Origins of the Apple: The Role of Megafaunal Mutualism in the Domestication of Malus and Rosaceous Trees

Seeking consensus on the domestication concept

The domestication of plants and animals permitted the development of cities and social hierarchies, as well as fostering cultural changes that ultimately led humanity into the modern world. Despite the importance of this set of related evolutionary phenomena, scholars have not reached a consensus on what the earliest steps in the domestication process looked like, how long the seminal portions of the process took to unfold, or whether humans played a conscious role in parts or all of it. Likewise, many scholars find it difficult to disentangle the cultural processes of cultivation from the biological processes of domestication. Over the past decade, the prevailing views among scholars have begun to shift towards unconscious and protracted models of early domestication; however, the nomenclature used to discuss these changes has been stagnant. Discussions of early domestication remain bound up in prevailing definitions and preconceived ideas of what the process looked like. In this paper, we seek to break down definitions of domestication and to construct a definition that serves equal utility regardless of the views that researchers hold about the process.This article is part of the theme issue 'Unravelling domestication: multi-disciplinary perspectives on human and non-human relationships in the past, present and future'.

Application of phytosynthesized silver nanoparticles (SNPs) against Erwinia amylovora causing fire blight disease

The bacterium Erwinia amylovora is responsible for the destructive disease known as fire blight in pear trees. This highly detrimental condition poses a significant threat to the health and vitality of these trees. The existing strategies for managing fire blight disease involve the regular use of copper compounds and streptomycin, particularly during periods when environmental factors are conducive to the spread of the infection. Silver nanoparticles, also known as SNPs, are tiny specks of silver ranging in size from 10 to 100 nm. These particles are created through various chemical and biological processes. Numerous studies have demonstrated their ability to exhibit antibacterial properties against a wide range of human and animal pathogens. In this investigation, the dimensions of SNPs were ascertained by employing aqueous extracts derived from apple, pear, and quince leaves. The average sizes of the SNPs were found to be approximately 30 nm, 38 nm, and 55 nm, apple, quince and pear respectively. The pear mature fruits successfully managed to control the rot caused by the disease-causing E. amylovora. This study shows the viability of utilizing leaves extract from apple, pear, and quince as a suitable medium for the production of silver nanoparticles. These nanoparticles hold potential for effectively managing fire blight disease.

Apple russeting-causes, physiology and control measures: A review

MAIN CONCLUSION

This review serves as a critical framework for guiding future research into the causes of russeting and the development of effective control strategies to enhance fruit quality. Russeting is a condition characterized by the formation of brown, corky patches on fruit skin which significantly impairs both the quality and market value of apples. This phenomenon arises from a complex interplay of various biotic and abiotic factors. Among the abiotic factors, environmental conditions, such as light, temperature, and relative humidity, as well as nutrient imbalances and the application of agrochemicals are important, whereas biotic factors include the influence of yeasts, fungi, viruses, and bacteria. The susceptibility of apple cultivars to russeting varies with yellow-fleshed varieties generally exhibiting higher incidences compared to red-fleshed ones. While russeting is partly determined by varietal and genetic factors, it can be mitigated through the implementation of effective cultural practices, nutrient management, plant growth regulators, biological agents, and pesticides. Understanding these dynamics provides valuable insights for developing future research strategies aimed at improving fruit quality and production.

Malus sieversii: a historical, genetic, and conservational perspective of the primary progenitor species of domesticated apples

Apples are one of the most valued tree fruit crops around the world. Currently, a few highly popular and economically successful apple cultivars dominate the commercial production and serve as main genetic contributors to the development of new apple cultivars. This limited level of genetic diversity grown as a clonally propagated monoculture renders the apple industry vulnerable to the wide range of weather events, pests, and pathogens. Wild apple species are an excellent source of beneficial alleles for the wide range of biotic and abiotic stressors challenging apple production. However, the biological barriers of breeding with small-fruited wild apples greatly limit their use. Using a closely related wild species of apple such as Malus sieversii can improve the efficiency of breeding efforts and broaden the base of available genetics. M. sieversii is the main progenitor of the domesticated apple, native to Central Asia. The similarity of fruit morphology to domesticated apples and resistances to abiotic and biotic stresses makes it appealing for apple breeding programs. However, this important species is under threat of extinction in its native range. Preserving the wild apple forests in Central Asia is vital for ensuring the sustainable protection of this important genetic resource. The insufficient awareness about the complete range of challenges and opportunities associated with M. sieversii hinders the maximization of its potential benefits. This review aims to provide comprehensive information on the cultural and historical context of M. sieversii, current genetic knowledge for breeding, and the conservation challenges of wild apple forests.

Domestication as the evolution of interspecies cooperative breeding

We propose that domestication is the result of interspecies cooperative breeding. Considering domestication as an outcome of cooperative breeding can explain how domestication occurs in both plants and animals, encompass cases of domestication that do not involve humans, and shed light on why humans are involved in so many domesticatory relationships. We review the cooperative breeding model of human evolution, which posits that care of human infants by alloparents enabled the evolution of costly human brains and long juvenile development, while selecting for tolerance of strangers. We then explore how human cooperation in the protection and provisioning of young plants and animals can explain the evolution of domestication traits such as changes in development; loss of aggressive, defensive, and bet-hedging aspects of the phenotype; and increased fertility. We argue that the importance of cooperative breeding to human societies has made humans especially likely to enter into interspecies cooperative breeding relationships.

The initial spread of peaches across eastern North America was structured by Indigenous communities and ecologies

We conduct a synthetic archaeological and ethnohistoric dating program to assess the timing and tempo of the spread of peaches, the first Eurasian domesticate to be adopted across Indigenous eastern North America, into the interior American Southeast by Indigenous communities who quickly "Indigenized" the fruit. In doing so, we present what may be the earliest absolute dates for archaeological contexts containing preserved peach pits in what is today the United States in the early to mid-16th century. Along with our broader chronological modeling, these early dates suggest that peaches were likely in the interior prior to permanent Spanish settlement in the American Southeast and that peaches spread independently of interactions with Spanish colonizers. We further argue that that eventual spread of peaches was structured exclusively by Indigenous communities and the ecologies produced through long-term Indigenous land management and land use practices, highlighting and centering the agency of Indigenous societies in the socioecological process of colonization.

