Identifying coffee: development of a low-cost and robust barcoding assay for wild African Coffea species

With an estimated consumption of more than two billion cups a day, coffee is one of the most popular beverages in the world. Nearly all coffee is produced from the seeds of two species: Coffea arabica (Arabica coffee) and Coffea canephora (Robusta coffee). Both Arabica and Robusta coffee production is threatened by climate fluctuations and disease outbreaks, reducing yields and ravaging coffee plantations. To overcome these challenges, the potential of other wild Coffea species for the improvement of existing coffee varieties or for the development of new varieties has been studied. The Coffea genus consists of circa 130 described species that are mainly found in sub-Saharan Africa and Madagascar. Coffea species on the African continent are more closely related to Arabica and Robusta coffee. Nevertheless, the identification of African Coffea species at species level based on morphological traits can be challenging as several species seem to have overlapping trait characteristics. In this study, we developed a molecular barcoding assay consisting of eight nuclear markers between ca 200 and 800 base pairs long that can be sequenced using Sanger sequencing. Marker regions were selected based on the output of publicly available genotyping-by-sequencing data, ensuring that each Coffea species included in this dataset had a unique allele for at least two out of eight markers. The resulting barcoding assay is a cost-efficient and accessible tool for the molecular identification of wild African Coffea species, facilitating their conservation and their application for the improvement of coffee cultivation

Banana seed genetic resources for food security: status, constraints, and future priorities

Open Access Journal; Published online: 15 Nov 2021Storing seed collections of crop wild relatives, wild plant taxa genetically related to crops, is an essential component in global food security. Seed banking protects genetic resources from degradation and extinction and provides material for use by breeders. Despite being among the most important crops in the world, banana and plantain crop wild relatives are largely under-represented in genebanks. Nevertheless, banana crop wild relative seed collections are in fact held in different countries, but these have not previously been part of reporting or analysis. To fill this gap, we firstly collated banana seed accession data from 13 institutions in 10 countries. These included 537 accessions containing an estimated 430,000 seeds of 56 species. We reviewed their taxonomic coverage and seed storage conditions including viability estimates. We found that seed accessions have low viability (25% mean) representing problems in seed storage and processing. Secondly, we surveyed 22 institutions involved in banana genetic resource conservation regarding the key constraints and knowledge gaps that institutions face related to banana seed conservation. Major constraints were identified including finding suitable material and populations to collect seeds from, lack of knowledge regarding optimal storage conditions and germination conditions. Thirdly, we carried out a conservation prioritization and gap analysis of Musaceae taxa, using established methods, to index representativeness. Overall, our conservation assessment showed that despite this extended data set banana crop wild relatives are inadequately conserved, with 51% of taxa not represented in seed collections at all; the average conservation assessment showing high priority for conservation according to the index. Finally, we provide recommendations for future collecting, research, and management, to conserve banana and plantain crop wild relatives in seed banks for future generations

Using seminatural and simulated habitats for seed germination ecology of banana wild relatives

Open Access JournalEcologically meaningful seed germination experiments are constrained by access to seeds and relevant environments for testing at the same time. This is particularly the case when research is carried out far from the native area of the studied species. Here, we demonstrate an alternative—the use of glasshouses in botanic gardens as simulated-natural habitats to extend the ecological interpretation of germination studies. Our focal taxa were banana crop wild relatives (Musa acuminata subsp. burmannica, Musa acuminata subsp. siamea, and Musa balbisiana), native to tropical and subtropical South-East Asia. Tests were carried out in Belgium, where we performed germination tests in relation to foliage-shading/exposure to solar radiation and seed burial depth, as well as seed survival and dormancy release in the soil. We calibrated the interpretation of these studies by also conducting an experiment in a seminatural habitat in a species native range (M. balbisiana—Los Baños, the Philippines), where we tested germination responses to exposure to sun/shade. Using temperature data loggers, we determined temperature dynamics suitable for germination in both these settings. In these seminatural and simulated-natural habitats, seeds germinated in response to exposure to direct solar radiation. Seed burial depth had a significant but marginal effect by comparison, even when seeds were buried to 7 cm in the soil. Temperatures at sun-exposed compared with shaded environments differed by only a few degrees Celsius. Maximum temperature of the period prior to germination was the most significant contributor to germination responses and germination increased linearly above a threshold of 23℃ to the maximum temperature in the soil (in simulated-natural habitats) of 35℃. Glasshouses can provide useful environments to aid interpretation of seed germination responses to environmental niches

Genetic diversity and structure of Musa balbisiana populations in Vietnam and its implications for the conservation of banana crop wild relatives

Open Access Journal; Published online: 23 Jun 2021Crop wild relatives (CWR) are an indispensable source of alleles to improve desired traits in related crops. While knowledge on the genetic diversity of CWR can facilitate breeding and conservation strategies, it has poorly been assessed. Cultivated bananas are a major part of the diet and income of hundreds of millions of people and can be considered as one of the most important fruits worldwide. Here, we assessed the genetic diversity and structure of Musa balbisiana, an important CWR of plantains, dessert and cooking bananas. Musa balbisiana has its origin in subtropical and tropical broadleaf forests of northern Indo-Burma. This includes a large part of northern Vietnam where until now, no populations have been sampled. We screened the genetic variation and structure present within and between 17 Vietnamese populations and six from China using 18 polymorphic SSR markers. Relatively high variation was found in populations from China and central Vietnam. Populations from northern Vietnam showed varying levels of genetic variation, with low variation in populations near the Red River. Low genetic variation was found in populations of southern Vietnam. Analyses of population structure revealed that populations of northern Vietnam formed a distinct genetic cluster from populations sampled in China. Together with populations of central Vietnam, populations from northern Vietnam could be subdivided into five clusters, likely caused by mountain ranges and connected river systems. We propose that populations sampled in central Vietnam and on the western side of the Hoang Lien Son mountain range in northern Vietnam belong to the native distribution area and should be prioritised for conservation. Southern range edge populations in central Vietnam had especially high genetic diversity, with a high number of unique alleles and might be connected with core populations in northern Laos and southwest China. Southern Vietnamese populations are considered imported and not native

