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.

Flavonoids are divided into several structural classes, including anthocyanins, which provide flower and leaf colors and other derivatives with diverse roles in plant development and interactions with the environment. This study characterized four Anthocyanidin Synthase (ANS) genes of Brassica rapa, a structural gene of anthocyanin biosynthetic pathway, and investigated their association with cold and freezing tolerance in B. rapa. Sequences of these genes were analyzed and compared with similar types of gene sequences of other species and found a high degree of homology with their respective functions. In the organ specific expression analysis, these genes showed expression only in the colored portion of leaves of different lines of B. rapa. On the other hand, BrANS genes also showed differential expression with certain time course of cold stress treatment in B. rapa. Thus, the above results suggest probable association of these genes with anthocyanin biosynthesis and cold and freezing tolerance and might be useful resources for developing cold resistant Brassica crops with desirable colors as well. The present work may help explore the molecular mechanism that regulates anthocyanin biosynthesis and its response to abiotic stress at the transcriptional level in plants.

sequence and more than fifty thousand proteins have been obtained to date. Transcription factors (TFs) are important regulators involved in plant development and physiological processes and the AP2/ERF protein family contains TFs that also plays a crucial role as well and response to biotic and abiotic stress conditions in plants. However, no detailed expression profile of AP2/ERF-like genes is available for B. oleracea. In the present study, 226 AP2/ERF TFs were identified from B. oleracea based on the available genome sequence. Based on sequence similarity, the AP2/ERF superfamily was classified into five groups (DREB, ERF, AP2, RAV and Soloist) and 15 subgroups. The identification, classification, phylogenetic construction, conserved motifs, chromosome distribution, functional annotation, expression patterns and interaction network were then predicted and analyzed. AP2/ERF TFs expression levels exhibited differences in response to varying abiotic stresses based on expressed sequence tags (ESTs). BoCBF1a, 1b, 2, 3 and 4, which were highly conserved in Arabidopsis and B. rapa CBF/DREB genes families were well characterized. Expression analysis enabled elucidation of the molecular and genetic level expression patterns of cold tolerance (CT) and susceptible lines (CS) of cabbage and indicated that all BoCBF genes responded to abiotic stresses. Comprehensive analysis of the physiological functions and biological roles of AP2/ERF superfamily genes and BoCBF family genes in B. oleracea is required to elucidate AP2/ERF, which will provide rich resources and opportunities to understand abiotic stress tolerance in crops.

Cabbage (Brassica oleracea) is one of the most important vegetable crops in the world. Yet, its sensitivity to cold stress, especially at the seedling stage, could limit the production. Until now, only, few studies about heritably durable cold tolerance were carried out in cabbage. Hence this study was done to characterize the transcriptome profiles of two cabbage genotypes with contrasting responses to cold stress using Illumina Hiseq short read (paired-end) sequencing technology. MicroRNAs (miRNAs) represent a class of short, non-coding, endogenous RNAs which play important roles in post-transcriptional regulation of gene expression. Thisstudy,wesoughttoprovideamorecomprehensivepredictionofB. oleracea cold responsive miRNAs based on high through put sequencing using two contrasting genotypes. The raw sequences were processed for removal of poor-quality and adaptor sequences. Then, the high quality unigenes (58,094) reads were applied for length filtering. Then, unigenes reads were used in a BLASTN search against of Rfam database and known miRNA database (miRBase 18.0) to removal of non-coding RNA’s and identifies conserved miRNA’s in B. oleracea. Further, novel reads were searched against B. oleracea genome. Their flanking sequences in the genome were used to predict their secondary structures, target prediction, and functional analysis. This is first report to identify novel miRNAs for cold stress through high throughput techniques. Our findings will provide an overview of potential miRNAs involved in cold stress, which may provide important clues on the function of miRNAs in from B. oleracea and other closely related Brassica species.

Flavonoids including anthocyanins provide flower and leaf colors and other derivatives that play diverse roles in plant development and interactions with the environment and dihydroflavonol 4-reductase (DFR) is part of an important step in the flavonoid biosynthesis pathway of anthocyanins. This study characterized 12 DFR genes of Brassica rapa and investigated their association with anthocyanin coloration, cold and freezing tolerance in several genotypes of B. rapa. Sequences of these genes were analyzed and compared with DFR gene sequences from other species and a high degree of homology was found. Constitutive expression of them in several pigmented and non-pigmented lines of B. rapa showed a correlation with anthocyanin accumulation only for BrDFR8 and 9. Conversely, BrDFR genes also showed responses to cold and freezing stress treatment in B. rapa. BrDFRs were also shown to be regulated by two transcription factors, BrMYB2-2 and BrTT8, contrasting with anthocyanin accumulation and cold and freezing stress. Thus, the above results suggest the association of these genes with anthocyanin biosynthesis and cold and freezing stress tolerance and might be useful resources for development cold and/or freezing resistant Brassica crops with desirable colors as well. The findings presented here may also help explore the molecular mechanism that regulates anthocyanin biosynthesis and its response to abiotic stress at the transcriptional level in plants.