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Avian metaavulavirus 8 (AMAV‐8), formerly known as avian paramyxovirus 8 (APMV‐8), has been detected sporadically in wild birds worldwide since it was first identified in a Canadian goose in 1976. However, the presence of AMAV‐8 in birds has never been reported in China. To understand the epidemiological situation of AMAV‐8 and its ability to infect chickens, we conducted a surveillance study and in vivo analysis of the AMAV‐8 isolate identified in total of 14,909 clinical samples collected from wild and domestic birds from 2014 to 2022 in China. However, in 2017, only one AMAV‐8 virus (Y7) was successful isolated from the fresh droppings of a migratory swan goose in Qinghai Lake in Northwest China. Thereafter, we report the complete genome sequence of the Y7 strain with a genome length of 15,342 nucleotides and the Y7 isolate was genetically closely‐related to wild bird‐origin AMAV‐8 viruses previously circulated in the United States, Japan, and Kazakhstan. Furthermore, AMAV‐8 infections of one‐day‐old specific pathogen‐free (SPF) chicks did not induce any clinical signs over the entire observation period but was associated with viral shedding for up to 8 days. Interestingly, although all birds infected with the Y7 strain seroconverted within the first week of infection, virus replication was only detected in the trachea but not in other tissues such as the brain, lung, or heart. Here, we report the complete genome, genetic and biological characterization, replication and pathogenicity analysis in vivo and first detection of AMAV‐8 in China. [ABSTRACT FROM AUTHOR]

Pterocarpus santalinus L.f. is an endangered tree species that is cherished worldwide for its valuable deep red-colored heartwood, which has multiple uses. This species exhibits a wide range of medicinal properties and offers immense potential for the discovery of bioactive compounds of pharmacological importance. The overharvesting of this species for heartwood has led to a gradual decline in its natural populations, thereby depleting its genetic resources and contributing to the loss of genetic diversity. Therefore, it is essential to assess genetic diversity, as such information allows for the effective conservation and utilization of genetic resources. In the present study, the genetic diversity and population structure among 40 germplasm accessions originating from 8 populations of P. santalinus were analyzed using six cross-species simple sequence repeats (SSR), 20 each of inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) markers. SSR markers revealed higher polymorphism (100 %), followed by ISSRs (82.81 %) and RAPDs (67.50 %), across all the accessions. The mean values of the polymorphic information content (PIC), effective multiplex ratio (EMR), and marker index (MI) were higher for SSRs (0.84, 9.17, and 7.7), followed by ISSRs (0.262, 4.474, and 1.251) and RAPDs (0.204, 3.268 and 0.970, respectively), indicating the superiority of SSRs in detecting polymorphisms in red sanders. Similarly, the estimates of Nei's gene diversity (H) and Shannon's information index (I) varied across the studied accessions, with the highest values for SSRs (H = 0.528, I = 0.923), followed by ISSRs (H = 0.287, I = 0.428) and RAPDs (H = 0.206, I = 0.307). However, the genetic statistic (Gst) or fixation statistic (Fst) and gene flow (Nm) values were higher for RAPDs (0.455 and 0.598) and ISSRs (0.446 and 0.620) than for SSRs (0.383 and 0.489, respectively), indicating significant genetic differentiation of the populations and moderate gene flow among the populations. Analysis of molecular variance (AMOVA) with SSR, ISSR, and RAPD markers revealed that a greater proportion of genetic variation resided within populations (74 %, 69 %, and 66 %, respectively) than among populations (26 %, 31 %, and 34 %, respectively). Hierarchical clustering on the basis of RAPDs grouped most of the accessions according to the population of origin; however, this clustering was different for the ISSR and SSR markers. STRUCTURE analysis divided the accessions into four, two, and three groups with SSR, ISSR, and RAPD markers, respectively, with admixtures detected in all the groups pointing toward shared genetic lineages and diverse genetic ancestry among the accessions of different populations. Overall, the populations of Gumudipoondi of Tamil Nadu and K.V. Bhavi of Andhra Pradesh were genetically more diverse than other populations, as revealed by genetic diversity estimates obtained with SSR and ISSR marker systems; therefore, the accessions of these populations must be prioritized for conservation and utilization in breeding programs for genetic improvement. [Display omitted] • Genetic diversity was assessed among 40 accessions of P. santalinus using 6 cross-species SSR, 20 each of ISSR and RAPD primers. • Cross-species SSRs were more efficient in detecting genetic diversity in the studied populations than ISSRs and RAPDs. • The populations of Gumidipoondi of Tamil Nadu (GTN) and K.V. Bhavi of Andhra Pradesh (KAP) exhibited higher genetic diversity than other populations according to SSR and ISSR marker analysis. • Analysis of molecular variance with SSR, ISSR and RAPD markers showed that genetic variations within populations (74 %, 69 % and 66 %) were greater than among populations (26 %, 31 % and 34 %). • STRUCTURE analysis using SSR, ISSR and RAPD markers divided the populations into four, two and three genetic groups, respectively, with admixtures detected in all genetic groups. [ABSTRACT FROM AUTHOR]

