Genetic structure and domestication history of the grape

Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health

Plants shape and interact continuously with their rhizospheric microbiota, which play a key role in plant health and resilience. However, plant-associated microbial community can be shaped by several factors including plant phenotype and cropping system. Thus, understanding the interplay between microbiome assembly during the onset of plant-pathogen interactions and long-lasting resistance traits in ligneous plants remains a major challenge. To date, such attempts were mainly investigated in herbaceous plants, due to their phenotypic characteristics and their short life cycle. However, only few studies have focused on the microbial structure, dynamic and their drivers in perennial ligneous plants. Ligneous plants coevolved in interaction with specific fungal and bacterial communities that differ from those of annual plants. The specificities of such ligneous plants in shaping their own functional microbial communities could be dependent on their high heterozygosis, physiological and molecular status associated to seasonality and their aging processes, root system and above-ground architectures, long-lasting climatic variations, and specific cultural practices. This article provides an overview of the specific characteristics of perennial ligneous plants that are likely to modulate symbiotic interactions in the rhizosphere, thus affecting the plant's fitness and systemic immunity. Plant and microbial traits contributing to the establishment of plant-microbiome interactions and the adaptation of this holobiont are also discussed.

Unearthing Grape Heritage: Morphological Relationships between Late Bronze-Iron Age Grape Pips and Modern Cultivars

The grapevine was one of the earliest domesticated fruit crops and has been cultivated since ancient times. It is considered one of the most important fruit crops worldwide for wine and table grape production. The current grape varieties are the outcome of prolonged selection initiated during the domestication process of their wild relative. Recent genetic studies have shed light on the origins of the modern domestic grapevine in western Europe, suggesting that its origin stems from the introgression between eastern domestic grapes and western wild grapes. However, the origin of ancient grapevines remains largely unexplored. In this study, we conducted an extensive analysis of 2228 well-preserved waterlogged archaeological grape pips from two sites in Sardinia (Italy), dated to the Late Bronze Age (ca. 1300-1100 BC) and the Iron Age (4th and 3rd centuries BC). Using morphometrics and linear discriminant analyses, we compared the archaeological grape pips with modern reference collections to differentiate between wild and domestic grape types and to investigate similarities with 330 modern cultivars. Grape pips from the Late Bronze Age displayed a high percentage of similarity with domesticated grapevines, with a small percentage assigned to wild ones, while the majority of grape pips from the Iron Age were classified as domestic. Discriminant analyses revealed that both white and red grape varieties were cultivated during the Late Bronze and Iron Ages, suggesting a high level of diversification in grape cultivation. Furthermore, a high percentage of archaeological grape pips from both periods showed strong similarities with modern cultivars from the Caucasus and Balkans. This suggests that the great diversity of grapevines present in Sardinia could result from interbreeding between western Asian cultivars and local grapevines that began in the Late Bronze Age. Additionally, a substantial proportion of archaeological grape pips exhibited similar morphometric characteristics to two important Mediterranean grape cultivars: "Muscat à petits grains blancs" and "Garnacha".

Adaptation and the Geographic Spread of Crop Species

Crops are plant species that were domesticated starting about 11,000 years ago from several centers of origin, most prominently the Fertile Crescent, East Asia, and Mesoamerica. From their domestication centers, these crops spread across the globe and had to adapt to differing environments as a result of this dispersal. We discuss broad patterns of crop spread, including the early diffusion of crops associated with the rise and spread of agriculture, the later movement via ancient trading networks, and the exchange between the Old and New Worlds over the last ∼550 years after the European colonization of the Americas. We also examine the various genetic mechanisms associated with the evolutionary adaptation of crops to their new environments after dispersal, most prominently seasonal adaptation associated with movement across latitudes, as well as altitudinal, temperature, and other environmental factors.

Integration of machine learning models with microsatellite markers: New avenue in world grapevine germplasm characterization

Development of efficient analytical techniques is required for effective interpretation of biological data to take novel hypotheses and finding the critical predictive patterns. Machine Learning algorithms provide a novel opportunity for development of low-cost and practical solutions in biology. In this study, we proposed a new integrated analytical approach using supervised machine learning algorithms and microsatellites data of worldwide vitis populations. A total of 1378 wild (V. vinifera spp. sylvestris) and cultivated (V. vinifera spp. sativa) accessions of grapevine were investigated using 20 microsatellite markers. Data cleaning, feature selection, and supervised machine learning classification models vis, Naive Bayes, Support Vector Machine (SVM) and Tree Induction methods were implied to find most indicative and diagnostic alleles to represent wild/cultivated and originated geography of each population. Our combined approaches showed microsatellite markers with the highest differentiating capacity and proved efficiency for our pipeline of classification and prediction of vitis accessions. Moreover, our study proposed the best combination of markers for better distinguishing of populations, which can be exploited in future germplasm conservation and breeding programs.

A history of olive and grape cultivation in Southwest Asia using charcoal and seed remains

Evaluating archaeobotanical data from over 3.9 million seeds and 124,300 charcoal fragments across 330 archaeological site phases in Southwest Asia, we reconstruct the history of olive and grape cultivation spanning a period of 6,000 years. Combining charcoal and seed data enables investigation into both the production and consumption of olive and grape. The earliest indication for olive and grape cultivation appears in the southern Levant around ca. 5000 BC and 4th millennium BC respectively, although cultivation may have been practiced prior to these dates. Olive and grape cultivation in Southwest Asia was regionally concentrated within the Levant until 600 BC, although there were periodic pushes to the East. Several indications for climate influencing the history of olive and grape cultivation were found, as well as a correlation between periods of high population density and high proportions of olive and grape remains in archaeological sites. While temporal uncertainty prevents a detailed understanding of the causal mechanisms behind these correlations, we suggest that long distance trade in olives, grapes and their associated products was integral to the economic, social, and demographic trajectories of the region.

From acidity to sweetness: a comprehensive review of carbon accumulation in grape berries

Most of the carbon found in fruits at harvest is imported by the phloem. Imported carbon provide the material needed for the accumulation of sugars, organic acids, secondary compounds, in addition to the material needed for the synthesis of cell walls. The accumulation of sugars during fruit development influences not only sweetness but also various parameters controlling fruit composition (fruit "quality"). The accumulation of organic acids and sugar in grape berry flesh cells is a key process for berry development and ripening. The present review presents an update of the research on grape berry development, anatomical structure, sugar and acid metabolism, sugar transporters, and regulatory factors.

Population comparative genomics discovers gene gain and loss during grapevine domestication

Plant domestication are evolutionary experiments conducted by early farmers since thousands years ago, during which the crop wild progenitors are artificially selected for desired agronomic traits along with dramatic genomic variation in the course of moderate to severe bottlenecks. However, previous investigations are mainly focused on small-effect variants, while changes in gene contents are rarely investigated due to the lack of population-level assemblies for both the crop and its wild relatives. Here, we applied comparative genomic analyses to discover gene gain and loss during grapevine domestication using long-read assemblies of representative population samples for both domesticated grapevines (V. vinifera ssp. vinifera) and their wild progenitors (V. vinifera ssp. sylvestris). Only ∼7% of gene families were shared by 16 Vitis genomes while ∼8% of gene families were specific to each accession, suggesting dramatic variations of gene contents in grapevine genomes. Compared to wild progenitors, the domesticated accessions exhibited an increased presence of genes associated with asexual reproduction, while the wild progenitors showcased a higher abundance of genes related to pollination, revealing the transition from sexual reproduction to clonal propagation during domestication processes. Moreover, the domesticated accessions harbored fewer disease-resistance genes than wild progenitors. The SVs occurred frequently in aroma and disease-resistance related genes between domesticated grapevines and wild progenitors, indicating the rapid diversification of these genes during domestication. Our study provides insights and resources for biological studies and breeding programs in grapevine.

