Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations

Recent advances in date palm genomics: A comprehensive review

As one of the oldest fruit trees of the Arabian peninsula, other Middle-Eastern countries, and also North Africa, the date palm (Phoenix dactylifera L.), is highly significant for the economy of the region. Listed as part of UNESCO’s Intangible Cultural Heritage of Humanity, the date palm is believed to be the first tree cultivated by human beings, and was probably first harvested for its fruit nearly 7,000 years ago. Initial research efforts in date palm genetics focused on understanding the genetic diversity of date palm germplasm collections and its phylogenetic history, both important prerequisites for plant improvement. Despite various efforts, the center of origin of the date palm is still unclear, although genomic studies suggest two probable domestication events: one in the Middle East and the other in North Africa, with two separate gene pools. The current review covers studies related to omics analyses that have sought to decipher the present genetic diversity of the date palm. With advances and cost reductions in sequencing technologies, rapid progress has been made in the past few years in date palm genomics research. Along with organellar genomes, several reference genomes of the date palm are now available. In addition, several genotypes have been re-sequenced, either to detect single nucleotide polymorphisms (SNPs), or to study domestication and identification of key genes/loci associated with important agronomic traits, such as sex, fruit color, and sugar composition. These genomics research progress has paved the way to perform fast-track and precise germplasm improvement processes in date palm. In this study, we review the advances made in the genetics and genomics of the date palm so as to strategize targeted crop improvement plans for marginal areas of the Middle Eastern peninsula, North Africa, and other parts of the world.

Panmixia and active colonisation of the invasive palm Trachycarpus fortunei (Arecaceae) in Southern Switzerland and Northern Italy as inferred by microsatellites and SNP markers

Trachycarpus fortunei (Arecaceae: Coryphoideae) is an Asian palm that was introduced during the nineteenth century in southern Switzerland and northern Italy as an ornamental plant. In the recent decades, the palm has become an aggressive invasive species in the region. Before this study, the genetic structure and diversity of the naturalised populations were unknown. We aimed at understanding the dynamics of invasion and at comparing the results obtained with two types of markers. This genetic approach aimed at tracing back as far as possible the source of invasive populations comparing historical information found in literature and invasive genetic patterns. The genetic diversity was analysed using eight microsatellites (five were developed for that purpose) and 31′000 SNPs identified through GBS analyses. Genetic analyses were carried out for 200 naturalised individuals sampled from 21 populations in the Canton Ticino (Switzerland) and the provinces of Lombardy and Piedmont (Italy). The observed general panmixia indicates that the expansion of T. fortunei is active in its naturalised areas. The genetic pattern found for both SNPs and microsatellites appears to be related to the colonisation process, with a lack of geographic structure and bottleneck signatures occurring at the colonisation front, distantly from historical sites. This study gives a better understanding of the expansion of T. fortunei and adds new insights to its ecology.

Genetic Structure of a Worldwide Germplasm Collection of Prunus armeniaca L. Reveals Three Major Diffusion Routes for Varieties Coming From the Species' Center of Origin

The characterization of the largest worldwide representative data set of apricot (Prunus armeniaca L.) germplasm was performed using molecular markers. Genetic diversity and structure of the cultivated apricot genetic resources were analyzed to decipher the history of diffusion of this species around the world. A common set of 25 microsatellite markers was used for genotyping a total of 890 apricot accessions in different collections from the center of origin to the more recent regions of apricot culture. Using a Bayesian model-based clustering approach, the apricot genotypes can be structured into five different genetic clusters (FST = 0.174), correlated with the geographical regions of origin of the accessions. Accessions from China and Central Asia were clustered together and exhibited the highest levels of diversity, confirming an origin in this region. A loss of genetic diversity was observed from the center of origin to both western and eastern zones of recent apricot culture. Altogether, our results revealed that apricot spread from China and Central Asia, defined as the center of origin, following three major diffusion routes with a decreasing gradient of genetic variation in each geographical group. The identification of specific alleles outside the center of origin confirmed the existence of different secondary apricot diversification centers. The present work provides more understanding of the worldwide history of apricot species diffusion as well as the field of conservation of the available genetic resources. Data have been used to define an apricot core collection based on molecular marker diversity which will be useful for further identification of genomic regions associated with commercially important horticultural traits through genome-wide association studies to sustain apricot breeding programs.