I n this study, we used three RAPD (Random Amplified Polymorphic DNA) primers, OPA 01, OPA 13, and OPA 09, to analyze the genetic diversity of Helicoverpa armigera (Hubner). These primers produced a total of 41 polymorphic markers, with each primer yielding a varying number of unique bands, ranging from 7 to 18 bands per primer. The amplicon sizes ranged from 150 to 10,000 base pairs (bp), with clear bands below 2000 bp observed for all three primers. Using these 41 RAPD markers, we assessed the genetic relationships among H. armigera populations collected from three districts: Peshawar, Bajaur, and Swat. The genetic similarity coefficients varied from 0.000 to 0.929, indicating diverse genetic relationships among the populations. The construction of a UPGMA dendrogram based on Jaccard's similarity coefficient revealed two distinct clades, Clade A and Clade B, with Clade A including populations from districts Swat and Bajaur and Clade B comprising populations from district Peshawar. This genetic differentiation among the populations based on geographical origin suggests significant genetic diversity influenced by environmental factors and local adaptation. These findings enhance our understanding of the genetic structure of H. armigera populations in the region and provide valuable know-how about developing targeted pest management strategies. Further research may explore additional genetic markers and expand the scope of genetic variation assessments across broader geographical areas. [ABSTRACT FROM AUTHOR]

The complexity of citrus phylogeny and taxonomy, influenced by polyembryony, genetic diversity, and extended generation cycles, necessitates assessing genetic relationships for improved production and disease resilience. DNA polymorphism markers are pivotal in genotyping and resolving phenotypic varietal ambiguities through accurate and objective genetic relatedness and distinctiveness assessments. In this study, 27 accessions of kagzi and ornamental lime were evaluated at morphological (based on IPGRI citrus descriptor), biochemical, and molecular levels using DNA-based markers, namely, random amplified polymorphic DNA (RAPD), start codon targeted (SCoT) polymorphism, and simple sequence repeats (SSR). Morphological analysis unveiled significant variation in leaf lamina attachment, shape, margins, fruit characteristics, and texture across all parameters. Biochemical research noted minimal differences, with total soluble solids (TSS) ranging from 5.7° to 8.0° Brix and titratable acidity (TA) from 0.36 to 0.50%. Notably, ornamental lime accessions exhibited higher TSS:TA ratios of 16.00. Molecular markers (RAPD, SCoT, and SSR) corroborated these findings, yielding 115, 74, and 64 amplicons, respectively, with polymorphic percentages varying from 33.33 to 100%. Polymorphic information content ranged from 0.20 to 0.90 for RAPD, 0.41 to 0.99 for SCoT, and 0.07 to 0.67 for SSR markers. Analysis of molecular variance (AMOVA) substantiated significant genetic differences among the kagzi and ornamental lime accessions (RAPD PhiPT = 0.267, SCoT PhiPT = 0.351, SSR PhiPT = 0.107). Furthermore, STRUCTURE software 2.3.4 revealed a ΔK value of two (K = 2), indicating two distinct genetic pools within the accessions, possibly attributable to bud mutations generating varying morphological traits within the same plant. Molecular marker-based germplasm characterization can mitigate confusion linked to morphological characteristics and multiple cultivar registrations. [ABSTRACT FROM AUTHOR]