Effects of apples (Malus domestica) and their derivatives on metabolic conditions related to inflammation and oxidative stress and an overview of by-products use in food processing

Apple (Malus domestica) is the third most produced fruit worldwide. It is a well-known source of bioactive compounds mainly represented by hydroxycinnamic acids, flavan-3-ols, dihydrochalcones, dehydroascorbic acid, carotenoids, chlorogenic acid, epicatechin, and phloridzin. Due to the lack of a recent evaluation of the clinical trials associated with apple consumption, this review investigated the effects of this fruit on metabolic conditions related to inflammation and oxidative stress and reviewed the applications of apple waste on food products. Thirty-three studies showed that apples or its derivatives exhibit anti-inflammatory and antioxidant actions, improve blood pressure, body fat, insulin resistance, dyslipidemia, and reduce cardiovascular risks. Apples have a great economic impact due to its several applications in the food industry and as a food supplement since it has impressive nutritional value. Dietary fiber from the fruit pomace can be used as a substitute for fat in food products or as an improver of fiber content in meat products. It can also be used in bakery and confectionary products or be fermented to produce alcohol. Pomace phytocompounds can also be isolated and applied as antioxidants in food products. The potential for the use of apples and by-products in the food industry can reduce environmental damage.

Investigating the spatiotemporal dynamics of apple tree phyllosphere bacterial and fungal communities across cultivars in orchards

The phyllosphere, a reservoir of diverse microbial life associated with plant health, harbors microbial communities that are subject to various complex ecological processes acting at multiple scales. In this study, we investigated the determinants of the spatiotemporal variation in bacterial and fungal communities within the apple tree phyllosphere, employing 16S and ITS amplicon sequencing. Our research assessed the impact of key factors-plant compartment, site, time, and cultivar-on the composition and diversity of leaf and flower microbial communities. Our analyses, based on samples collected from three cultivars in three orchards in 2022, revealed that site and time are the strongest drivers of apple tree phyllosphere microbial communities. Conversely, plant compartment and cultivar exhibited minor roles in explaining community composition and diversity. Predominantly, bacterial communities comprised Hymenobacter (25%) and Sphingomonas (10%), while the most relatively abundant fungal genera included Aureobasidium (27%) and Sporobolomyces (10%). Additionally, our results show a gradual decrease in alpha-diversity throughout the growth season. These findings emphasize the necessity to consider local microbial ecology dynamics in orchards, especially as many groups worldwide aim for the development of biocontrol strategies (e.g., by manipulating plant-microbe interactions). More research is needed to improve our understanding of the determinants of time and site-specific disparities within apple tree phyllosphere microbial communities across multiple years, locations, and cultivars.

The potential range of west Asian apple species Malus orientalis Uglitzk. under climate change

The wild relatives of cultivated apples would be an ideal source of diversity for breeding new varieties, which could potentially grow in diverse habitats shaped by climate change. However, there is still a lack of knowledge about the potential distribution of these species. The aim of the presented work was the understand the impacts of climate change on the potential distribution and habitat fragmentation of Caucasian crab apple (Malus orientalis Uglitzk.) and the designation of areas of high interest according to climatic conditions. We used the MaxEnt models and Morphological-Spatial Analysis (MSPA) to evaluate the potential distribution, suitability changes, habitat fragmentation, and connectivity throughout the species range in Turkey, Armenia, Georgia, Russia, and Iran. The results revealed that the potentially suitable range of M. orientalis encompasses 858,877 km², 635,279 km² and 456,795 km² under the present, RCP4.5 and RCP8.5 scenario, respectively. The range fragmentation analysis demonstrated a notable shift in the edge/core ratio, which increased from 50.95% in the current scenario to even 67.70% in the future. The northern part of the range (Armenia, northern Georgia, southern Russia), as well as the central and western parts of Hyrcania will be a core of the species range with suitable habitats and a high connectivity between M. orientalis populations and could work as major refugia for the studied species. However, in the Zagros and central Turkey, the potential range will shrink due to the lack of suitable climatic conditions, and the edge/core ratio will grow. In the southern part of the range, a decline of M. orientalis habitats is expected due to changing climatic conditions. The future outlook suggests that the Hyrcanian forest and the Caucasus region could serve as important refuges for M. orientalis. This study helps to understand spatial changes in species' range in response to climate change and can help develop conservation strategies. This is all the more important given the species' potential use in future breeding programs aimed at enriching the gene pool of cultivated apple varieties.

The seed dispersal syndrome hypothesis in ungulate-dominated landscapes

The Seed Dispersal Syndrome Hypothesis (SDSH) posits that fruit traits predict the main dispersers interacting with plant species. Mammalian dispersers, relying heavily on olfactory cues, are expected to select dull-colored, scented, and larger fruits compared to birds. However, challenges like overabundant seed predators and context-dependency of frugivore-plant interactions complicate SDSH expectations. We studied the Iberian pear, Pyrus bourgaeana, an expected mammal-dispersed tree based on its fruit traits. Extensive camera-trapping data (over 35,000 records) from several tree populations and years revealed visits from seven frugivore groups, with ungulate fruit predators (59-97%) and carnivore seed dispersers (1-20%) most frequent, while birds, lagomorphs, and rodents were infrequent (0-10%). Red deer and wild boar were also the main fruit removers in all sites and years but acted as fruit and seed predators, and thus likely exert conflicting selection pressures to those exerted by seed dispersers. Although, as predicted by the SDSH, most Iberian pear fruits were consumed by large and medium-sized mammals, the traits of Iberian pear fruits likely reflect selection pressures from dispersal vectors in past times. Our results do not challenge the SDHS but do reveal the importance of considering frugivore functional roles for its adequate evaluation.