Genetic relationships and introgression events between wild and cultivated grapevines (Vitis vinifera L.): focus on Italian Lambruscos

Research efforts on genomic structure and ecology of wild populations of Vitis vinifera L. offer insights on grape domestication processes and on the assortment evolution of the cultivated forms. Attention is also paid to the origin of traditional, long-cultivated varieties, often producing renowned and valuable wines. The genetic relationships between 283 Vitis vinifera cultivated varieties (subsp. sativa) and 65 individuals from 9 populations of the sylvestris subspecies mainly from northern Italy were explored by means of molecular markers (27 nuclear and 4 chloroplastic microsatellites). Several episodes of contamination of the wild germplasm by the pollen of specific grape cultivars were detected, implying concern for maintaining the purity of the wild form. At the same time, events of introgression from the wild subspecies resulted playing a crucial role in the emergence of several cultivated varieties with a clear admixed genome ancestry sativa-sylvestris. These included Lambruscos originated from the flat areas crossed by the Po and Adige rivers in northern Italy, while other cultivars still called Lambrusco but typical of hilly areas did not show the same admixed genome. Historical and ecological evidences suggesting an adaptative recent post-domestication process in the origin of several Italian Lambruscos are discussed.

Unraveling the diversity and cultural heritage of fruit crops through paleogenomics

Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying and understanding genetic traits crucial for crop resilience, disease resistance, and nutritional value. The approach not only tracks landrace dispersal and introgression but also sheds light on domestication events. In the face of major future environmental challenges, integrating paleogenomics with modern breeding strategies emerges as a promising avenue to significantly bolster fruit crop sustainability.

Acquisition and transmission of Grapevine fanleaf virus (GFLV) by Xiphinema index and Xiphinema italiae (Longidoridae)

Grapevine fanleaf virus (GFLV) is one of the most severe virus diseases of grapevines, causing fanleaf degeneration that is transmitted by Xiphinema index. This paper aims to isolate Xiphinema species from Tunisian vineyard soil samples and assess their ability to acquire and transmit GFLV under natural and controlled conditions. Based on morphological and morphometric analyses, Tunisian dagger nematodes were identified as X. index and Xiphinema italiae. These results were confirmed with molecular identification tools using species-specific polymerase chain reaction primers. The total RNA of GFLV was extracted from specimens of Xiphinema and amplified based on real-time polymerase chain reaction using virus-specific primers. Our results showed that X. index could acquire and transmit the viral particles of GFLV. This nepovirus was not detected in X. italiae, under natural conditions; however, under controlled conditions, this nematode was able to successfully acquire and transmit the viral particles of GFLV.

Current Status and Future Perspectives on Distribution of Fungal Endophytes and Their Utilization for Plant Growth Promotion and Management of Grapevine Diseases

Grapevine is one of the economically most important fruit crops cultivated worldwide. Grape production is significantly affected by biotic constraints leading to heavy crop losses. Changing climatic conditions leading to widespread occurrence of different foliar diseases in grapevine. Chemical products are used for managing these diseases through preventive and curative application in the vineyard. High disease pressure and indiscriminate use of chemicals leading to residue in the final harvest and resistance development in phytopathogens. To mitigate these challenges, the adoption of potential biocontrol control agents is necessary. Moreover, multifaceted benefits of endophytes made them eco-friendly, and environmentally safe approach. The genetic composition, physiological conditions, and ecology of their host plant have an impact on their dispersion patterns and population diversity. Worldwide, a total of more than 164 fungal endophytes (FEs) have been characterized originating from different tissues, varieties, crop growth stages, and geographical regions of grapevine. These diverse FEs have been used extensively for management of different phytopathogens globally. The FEs produce secondary metabolites, lytic enzymes, and organic compounds which are known to possess antimicrobial and antifungal properties. The aim of this review was to understand diversity, distribution, host-pathogen-endophyte interaction, role of endophytes in disease management and for enhanced, and quality production.

A super-pangenome of the North American wild grape species

BACKGROUND

Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations.

RESULTS

Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce's disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes.

CONCLUSIONS

This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.

Wild grapes of Armenia: unexplored source of genetic diversity and disease resistance

The present study is the first in-depth research evaluating the genetic diversity and potential resistance of Armenian wild grapes utilizing DNA-based markers to understand the genetic signature of this unexplored germplasm. In the proposed research, five geographical regions with known viticultural history were explored. A total of 148 unique wild genotypes were collected and included in the study with 48 wild individuals previously collected as seed. A total of 24 nSSR markers were utilized to establish a fingerprint database to infer information on the population genetic diversity and structure. Three nSSR markers linked to the Ren1 locus were analyzed to identify potential resistance against powdery mildew. According to molecular fingerprinting data, the Armenian V. sylvestris gene pool conserves a high genetic diversity, displaying 292 different alleles with 12.167 allele per loci. The clustering analyses and diversity parameters supported eight genetic groups with 5.6% admixed proportion. The study of genetic polymorphism at the Ren1 locus revealed that 28 wild genotypes carried three R-alleles and 34 wild genotypes carried two R-alleles associated with PM resistance among analyzed 107 wild individuals. This gene pool richness represents an immense reservoir of under-explored genetic diversity and breeding potential. Therefore, continued survey and research efforts are crucial for the conservation, sustainable management, and utilization of Armenian wild grape resources in the face of emerging challenges in viticulture.

Genealogical Analyses of 3 Cultivated and 1 Wild Specimen of Vitis vinifera from Greece

Grapevine (Vitis vinifera) has been an important crop with considerable cultural and economic significance for over 2,500 years, and Greece has been an important entry point into Europe for lineages that were domesticated in Western Asia and the Caucasus. However, whole-genome-based investigation of the demographic history of Greek cultivars relative to other European lineages has only started recently. To understand how Greek cultivars relate to Eurasian domesticated and wild populations, we sequenced 3 iconic domesticated strains ('Xinomavro,' 'Agiorgitiko,' 'Mavrotragano') along with 1 wild accession (the vinetree of Pausanias-a historically important wild specimen) and analyzed their genomic diversity together with a large sample of publicly available domesticated and wild strains. We also reconstructed genealogies by leveraging the powerful tsinfer methodology which has not previously been used in this system. We show that cultivated strains from Greece differ genetically from other strains in Europe. Interestingly, all the 3 cultivated Greek strains clustered with cultivated and wild accessions from Transcaucasia, South Asia, and the Levant and are amongst the very few cultivated European strains belonging to this cluster. Furthermore, our results indicate that 'Xinomavro' shares close genealogical proximity with European elite cultivars such as 'Chardonnay,' 'Riesling,' and 'Gamay' but not 'Pinot.' Therefore, the proximity of 'Xinomavro' to Gouais/Heunisch Weiss is confirmed and the utility of ancestral recombination graph reconstruction approaches to study genealogical relationships in crops is highlighted.

Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits

The ease and throughput of single-cell genomics have steadily improved, and its current trajectory suggests that surveying single-cell populations will become routine. We discuss the merger of quantitative genetics with single-cell genomics and emphasize how this synergizes with advantages intrinsic to plants. Single-cell population genomics provides increased detection resolution when mapping variants that control molecular traits, including gene expression or chromatin accessibility. Additionally, single-cell population genomics reveals the cell types in which variants act and, when combined with organism-level phenotype measurements, unveils which cellular contexts impact higher-order traits. Emerging technologies, notably multiomics, can facilitate the measurement of both genetic changes and genomic traits in single cells, enabling single-cell genetic experiments. The implementation of single-cell genetics will advance the investigation of the genetic architecture of complex molecular traits and provide new experimental paradigms to study eukaryotic genetics.

Differences in the genomic diversity, structure, and inbreeding patterns in wild and managed populations of Agave potatorum Zucc. used in the production of Tobalá mezcal in Southern Mexico

Agave potatorum Zucc. locally known as Tobalá, is an important species for mezcal production. It is a perennial species that takes 10 to 15 years to reach reproductive age. Because of high demand of Tobalá mezcal and the slow maturation of the plants, its wild populations have been under intense anthropogenic pressure. The main objective of this study was to estimate the genome-wide diversity in A. potatorum and determine if the type of management has had any effect on its diversity, inbreeding and structure. We analyzed 174 individuals (105 wild, 42 cultivated and 27 from nurseries) from 34 sites with a reduced representation genomic method (ddRADseq), using 14,875 SNPs. The diversity measured as expected heterozygosity was higher in the nursery and wild plants than in cultivated samples. We did not find private alleles in the cultivated and nursery plants, which indicates that the individuals under management recently derived from wild populations, which was supported by higher gene flow estimated from wild populations to the managed plants. We found low but positive levels of inbreeding (FIS = 0.082), probably related to isolation of the populations. We detected low genetic differentiation among populations (FST = 0.0796), with positive and significant isolation by distance. The population genetic structure in the species seems to be related to elevation and ecology, with higher gene flow among populations in less fragmented areas. We detected an outlier locus related to the recognition of pollen, which is also relevant to self-incompatibility protein (SI). Due to seed harvest and long generation time, the loss of diversity in A. potatorum has been gradual and artificial selection and incipient management have not yet caused drastic differences between cultivated and wild plants. Also, we described an agroecological alternative to the uncontrolled extraction of wild individuals.

Genomic analysis of the emergent aquatic plant Sparganium stoloniferum provides insights into its clonality, local adaptation and demographic history

Clonal propagation and extensive dispersal of seeds and asexual propagules are two important features of aquatic plants that help them adapt to aquatic environments. Accurate measurements of clonality and effective clonal dispersal are essential for understanding the evolution of aquatic plants. Here, we first assembled a high-quality chromosome-level genome of a widespread emergent aquatic plant Sparganium stoloniferum to provide a reference for its population genomic study. We then performed high-depth resequencing of 173 individuals from 20 populations covering different basins across its range in China. Population genomic analyses revealed three genetic lineages reflecting the northeast (NE), southwest (SW) and northwest (NW) of its geographical distribution. The NE lineage diverged in the middle Pleistocene while the SW and NW lineages diverged until about 2400 years ago. Clonal relationship analyses identified nine populations as monoclonal population. Dispersal of vegetative propagules was identified between five populations covering three basins in the NE lineage, and dispersal distance was up to 1041 km, indicating high dispersibility in emergent aquatic plant species. We also identified lineage-specific positively selected genes that are likely to be involved in adaptations to saline wetlands and high-altitude environments. Our findings accurately measure the clonality, determine the dispersal range and frequency of vegetative propagules, and detect genetic signatures of local adaptation in a widespread emergent aquatic plant species, providing new perspectives on the evolution of aquatic plants.

Dissecting the genetic architecture of root-related traits in a grafted wild Vitis berlandieri population for grapevine rootstock breeding

In woody perennial plants, quantitative genetics and association studies remain scarce for root-related traits, due to the time required to obtain mature plants and the complexity of phenotyping. In grapevine, a grafted cultivated plant, most of the rootstocks used are hybrids between American Vitis species (V. rupestris, V. riparia, and V. berlandieri). In this study, we used a wild population of an American Vitis species (V. berlandieri) to analyze the genetic architecture of the root-related traits of rootstocks in a grafted context. We studied a population consisting of 211 genotypes, with one to five replicates each (n = 846 individuals), plus four commercial rootstocks as control genotypes (110R, 5BB, Börner, and SO4). After two independent years of experimentation, the best linear unbiased estimates method revealed root-related traits with a moderate-to-high heritability (0.36-0.82) and coefficient of genetic variation (0.15-0.45). A genome-wide association study was performed with the BLINK model, leading to the detection of 11 QTL associated with four root-related traits (one QTL was associated with the total number of roots, four were associated with the number of small roots (< 1 mm in diameter), two were associated with the number of medium-sized roots (1 mm < diameter < 2 mm), and four were associated with mean diameter) accounting for up to 25.1% of the variance. Three genotypes were found to have better root-related trait performances than the commercial rootstocks and therefore constitute possible new candidates for use in grapevine rootstock breeding programs.

Disentangling the origins of viticulture in the western Mediterranean

We present direct evidence of early grape domestication in southern Italy via a multidisciplinary study of pip assemblage from one site, shedding new light on the spread of viticulture in the western Mediterranean during the Bronze Age. This consist of 55 waterlogged pips from Grotta di Pertosa, a Middle Bronze Age settlement in the south of the Italian peninsula. Direct radiocarbon dating of pips was carried out, confirming the chronological consistency of the samples with their archaeological contexts (ca. 1450-1200 BCE). The extraordinary state of conservation of the sample allowed to perform geometric morphometric (GMM) and paleogenetic analyses (aDNA) at the same time. The combination of the two methods has irrefutably shown the presence of domestic grapevines, together with wild ones, in Southern Italy during the Middle/Late Bronze Age. The results converge towards an oriental origin of the domestic grapes, most likely arriving from the Aegean area through the Mycenaeans. A parent/offspring kinship was also recognised between a domestic/wild hybrid individual and a domestic clonal group. This data point out a little known aspect of the diffusion of the first viticulture in Italy, and therefore in the western Mediterranean, which involved the hybridization between imported domestic varieties with, likely local, wild vines.

Molecular mechanisms of drought resistance using genome-wide association mapping in maize (Zea mays L.)

BACKGROUND

Drought is a critical abiotic stress that influences maize yield and reduces grain yield when it occurs at the flowering or filling stage. To dissect the genetic architecture of grain yield under drought stress (DS), a genome-wide association analysis was conducted in a maize population composed of diverse inbred lines from five locations under well-watered and DS conditions at flowering in 2019 and 2020.