In the study, it was aimed to determine the molecular characterization and genetic relationships of Mentha species obtained from different countries and regions at the molecular level and to ensure the sustainability of these species. For this purpose, ISSR marker technique, which is effective in detecting polymorphism and genetic variation within and between Mentha species, was used. In the study a total of 460 allelic bands were detected, and all bands were found to be 100% polymorphic. The maximum number of bands was produced by the ISSR7 primer (25), but the minimum number of bands was produced by the ISSR12 primer (13). The highest PIC (Polymorphism Information Content) value was detected in the ISSR3 primer (0.521) but the lowest PIC value was determined in the 903 primer (0.203). Molecular datas were analyzed using the NTSYSpc 2.02 software and it was determined that the mint species were divided into two main groups. In the results obtained, it was determined that there was no relationship between the genetic diversity and geographical origins, and the populations from different geographical regions were in the same clusters. In the study, it was concluded that there was a significant molecular diversity among the species, and that some Mentha clones, which are defined by morphological features and still remain taxonomically uncertain, were belong to which species at the molecular level. Therefore, it is insufficient to classify species with morphochemical, morphological and phenotypic characteristics. [ABSTRACT FROM AUTHOR]

Escherichia coli is one of the key bacteria responsible for a variety of diseases in humans and livestock-associated infections around the globe. It is the leading cause of mortality in neonatal and weaned piglets in pig husbandry, causing diarrhea and significant harm to the industry. Furthermore, the frequent and intensive use of antimicrobials for the prevention of diseases, particularly gastrointestinal diseases, may promote the selection of multidrug-resistant (MDR) strains. These resistant genotypes can be transmitted through the excrement of animals, including swine. It is common practice to use porcine manure processed by biodigesters as fertilizer. This study aimed to examine the antimicrobial susceptibility, the presence of virulence genes frequently associated with pathotypes of intestinal pathogenic E. coli (InPEC), and antimicrobial resistance genes (ARGs) of 28 E. coli isolates collected from swine manure fertilizers. In addition, the enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) technique was used to investigate the genetic relationship among the strains. Using disk diffusion, the antimicrobial susceptibility profiles of the strains were determined. Using polymerase chain reaction (PCR), 14 distinct virulence genes associated with the most prevalent diarrhea and intestinal pathogenic E. coli (DEC/InPEC) and five ARGs were analyzed. All isolates tested positive for multidrug resistance. There was no detection of any of the 14 virulence genes associated with InPECs, indicating the presence of an avirulent commensal microbiota. Molecular classification by ERIC-PCR revealed that the majority of isolates (27 isolates) coalesced into a larger cluster with a genetic similarity of 47.7%; only one strain did not cluster in this cluster, indicating a high level of genetic diversity among the analyzed isolates. Thus, it is of the utmost importance to conduct epidemiological surveillance of animal breeding facilities in order to determine their microbiota and formulate plans to reduce the use of antimicrobials and improve animal welfare. [ABSTRACT FROM AUTHOR]