Polysaccharides (pectin, mucilage, and fructan inulin) and their fermented products: A critical analysis of their biochemical, gut interactions, and biological functions as antidiabetic agents

Diabetes mellitus is a globally metabolic endocrine syndrome marked by a deficiency of insulin secretion (type-1 DM) or glucose intolerance arising from insulin response impairment (type-2 DM) leading to abnormal glucose metabolism. With an increasing interest in natural dietary components for diabetes management, the identification of novel agents witnessed major discoveries. Plant-derived mucilage, pectin, and inulin are important non-starch polysaccharides that exhibit effective antidiabetic properties often termed soluble dietary fiber (SDF). SDF affects sugar metabolism through multiple mechanisms affecting glucose absorption and diffusion, modulation of carbohydrate metabolizing enzymes (α-amylase and α-glucosidase), ameliorating β-pancreatic cell dysfunction, and improving insulin release or sensitivity. Certain SDFs inhibit dipeptidyl peptidase-4 and influence the expression levels of genes related to glucose metabolism. This review is designed to discuss holistically and critically the antidiabetic effects of major SDF and their underlying mechanisms of action. This review should aid drug discovery approaches in developing novel natural antidiabetic drugs from SDF.

Large mammals and trees in eastern monsoonal China: anthropogenic losses since the Late Pleistocene and restoration prospects in the Anthropocene

Massive human-induced declines of large-sized animals and trees (megabiota) from the Late Pleistocene to the Anthropocene have resulted in downsized ecosystems across the globe, in which components and functions have been greatly simplified. In response, active restoration projects of extant large-sized species or functional substitutes are needed at large scales to promote ecological processes that are important for ecosystem self-regulation and biodiversity maintenance. Despite the desired global scope of such projects, they have received little attention in East Asia. Here, we synthesise the biogeographical and ecological knowledge of megabiota in ancient and modern China, with relevant data mostly located in eastern monsoonal China (EMC), aiming to assess its potential for restoring functionally intact ecosystems modulated by megabiota. We found that during the Late Pleistocene, 12 mammalian megafaunal (carnivores ≥15 kg and herbivores ≥500 kg) species disappeared from EMC: one carnivore Crocuta ultima (East Asian spotted hyena) and 11 herbivores including six megaherbivores (≥1000 kg). The relative importance of climate change and humans in driving these losses remains debated, despite accumulating evidence in favour of the latter. Later massive depletion of megafauna and large-sized (45-500 kg) herbivores has been closely associated with agricultural expansion and societal development, especially during the late Holocene. While forests rich in large timber trees (33 taxa in written records) were common in the region 2000-3000 years ago, millennial-long logging has resulted in considerable range contractions and at least 39 threatened species. The wide distribution of C. ultima, which likely favoured open or semi-open habitats (like extant spotted hyenas), suggests the existence of mosaic open and closed vegetation in the Late Pleistocene across EMC, in line with a few pollen-based vegetation reconstructions and potentially, or at least partially, reflecting herbivory by herbivorous megafauna. The widespread loss of megaherbivores may have strongly compromised seed dispersal for both megafruit (fleshy fruits with widths ≥40 mm) and non-megafruit plant species in EMC, especially in terms of extra-long-distance (>10 km) dispersal, which is critical for plant species that rely on effective biotic agents to track rapid climate change. The former occurrence of large mammals and trees have translated into rich material and non-material heritages passed down across generations. Several reintroduction projects have been implemented or are under consideration, with the case of Elaphurus davidianus a notable success in recovering wild populations in the middle reaches of the Yangtze River, although trophic interactions with native carnivorous megafauna have not yet been restored. Lessons of dealing with human-wildlife conflicts are key to public support for maintaining landscapes shared with megafauna and large herbivores in the human-dominated Anthropocene. Meanwhile, potential human-wildlife conflicts, e.g. public health risks, need to be scientifically informed and effectively reduced. The Chinese government's strong commitment to improved policies of ecological protection and restoration (e.g. ecological redlines and national parks) provides a solid foundation for a scaling-up contribution to the global scope needed for solving the crisis of biotic downsizing and ecosystem degradation.

The East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (Pamp.) Rehder., are additional contributors to the genomes of cultivated European and Chinese varieties

The domestication process in long-lived plant perennials differs dramatically from that of annuals, with a huge amount of genetic exchange between crop and wild populations. Though apple is a major fruit crop grown worldwide, the contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense study. We used population genomics approaches to investigate the contributions of several wild apple species to European and Chinese rootstock and dessert genomes, with a focus on the extent of wild-crop gene flow. Population genetic structure inferences revealed that the East Asian wild apples, Malus baccata (L.) Borkh and M. hupehensis (Pamp.), form a single panmictic group, and that the European dessert and rootstock apples form a specific gene pool whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools, suggesting different evolutionary histories of European and Chinese apple varieties. Coalescent-based inferences and gene flow estimates indicated that M. baccata - M. hupehensis contributed to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions, and not as an initial contributor as previously supposed. We also confirmed the contribution through wild-to-crop introgressions of Malus sylvestris Mill. to the cultivated apple genome. Apple tree domestication is therefore one example in woody perennials that involved gene flow from several wild species from multiple geographical areas. This study provides an example of a complex protracted process of domestication in long-lived plant perennials, and is a starting point for apple breeding programmes.

Food globalization in southern Central Asia: archaeobotany at Bukhara between antiquity and the Middle Ages

The Silk Road is a modern name for a globalization phenomenon that marked an extensive network of communication and exchange in the ancient world; by the turn of the second millennium AD, commercial trade linked Asia and supported the development of a string of large urban centers across Central Asia. One of the main arteries of the medieval trade routes followed the middle and lower Zarafshan River and was connected by mercantile cities, such as Samarkand and Bukhara. Bukhara developed into a flourishing urban center between the fourth and sixth centuries AD, served as the capital of the Samanid court between AD 893 and 999, and remained prosperous into the Qarakhanid period (AD 999-1220), until the Mongol invasion in AD 1220. We present the first archaeobotanical study from this ancient center of education, craft production, artistic development, and commerce. Radiocarbon dates and an archaeological chronology that has been developed for the site show that our samples cover a range between the third and eleventh centuries AD. These samples from Bukhara represent the richest systematically collected archaeobotanical assemblage thus far recovered in Central Asia. The assemblage includes spices and both annual and perennial crops, which allowed Sogdians and Samanids to feed large cities in river oases surrounded by desert and arid steppe and supported a far-reaching commercial market in the first millennium AD.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12520-023-01827-z.