Photoinhibition of seed germination: Occurrence, ecology and phylogeny

Light conditions provide important information about the best time and place for seedling establishment. Photoinhibition of seed germination (PISG), defined as the partial or complete suppression of germination under white light, has been interpreted as a physiological adaptation to avoid germination at or near the soil surface. This review is the first report of an all-inclusive, fully quantitative analysis of PISG in seed plants. Pertinent data available from the published literature for 301 taxa from 59 families and 27 orders were assessed. The association of PISG with several plant and seed traits allowed us to consider the adaptive significance of PISG in relation to plant life histories and the natural environments. As no gymnosperm has been found to be truly photoinhibited, it seems that PISG is apomorphic to flowering plants (especially monocots). Seeds of most taxa with PISG have a dark colour and intermediate mass, mostly in the range 1 to 27 mg. PISG is absent from humid tropical regions and from cold climates, but it is strongly associated with open, disturbed and dry habitats. An intriguing implication of PISG is the formation of a soil-surface seed bank. Taken together, these results clearly indicate that PISG is a physiological adaptation to avoid germination on the soil surface, where conditions are not suitable for seedling establishment. PISG is probably much more frequent in seed plants than previously thought. Thus, laboratory experiments should be conducted under well-characterized light and dark conditions. Copyright © Cambridge University Press 2017

Photoinhibition of seed germination: occurrence, ecology and phylogeny

Light conditions provide important information about the best time and place for seedling establishment. Photoinhibition of seed germination (PISG), defined as the partial or complete suppression of germination under white light, has been interpreted as a physiological adaptation to avoid germination at or near the soil surface. This review is the first report of an all-inclusive, fully quantitative analysis of PISG in seed plants. Pertinent data available from the published literature for 301 taxa from 59 families and 27 orders were assessed. The association of PISG with several plant and seed traits allowed us to consider the adaptive significance of PISG in relation to plant life histories and the natural environments. As no gymnosperm has been found to be truly photoinhibited, it seems that PISG is apomorphic to flowering plants (especially monocots). Seeds of most taxa with PISG have a dark colour and intermediate mass, mostly in the range 1 to 27 mg. PISG is absent from humid tropical regions and from cold climates, but it is strongly associated with open, disturbed and dry habitats. An intriguing implication of PISG is the formation of a soil-surface seed bank. Taken together, these results clearly indicate that PISG is a physiological adaptation to avoid germination on the soil surface, where conditions are not suitable for seedling establishment. PISG is probably much more frequent in seed plants than previously thought. Thus, laboratory experiments should be conducted under well-characterized light and dark conditions

Phylogeography and conservation gaps of Musa balbisiana Colla genetic diversity revealed by microsatellite markers

Open Access Article; Published online: 07 May 2022Collection and storage of crop wild relative (CWR) germplasm is crucial for preserving species genetic diversity and crop improvement. Nevertheless, much of the genetic variation of CWRs is absent in ex situ collections and detailed passport data are often lacking. Here, we focussed on Musa balbisiana, one of the two main progenitor species of many banana cultivars. We investigated the genetic structure of M. balbisiana across its distribution range using microsatellite markers. Accessions stored at the International Musa Germplasm Transit Centre (ITC) ex situ collection were compared with plant material collected from multiple countries and home gardens from Vietnam. Genetic structure analyses revealed that accessions could be divided into three main clusters. Vietnamese and Chinese populations were assigned to a first and second cluster respectively. A third cluster consisted of ITC and home garden accessions. Samples from Papua New Guinea were allocated to the cluster with Chinese populations but were assigned to a separate fourth cluster if the number of allowed clusters was set higher. Only one ITC accession grouped with native M. balbisiana populations and one group of ITC accessions was nearly genetically identical to home garden samples. This questioned their wild status, including accessions used as reference for wild M. balbisiana. Moreover, most ITC accessions and home garden samples were genetically distinct from wild populations. Our results highlight that additional germplasm should be collected from the native distribution range, especially from Northeast India, Myanmar, China, and the Philippines and stored for ex situ conservation at the ITC. The lack of passport data for many M. balbisiana accessions also complicates the interpretation of genetic information in relation to cultivation and historical dispersal routes

The seed germination spectrum of alpine plants: a global meta-analysis

Assumptions about the germination ecology of alpine plants are presently based on individual species and local studies. A current challenge is to synthesise, at the global level, the alpine seed ecological spectrum. We performed a meta-analysis of primary data from laboratory experiments conducted across four continents (excluding the tropics) and 661 species, to estimate the influence of six environmental cues on germination proportion, mean germination time and germination synchrony; accounting for seed morphology (mass, embryo : seed ratio) and phylogeny. Most alpine plants show physiological seed dormancy, a strong need for cold stratification, warm-cued germination and positive germination responses to light and alternating temperatures. Species restricted to the alpine belt have a higher preference for warm temperatures and a stronger response to cold stratification than species whose distribution extends also below the treeline. Seed mass, embryo size and phylogeny have strong constraining effects on germination responses to the environment. Globally, overwintering and warm temperatures are key drivers of germination in alpine habitats. The interplay between germination physiology and seed morphological traits further reflects pressures to avoid frost or drought stress. Our results indicate the convergence, at the global level, of the seed germination patterns of alpine species