Abstract Background Coccidiosis caused by Eimeria zuernii (Eimeriidae: Coccidia) represents a significant economic threat to the bovine industry. Understanding the evolutionary and genetic biology of E. zuernii can assist in new interaction developments for the prevention and control of this protozoosis. Methods We defined the evolutionary and genetic characteristics of E. zuernii by sequencing the complete mitogenome and analyzing the genetic diversity and population structure of 51 isolates collected from eight yak breeding parks in China. Results The 6176-bp mitogenome of E. zuernii was linear and encoded typical mitochondrial contents of apicomplexan parasites, including three protein-coding genes [PCGs; cytochrome c oxidase subunits I and III (cox1 and cox3), and cytochrome b (cytb)], seven fragmented small subunit (SSU) and 12 fragmented large subunit (LSU) rRNAs. Genome-wide comparative and evolutionary analyses showed cytb and cox3 to be the most and least conserved Eimeria PCGs, respectively, and placed E. zuernii more closely related to Eimeria mephitidis than other Eimeria species. Furthermore, cox1-based genetic structure defined 24 haplotypes of E. zuernii with high haplotype diversities and low nucleotide diversities across eight geographic populations, supporting a low genetic structure and rapid evolutionary rate as well as a previous expansion event among E. zuernii populations. Conclusions To our knowledge, this is the first study presenting the phylogeny, genetic diversity, and population structure of the yak E. zuernii, and such information, together with its mitogenomic data, should contribute to a better understanding of the genetic and evolutionary biological studies of apicomplexan parasites in bovines. Graphical Abstract

Abstract Background Mulberry (Morus spp.) is an economically important woody plant, which has been used for sericulture (silk farming) for thousands of years. The genetic background of mulberry is complex due to polyploidy and frequent hybridization events. Results Comparative genomic in situ hybridization (cGISH) and self-GISH were performed to illustrate the chromosome constitution and genetic relationships of 40 mulberry accessions belonging to 12 species and three varietas in the Morus genus and containing eight different ploidy levels. We identified six homozygous cGISH signal patterns and one heterozygous cGISH signal pattern using four genomic DNA probes. Using cGISH and self-GISH data, we defined five mulberry sections (Notabilis, Nigra, Wittiorum, and Cathayana, all contained only one species; and Alba, which contained seven closely related species and three varietas, was further divided into two subsections) and proposed the genetic relationships among them. Differential cGISH signal patterns detected in section Alba allowed us to refine the genetic relationships among the closely related members of this section. Conclusions We propose that GISH is an efficient tool to investigate the chromosome constitution and genetic relationships in mulberry. The results obtained here can be used to guide outbreeding of heterozygous perennial crops like mulberry.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases threatening wheat production both in Turkey and worldwide. However, the underlying genetic dynamics of Pst populations are not fully known in Turkey. To determine the population genetic structure and migration network among regional Pst populations, a total of 140 Pst isolates collected from six geographical regions of Turkey from 2018 to 2020 were sampled and genotyped using 21 simple sequence repeat loci. A total of 70 multilocus genotypes were identified and classified into the three major genetic groups by Bayesian assignment. The highest genotypic diversity was detected in Southeastern Anatolia, showing its critical role as one of the source populations to trigger possible stripe rust epidemics. Analysis of molecular variance revealed the highest variation (90.25%) within isolates. The migration network generated by the number of effective migrants showed that the highest migration (1.0) was determined between Southeastern Anatolia and Central Anatolia, and considerable levels of migration (>0.2) were determined among the other regions, except for the Black Sea. Linkage equilibrium (P > 0.05) was detected for many geographical regions, except for Marmara (P = 0.00) and the Mediterranean (P = 0.03), suggesting that reproduction of Pst populations is most likely sexual or mixed (sexual and clonal). To sum up, this is the first study on the genetic relationships and population genetic structure of the Pst population in Turkey, and these findings may provide critical information to develop management strategies for wheat stripe rust. [ABSTRACT FROM AUTHOR]

