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Principal coordinates analysis (PCoA) on five Prunophora species performed with DARwin. The sampling for this analysis included P. cerasifera (N = 66) in blue, P. armeniaca (N = 87) in pink, P. brigantina (N = 73) in green, the Chinese apricot tree P. mume (N = 9) in grey and Japanese plum, P. salicina (N = 10) in orange. Black dots correspond to Prunocerasus species (P. mexicana, P. munsoniana and P. maritima). Colours refer to the genetic clusters inferred from the STRUCTURE analysis, according to the barplots at K = 8 in Figure S4
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In-depth characterization of the genetic diversity and population structure of wild relatives is of paramount importance for genetic improvement and biodiversity conservation, and is particularly crucial when the wild relatives of crops are endangered. In this study, we sampled the Alpine plum (Briançon apricot) Prunus brigantina Vill. across its n...
Context in source publication
Context 1
... closer to the Armeniaca species (P. armeniaca and P. mume) than to other Prunus and Prunocerasus species, which is consistent with taxonomy of Rehder (1940). The principal coordinates analysis (PCoA) supported the differentiation of P. brigantina from other species of the Armeniaca section, and from the Prunus and Prunocerasus sections (Fig. 5). Both the NJ tree and the PCoA indicated that plum species (P. cerasifera and P. salicina) were partly overlapping, in particular the cultivated Japanese plums and cherry plums; the wild P. salicina trees in contrast appeared well separated from P. cerasifera (Figs. 4 and 5). The overlapping may be the result of low power to ...
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Citations
... He = 0.732, and I = 1.837) 21 , and a significantly higher diversity compared with sweet cherry (Prunus avium L.) (Na = 9.800 and He = 0.700) 52 , peach (Prunus persica L.) (Na = 6.410 and He = 0.490) 53 and alpine plum (Prunus brigantina Vill.) (Na = 5.040 and He = 0.430) 54 . Moreover, compared with xylophyta in the Rosaceae family, the diversity is lower than that of apple (Malus × domestica Borkh.) ...
Siberian apricot (Prunus sibirica L.) is a woody tree species of ecological, economic, and social importance. To evaluate the genetic diversity, differentiation, and structure of P. sibirica, we analyzed 176 individuals from 10 natural populations using 14 microsatellite markers. These markers generated 194 alleles in total. The mean number of alleles (13.8571) was higher than the mean number of effective alleles (6.4822). The average expected heterozygosity (0.8292) was higher than the average observed heterozygosity (0.3178). Shannon information index and polymorphism information content were separately 2.0610 and 0.8093, demonstrating the rich genetic diversity of P. sibirica. Analysis of molecular variance revealed that 85% of the genetic variation occurred within populations, with only 15% among them. The genetic differentiation coefficient and gene flow were separately 0.151 and 1.401, indicating a high degree of genetic differentiation. Clustering results showed that a genetic distance coefficient of 0.6 divided the 10 natural populations into two subgroups (subgroups A and B). STRUCTURE and principal coordinate analysis divided the 176 individuals into two subgroups (clusters 1 and 2). Mantel tests revealed that genetic distance was correlated with geographical distance and elevation differences. These findings can contribute to the effective conservation and management of P. sibirica resources.
... Mountains and rivers function as natural geographical barriers affecting gene flow in plants [6][7][8]. Moreover, human disturbances, such as road or bridge construction and mining, can significantly increase geographical isolation and habitat fragmentation of populations, resulting in reduced gene flow and genetic diversity of populations, thus affecting the genetic structure and population dynamics of the species [9][10][11][12]. Even forest park tourism and farming, which have recently become popular in China, pose a threat to rare species. ...
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.
... Mountains and rivers function as natural geographical barriers affecting gene ow in plants [6][7][8]. Moreover, human disturbances, such as road or bridge construction and mining, can signi cantly increase geographical isolation and habitat fragmentation of populations, resulting in reduced gene ow and genetic diversity of populations, thus affecting the genetic structure and population dynamics of the species [9][10][11][12]. Even forest park tourism and farming, which have recently become popular in China, pose a threat to rare species. ...