RESULTS

Using a fixed and random model circulating probability unification model, a total of 147 loci associated with grain yield or the drought resistance index (DRI) were identified, of which 54 loci were associated with a DRI with an average phenotypic variation explanation of 4.03%. Further, 10 of these loci explained more than 10% of the phenotypic variation. By integrating two public transcriptome datasets, 22 differentially expressed genes were considered as candidate genes, including the cloned gene ZmNAC49, which responds to drought by regulating stomatal density. Enrichment and protein interaction network showed that signaling pathways responded to drought resistance, including jasmonic acid and salicylic acid, mitogen-activated protein kinase, and abscisic acid-activated. Additionally, several transcription factors involved in DS were identified, including basic leucine zipper (GRMZM2G370026), NAC (GRMZM2G347043), and ethylene-responsive element binding protein (GRMZM2G169654).

CONCLUSIONS

In this study, we nominated several genes as candidate genes for drought resistance by intergrating association maping and transcription analysis. These results provide valuable information for understanding the genetic basis of drought tolerance at the mature stage and for designing drought-tolerant maize breeding.

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.

Transcriptional repression of MdMa1 by MdMYB21 in Ma locus decreases malic acid content in apple fruit

Malic acid is a major organic acid component of apples and a crucial determinant of fruit organoleptic quality. A candidate gene for malic acid content, designated MdMa1, was previously identified in the Ma locus, which is a major quantitative trait locus (QTL) for apple fruit acidity located on the linkage group 16. Region-based association mapping to detect candidate genes in the Ma locus identified MdMa1 and an additional MdMYB21 gene putatively associated with malic acid. MdMYB21 was significantly associated with fruit malic acid content, accounting for ~7.48% of the observed phenotypic variation in the apple germplasm collection. Analyses of transgenic apple calli, fruits and tomatoes demonstrated that MdMYB21 negatively regulated malic acid accumulation. The apple fruit acidity-related MdMa1 and its tomato ortholog, SlALMT9, exhibited lower expression profiles in apple calli, mature fruits and tomatoes in which MdMYB21 was overexpressed, compared with their corresponding wild-type variety. MdMYB21 directly binds to the MdMa1 promoter and represses its expression. Interestingly, a 2-bp variation in the MdMYB21 promoter region altered its expression and regulation of its target gene, MdMa1, expression. Our findings not only demonstrate the efficiency of integrating QTL and association mapping in the identification of candidate genes controlling complex traits in apples, but also provide insights into the complex regulatory mechanism of fruit malic acid accumulation.

Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes

Wild grapevines are important genetic resources in breeding programs to confer adaptive fitness traits and unique fruit characteristics, but the genetics underlying these traits, and their evolutionary origins, are largely unknown. To determine the factors that contributed to grapevine genome diversification, we performed comprehensive intragenomic and intergenomic analyses with three cultivated European (including the PN40024 reference genome) and two wild North American grapevine genomes, including our newly released Vitis labrusca genome. We found the heterozygosity of the cultivated grapevine genomes was twice as high as the wild grapevine genomes studied. Approximately 30% of V. labrusca and 48% of V. vinifera Chardonnay genes were heterozygous or hemizygous and a considerable number of collinear genes between Chardonnay and V. labrusca had different gene zygosity. Our study revealed evidence that supports gene gain-loss events in parental genomes resulted in the inheritance of hemizygous genes in the Chardonnay genome. Thousands of segmental duplications supplied source material for genome-specific genes, further driving diversification of the genomes studied. We found an enrichment of recently duplicated, adaptive genes in similar functional pathways, but differential retention of environment-specific adaptive genes within each genome. For example, large expansions of NLR genes were discovered in the two wild grapevine genomes studied. Our findings support variation in transposable elements contributed to unique traits in grapevines. Our work revealed gene zygosity, segmental duplications, gene gain-and-loss variations, and transposable element polymorphisms can be key driving forces for grapevine genome diversification.

Proteome-Wide Identification of Non-histone Lysine Methylation during Grape Berry Ripening

To gain a comprehensive understanding of non-histone methylation during berry ripening in grape (Vitis vinifera L.), the methylation of non-histone lysine residues was studied using a 4D label-free quantitative proteomics approach. In total, 822 methylation sites in 416 methylated proteins were identified, with xxExxx_K_xxxxxx as the conserved motif. Functional annotation of non-histone proteins with methylated lysine residues indicated that these proteins were mostly associated with "ripening and senescence", "energy metabolism", "oxidation-reduction process", and "stimulus response". Most of the genes encoding proteins subjected to methylation during grape berry ripening showed a significant increase in expression during maturation at least at one developmental stage. The correlation of methylated proteins with QTLs, SNPs, and selective regions associated with fruit quality and development was also investigated. This study reports the first proteomic analysis of non-histone lysine methylation in grape berry and indicates that non-histone methylation plays an important role in grape berry ripening.

Genomic analysis unveils reduced genetic variability but increased proportion of heterozygotic genotypes of the intensively managed mezcal agave, Agave angustifolia

PREMISE

The central Oaxaca Basin has a century-long history of agave cultivation and is hypothesized to be the region of origin of other cultivated crops. Widely cultivated for mezcal production, the perennial crop known as "espadín" is putatively derived from wild Agave angustifolia. Nevertheless, little is known about its genetic relationship to the wild A. angustifolia or how the decades-long clonal propagation has affected its genetics.

METHODS

Using restriction-site-associated DNA sequencing and over 8000 single-nucleotide polymorphisms, we studied aspects of the population genomics of wild and cultivated A. angustifolia in Puebla and Oaxaca, Mexico. We assessed patterns of genetic diversity, inbreeding, distribution of genetic variation, and differentiation among and within wild populations and plantations.

RESULTS

Genetic differentiation between wild and cultivated plants was strong, and both gene pools harbored multiple unique alleles. Nevertheless, we found several cultivated individuals with high genetic affinity with wild samples. Higher heterozygosity was observed in the cultivated individuals, while in total, they harbored considerably fewer alleles and presented higher linkage disequilibrium compared to the wild plants. Independently of geographic distance among sampled plantations, the genetic relatedness of the cultivated plants was high, suggesting a common origin and prevalent role of clonal propagation.

CONCLUSIONS

The considerable heterozygosity found in espadín is contained within a network of highly related individuals, displaying high linkage disequilibrium generated by decades of clonal propagation and possibly by the accumulation of somatic mutations. Wild A. angustifolia, on the other hand, represents a significant genetic diversity reservoir that should be carefully studied and conserved.

