Summary Cannabis (Cannabis sativa L.) is one of the oldest cultivated plants purported to have unique medicinal properties. However, scientific research of cannabis has been restricted by the Single Convention on Narcotic Drugs of 1961, an international treaty that prohibits the production and supply of narcotic drugs except under license. Legislation governing cannabis cultivation for research, medicinal and even recreational purposes has been relaxed recently in certain jurisdictions. As a result, there is now potential to accelerate cultivar development of this multi‐use and potentially medically useful plant species by application of modern genomics technologies. Whilst genomics has been pivotal to our understanding of the basic biology and molecular mechanisms controlling key traits in several crop species, much work is needed for cannabis. In this review we provide a comprehensive summary of key cannabis genomics resources and their applications. We also discuss prospective applications of existing and emerging genomics technologies for accelerating the genetic improvement of cannabis.

White Guinea yam (Dioscorea rotundata) is an important staple tuber crop in West Africa. However, its origin remains unclear. In this study, we resequenced 336 accessions of white Guinea yam and compared them with the sequences of wild Dioscorea species using an improved reference genome sequence of D. rotundata. In contrast to a previous study suggesting that D. rotundata originated from a subgroup of Dioscorea praehensilis, our results suggest a hybrid origin of white Guinea yam from crosses between the wild rainforest species D. praehensilis and the savannah-adapted species Dioscorea abyssinica. We identified a greater genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improving this crop through molecular breeding.

Opium poppy (Papaver somniferum) is one of the world’s oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the extent of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations using discriminate analysis of principal components and STRUCTURE analysis. Most accessions obtained from the same country were grouped together within subpopulations, likely a consequence of the restriction on movement of poppy germplasm. Alkaloid profiles of accessions were highly diverse, with morphine being dominant. Phylogenetic analysis identified genetic groups that were largely consistent with the subpopulations detected and that could be differentiated broadly based on traits such as number of branches and seed weight. These accessions and the associated genotypic data are valuable resources for further genetic diversity analysis, which could include definition of poppy core sets to facilitate genebank management and use of the diversity for genetic improvement of this valuable crop.

Opium poppy is the only commercially viable source of narcotic raw materials used by the alkaloid pharmaceutical industry. Considerable advances in our knowledge of basic poppy biology and the alkaloid biosynthetic pathway have been driven by recent progress in transcriptomics, genomics, and functional genetics. However, much work remains for this knowledge to be translated into improvements in crop performance. The genetic diversity of poppy is poorly characterised and the available information is highly fragmented. The recent release of a poppy genome sequence adds a new dimension to poppy genomic research, enabling characterisation of diversity and identification of genes and molecular markers associated with valuable traits. This will create opportunities for functional genomics studies and the incorporation of more diverse germplasm into poppy improvement programmes. This review discusses the current state of poppy genetic and genomic resources, highlights the advances made in elucidating the alkaloid biosynthetic pathway that led to the emergence of poppy as a model system to study secondary metabolism in plants, and presents perspectives for future research.

A core subset with a small number of accessions representing the genetic diversity of the base collection plays a vital role in facilitating efficient utilization of plant genetic resources. This is particularly relevant for vegetatively propagated large plant size tuber crops with a long growing period, such as white Guinea yam (Dioscorea rotundata Poir.). For the efficient utilization of D. rotundata genetic resources, this study was aimed at developing a mini-core collection from a core collection of 447 D. rotundata accessions maintained at the International Institute of Tropical Agriculture (IITA). Accordingly, a D. rotundata mini-core collection representing 102 accessions was selected using 16 simple sequence repeat (SSR) markers, retaining ∼98% of the SSR allelic diversity of the base collection. A similar level of diversity was captured within the mini-core collection and the base collection with respect to 21 morphological traits, ploidy level, and geographic origin. The mini-core collection demonstrated a wide range of variation in agronomic traits such as growth period, number of tubers, average tuber weight, and total yield per plant. This variation was considerable when compared with the variation observed for the same traits among the 10 lines or genotypes conventionally used in the breeding program at IITA, which were included in this study as checks. The selected mini-core accessions could serve as a working collection to broaden the genetic variation for use in practical breeding programs, as well as in future genomic analyses aimed at the genetic improvement of D. rotundata in West Africa.

Advances in next generation sequencing (NGS)-based methodologies have accelerated the identifications of simple genetic variants such as point mutations and small insertions/deletions (InDels). Structural variants (SVs) including large InDels and rearrangements provide vital sources of genetic diversity for plant breeding. However, their analysis remains a challenge due to their complex nature. Consequently, novel NGS-based approaches are needed to rapidly and accurately identify SVs. Here, we present an NGS-based bulkedsegregant analysis (BSA) technique called Sat-BSA (SVs associated with traits) for identifying SVs controlling traits of interest in crops. Sat-BSA targets allele frequencies at all SNP positions to first identify candidate genomic regions associated with a trait, which is then reconstructed by long reads-based local de novo assembly. Finally, the association between SVs, RNA-seq-based gene expression patterns and trait is evaluated for multiple cultivars to narrow down the candidate genes. We applied Sat-BSA to segregating F 2 progeny obtained from crosses between turnip cultivars with different tuber colors and successfully isolated two genes harboring SVs that are responsible for tuber phenotypes. The current study demonstrates the utility of Sat-BSA for the identification of SVs associated with traits of interest in species with large and heterozygous genomes.

White Guinea yam (Dioscorea rotundata) is an important staple tuber crop of West Africa. However, its origin remains unclear. In this study, we re-sequenced 336 accessions of white Guinea yam and compared them with the sequences of the wild Dioscorea species using an improved reference genome sequence of D. rotundata. Our results suggest a hybrid origin of white Guinea yam from crosses between the rainforest wild species D. praehensilis and the savannah-adapted D. abyssinica. We identified a higher genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and an extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improvement of this crop through molecular breeding.

Germination involves highly dynamic transcriptional programs as the cells of seeds reactivate and express the functions necessary to establish in the environment. Individual cell types have distinct roles within the embryo, so must therefore have cell-type specific gene expression and gene regulatory networks. We can better understand how the functions of different cell types are established and contribute to the embryo by determining how cell-type specific transcription begins and changes through germination. Here we describe a temporal analysis of the germinating Arabidopsis embryo at single-cell resolution. We define the highly dynamic cell-type specific patterns of gene expression and how these relate to changing cellular function as germination progresses. Underlying these are unique gene regulatory networks and transcription factor activity. We unexpectedly discover that most embryo cells transition through the same initial transcriptional state early in germination, after which cell-type specific gene expression is established. Furthermore, our analyses support previous findings that the earliest events leading to the induction of embryo growth take place in the vasculature. Overall, our study constitutes a general framework to characterise Arabidopsis cell states through embryo growth, allowing investigation of different genotypes and other plant species whose seed strategies may differ.