Background: Genetic diversity, genetic structure, and gene flow in plant populations and their influencing factors are important in conservation biology. Cypripedium macranthos isone 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 northeastChina were analyzed to evaluate the genetic diversity, gene flow among populations, and genetic structure by genotyping-by-sequencing. More than 68.44 Gbhigh-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 andgenetic structure of C. macranthos populations weremainly 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.
... In particular, the apricot accession A1915 found to be infected by a novel cheravirus is an old variety (San Castrese) from the Campania region in southern Italy, introduced from Venturina Pisa University experimental repository in the collection. In addition, similar leaf samples were collected in the French Alps in 2017 [17] and 2021, respectively, for wild growing P. brigantina and P. mahaleb trees. The original, partially sequenced StPV isolate [4] was maintained in GF305 peach seedlings in collection at INRAE virus repository under greenhouse conditions. ...
As part of a virome characterization of Prunus species, a novel cheravirus was discovered in two wild species, Prunus brigantina and P. mahaleb, and in an apricot (P. armeniaca) accession. The sequence of the two genomic RNAs was completed for two isolates. The Pro-Pol conserved region showed 86% amino acid (aa) identity with the corresponding region of trillium govanianum cheravirus (TgCV), a tentative Cheravirus member, whereas the combined coat proteins (CPs) shared only 40% aa identity with TgCV CPs, well below the species demarcation threshold for the genus. This suggests that the new virus should be considered a new species for which the name alpine wild prunus virus (AWPV) is proposed. In parallel, the complete genome sequence of stocky prune virus (StPV), a poorly known cheravirus for which only partial sequences were available, was determined. A phylogenetic analysis showed that AWPV, TgCV and StPV form a distinct cluster, away from other cheraviruses.
... ansu population revealed high levels of genetic diversity (He = 0.696). This level of diversity was higher than that of Prunus mume (He = 0.497) [47], and Prunus brigantina (He = 0.48) [48], but lower than that of Prunus sibirica (He = 0.774) [21] and Prunus armeniaca (He = 0.792) [13]. The level of genetic diversity may be related to molecular markers, samples, environmental conditions, and other factors. ...
The genetic diversity and genetic structure of P . armeniaca var. ansu were analyzed based on SSR markers. The aim was to provide scientific basis for conservation, efficient utilization, molecular marker assisted breeding and improved variety selection of P . armeniaca var. ansu germplasm resources. The results showed that the level of genetic diversity within the population was high. Among the 30 SSR markers, the mean number of observed alleles was 11.433, the mean number of effective alleles was 4.433, the mean of Shannon information index was 1.670, and the mean of polymorphic information content was 0.670. Among the eight provenances, Tuanjie Township, Xinyuan County, Xinjiang had the highest genetic diversity. The observed alleles, effective alleles, Shannon information index and Nei’s gene diversity index among provenances were higher than those within provenances. Based on Bayesian mathematical modeling and UPGMA cluster analysis, 86 P . armeniaca var. ansu accessions were divided into three subpopulations and four groups, which reflected individual differences in provenances. Subpopulations classified by Bayesian mathematical modeling and groups classified by UPGMA cluster analysis were significantly correlated with geographical provenance (Sig<0.01) and the provenances significantly impacted classification of groups. The provenances played an important role in classification of groups. The genetic distance between Tuanjie Township of Xinyuan County and Alemale Township of Xinyuan County was the smallest, while the genetic relationship between them was the closest and the degree of genetic differentiation was small.
... They have accelerated the development of tea plant genomics, genetics, and breeding [57][58][59][60][61]. Here, the core set was used to detect novel variations, select superior varieties, and furnish optimal germplasms because it consists of relatively smaller populations with comparatively higher genetic diversity [62]. Core collection development has been applied for cowpea [63], alpine plum [64], walnut [65], tea [50,57] and other plants. However, no core collection has yet been developed for the cultivated-type tea accessions in Guizhou Plateau. ...