Dissipation, residue, and dietary risk assessment of dimethachlon in grapes

Dimethachlon, a dicarboximide fungicide, has gained widespread usage in Asian countries. While considered a low-toxicity fungicide, concerns regarding potential health effects, such as nephrotoxicity, have emerged. To date, neither China nor other countries have established maximum residue limit (MRL) for dimethachlon on grapes, and exposure risk assessment of dimethachlon is lacking. Here, we developed a QuEChERS method coupled with gas chromatography-mass spectrometry (GC-MS) to investigate the dissipation rates and terminal residues of dimethachlon in grapes, along with an assessment of dietary risk to consumers. Our results indicated that the average recoveries of dimethachlon in grapes ranged from 74 to 76%. The limit of quantification (LOQ) was 0.050 mg/kg. After undergoing 112 days of storage at -18 °C, the dissipation rate of dimethachlon in grapes was found to be less than 30%, suggesting a state of stable storage. In the context of good agricultural practice (GAP) guidelines, the half-lives of dimethachlon in grapes were 14.3-18.1 days, which is notably longer compared to the reported values for other crops. The terminal residues of dimethachlon in grapes at 14 and 21 days were found to be < 0.05-0.53 mg/kg and < 0.05-0.29 mg/kg, respectively. Regarding the dietary risk assessment, the calculated risk quotient (RQ) value was significantly below 100%, indicating a negligible chronic risk of dimethachlon in grapes at the recommended dosage. This study provides an important reference for the analysis of dimethachlon and offers valuable empirical data to support the establishment of MRL.

Species relationships within the genus Vitis based on molecular and morphological data

The grape genus Vitis L. includes the domesticated V. vinifera, which is one of the most important fruit crop, and also close relatives recognized as valuable germplasm resources for improving cultivars. To resolve some standing problems in the species relationships within the Vitis genus we analyzed diversity in a set of 90 accessions comprising most of Vitis species and some putative hybrids. We discovered single nucleotide polymorphisms (SNPs) in SANGER sequences of twelve loci and genotyped accessions at a larger number of SNPs using a previously developed SNP array. Our phylogenic analyses consistently identified: three clades in North America, one in East Asia, and one in Europe corresponding to V. vinifera. Using heterozygosity measurement, haplotype reconstruction and chloroplast markers, we identified the hybrids existing within and between clades. The species relationships were better assessed after discarding these hybrids from analyses. We also studied the relationships between phylogeny and morphological traits and found that several traits significantly correlated with the phylogeny. The American clade that includes important species such as V. riparia and V. rupestris showed a major divergence with all other clades based on both DNA polymorphisms and morphological traits.

Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple [Malus sylvestris (L.) Mill.], a wild relative of the cultivated apple

BACKGROUND AND AIMS

Studying the relationship between phenotypic and genetic variation in populations distributed across environmental gradients can help us to understand the ecological and evolutionary processes involved in population divergence. We investigated the patterns of genetic and phenotypic diversity in the European crabapple, Malus sylvestris, a wild relative of the cultivated apple (Malus domestica) that occurs naturally across Europe in areas subjected to different climatic conditions, to test for divergence among populations.

METHODS

Growth rates and traits related to carbon uptake in seedlings collected across Europe were measured in controlled conditions and associated with the genetic status of the seedlings, which was assessed using 13 microsatellite loci and the Bayesian clustering method. Isolation-by-distance, isolation-by-climate and isolation-by-adaptation patterns, which can explain genetic and phenotypic differentiation among M. sylvestris populations, were also tested.

KEY RESULTS

A total of 11.6 % of seedlings were introgressed by M. domestica, indicating that crop-wild gene flow is ongoing in Europe. The remaining seedlings (88.4 %) belonged to seven M. sylvestris populations. Significant phenotypic trait variation among M. sylvestris populations was observed. We did not observe significant isolation by adaptation; however, the significant association between genetic variation and the climate during the Last Glacial Maximum suggests that there has been local adaptation of M. sylvestris to past climates.

CONCLUSIONS

This study provides insight into the phenotypic and genetic differentiation among populations of a wild relative of the cultivated apple. This might help us to make better use of its diversity and provide options for mitigating the impact of climate change on the cultivated apple through breeding.

Genome assembly of the hybrid grapevine Vitis 'Chambourcin'

'Chambourcin' is a French-American interspecific hybrid grape grown in the eastern and midwestern United States and used for making wine. Few genomic resources are available for hybrid grapevines like 'Chambourcin'. Here, we assembled the genome of 'Chambourcin' using PacBio HiFi long-read, Bionano optical map, and Illumina short-read sequencing technologies. We generated an assembly for 'Chambourcin' with 26 scaffolds, with an N50 length of 23.3 Mb and an estimated BUSCO completeness of 97.9%. We predicted 33,791 gene models and identified 16,056 common orthologs between 'Chambourcin', V. vinifera 'PN40024' 12X.v2, VCOST.v3, Shine Muscat and V. riparia Gloire. We found 1,606 plant transcription factors from 58 gene families. Finally, we identified 304,571 simple sequence repeats (up to six base pairs long). Our work provides the genome assembly, annotation and the protein and coding sequences of 'Chambourcin'. Our genome assembly is a valuable resource for genome comparisons, functional genomic analyses and genome-assisted breeding research.

Hybrid Vitis Cultivars with American or Asian Ancestries Show Higher Tolerance towards Grapevine Trunk Diseases

Grape production worldwide is increasingly threatened by grapevine trunk diseases (GTDs). No grapevine cultivar is known to be entirely resistant to GTDs, but susceptibility varies greatly. To quantify these differences, four Hungarian grape germplasm collections containing 305 different cultivars were surveyed to determine the ratios of GTDs based on symptom expression and the proportion of plant loss within all GTD symptoms. The cultivars of monophyletic Vitis vinifera L. origin were amongst the most sensitive ones, and their sensitivity was significantly (p < 0.01) higher than that of the interspecific (hybrid) cultivars assessed, which are defined by the presence of Vitis species other than V. vinifera (e.g., V. labrusca L., V. rupestris Scheele, and V. amurensis Rupr.) in their pedigree. We conclude that the ancestral diversity of grapes confers a higher degree of resilience against GTDs.

Adaptive and maladaptive introgression in grapevine domestication

Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these introgression events have not been investigated. Here, we studied resequencing data from 345 samples spanning the distributional range of wild (Vitis vinifera ssp. sylvestris) and cultivated (V. vinifera ssp. vinifera) grapes. Based on machine learning-based population genetic analyses, we detected evidence for a single domestication of grapevine, followed by continuous gene flow between European wild grapes (EU) and cultivated grapes over the past ~2,000 y, especially from EU to wine grapes. We also inferred that soft-selective sweeps were the dominant signals of artificial selection. Gene pathways associated with the synthesis of aromatic compounds were enriched in regions that were both selected and introgressed, suggesting EU wild grapes were an important resource for improving the flavor of cultivated grapes. Despite the potential benefits of introgression in grape improvement, the introgressed fragments introduced a higher deleterious burden, with most deleterious SNPs and structural variants hidden in a heterozygous state. Cultivated wine grapes have benefited from adaptive introgression with wild grapes, but introgression has also increased the genetic load. In general, our study of beneficial and harmful effects of introgression is critical for genomic breeding of grapevine to take advantage of wild resources.

