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Background Understanding the molecular basis of sport mutations in fruit trees has the potential to accelerate generation of improved cultivars. Results For this, we analyzed the genome of the apple tree that developed the RubyMac phenotype through a sport mutation that led to the characteristic fruit coloring of this variety. Overall, we found 46 somatic mutations that distinguished the mutant and wild-type branches of the tree. In addition, we found 54 somatic gene conversions (i.e., loss-of-heterozygosity mutations) that also distinguished the two parts of the tree. Approximately 20% of the mutations were specific to individual cell lineages, suggesting that they originated from the corresponding meristematic layers. Interestingly, the de novo mutations were enriched for GC =  > AT transitions while the gene conversions showed the opposite bias for AT =  > GC transitions, suggesting that GC-biased gene conversions have the potential to counteract the AT-bias of de novo mutations. By comparing the gene expression patterns in fruit skins from mutant and wild-type branches, we found 56 differentially expressed genes including 18 involved in anthocyanin biosynthesis. While none of the differently expressed genes harbored a somatic mutation, we found that some of them in regions of the genome that were recently associated with natural variation in fruit coloration. Conclusion Our analysis revealed insights in the characteristics of somatic change, which not only included de novo mutations but also gene conversions. Some of these somatic changes displayed strong candidate mutations for the change in fruit coloration in RubyMac .

The physiology and biology of blueberry fruit is the most important consideration for understanding postharvest storage. Fruit physiology is responsive to many stimuli including biotic, genetic, and environmental inputs. The extent to which a blueberry fruit are affected by these factors is largely cultivar dependent. The following studies address two aspects of blueberry fruit postharvest biology as it relates to pest control: In Chapter 2, we explore the effect of SO2 fumigation on five blueberry cultivars: ‘Bluecrop’, ‘Draper’, ‘Elliott’, ‘Jersey’, and ‘Liberty’ and the extent to which SO2 fumigation can be used to disinfest blueberry fruit of blueberry maggot (BBM) Rhagoletis mendax Curran. In Chapter 3, we use RNA sequencing (RNA-seq) to reveal genes differentially expressed (DE) in ‘Elliott’ fruit in response to infection by Colletotrichum fioriniae compared to mock- (water-) inoculated fruit. By filtering out DE genes in mock-inoculated fruit postharvest, as well as DE genes in infected ‘Jersey’ and ‘Draper’ fruit, we discovered 113 genes unique to ‘Elliott’ fruit that are inoculation-responsive. This set of genes include canonical plant resistance genes as well as genes associated with secondary metabolite biosynthesis, cell wall metabolism, reactive oxygen species production and scavenging, and the hypersensitive response. These studies provide important groundwork for future blueberry breeding by identifying cultivars with genetics and physiology amenable to different interventions for reducing postharvest fruit losses.

Understanding the molecular basis of sport mutations in fruit trees can accelerate breeding of novel cultivars. For this, we analyzed the DNA of the apple tree that evolved the RubyMac phenotype through a sport mutation that introduced changes in fruit coloration in upper branches of the tree. Unexpectedly, we not only found 46 de novo mutations, but also 54 somatic gene conversions (i.e., loss-of-heterozygosity mutations) distinguishing the mutant and wild-type branches of the tree. Approximately 30% of the de novo mutations and 80% of the gene conversions were observed only in specific cells layers suggesting that they occurred in the corresponding meristematic layers. Interestingly, the de novo mutations were enriched for GC=>AT transitions, while the gene conversions showed the opposite bias for AT=>GC transitions suggesting that GC-biased gene conversions have the potential to counteract the AT-bias of de novo mutations. By comparing the gene expression patterns in fruit skins from mutant and wild-type branches, we found 56 differentially expressed genes including 18 that were involved in anthocyanin biosynthesis. While none of the differently expressed genes harbored a mutation, we found that some of the mutations affected the integrity of candidate genes in regions of the genome that were recently associated with natural variation in fruit coloration.Competing Interest StatementThe authors have declared no competing interest.

Aim Understanding the resilience and adaptability of alpine flora under climate change is crucial for biodiversity conservation. While functional traits are key to predicting alpine plants' responses to climate change, the role of regeneration traits remains underexplored. We hypothesised that alpine species thriving under climate change produce seeds with higher dispersal ability, longer soil persistence, lower dormancy requirements, and faster germination, while declining species would show opposite traits. Location Twenty‐three summits across six mountain ranges in Central and Southern Europe: Sierra Nevada, Northern and Central Apennines, and Northeastern, Central, and Southern Alps. Methods We analysed long‐term data on frequency and abundance changes and eight seed traits related to dispersal, establishment, and soil persistence for 177 alpine species using linear mixed‐effect models. Results Over two decades, alpine plant populations remained stable, with nearly 90% of species showing minimal frequency change and 70% showing minimal abundance change. However, abundance shifts varied by region: 16%–25% of species declined in Sierra Nevada, the Central Apennines, and the Southern Alps, while the Northeastern Alps and the Northern Apennines showed the largest increases (27% and 17%, respectively). Significant but limited relationships between seed traits and population dynamics were captured, primarily in the Central and Northern Apennines. Species with lower potential for epizoochory or anemochory were more likely to increase in abundance, while smaller seeds were linked to ‘winners’ in some regions. Germination traits, such as broader temperature requirements and slower germination, characterised species with increased abundance in the Northern Apennines. Main Conclusions Seed traits had limited predictive power in distinguishing ‘losers’ and ‘winners’ of climate change among European alpine plants. This likely reflects the longevity of alpine plants, short observation periods, and potential mismatches between seed‐level microenvironmental conditions and broader climatic trends.

Seventeen European endemic plant species were considered extinct, but improved taxonomic and distribution knowledge as well as ex situ collecting activities brought them out of the extinct status. These species have now been reported into a conservation framework that may promote legal protection and in situ and ex situ conservation. Species once considered extinct have now, through improved taxonomic knowledge and collection activities, been restored, with lessons for conservation policies both in Europe and globally.

Resurrecting extinct species is a fascinating and challenging idea for scientists and the general public. Whereas some theoretical progress has been made for animals, the resurrection of extinct plants (de-extinction sensu lato) is a relatively recently discussed topic. In this context, the term ‘de-extinction’ is used sensu lato to refer to the resurrection of ‘extinct in the wild’ species from seeds or tissues preserved in herbaria, as we acknowledge the current impossibility of knowing a priori whether a herbarium seed is alive and can germinate. In plants, this could be achieved by germinating or in vitro tissue-culturing old diaspores such as seeds or spores available in herbarium specimens. This paper reports the first list of plant de-extinction candidates based on the actual availability of seeds in herbarium specimens of globally extinct plants. We reviewed globally extinct seed plants using online resources and additional literature on national red lists, resulting in a list of 361 extinct taxa. We then proposed a method of prioritizing candidates for seed-plant de-extinction from diaspores found in herbarium specimens and complemented this with a phylogenetic approach to identify species that may maximize evolutionarily distinct features. Finally, combining data on seed storage behaviour and longevity, as well as specimen age in the novel ‘best de-extinction candidate’ score (DEXSCO), we identified 556 herbarium specimens belonging to 161 extinct species with available seeds. We expect that this list of de-extinction candidates and the novel approach to rank them will boost research efforts towards the first-ever plant de-extinction.Reviewing online resources and additional literature on national red lists, 361 extinct seed-plant taxa were identified. Of these, 556 herbarium specimens belonging to 161 extinct species were found to have a high ‘de-extinction candidate’ score.