Objective  Mechanism of red bud taro in response to cryotherapy was studied by transcriptome analysis for extended application of the virus-free seedlings at Yanshan, Jiangxi.

  Method  Transcriptomes of virus-free (VF) and virus-carrying (V) red bud taro plantlets that had been cryo-therapeutically treated were analyzed and compared.

  Result  In the VF plantlets, the clean reads were 42 406 188 with a GC content of 54.09%; while, in the V plantlets, the clean reads were 46 818 060 with a GC content of 50.36%. For either group, the FPKM was between 0-2, and the expression density between 0-0.8. There were 23 820 genes commonly expressed in both VF and V, while 4 477 independently expressed in VF, and 10 298 in V. There was a low correlation between VF and V with a coefficient of 0.287, and were 5 282 differentially expressed genes (DEG) in them. Compared to V, VF had 3 011 genes were up-regulated and 2 271 down-regulated. The Go enrichment analysis showed that the differential genes were annotated mainly in the processes of hydrogen peroxide catabolism, hydrogen peroxide metabolism, monocarboxylic acid biosynthesis, and polysaccharide catabolism, metal ion transport, extracellular region, cell wall, external encapsulating structure, intrinsic components of membrane and plasma membrane as well as the activities of nucleic acid binding transcription factor, transcription factor, sequence-specific DNA binding, monooxygenase, iron ion binding, heme binding, etc. The KEGG enrichment analysis indicated that the differential genes were annotated largely to the biosynthesis of phenylpropanoid, flavonoid, stilbenoid, diarylheptanoid, gingerol, carotenoid, isoquinoline alkaloid, ubiquinone, and other terpenoid-quinones, the metabolisms of starch, sucrose, tyrosine, alpha-Linolenic acid, phenylalanine, cyanoamino acid, glycine, serine, threonine, fructose, mannose, galactose, amino sugar, and nucleotide sugar, and the pathways of MAPK signaling-plant, plant hormone signal transduction, pentose and glucuronate interconversions, peroxisome, circadian rhythm-plant, and others,

  Conclusion  The genes of F-box family protein, abscisic acid receptor PYR1, ethylene receptor 2, auxin response factor 1, BZIP transcription factor family protein, peroxidase, catalase 1, superoxide dismutase Cu-Zn, plant disease resistance response protein, disease resistance protein, disease resistance protein RPS2, disease resistance protein RPS5, disease resistance protein RGA2, disease resistance response protein, retrovirus-related Pol polyprotein from transposon TNT, retrovirus-related Pol polyprotein LINE-1, tobamovirus multiplication protein 3-like, tobamovirus multiplication protein 1, retrovirus-related Pol polyprotein from transposon RE1, sucrose synthase, etc. were the predominant genes in the virus-free red bud taro plantlets that responded to the cryotherapy.