these genes in our ongoing QTL and association mapping studies to identify functional markers associated with cold tolerance in sugar/energycane.