Evolution and biogeography of apple stem grooving virus

BACKGROUND

Apple stem grooving virus (ASGV) has a wide host range, notably including apples, pears, prunes and citrus. It is found worldwide.

METHOD

In this study, two near complete genomes, and seven coat protein (CP) sequences of Iranian isolates from apple were determined. Sequences added from GenBank provided alignments of 120 genomic sequences (54 of which were recombinant), and 276 coat protein genes (none of them recombinant).

RESULT

The non-recombinant genomes gave a well supported phylogeny with isolates from diverse hosts in China forming the base of the phylogeny, and a monophyletic clade of at least seven clusters of isolates from around the world with no host or provenace groupings among them, and all but one including isolates from China. The six regions of the ASGV genome (five in one frame, one - 2 overlapping) gave significantly correlated phylogenies, but individually had less statistical support. The largest cluster of isolates contained those from Iran and had isolates with worldwide provenances, and came from a wide range of mono- and dicotyledonous hosts. Population genetic comparisons of the six regions of the ASGV genome showed that four were under strong negative selection, but two of unknown function were under positive selection.

CONCLUSION

ASGV most likely originated and spread in East Asia in one or more of various plant species, but not in Eurasia; the ASGV population of China had the greatest overall nucleotide diversity and largest number of segregating sites.

Detection of Cytb Point Mutation (G143A) that Confers High-Level Resistance to Pyraclostrobin in Glomerella cingulata Using LAMP Method

Glomerella leaf spot (GLS) caused by Glomerella cingulata is a newly emerging disease that results in severe defoliation and fruit spots in apples. In China, the compound of pyraclostrobin and tebuconazole was registered to control GLS in 2018 and has achieved excellent control efficiency. In this study, we showed that the high-level resistant isolates of G. cingulata to pyraclostrobin, caused by the point mutation at codon 143 (GGT→GCT, G143A) in the cytochrome b gene, has appeared in apple orchards in Shandong Province in 2020, and the resistance frequency was 4.8%. Based on the genotype of the resistant isolates, we developed a loop-mediated isothermal amplification (LAMP) assay for detection of the pyraclostrobin resistance. The LAMP assay was demonstrated to have good specificity, sensitivity, and repeatability, and it exhibited high accuracy in detecting pyraclostrobin resistance in the field. This study reported the resistance status of GLS to pyraclostrobin in Shandong Province and developed a molecular tool for the detection of pyraclostrobin resistance, which is of practical significance for the scientific control of GLS.

Bearing Fruit: Miocene Apes and Rosaceous Fruit Evolution

Extinct megafaunal mammals in the Americas are often linked to seed-dispersal mutualisms with large-fruiting tree species, but large-fruiting species in Europe and Asia have received far less attention. Several species of arboreal Maloideae (apples and pears) and Prunoideae (plums and peaches) evolved large fruits starting around nine million years ago, primarily in Eurasia. As evolutionary adaptations for seed dispersal by animals, the size, high sugar content, and bright colorful visual displays of ripeness suggest that mutualism with megafaunal mammals facilitated the evolutionary change. There has been little discussion as to which animals were likely candidate(s) on the late Miocene landscape of Eurasia. We argue that several possible dispersers could have consumed the large fruits, with endozoochoric dispersal usually relying on guilds of species. During the Pleistocene and Holocene, the dispersal guild likely included ursids, equids, and elephantids. During the late Miocene, large primates were likely also among the members of this guild, and the potential of a long-held mutualism between the ape and apple clades merits further discussion. If primates were a driving factor in the evolution of this large-fruit seed-dispersal system, it would represent an example of seed-dispersal-based mutualism with hominids millions of years prior to crop domestication or the development of cultural practices, such as farming.

The potential chemo-preventive roles of Malus domestica against the risk of colorectal cancer: A suggestive insight into clinical application

Biologically active compounds in fruit-derived ingredients, particularly phytochemicals, have significant potential to modulate and mitigate many pathological processes in the development of disease conditions, including cancer. Colorectal cancer (CRC) remains a major public health issue. Nonetheless, prevention is an important step in lowering the rate of mortality from this cancer. Currently, the link between apple consumption and improved health is becoming remarkably evident and is reported to be beneficial for human health. Phytochemicals, such as flavonoids and other polyphenol compounds extensively available in apple fruits, have well-known positive effects on health outcomes and the potential to combat and prevent the development of CRC, including antioxidant, anti-proliferative, and anti-carcinogenic effects. This review describes the bioactive compounds derived from apple fruits, particularly the polyphenols and flavonoids, their proposed mechanisms responsible for their bioactive properties and health-promoting attributes that could provide potential chemo-preventive effects against the risk of CRC development. The conclusion of the review provides insights into the potential effects of apple-derived bioactive compounds and proposes the need for more clinical studies in large trials for future strategies regarding the valuable effects of apple phytochemicals, which might be therapeutic candidates in the campaign against CRC.

Natural Polyphenol Recovery from Apple-, Cereal-, and Tomato-Processing By-Products and Related Health-Promoting Properties

Polyphenols of plant origin are a broad family of secondary metabolites that range from basic phenolic acids to more complex compounds such as stilbenes, flavonoids, and tannins, all of which have several phenol units in their structure. Considerable health benefits, such as having prebiotic potential and cardio-protective and weight control effects, have been linked to diets based on polyphenol-enriched foods and plant-based products, indicating the potential role of these substances in the prevention or treatment of numerous pathologies. The most representative phenolic compounds in apple pomace are phloridzin, chlorogenic acid, and epicatechin, with major health implications in diabetes, cancer, and cardiovascular and neurocognitive diseases. The cereal byproducts are rich in flavonoids (cyanidin 3-glucoside) and phenolic acids (ferulic acid), all with significant results in reducing the incidence of noncommunicable diseases. Quercetin, naringenin, and rutin are the predominant phenolic molecules in tomato by-products, having important antioxidant and antimicrobial activities. The present understanding of the functionality of polyphenols in health outcomes, specifically, noncommunicable illnesses, is summarized in this review, focusing on the applicability of this evidence in three extensive agrifood industries (apple, cereal, and tomato processing). Moreover, the reintegration of by-products into the food chain via functional food products and personalized nutrition (e.g., 3D food printing) is detailed, supporting a novel direction to be explored within the circular economy concept.