Genetic structure and first genome-wide insights into the adaptation of a wild relative of grapevine, Vitis berlandieri

In grafted plants, such as grapevine, increasing the diversity of rootstocks available to growers is an ideal strategy for helping plants to adapt to climate change. The rootstocks used for grapevine are hybrids of various American Vitis, including V. berlandieri. The rootstocks currently use in vineyards are derived from breeding programs involving very small numbers of parental individuals. We investigated the structure of a natural population of V. berlandieri and the association of genetic diversity with environmental variables. In this study, we collected seeds from 78 wild V. berlandieri plants in Texas after open fertilization. We genotyped 286 individuals to describe the structure of the population, and environmental information collected at the sampling site made it possible to perform genome-environment association analysis (GEA). De novo long-read whole-genome sequencing was performed on V. berlandieri and a STRUCTURE analysis was performed. We identified and filtered 104,378 SNPs. We found that there were two subpopulations associated with differences in elevation, temperature, and rainfall between sampling sites. GEA identified three QTL for elevation and 15 QTL for PCA coordinates based on environmental parameter variability. This original study is the first GEA study to be performed on a population of grapevines sampled in natural conditions. Our results shed new light on rootstock genetics and could open up possibilities for introducing greater diversity into genetic improvement programs for grapevine rootstocks.

Genetic diversity, population genetic structure and gene flow in the rare and endangered wild plant Cypripedium macranthos revealed by genotyping-by-sequencing

BACKGROUND

Genetic diversity, genetic structure, and gene flow in plant populations and their influencing factors are important in conservation biology. Cypripedium macranthos is one of the few wild orchids with high ornamental value in northern China. However, over the past decade, excessive collection, trading, tourism development, habitat fragmentation, deceptive pollination, and seed germination difficulties have all caused a sharp decline in the number of C. macranthos individuals and its population. In order to propose a scientific and effective conservation strategy, the genetic diversity, genetic structure and gene flow of the current CM population are urgent scientific issues to be clarified.

RESULTS

Here, 99 individuals of C. macranthos from north and northeast China were analyzed to evaluate the genetic diversity, gene flow among populations, and genetic structure by genotyping-by-sequencing. More than 68.44 Gb high-quality clean reads and 41,154 SNPs were obtained. Our data based on bioinformatics methods revealed that C. macranthos has lower genetic diversity, high levels of historical gene flow, and moderate-to-high genetic differentiation between populations. The gene migration model revealed that the direction of gene flow was mainly from northeast populations to north populations in China. The results of genetic structure analysis showed that 11 C. macranthos populations can be considered as two groups, and further divided into four subgroups. Moreover, the Mantel test detected no significant "Isolation by Distance" between populations.

CONCLUSIONS

Our study demonstrates that the present genetic diversity and genetic structure of C. macranthos populations were mainly caused by biological characteristics, human interference, habitat fragmentation, and restricted gene flow. Finally, constructive measures, which can provide a basis for the proposal of conservation strategies, have been suggested.

Exploring genetic diversity and population structure of a large grapevine (Vitis vinifera L.) germplasm collection in Türkiye

Grapevine (Vitis Vinifera L.) has been one of the significant perennial crops in widespread temperate climate regions since its domestication around 6000 years ago. Grapevine and its products, particularly wine, table grapes, and raisins, have significant economic importance not only in grapevine-growing countries but also worldwide. Grapevine cultivation in Türkiye dates back to ancient times, and Anatolia is considered one of the main grapevine migration routes around the Mediterranean basin. Turkish germplasm collection, conserved at the Turkish Viticulture Research Institutes, includes cultivars and wild relatives mainly collected in Türkiye, breeding lines, rootstock varieties, and mutants, but also cultivars of international origin. Genotyping with high-throughput markers enables the investigation of genetic diversity, population structure, and linkage disequilibrium, which are crucial for applying genomic-assisted breeding. Here, we present the results of a high-throughput genotyping-by-sequencing (GBS) study of 341 genotypes from grapevine germplasm collection at Manisa Viticulture Research Institute. A total of 272,962 high-quality single nucleotide polymorphisms (SNP) markers on the nineteen chromosomes were identified using genotyping-by-sequencing (GBS) technology. The high-density coverage of SNPs resulted in an average of 14,366 markers per chromosome, an average polymorphism information content (PIC) value of 0.23 and an expected heterozygosity (He) value of 0.28 indicating the genetic diversity within 341 genotypes. LD decayed very fast when r² was between 0.45 and 0.2 and became flat when r² was 0.05. The average LD decay for the entire genome was 30 kb when r^2 = 0.2. The PCA and structure analysis did not distinguish the grapevine genotypes based on different origins, highlighting the occurrence of gene flow and a high amount of admixture. Analysis of molecular variance (AMOVA) results indicated a high level of genetic differentiation within populations, while variation among populations was extremely low. This study provides comprehensive information on the genetic diversity and population structure of Turkish grapevine genotypes.

A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus

A diploid genome in the Saccharum complex facilitates our understanding of evolution in the highly polyploid Saccharum genus. Here we have generated a complete, gap-free genome assembly of Erianthus rufipilus, a diploid species within the Saccharum complex. The complete assembly revealed that centromere satellite homogenization was accompanied by the insertions of Gypsy retrotransposons, which drove centromere diversification. An overall low rate of gene transcription was observed in the palaeo-duplicated chromosome EruChr05 similar to other grasses, which might be regulated by methylation patterns mediated by homologous 24 nt small RNAs, and potentially mediating the functions of many nucleotide-binding site genes. Sequencing data for 211 accessions in the Saccharum complex indicated that Saccharum probably originated in the trans-Himalayan region from a diploid ancestor (x = 10) around 1.9-2.5 million years ago. Our study provides new insights into the origin and evolution of Saccharum and accelerates translational research in cereal genetics and genomics.

Dual domestications and origin of traits in grapevine evolution

We elucidate grapevine evolution and domestication histories with 3525 cultivated and wild accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape ecotypes caused by continuous habitat fragmentation. Then, domestication occurred concurrently about 11,000 years ago in Western Asia and the Caucasus to yield table and wine grapevines. The Western Asia domesticates dispersed into Europe with early farmers, introgressed with ancient wild western ecotypes, and subsequently diversified along human migration trails into muscat and unique western wine grape ancestries by the late Neolithic. Analyses of domestication traits also reveal new insights into selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These data demonstrate the role of the grapevines in the early inception of agriculture across Eurasia.

Genetic changes in the genus Vitis and the domestication of vine

The genus Vitis belongs to the Vitaceae family and is divided into two subgenera: Muscadinia and Vitis, the main difference between these subgenera being the number of chromosomes. There are many hypotheses about the origin of the genus, which have been formed with archaeological studies and lately with molecular analyses. Even though there is no consensus on the place of origin, these studies have shown that grapes have been used by man since ancient times, starting later on its domestication. Most studies point to the Near East and Greece as the beginning of domestication, current research suggests it took place in parallel in different sites, but in all cases Vitis vinifera (L.) subsp. sylvestris [Vitis vinifera (L.) subsp. sylvestris (Gmelin) Hagi] seems to be the species chosen by our ancestors to give rise to the now known Vitis vinifera (L.) subsp. vinifera [=sativa (Hegi)= caucasica (Vavilov)]. Its evolution and expansion into other territories followed the formation of new empires and their expansion, and this is where the historical importance of this crop lies. In this process, plants with hermaphrodite flowers were preferentially selected, with firmer, sweeter, larger fruits of different colors, thus favoring the selection of genes associated with these traits, also resulting in a change in seed morphology. Currently, genetic improvement programs have made use of wild species for the introgression of disease resistance genes and tolerance to diverse soil and climate environments. In addition, the mapping of genes of interest, both linked to agronomic and fruit quality traits, has allowed the use of molecular markers for assisted selection. Information on the domestication process and genetic resources help to understand the gene pool available for the development of cultivars that respond to producer and consumer requirements.

