Bulb onion (Allium cepa L.) is an ancient crop that is thought to have originated in Central Asia and has been cultivated for over 5000 years. Classical genetic and plant breeding approaches have been used to improve onion yield, quality, and resistance against biotic and abiotic stresses. However, its biennial life cycle, cross-pollinated nature and high inbreeding depression have proved challenging for the characterization and breeding of improved traits. New technologies, notably next-generation sequencing, are providing researchers with the genomic resources and approaches to overcome these challenges. Using these genomic technologies, molecular markers are being rapidly developed and utilized for germplasm analysis and mapping in onion. These new tools and knowledge are allowing the integration of molecular and conventional breeding to speed up onion improvement programmes. In this review, we outline recent progress in onion genomics and molecular genetics and prospects for enhancing onion yield and quality in the future.

Geophytes, the plants that form vegetative storage organs, are characterized by a dual reproduction system, in which vegetative and sexual propagation are tightly regulated to ensure fitness in harsh climatic conditions. Recent findings highlight the role of the PEBP (PHOSPHATIDYLETHANOLAMINE-BINDING PROTEINS) gene family in geophytes as major players in the molecular cascades underlying both types of reproduction. In this review, we briefly explain the life cycle and reproduction strategies of different geophytes and what is known about the physiological aspects related to these processes. Subsequently, an in-depth overview is provided of the molecular and genetic pathways driving these processes. In the evolution of plants, the PEBP gene family has expanded followed by neo- and sub-functionalization. Careful characterization revealed that differential expression and differential protein complex formation provides the members of this gene family with unique functions, enabling to mediate the crosstalk between the two reproductive events in geophytes in response to environmental and endogenous cues. Taken all these studies into account, we propose to regard the PEBPs as conductors of geophytes reproductive development.

Additional index words. growth conditions, photoperiod, light quality, sciarid fly Abstract. Bulb onion (Allium cepa L.) is a challenging subject for experimental studies because of its slow growth, genetic heterogeneity, and sensitivity to environmental and biotic stresses. Sharing of common germplasm and controlled propagation practices has underpinned research on model plants, such as Arabidopsis and tomato, but not in onion. To encourage wider evaluation of onion for physiological and molecular studies in controlled environments, we describe the growing practices we have developed over two decades of research on adaptive and nutrient assimilation traits. Key aspects covered include choice of germplasm, propagation media, nutrition, and environmental control. Adopting common onion genetics and cultivation techniques across laboratories will allow researchers to answer deeper research questions and increase the reproducibility of the research.

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.

The hull-less pumpkin (Cucurbita pepo) seed does not require de-hulling before use for human consumption, as a result highly preferred by the oil, nut, and baking industries. In hull-less seeds, a single recessive gene is responsible for the absence of outer thick seed coat layers; however, the genomic region and gene(s) controlling the trait are unclear to date. In this study, four crosses attempted to derive F2 and backcross populations confirmed the single recessive gene inheritance of hull-less seed trait in populations adapted to the sub-tropical climate. The candidate genomic region for hull-less seed trait was identified through the BSA-QTLseq approach using bulks of F2:3 progenies from a cross of HP111 (hulled) and HLP36 (hull-less). A novel genomic region on chromosome 12 ranging from 1.80 to 3.86 Mb was associated with the hull-less seed trait. The re-sequencing data identified a total of 396 SNPs within this region and eight were successfully converted into polymorphic KASP assays. The genotyping of segregating F2 (n = 160) with polymorphic KASP assays resulted in a 40.3 cM partial linkage map and identified Cp_3430407 (10 cM) and Cp_3498687 (16.1 cM) as flanking markers for hull-less locus (Cphl-1). These flanking markers correspond to the 68.28 kb region in the reference genome, and the marker, Cp_3430407 successfully predicted the genotype in 93.33% of the C. pepo hull-less germplasm lines, thus can be used for marker-assisted selection in parents polymorphic for the hull-less seed trait. The Cphl-1-linked genomic region (2.06 Mb) encompasses a total of 182 genes, including secondary cell wall and lignin biosynthesis-related transcriptional factors viz., “NAC” (Cp4.1LG12g04350) and “MYB” (Cp4.1LG12g03120). These genes were differentially expressed in the seeds of hulled and hull-less genotypes, and therefore could be the potential candidate genes governing the hull-less seed trait in pumpkin.