Evidence of an additional centre of apple domestication in Iran, with contributions from the Caucasian crab apple Malus orientalis Uglitzk. to the cultivated apple gene pool

Divergence processes in crop-wild fruit tree complexes in pivotal regions for plant domestication such as the Caucasus and Iran remain little studied. We investigated anthropogenic and natural divergence processes in apples in these regions using 26 microsatellite markers amplified in 550 wild and cultivated samples. We found two genetically distinct cultivated populations in Iran that are differentiated from Malus domestica, the standard cultivated apple worldwide. Coalescent-based inferences showed that these two cultivated populations originated from specific domestication events of Malus orientalis in Iran. We found evidence of substantial wild-crop and crop-crop gene flow in the Caucasus and Iran, as has been described in apple in Europe. In addition, we identified seven genetically differentiated populations of wild apple (M. orientalis), not introgressed by the cultivated apple. Niche modelling combined with genetic diversity estimates indicated that these wild populations likely resulted from range changes during past glaciations. This study identifies Iran as a key region in the domestication of apple and M. orientalis as an additional contributor to the cultivated apple gene pool. Domestication of the apple tree therefore involved multiple origins of domestication in different geographic locations and substantial crop-wild hybridization, as found in other fruit trees. This study also highlights the impact of climate change on the natural divergence of a wild fruit tree and provides a starting point for apple conservation and breeding programmes in the Caucasus and Iran.

Home gardens of Central Asia: Reservoirs of diversity of fruit and nut tree species

Central Asia is an important center of origin for many globally valued fruit and nut tree species. Forest degradation and deforestation are cause for concern for the conservation of these valuable species, now confined to small remnant populations. Home gardens have the important function of sustaining household food consumption and income generation, and can potentially play a critical role in conserving diversity of fruit and nut trees. These systems have been very poorly documented in the scientific literature. This study contributes to filling this gap by describing the diversity of fruit and nut trees in home gardens of Kyrgyzstan, Uzbekistan, and Tajikistan, examining their dynamic flow of planting material and its sources, understanding their future prospects, and looking at significant differences between the three countries. Home gardens show a similar portfolio of the most abundant tree species (apple, apricot, walnut, pear, and plum). Although the diversity of tree species and varieties recorded is significant, small population sizes can limit future possibilities for this diversity to thrive, given the pressure on natural stands and on habitats where the preferred species are found. Furthermore, the selection of species and varieties to be planted in home gardens is increasingly influenced by market opportunities and availability of exotic material. Some of the most abundant tree species recorded are represented largely by exotic varieties (apple, pear), while others (e.g., apricot, walnut, plum) are still mainly characterized by traditional local varieties that are not formally registered. Home gardens continue to play a critical role in rural livelihoods and in national economies, and many rural inhabitants still aspire to maintain them. Thus, home gardens should be integrated in national research and extension systems and closely linked to national conservation efforts. Changes and possible declines in the diversity they host, their health status, and resilience should be carefully monitored.

Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication

Background

Persian walnut, Juglans regia, occurs naturally from Greece to western China, while its closest relative, the iron walnut, Juglans sigillata, is endemic in southwest China; both species are cultivated for their nuts and wood. Here, we infer their demographic histories and the time and direction of possible hybridization and introgression between them.

Results

We use whole-genome resequencing data, different population-genetic approaches (PSMC and GONE), and isolation-with-migration models (IMa3) on individuals from Europe, Iran, Kazakhstan, Pakistan, and China. IMa3 analyses indicate that the two species diverged from each other by 0.85 million years ago, with unidirectional gene flow from eastern J. regia and its ancestor into J. sigillata, including the shell-thickness gene. Within J. regia, a western group, located from Europe to Iran, and an eastern group with individuals from northern China, experienced dramatically declining population sizes about 80 generations ago (roughly 2400 to 4000 years), followed by an expansion at about 40 generations, while J. sigillata had a constant population size from about 100 to 20 generations ago, followed by a rapid decline.

Conclusions

Both J. regia and J. sigillata appear to have suffered sudden population declines during their domestication, suggesting that the bottleneck scenario of plant domestication may well apply in at least some perennial crop species. Introgression from introduced J. regia appears to have played a role in the domestication of J. sigillata.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02720-z.

Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii)

An understanding of the relationship between the cultivated apple (Malus domestica) and its primary wild progenitor species (M. sieversii) not only provides an understanding of how apples have been improved in the past, but may be useful for apple improvement in the future. We measured 10 phenotypes in over 1000 unique apple accessions belonging to M. domestica and M. sieversii from Canada's Apple Biodiversity Collection. Using principal components analysis (PCA), we determined that M. domestica and M. sieversii differ significantly in phenotypic space and are nearly completely distinguishable as two separate groups. We found that M. domestica had a shorter juvenile phase than M. sieversii and that cultivated trees produced flowers and ripe fruit later than their wild progenitors. Cultivated apples were also 3.6 times heavier, 43% less acidic, and had 68% less phenolic content than wild apples. Using historical records, we found that apple breeding over the past 200 years has resulted in a trend towards apples that have higher soluble solids, are less bitter, and soften less during storage. Our results quantify the significant changes in phenotype that have taken place since apple domestication, and provide evidence that apple breeding has led to continued phenotypic divergence of the cultivated apple from its wild progenitor species.

Pljushtchia argoi sp. n., a new geometrid moth from the Western Tien Shan Mountains (Lepidoptera, Geometridae, Larentiinae)

Background

This paper focuses on the morphological description and illustration of the wing pattern and genitalia structures of the known species of the genus Pljushtchia. The possibility of co-evolution of Pljushtchia moths and fruit tree forests of Tien Shan is discussed. The maple tree is supposed to have evolved in the Ili River valley in NW China and in Kazakhstan. Malussieversii, the wild apple tree, is distributed in Miocene nemoral forest belt to Europe in the West an to western North America in the East. The last remnants of fruit tree forests are now localised in biodiversity hotspots in China and in Middle Asian mountains.

