Bulb onion (Allium cepa) is one of the second most widely cultivated and consumed vegetable crops in the world. During winter where the temperature can be as low, plant could get cold injury and limit the production of bulb onion. However, the genomic resources available for bulb onion are still very limited. To date, no studies about heritably durable cold and freezing tolerance were carried out in bulb onion genotypes using high-throughput sequencing technology was applied. We sequenced cold (2°C) freezing (-5 and -15°C) treated and control (25°C) samples of contrasting genotypes of A. cepa lines and obtained 4,52,194,370 total high quality reads. After de novo assembly reads were assembled into 54,047 genes finally generated with an average length of 1,331 bp. Based on the similarity search aligning all genes with known public non-redundant (NR) database, including Swiss-prot, KEGG and COG. Differentially expressed genes (DEGs) were investigated using FPKM method. Overall, 92,862 genes were differentially regulated in all libraries were identified. Additionally, increase our understanding of the DEGs, we performed GO and KEGG pathway enrichment analyses. Based on FDR<=0.01 value in cold freezing tolerant line candidate genes were selected and discussed. Finally 25 candidate genes were examined using qRT-PCR were differentially regulated and known to be associated with cold and freezing stresses. Moreover, in silico prediction of putative molecular marker 4,437 SSRs and 6,076 SNPs. Our study is the first to provide the transcriptome sequence resource of Allium spp., for cold and freezing stress. We identified large set of genes to determine its DEGs profile under cold and freezing condition using two different genotypes. These data provides a valuable resource of genetic and genomic studies of Allium spp.

Onion and other Allium vegetables have been valued since antiquity for their pungent flavor and aroma. Modern science has confirmed traditional benefits that the organosulfur compounds that impart flavor also confer significant human health benefits such as reduced blood clotting and antimicrobial properties. Glucose, fructose and sucrose comprises majority of onion bulb dry matter content. The sugars, pyruvic acid accumulation and transcript level of some transcription factors involved in the biosynthesis of high sugars and pyruvic acid. These profiles were compared with two different lines 36101 (early) and 36122(Late) of bulb onion (Allium cepa L.) growing under drought and photoperiod condition using High Performance Liquid Chromatography (HPLC) and Quantitative real time PCR using FT genes. We identified the gene AcFT4 was responsible for early and late bulb intiation in the onion lines. The cultivar lines 36101and 36122 were used to identify potential genes controlling pungency and sugar. The comparative analysis of two lines showed significant positive phenotypic and genetic correlations. Sugar and pungency profile showed significant difference between two lines. FT gene expression and pungency level was high in onion lines during drought stress. In this study, we proposed the biochemical characterization of two line and genes involved in the bulb formation were also studied. There is a correlation between sugars and pungency level during the drought stress. These results could be presumably used as useful information to obtain onion varieties rich in sugars and pungency.