Whole-genome re-sequencing, diversity analysis, and stress-resistance analysis of 77 grape rootstock genotypes

INTRODUCTION

Grape rootstocks play critical role in the development of the grape industry over the globe for their higher adaptability to various environments, and the evaluation of their genetic diversity among grape genotypes is necessary to the conservation and utility of genotypes.

METHODS

To analyze the genetic diversity of grape rootstocks for a better understanding multiple resistance traits, whole-genome re-sequencing of 77 common grape rootstock germplasms was conducted in the present study.

RESULTS

About 645 billion genome sequencing data were generated from the 77 grape rootstocks at an average depth of ~15.5×, based on which the phylogenic clusters were generated and the domestication of grapevine rootstocks was explored. The results indicated that the 77 rootstocks originated from five ancestral components. Through phylogenetic, principal components, and identity-by-descent (IBD) analyses, these 77 grape rootstocks were assembled into ten groups. It is noticed that the wild resources of V. amurensis and V. davidii, originating from China and being generally considered to have stronger resistance against biotic and abiotic stresses, were sub-divided from the other populations. Further analysis indicated that a high level of linkage disequilibrium was found among the 77 rootstock genotypes, and a total of 2,805,889 single nucleotide polymorphisms (SNPs) were excavated, GWAS analysis among the grape rootstocks located 631, 13, 9, 2, 810, and 44 SNP loci that were responsible to resistances to phylloxera, root-knot nematodes, salt, drought, cold and waterlogging traits.

DISCUSSION

This study generated a significant amount of genomic data from grape rootstocks, thus providing a theoretical basis for further research on the resistance mechanism of grape rootstocks and the breeding of resistant varieties. These findings also reveal that China originated V. amurensis and V. davidii could broaden the genetic background of grapevine rootstocks and be important germplasm used in breeding high stress-resistant grapevine rootstocks.

Review: Status and prospects of association mapping in grapevine

Thanks to current advances in sequencing technologies, novel bioinformatics tools, and efficient modeling solutions, association mapping has become a widely accepted approach to unravel the link between genotype and phenotype diversity in numerous crops. In grapevine, this strategy has been used in the last decades to understand the genetic basis of traits of agronomic interest (fruit quality, crop yield, biotic and abiotic resistance), of special relevance nowadays to improve crop resilience to cope with future climate scenarios. Genome-wide association studies have identified many putative causative loci for different traits, some of them overlapping well-known causal genes identified by conventional quantitative trait loci studies in biparental progenies, and/or validated by functional approaches. In addition, candidate-gene association studies have been useful to pinpoint the causal mutation underlying phenotypic variation for several traits of high interest in breeding programs (like berry color, seedlessness, and muscat flavor), information that has been used to develop highly informative and useful markers already in use in marker-assisted selection processes. Thus, association mapping has proved to represent a valuable step towards high quality and sustainable grape production. This review summarizes current applications of association mapping in grapevine research and discusses future prospects in view of current viticulture challenges.

Exchanges of economic plants along the land silk road

BACKGROUD

The greatest contribution of the Silk Road is to communicate among different countries and nationalities, and promote two-way cultural exchanges between the East and the West. We now have clearer understanding about how material civilization and religious culture of Central Asia and West Asia spread eastward along the Land Silk Road. However, there is controversial about how crops migrate along the Land Silk Road.

RESULTS

We summarize archaeology, genetics, and genomics data to explore crop migration patterns. Of the 207 crops that were domesticated along the Land Silk Road, 19 for which genomic evidence was available were selected for discussion.

CONCLUSIONS

There were conflicting lines of evidence for the domestication of Tibetan barley, mustard, lettuce, buckwheat, and chickpea. The main reasons for the conflicting results may include incomplete early knowledge, record differences in different period, sample sizes, and data analysis techniques. There was strong evidence that Tibetan barley, barley, wheat, and jujube were introduced into China before the existence of the Land Silk Road; and mustard, lettuce, buckwheat, chickpea, alfalfa, walnut, cauliflower, grape, spinach, apple, cucumber, mulberry, and pea spread to China via trade and human migration along the Land Silk Road.

Domestication and selection footprints in Persian walnuts (Juglans regia)

Walnut (Juglans) species are economically important hardwood trees cultivated worldwide for both edible nuts and high-quality wood. Broad-scale assessments of species diversity, evolutionary history, and domestication are needed to improve walnut breeding. In this study, we sequenced 309 walnut accessions from around the world, including 55 Juglans relatives, 98 wild Persian walnuts (J. regia), 70 J. regia landraces, and 86 J. regia cultivars. The phylogenetic tree indicated that J. regia samples (section Dioscaryon) were monophyletic within Juglans. The core areas of genetic diversity of J. regia germplasm were southwestern China and southern Asia near the Qinghai-Tibet Plateau and the Himalayas, and the uplift of the Himalayas was speculated to be the main factor leading to the current population dynamics of Persian walnut. The pattern of genomic variation in terms of nucleotide diversity, linkage disequilibrium, single nucleotide polymorphisms, and insertions/deletions revealed the domestication and selection footprints in Persian walnut. Selective sweep analysis, GWAS, and expression analysis further identified two transcription factors, JrbHLH and JrMYB6, that influence the thickness of the nut diaphragm as loci under selection during domestication. Our results elucidate the domestication and selection footprints in Persian walnuts and provide a valuable resource for the genomics-assisted breeding of this important crop.

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.

Genomic-environmental associations in wild cranberry (Vaccinium macrocarpon Ait.)

Understanding the genetic basis of local adaptation in natural plant populations, particularly crop wild relatives, may be highly useful for plant breeding. By characterizing genetic variation for adaptation to potentially stressful environmental conditions, breeders can make targeted use of crop wild relatives to develop cultivars for novel or changing environments. This is especially appealing for improving long-lived woody perennial crops such as the American cranberry (Vaccinium macrocarpon Ait.), the cultivation of which is challenged by biotic and abiotic stresses. In this study, we used environmental association analyses in a collection of 111 wild cranberry accessions to identify potentially adaptive genomic regions for a range of bioclimatic and soil conditions. We detected 126 significant associations between SNP marker loci and environmental variables describing temperature, precipitation, and soil attributes. Many of these markers tagged genes with functional annotations strongly suggesting a role in adaptation to biotic or abiotic conditions. Despite relatively low genetic variation in cranberry, our results suggest that local adaptation to divergent environments is indeed present, and the identification of potentially adaptive genetic variation may enable a selective use of this germplasm for breeding more stress-tolerant cultivars.