New information

This paper provides a description of a new species of geometrid moth, Pljushtchiaargoi sp. n. As the ancestral Malussieversii has diverged in Malussilvestris in Europe, Malusturkestanica in Kyrgyzstan and Malushissarica in Tajikistan, a co-divergence of geometrid moths and their food plants is possible. We found Chlorissaarkitensis Viidalepp in the Chatkal area, Tien Shan, its sister species Chlorissatalvei Viidalepp in Hissar and Pamirs and Chlorissapretiosaria Staudinger in Transcaucasus. Pljushtchiaprima is associated with a biodiversity hotspot in Tajikistan and Pljushtchiaargoi with another biodiversity hotspot in southern Tien Shan.

Sidon on the breadth of the wild sea: Movement and diet on the Mediterranean coast in the Middle Bronze Age

OBJECTIVES

Excavations at Sidon (Lebanon) have revealed dual identities during the Middle Bronze Age (ca. 2000-1600 BCE): a maritime port and center for local distribution, as well as a settlement with a heavy subsistence dependence on the extensive inland hinterlands. We aim to investigate residential mobility at Sidon using isotopic analyses of 112 individuals from 83 burials (20 females, 26 males, and 37 subadults). Veneration and remembrance of the dead is evident from funerary offerings in and near the tombs. With marine fish a major component in funerary offerings, we predict major marine reliance in this coastal population.

MATERIALS AND METHODS

New isotopic evidence of paleomobility (87 Sr/86 Sr, δ18 O) and diet (δ13 Ccarbonate ) is the focus of this research. Previous bulk bone collagen δ13 C and δ15 N analysis is strengthened by further sampling, along with δ34 S where collagen yield was sufficient.

RESULTS

The five non-locals identified (8.9% of the 56 analyzed) come from constructed tombs with high-status grave goods except for one, which was heavily disturbed in antiquity. Dietary investigation of the population confirms reliance on terrestrial resources with no significant marine input. No significant differences in diet between the sexes or burial types are present.

CONCLUSIONS

Although Sidon was part of a growing Mediterranean network evidenced through artefactual finds, relatively low immigration is evident. While religious feasts venerating the dead may have involved significant piscine components, no appreciable marine input in diet is observed. Fish may have been reserved for the deceased or only consumed on feast days alongside the dead rather than a regular part of the Bronze Age menu.

Apple Pomace as a Sustainable Substrate in Sourdough Fermentation

Innovations range from food production, land use, and emissions all the way to improved diets and waste management. Global apple production has amounted to over 87 million tons/year, while 18% are processed, resulting in 20-35% (apple fruit fresh weight) apple pomace (AP). Using modern AP management, integrated knowledge in innovative fermentation demonstrates opportunities for reducing environmental pollution and integration into a circular economy. With this association in view, integrating AP flour during sourdough fermentation increases the nutritional value, highlighting a new approach that could guide innovative fermented foods. In this study, the wheat flour (WF) and AP flour were mixed at different ratios, hydrated with water (1:1 w/v), and fermented using a selective culture of Fructilactobacillus florum DSM 22689 and baker's yeast (single and co-culture). Sourdough fermentation was monitored and analyzed for 72 h. Results suggested that AP may be an important source of organic acids and fermentable sugars that increase nutritional sourdough value. AP flour addition in WF had a positive effect, especially in fermentations with 95% WF and 5% AP, mainly in co-culture fermentation.

The Taming of Psidium guajava: Natural and Cultural History of a Neotropical Fruit

Guava (Psidium guajava L., Myrtaceae) is a Neotropical fruit that is widely consumed around the world. However, its evolutionary history and domestication process are unknown. Here we examine available ecological, taxonomic, genetic, archeological, and historical evidence about guava. Guava needs full sunlight, warm temperatures, and well-distributed rainfall throughout the year to grow, but tolerates drought. Zoochory and anthropochory are the main forms of dispersal. Guava's phylogenetic relationships with other species of the genus Psidium are unclear. A group of six species that share several morphological characteristics are tentatively accepted as the Psidium guajava complex. DNA analyses are limited to the characterization of crop genetic diversity within localities and do not account for possible evolutionary and domestication scenarios. A significant amount of archeological information exists, with a greater number and older records in South America than in Mesoamerica, where there are also numerous historical records. From this information, we propose that: (1) the guava ancestor may have originated during the Middle or Late Miocene, and the savannas and semi-deciduous forests of South America formed during the Late Pleistocene would have been the most appropriate ecosystems for its growth, (2) the megafauna were important dispersers for guava, (3) dispersal by humans during the Holocene expanded guava's geographic range, including to the southwestern Amazonian lowlands, (4) where its domestication may have started, and (5) with the European conquest of the Neotropics, accompanied by their domestic animals, new contact routes between previously remote guava populations were established. These proposals could direct future research on the evolutionary and domestication process of guava.

Postharvest quality assessment of apple during storage at ambient temperature

In this study, the physical and chemical quality attributes of apples were measured experimentally during the storage after harvesting, using well-defined procedures and techniques. Overall quality index (OQi) models were formulated in terms of measured quality attributes. Firmness (F) and total soluble solids (TSS) varied from 11.88 ± 0.25 to 7.68 ± 0.24 N and 14.1 ± 0.1 to 12.7 ± 0.1 % Brix, respectively, whereas acidity and density varied from 0.163 ± 0.003 to 0.081 ± 0.001 % and 0.995 ± 0.003 to 0.951 ± 0.004 gm/cm³, respectively. The gloss values at 45° and 60° angles of incidence were found to be in the range of 7.9 ± 0.2 to 4.1 ± 0.3 and 6.8 ± 0.1 to 2.5 ± 0.3, respectively whereas, the Hunter color values L, a, b were found to be in the range of 51.75 ± 1.33 to 57.01 ± 0.98, 24.20 ± 0.86 to 30.12 ± 1.13, and 19.53 ± 1.61 to 22.96 ± 1.12, respectively. Formulated models were validated with the sensory scores. OQi predicted by the Model ML2 was found to be in consonance with the variation in the sensory overall quality scores. The OQi, as per the model ML2, was estimated as the ratio of the product of the constant C (265.5), acidity (A), and firmness (F) to the mod of the product of Hunter color values a and b. Finally, the predicted values of OQi were correlated with the measured quality parameters to check the possibility of predicting OQi non-destructively by using any one of those measured attributes during the storage.