Background
Tea plants originated in southwestern China. Guizhou Plateau is an original center of tea plants, and is rich in germplasm resources. However, the genetic diversity, population structure and distribution characteristics of cultivated-type tea plants in the region are unknown. In this study, we explored the genetic diversity and geographical distribution of cultivated-type tea accessions in Guizhou Plateau.
Results
We used 112,072 high-quality genotyping-by-sequencing to analyze the genetic diversity, principal components, phylogeny, population structure, and linkage disequilibrium, and develop a core collection of 253 cultivated-type tea plant accessions from Guizhou Plateau. The results showed Genetic diversity of the cultivated-type tea accessions of the Pearl River Basin was significantly higher than that of the cultivated-type tea accessions of the Yangtze River Basin. Three inferred pure groups (CG-1, CG-2 and CG-3) and one inferred admixture group (CG-4), were identified by a population structure analysis, and verified by principal component and phylogenetic analyses. The highest genetic distance and differentiation coefficients were determined for CG-2 vs CG-3. The lower genetic distance and differentiation coefficients were determined for CG-4 vs CG-2 and CG-4 vs CG-3, respectively. We developed a core set and a primary set. The primary and core sets contained 77.0 and 33.6% of all individuals in the initial set, respectively. The primary set may serve as the primary population in genome-wide association studies, while the core collection may serve as the core population in multiple treatment setting studies.
Conclusions
The present study demonstrated the genetic diversity and geographical distribution characteristics of cultivated-type tea plants in Guizhou Plateau. Significant differences in genetic diversity and evolutionary direction were detected between the ancient landraces of the Pearl River Basin and the those of the Yangtze River Basin. Major rivers and ancient hubs were largely responsible for the genetic exchange between the Pearl River Basin and the Yangtze River Basin ancient landraces as well as the formation of the ancient hubs evolutionary group. Genetic diversity, population structure and core collection elucidated by this study will facilitate further genetic studies, germplasm protection, and breeding of tea plants.
... The core collection was used for detecting the novel variation, selecting excellent varieties, and providing the excellent germplasms for breeders by using smaller populations and greater genetic diversity [53]. So far, development of core collection was widely used in many plants, such as cowpea [54], alpine plum [55], walnut [56], tea plant [27,48] and so on. However, development of the core collection of cultivated-type tea accessions from Guizhou Plateau has not been reported. ...
Background
Tea plants originated from the southwest of China. Guizhou is one of the origin center of tea plants, which is rich in tea plant germplasm resources. However, the distribution characteristics and transmission model of tea plant were still unclear.
Results
We collected 253 cultivated-type tea plant accessions from Guizhou plateau and analyzed the genetic diversity, PCA, phylogenetic, population structure, LD, and development of core collection using the genotyping-by-sequencing (GBS) approach. A total of 112,072 high-quality SNPs were identified, which was further used to analyze the genetic diversity and population structure. In this study, we found that the genetic diversity in cultivated-type tea accessions of PR Basin were significantly higher than that in cultivated-type tea accessions of YR Basin. Moreover, four groups, including three pure groups (CG-1, CG-2 and CG-3) and one admixture group (CG-4), were identified based on population structure analysis, which was verified by PAC and phylogenetic analysis. Our results showed that the highest GD and Fst values were found in CG-2 vs CG-3, followed by CG-1 vs CG-2 and CG-1 vs CG-3. The lowest GD and Fst values were detected in CG-4 vs CG-1, CG-4 vs CG-2, and CG-4 vs CG-3.
Conclusions
This study provided the evidence to confirm the contribution of PR and YR Basins and ancient hub road section to the transmission of cultivated-type tea accessions in Guizhou plateau. The genetic diversity, population structure and core collection revealed by our study will benefit further genetic studies, germplasm protection, and breeding.
... Apricot has a long history of cultivation in China [3]. A total of ten species belongs to the Armeniaca section, among these species, nine species, including Prunus armeniaca, P. sibirica, P. mandshurica, P. holosericeae, Prunus × dasycarpa, P. zhidanensis, P. zhengheeniss, P. limeixing, and P. mume, are native to China [3][4][5], whereas, P. brigantina is endemic in French Alps [6]. ...
