Recent Advances in Molecular Genetics of Onion

Onion is an important vegetable crop because it adds nutritional value and diversity to food preparation. Understanding recent advancements in onion molecular genetics is essential to improve production, quality, and disease resistance. Cutting-edge genomic technologies like genetic mapping and RNA sequencing reveal important genes and pathways. The review examines the progress in utilizing various molecular markers to study genetic divergence. The exploration extends to understanding the genes and pathways responsible for bulb color and chemical composition and the genetic factors influencing bulbing, flowering, and vernalization. Additionally, the article explores quantitative trait loci associated with resistance to major damaging diseases and delves into the role of different loci in male sterility and hybrid development. The recent publication of the whole genome sequence of onions will lead to further identification of genes and understanding their roles and functions in metabolic pathways

Length distribution of assembled transcripts in the extensive (Total) and abundant (Reduced) transcriptome datasets.

<p>Length distribution of assembled transcripts in the extensive (Total) and abundant (Reduced) transcriptome datasets.</p

Doubled Haploid ‘CUDH2107’ as a Reference for Bulb Onion (<i>Allium cepa</i> L.) Research: Development of a Transcriptome Catalogue and Identification of Transcripts Associated with Male Fertility

<div><p>Researchers working on model plants have derived great benefit from developing genomic and genetic resources using ‘reference’ genotypes. Onion has a large and highly heterozygous genome making the sharing of germplasm and analysis of sequencing data complicated. To simplify the discovery and analysis of genes underlying important onion traits, we are promoting the use of the homozygous double haploid line ‘CUDH2107’ by the onion research community. In the present investigation, we performed transcriptome sequencing on vegetative and reproductive tissues of CUDH2107 to develop a multi-organ reference transcriptome catalogue. A total of 396 million 100 base pair paired reads was assembled using the Trinity pipeline, resulting in 271,665 transcript contigs. This dataset was analysed for gene ontology and transcripts were classified on the basis of putative biological processes, molecular function and cellular localization. Significant differences were observed in transcript expression profiles between different tissues. To demonstrate the utility of our CUDH2107 transcriptome catalogue for understanding the genetic and molecular basis of various traits, we identified orthologues of rice genes involved in male fertility and flower development. These genes provide an excellent starting point for studying the molecular regulation, and the engineering of reproductive traits.</p></div

Statistics of De novo assembly and abundance estimation.

<p>Statistics of De novo assembly and abundance estimation.</p

Bulb onion orthologues of rice genes involved in male fertility and floral development identified using BLAST searches.

<p>Bulb onion orthologues of rice genes involved in male fertility and floral development identified using BLAST searches.</p

Comparisons of transcriptional profiles across samples.

<p>Heat map showing hierarchical clustered Spearman correlation matrix resulting from a pairwise comparison of transcript expression values.</p

Relative expression of the floral meristem identity genes <i>AGAMOUS</i> (<i>AG</i>), <i>APETALLA3</i> (<i>AP3</i>), <i>PISTILLATA</i> (<i>PI</i>) and <i>SEPALLATA3</i> (<i>SEP3</i>) across different onion organs.

<p>Expression determined from the RNAseq data is shown in red and RT-PCR data is shown in blue, with data represented by an average ± S.E. of three samples, with transcripts normalized to actin and β-tubulin.</p

GO terms in bulb onion compared with rice.

<p>(A) Total number of GO terms associated with cellular component, molecular function and biological process in onion (brown) and rice (green). (B-D) GO terms in onion (brown) and rice (green) associated with; (B) cellular component, (C) molecular function, and (D) biological process.</p

Sequence conservation between the bulb onion abundant transcriptome dataset and other <i>Allium</i> species.

<p>Sequence conservation between the bulb onion abundant transcriptome dataset and other <i>Allium</i> species.</p