Induced Genetic Variations in Fruit Trees Using New Breeding Tools: Food Security and Climate Resilience

Fruit trees provide essential nutrients to humans by contributing to major agricultural outputs and economic growth globally. However, major constraints to sustainable agricultural productivity are the uncontrolled proliferation of the population, and biotic and abiotic stresses. Tree mutation breeding has been substantially improved using different physical and chemical mutagens. Nonetheless, tree plant breeding has certain crucial bottlenecks including a long life cycle, ploidy level, occurrence of sequence polymorphisms, nature of parthenocarpic fruit development and linkage. Genetic engineering of trees has focused on boosting quality traits such as productivity, wood quality, and resistance to biotic and abiotic stresses. Recent technological advances in genome editing provide a unique opportunity for the genetic improvement of woody plants. This review examines application of the CRISPR-Cas system to reduce disease susceptibility, alter plant architecture, enhance fruit quality, and improve yields. Examples are discussed of the contemporary CRISPR-Cas system to engineer easily scorable PDS genes, modify lignin, and to alter the flowering onset, fertility, tree architecture and certain biotic stresses.

Fruit crops in the era of genome editing: closing the regulatory gap

The conventional breeding of fruits and fruit trees has led to the improvement of consumer-driven traits such as fruit size, yield, nutritional properties, aroma and taste, as well as the introduction of agronomic properties such as disease resistance. However, even with the assistance of modern molecular approaches such as marker-assisted selection, the improvement of fruit varieties by conventional breeding takes considerable time and effort. The advent of genetic engineering led to the rapid development of new varieties by allowing the direct introduction of genes into elite lines. In this review article, we discuss three such case studies: the Arctic^® apple, the Pinkglow pineapple and the SunUp/Rainbow papaya. We consider these events in the light of global regulations for the commercialization of genetically modified organisms (GMOs), focusing on the differences between product-related systems (the USA/Canada comparative safety assessment) and process-related systems (the EU "precautionary principle" model). More recently, genome editing has provided an efficient way to introduce precise mutations in plants, including fruits and fruit trees, replicating conventional breeding outcomes without the extensive backcrossing and selection typically necessary to introgress new traits. Some jurisdictions have reacted by amending the regulations governing GMOs to provide exemptions for crops that would be indistinguishable from conventional varieties based on product comparison. This has revealed the deficiencies of current process-related regulatory frameworks, particularly in the EU, which now stands against the rest of the world as a unique example of inflexible and dogmatic governance based on political expediency and activism rather than rigorous scientific evidence.

Exploring microbial determinants of apple replant disease (ARD): a microhabitat approach under split-root design

Apple replant disease (ARD) occurs worldwide in apple orchards and nurseries and leads to a severe growth and productivity decline. Despite research on the topic, its causality remains unclear. In a split-root experiment, we grew ARD-susceptible 'M26' apple rootstocks in different substrate combinations (+ARD: ARD soil; -ARD: gamma-irradiated ARD soil; and Control: soil with no apple history). We investigated the microbial community composition by 16S rRNA gene amplicon sequencing (bacteria and archaea) along the soil-root continuum (bulk soil, rhizosphere and rhizoplane). Significant differences in microbial community composition and structure were found between +ARD and -ARD or +ARD and Control along the soil-root continuum, even for plants exposed simultaneously to two different substrates (-ARD/+ARD and Control/+ARD). The substrates in the respective split-root compartment defined the assembly of root-associated microbial communities, being hardly influenced by the type of substrate in the respective neighbor compartment. Root-associated representatives from Actinobacteria were the most dynamic taxa in response to the treatments, suggesting a pivotal role in ARD. Altogether, we evidenced an altered state of the microbial community in the +ARD soil, displaying altered alpha- and beta-diversity, which in turn will also impact the normal development of apple rhizosphere and rhizoplane microbiota (dysbiosis), concurring with symptom appearance.

Harvesting strategies as evidence for 4000 years of camas (Camassia quamash) management in the North American Columbia Plateau

One of the greatest archaeological enigmas is in understanding the role of decision-making, intentionality and interventions in plant life cycles by foraging peoples in transitions to and from low-level food production practices. We bring together archaeological, palaeoclimatological and botanical data to explore relationships over the past 4000 years between people and camas (Camassia quamash), a perennial geophyte with an edible bulb common across the North American Pacific Northwest. In this region throughout the late Holocene, people began experimenting with selective harvesting practices through targeting sexually mature bulbs by 3500 cal BP, with bulb harvesting practices akin to ethnographic descriptions firmly established by 1000 cal BP. While we find no evidence that such interventions lead to a selection for larger bulbs or a reduction in time to maturity, archaeological bulbs do exhibit several other domestication syndrome traits. This establishes considerable continuity to human intervention into camas life cycles, but these dynamic relationships did not result in unequivocal morphological indications of domestication. This approach to tracking forager plant management practices offers an alternative explanatory framework to conventional management studies, supplements oral histories of Indigenous traditional resource management and can be applied to other vegetatively propagated species.