Background
Apricot is cultivated worldwide because of its high nutritive content and strong adaptability. Its flesh is delicious and has a unique and pleasant aroma. Apricot kernel is also consumed as nuts. The genome of apricot has been sequenced, and the transcriptome, resequencing, and phenotype data have been increasely generated. However, with the emergence of new information, the data are expected to integrate, and disseminate.
Results
To better manage the continuous addition of new data and increase convenience, we constructed the apricot genomic and phenotypic database (AprGPD, http://apricotgpd.com). At present, AprGPD contains three reference genomes, 1692 germplasms, 306 genome resequencing data, 90 RNA sequencing data. A set of user-friendly query, analysis, and visualization tools have been implemented in AprGPD. We have also performed a detailed analysis of 59 transcription factor families for the three genomes of apricot.
Conclusion
Six modules are displayed in AprGPD, including species, germplasm, genome, variation, product, tools. The data integrated by AprGPD will be helpful for the molecular breeding of apricot.
... holosericea Batalin 25 ) and P. brigantina; the first three are endemic in Eastern Asia (mostly China), while the more distant P. brigantina Vill. occurs in the French and Italian Alps [26][27][28] . All these species are diploid (2n = 16) with relatively small genome sizes (~220-230 Mbp), which, together with the availability of wild gene pools, make apricot an excellent system to study the domestication process in perennial tree crops. ...
... Based on morphological and botanical data, apricot was considered for a long time to have originated in China 29 . However, recent population genetics studies showed a closer relationship of European P. armeniaca apricots with wild Central Asian populations than with Chinese apricots, suggesting the existence of multiple independent domestication events in Central Asia, Europe and China, although the populations-of-origin could not be identified 24,27,30 . European and Chinese cultivated apricots share similar specific crop features, such as fruit shape and size, as well as tree phenology, suggesting convergent adaptation during parallel domestication. ...
... To investigate the genetic diversity and evolutionary history of Armeniaca lineages, we analysed the genomes (ca 21x coverage) of 564 We also used previously published genomes of P. mume (N = 348) 31 . Fourteen accessions of P. brigantina were used as outgroups 27 . SNPs were called using GATK best practices for this collection of 926 individuals (Supplementary Note 9). ...
Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding. The evolutionary and domestication history of apricots is poorly understood. Here, the authors provide four apricot high-quality genome assemblies, the genomes of 578 accessions from natural and cultivated populations, and show that Chinese and European apricots constitute two different gene pools, resulting from independent domestication events.
The economically significant genus Prunus includes fruit and nut crops that have been domesticated for shared and specific agronomic traits, however, the genomic signals of convergent and divergent selection have not been elucidated. In this study, we aim to detect genomic signatures of convergent and divergent selection by conducting comparative population genomic analyses of the Apricot-Peach-Plum-Mei (APPM) complex, utilizing a haplotype-resolved telomere-to-telomere (T2T) genome assembly and population resequencing data. The haplotype-resolved T2T reference genome for the plum cultivar was assembled through HiFi and Hi-C reads, resulting in two haplotypes with 251.25 Mb and 251.29 Mb in size, respectively. Comparative genomics reveals a chromosomal translocation of approximately 1.17 Mb in the apricot genomes compared to peach, plum, and mei. Notably, the translocation involves the D locus, significantly impacting acidity (TA), pH, and sugar content. Population genetic analysis detected substantial gene flow between plum and apricot, with introgression regions enriched in post-embryonic development and pollen germination processes. Comparative population genetic analyses revealed convergent selection for stress resistance, flower development, and fruit ripening, along with divergent selection shaping crop-specific genes, such as somatic embryogenesis in plum, pollen germination in mei, and hormone regulation in peach. Notably, selective sweeps on chromosome 7 coincide with a chromosomal co-linearity from the comparative genomics, impacting key fruit-softening genes such as PG, regulated by ERF and RMA1H1. Overall, this study provides insights into the genetic diversity, evolutionary history, and domestication of the APPM complex, offering valuable implications for genetic studies and breeding programs of Prunus crops.