Morphotype broadening of the grapevine (Vitis vinifera L.) from Oxus civilization 4000 BP, Central Asia

The region of Transoxiana underwent an early agricultural-demographic transition leading to the earliest proto-urban centers in Central Asia. The agronomic details of this cultural shift are still poorly studied, especially regarding the role that long-generation perennials, such as grapes, played in the cultivation system. In this paper, we present directly dated remains of grape pips from the early urban centers of Sapalli and Djarkutan, in south Uzbekistan. We also present linear morphometric data, which illustrate a considerable range of variation under cultivation that we divide into four distinct morphotypes according to pip shape. While some of the pips in these two assemblages morphologically fall within the range of wild forms, others more closely resemble modern domesticated populations. Most of the specimens measure along a gradient between the two poles, showing a mixed combination of domesticated and wild features. We also point out that the seeds recovered from the Djarkutan temple were, on average, larger and contained more affinity towards domesticated forms than those from domestic contexts. The potential preference of morphotypes seems to suggest that there were recognized different varieties that local cultivators might aware and possibly propagating asexually.

A Field Collection of Indigenous Grapevines as a Valuable Repository for Applied Research

The grapevine is an economically important plant, with a historical connection to the development of human culture. Currently, over 6000 accessions are known as individual grapevine varieties, some of which are important to national heritage, valuable for current viticultural practices, and as genetic resources to maintain plasticity under changing climatic conditions, environmental sustainability, and market demands. Recently, the diversity of cultivated grapevines has declined significantly, due to the increased focus of global wine industries on a few major cultivars. Moreover, due to biotic and abiotic stresses, the wild V. vinifera germplasm's genetic diversity has declined, with some varieties on the verge of extinction. Vitis germplasm conservation can be achieved via either in situ (e.g., protected areas) or Ex situ (e.g., field collections, seed banks, and tissue culture collections) methods. This study aims to highlight the importance of Vitis field bank collections. We demonstrate the research done in the Israeli indigenous Vitis vinifera collection. The multi-layer analysis of the varieties enabled the identification of drought stress-resistant varieties, and suggested a mechanism for this resistance through noting the dramatic phenological differences in foliage development between resistant and sensitive varieties. In addition, we show a general characterization of the varieties via major grape characteristics, including bunch and berry shape, as well as their possible utilization based on their aromatic and phenolic profiles.

A recessive mutation in muscadine grapes causes berry color-loss without influencing anthocyanin pathway

Anthocyanins, a major class of flavonoids, are important pigments of grape berries. Despite the recent discovery of the genetic cause underlying the loss of color, the metabolomic and molecular responses are unknown. Anthocyanin quantification among diverse berry color muscadines suggests that all genotypes could produce adequate anthocyanin quantities, irrespective of berry color. Transcriptome profiling of contrasting color muscadine genotypes proposes a potential deficiency that occurs within the anthocyanin transport and/or degradation mechanisms and might cause unpigmented berries. Genome-wide association studies highlighted a region on chromosome-4, comprising several genes encoding glutathione S-transferases involved in anthocyanin transport. Sequence comparison among genotypes reveals the presence of two GST4b alleles that differ by substituting the conserved amino acid residue Pro₁₇₁-to-Leu. Molecular dynamics simulations demonstrate that GST4b2–Leu₁₇₁ encodes an inactive protein due to modifications within the H-binding site. Population genotyping suggests the recessive inheritance of the unpigmented trait with a GST4b2/2 homozygous. A model defining colorless muscadines’ response to the mutation stimulus, avoiding the impact of trapped anthocyanins within the cytoplasm is established.

Transcriptome profiling and mutational analysis suggest a potential deficiency in anthocyanin transport by glutathione S-transferases and/or degradation mechanisms that might cause unpigmented berries.

Genome-wide association analysis of 101 accessions dissects the genetic basis of shell thickness for genetic improvement in Persian walnut (Juglans regia L.)

BACKGROUND

Understanding the underlying genetic mechanisms that drive phenotypic variations is essential for enhancing the efficacy of crop improvement. Persian walnut (Juglans regia L.), which is grown extensively worldwide, is an important economic tree fruit due to its horticultural, medicinal, and material value. The quality of the walnut fruit is related to the selection of traits such as thinner shells, larger filling rates, and better taste, which is very important for breeding in China. The complex quantitative fruit-related traits are influenced by a variety of physiological and environmental factors, which can vary widely between walnut genotypes.

RESULTS

For this study, a set of 101 Persian walnut accessions were re-sequenced, which generated a total of 906.2 Gb of Illumina sequence data with an average read depth of 13.8× for each accession. We performed the genome-wide association study (GWAS) using 10.9 Mb of high-quality single-nucleotide polymorphisms (SNPs) and 10 agronomic traits to explore the underlying genetic basis of the walnut fruit. Several candidate genes are proposed to be involved in walnut characteristics, including JrPXC1, JrWAKL8, JrGAMYB, and JrFRK1. Specifically, the JrPXC1 gene was confirmed to participate in the regulation of secondary wall cellulose thickening in the walnut shell.

CONCLUSION

In addition to providing considerable available genetic resources for walnut trees, this study revealed the underlying genetic basis involved in important walnut agronomic traits, particularly shell thickness, as well as providing clues for the improvement of genetic breeding and domestication in other perennial economic crops.

Genomic consequences of artificial selection during early domestication of a wood fibre crop

From its origins in Australia, Eucalyptus grandis has spread to every continent, except Antarctica, as a wood crop. It has been cultivated and bred for over 100 yr in places such as South Africa. Unlike most annual crops and fruit trees, domestication of E. grandis is still in its infancy, representing a unique opportunity to interrogate the genomic consequences of artificial selection early in the domestication process. To determine how a century of artificial selection has changed the genome of E. grandis, we generated single nucleotide polymorphism genotypes for 1080 individuals from three advanced South African breeding programmes using the EUChip60K chip, and investigated population structure and genome-wide differentiation patterns relative to wild progenitors. Breeding and wild populations appeared genetically distinct. We found genomic evidence of evolutionary processes known to have occurred in other plant domesticates, including interspecific introgression and intraspecific infusion from wild material. Furthermore, we found genomic regions with increased linkage disequilibrium and genetic differentiation, putatively representing early soft sweeps of selection. This is, to our knowledge, the first study of genomic signatures of domestication in a timber species looking beyond the first few generations of cultivation. Our findings highlight the importance of intra- and interspecific hybridization during early domestication.

Alternative modes of introgression-mediated selection shaped crop adaptation to novel climates

Recent plant genomic studies provide fine-grained details on the evolutionary consequences of adaptive introgression during crop domestication. Modern genomic approaches and analytical methods now make it possible to better separate the introgression signal from the demographic signal thus providing a more comprehensive and complex picture of the role of introgression in local adaptation. Adaptive introgression has been fundamental for crop expansion and has involved complex patterns of gene flow. In addition to providing new and more favorable alleles of large effect, introgression during the early stages of domestication also increased allelic diversity at adaptive loci. Previous studies have largely underestimated the effect of such increased diversity following introgression. Recent genomic studies in wheat, potato, maize, grapevine, and ryegrass show that introgression of multiple genes, of as yet unknown effect, increased the effectiveness of purifying selection, and promoted disruptive or fluctuating selection in early cultivars and landraces. Historical selection processes associated with introgression from crop wild relatives provide an instructive analog for adaptation to current climate change and offer new avenues for crop breeding research that are expected to be instrumental for strengthening food security in the coming years.