Transcriptome in two sugarcane varieties under low nitrogen stress

Leaves (RLT, RLCK,BLT, and BLCK) and roots (RRT, RRCK,BRT, and BRCK) in sugarcane varieties ROC22 and Badila under low nitrogen condition were selected for RNA-Seq analysis. In RNA-Seq, 237.4 Gb of data was obtained from 24 samples. The Q20 of the sequencing data was higher than 96.0%, and Q30 was above 90.5%. A total of 976,881 transcripts and 482,675 unigenes were obtained. The unigene splicing length (N50) was over the size of 1,200 bp. In the leaves, under low N stress, the number of differentially expressed genes (DEGs, 11,953) in the leaves of ROC22 were significantly higher than that of Badila (4,874) under low N stress, and the number of upregulated DEGs (6,003) was higher than that of downregulated (5,950) DEGs in the leaves of ROC22. In the roots, under low N stress, the number of DEGs in DRR was 3,153, including 2,195 upregulated and 958 downregulated. The number of DEGs in DBR was 1,521, including 1,171 upregulated and 350 downregulated. This study may explain the observed differences in low N tolerance between ROC22 and Badila. This study has provided a basis for improvement of sugarcane in adapting to low N conditions.