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Amaranthus tricolor  L. is a C 4  plant, which is consumed as a major leafy vegetable in some tropical countries. Under conditions of high temperature and short daylight,  Am. tricolor  readily bolts and blooms, degrading leaf quality. A preliminary  in vitro  flowering study demonstrated that the flowering control pathway in  Am. tricolor  may differ from that of  Arabidopsis . Nevertheless, no transcriptome analysis of the flowering process in  Amaranthus  has been conducted. To study  Am. tricolor  floral regulatory mechanisms, we conducted a large-scale transcriptome analysis—based on Illumina HiSeq sequencing of cDNA libraries generated from  Am. tricolor  at young seedling (YSS), adult seedling (ASS), flower bud (FBS), and flowering (FS) stages. A total of 99,312 unigenes were obtained. Using BLASTX, 43,088 unigenes (43.39%) were found to have significant similarity with accessions in Nr, Nt, and Swiss-Prot databases. Of these unigenes, 11,291 were mapped to 266 KEGG pathways. Further analysis of the four digital transcriptomes revealed that 735, 17,184, 274, and 206 unigenes were specifically expressed during YSS, ASS, FBS, and FS, respectively, with 59,517 unigenes expressed throughout the four stages. These unigenes were involved in many metabolic pathways related to  in vitro  flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for  in vitro  flowering in  Am. tricolor . Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from  Am. tricolor  at YSS, ASS, FBS, and FS; their differential expressions at the various stages indicate their possible roles in  Am. tricolor  growth and development, but the results were somewhat similar to  Arabidopsis . Because unigenes involved in many metabolic pathways or of unknown function were revealed to regulate  in vitro  plantlet growth and flowering in  Am. tricolor , the process appears to be highly complex in this species.

plos one

Transcriptome Analysis by Illumina High-Throughout Paired-End Sequencing Reveals the Complexity of Differential Gene Expression during In Vitro Plantlet Growth and Flowering in Amaranthus tricolor L.