Exaptation Traits for Megafaunal Mutualisms as a Factor in Plant Domestication

Megafaunal extinctions are recurring events that cause evolutionary ripples, as cascades of secondary extinctions and shifting selective pressures reshape ecosystems. Megafaunal browsers and grazers are major ecosystem engineers, they: keep woody vegetation suppressed; are nitrogen cyclers; and serve as seed dispersers. Most angiosperms possess sets of physiological traits that allow for the fixation of mutualisms with megafauna; some of these traits appear to serve as exaptation (preadaptation) features for farming. As an easily recognized example, fleshy fruits are, an exaptation to agriculture, as they evolved to recruit a non-human disperser. We hypothesize that the traits of rapid annual growth, self-compatibility, heavy investment in reproduction, high plasticity (wide reaction norms), and rapid evolvability were part of an adaptive syndrome for megafaunal seed dispersal. We review the evolutionary importance that megafauna had for crop and weed progenitors and discuss possible ramifications of their extinction on: (1) seed dispersal; (2) population dynamics; and (3) habitat loss. Humans replaced some of the ecological services that had been lost as a result of late Quaternary extinctions and drove rapid evolutionary change resulting in domestication.

Malus domestica: A Review on Nutritional Features, Chemical Composition, Traditional and Medicinal Value

Fruit-derived bioactive substances have been spotlighted as a regulator against various diseases due to their fewer side effects compared to chemical drugs. Among the most frequently consumed fruits, apple is a rich source of nutritional molecules and contains high levels of bioactive compounds. The main structural classes of apple constituents include polyphenols, polysaccharides (pectin), phytosterols, and pentacyclic triterpenes. Also, vitamins and trace elements complete the nutritional features of apple fruit. There is now considerable scientific evidence that these bioactive substances present in apple and peel have the potential to improve human health, for example contributing to preventing cardiovascular disease, diabetes, inflammation, and cancer. This review will focus on the current knowledge of bioactive substances in apple and their medicinal value for human health.

Genetic integrity is still maintained in natural populations of the indigenous wild apple species Malus sylvestris (Mill.) in Saxony as demonstrated with nuclear SSR and chloroplast DNA markers

Malus sylvestris (Mill.) is the only indigenous wild apple species in Central Europe. Agriculture, forestry, and urbanization increasingly endanger Malus sylvestris natural habitats. In addition, the risks of cross-hybridization associated with increase in the cultivation of the domesticated apple Malus × domestica (Borkh.) threaten the genetic integrity of M. sylvestris. The present study investigated the number of hybrids, genetic diversity, and genetic structure of 292 putative M. sylvestris that originate from five different natural M. sylvestris populations in Saxony, Germany. All samples were genetically analyzed using nine nuclear microsatellite markers (ncSSR) and four maternally inherited chloroplast markers (cpDNA) along with 56 apple cultivars commonly cultivated in Saxony. Eighty-seven percent of the wild apple accessions were identified as pure M. sylvestris. The cpDNA analysis showed six private haplotypes for M. sylvestris, whereas three haplotypes were present in M. sylvestris and M. × domestica. The analysis of molecular variance (AMOVA) resulted in a moderate (ncSSR) and great (cpDNA) variation among pure M. sylvestris and M. × domestica individuals indicating a low gene flow between both species. The genetic diversity within the pure M. sylvestris populations was high with a weak genetic structure between the M. sylvestris populations indicating an unrestricted genetic exchange between these M. sylvestris populations. The clear distinguishing of M. sylvestris and M. ×domestica confirms our expectation of the existence of pure M. sylvestris accessions in this area and supports the argument for the implementation of preservation measures to protect the M. sylvestris populations in Saxony.

Anthropogenic Seed Dispersal: Rethinking the Origins of Plant Domestication

It is well documented that ancient sickle harvesting led to tough rachises, but the other seed dispersal properties in crop progenitors are rarely discussed. The first steps toward domestication are evolutionary responses for the recruitment of humans as dispersers. Seed dispersal-based mutualism evolved from heavy human herbivory or seed predation. Plants that evolved traits to support human-mediated seed dispersal express greater fitness in increasingly anthropogenic ecosystems. The loss of dormancy, reduction in seed coat thickness, increased seed size, pericarp density, and sugar concentration all led to more-focused seed dispersal through seed saving and sowing. Some of the earliest plants to evolve domestication traits had weak seed dispersal processes in the wild, often due to the extinction of animal dispersers or short-distance mechanical dispersal.

Genotyping-by-Sequencing Identifies Historical Breeding Stages of the Recently Domesticated American Cranberry

The cranberry (Vaccinium macrocarpon Ait.) is a North American fruit crop domesticated less than 200 years ago. The USDA began the first cranberry breeding program in response to false-blossom disease in 1929, but after the first generation of cultivars were released in the 1950s, the program was discontinued. Decades later, renewed efforts for breeding cranberry cultivars at Rutgers University and the University of Wisconsin yielded the first modern cultivars in the 2000's. Phenotypic data suggests that current cultivars have changed significantly in terms of fruiting habits compared to original selections from endemic populations. However, due to the few breeding and selection cycles and short domestication period of the crop, it is unclear how much cultivated germplasm differs genetically from wild selections. Moreover, the extent to which selection for agricultural superior traits has shaped the genetic and phenotypic variation of cranberry remains mostly obscure. Here, a historical collection composed of 362 accessions, spanning wild germplasm, first-, second-, and third-generation selection cycles was studied to provide a window into the breeding and domestication history of cranberry. Genome-wide sequence variation of more than 20,000 loci showed directional selection across the stages of cranberry domestication and breeding. Diversity analysis and population structure revealed a partially defined progressive bottleneck when transitioning from early domestication stages to current cranberry forms. Additionally, breeding cycles correlated with phenotypic variation for yield-related traits and anthocyanin accumulation, but not for other fruit metabolites. Particularly, average fruit weight, yield, and anthocyanin content, which were common target traits during early selection attempts, increased dramatically in second- and third-generation cycle cultivars, whereas other fruit quality traits such as Brix and acids showed comparable variation among all breeding stages. Genome-wide association mapping in this diversity panel allowed us to identify marker-trait associations for average fruit weight and fruit rot, which are two traits of great agronomic relevance today and could be further exploited to accelerate cranberry genetic improvement. This study constitutes the first genome-wide analysis of cranberry genetic diversity, which explored how the recurrent use of wild germplasm and first-generation selections into cultivar development have shaped the evolutionary history of this crop species.

A Multifaceted Overview of Apple Tree Domestication

The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.