Copyright of Anadolu (1300-0225) is the property of Anadolu Dergisi and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Common lilac (Syringa vulgaris L.) is a popular landscaping plant. Our aim was to obtain a large set of single nucleotide polymorphism (SNP) markers, to reveal the precise identities of the investigated S. vulgaris accessions, and to discover genetic relationships among them. The studied plant material included local Finnish, previously unidentified accessions, known reference cultivars, and so-called historical accessions i.e., old shrubs growing in historic cultural landscapes. We intended to verify cultivar names for some valuable local common lilac accessions and to provide insights into the history of common lilac cultivation in Finland. In the analyses, we used a set of 15,007 SNP markers. First, polymorphic information contents were calculated (mean 0.190, range 0.012–0.500 per marker). Then, to investigate genetic relationships among genotypes, a phylogenetic tree was constructed, and a principal coordinate analysis was conducted. A Bayesian analysis of population structure was performed to determine the number and distribution of genetic clusters among samples. Genetic marker data combined with existing historical and phenotypic knowledge revealed novel information on the unidentified cultivars and on the genetic relationships among studied accessions and solved the arrival and early history of common lilac in Finland. Overall, such comprehensive genomic characterization and deep understanding of genetic relationships of S. vulgaris can be used when utilizing present cultivars and developing new ones in future breeding programs. [ABSTRACT FROM AUTHOR]

Background: The correlation between gut microbiota and infections has garnered significant attention in previous studies; nevertheless, our understanding of the causal relationships and mechanisms between specific microbial species and infections remains limited. Methods: This study aimed to employ Mendelian randomization (MR) using single-nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) data of European ancestry to explore the genetic-level relationships between distinct types of gut microbiota and susceptibility to infections. Our analysis encompassed three prevalent infections: intestinal infections, pneumonia, and urinary tract infections, while concurrently examining various types of gut microbiota. Results: We identified 18 protective gut microbiotas alongside 13 associated with increased infection risk. Particularly noteworthy are certain microbial communities capable of producing butyrate, such as the Ruminococcaceae and Lachnospiraceae families, which exhibited both favorable and unfavorable effects. Additionally, we observed a few certain communities linked to infection susceptibility, including ErysipelotrichaceaeUCG003 (OR = 0.13, 95% CI: 0.054-0.33, p = 1.24E-05), Collinsella (OR = 3.25, 95% CI: 2.00-5.27, p = 1.87E-06), and NB1n (OR = 1.24, 95% CI: 1.09-1.40, p = 1.12E-03). Conclusion: This study reveals complex relationships between gut microbiota and various infections. Our findings could potentially offer new avenues for exploring prevention and treatment strategies for infectious diseases. [ABSTRACT FROM AUTHOR]

Vibrio spp. including Vibrio cholerae and V. parahaemolyticus are the major causative agent of diarrhea involved in seafood consumption. Yala is a southern border province in Thailand where no seafood sources are provided. Thus, it is necessary to import several seafood products from neighboring provinces. The risk of Vibrio spp. replication is increased during seafood transport. Therefore, the objectives of this study were to isolate and characterize V. cholerae and V. parahaemolyticus from seafood in Yala and to investigate their genetic relationships with virulent and clinical strains. A total of 100 Vibrio isolates were obtained from four different sample types in retail markets. It was found that two-thirds of all isolates were yellow colonies on TCBS agar. Using PCR with specific primers, 34 % of V. cholerae and 8 % of V. parahaemolyticus were identified. To classify the virulence strains, Vibrio spp. were positive for hlyA and tdh, 17 and 1 %, respectively. Moreover, 54 % of Vibrio isolates were able to produce biofilm and 28 % of those isolates showed a high level of biofilm production. All representative strains of V. cholerae presented ß-hemolysin on blood agar correlated to hlyA while representative strains of V. parahaemolyticus presented ?-hemolysin and ß-hemolysin on blood agar. In addition, ERIC-PCR provided different DNA profiles of representative V. cholerae and V. parahaemolyticus which some strains showed a correlation with clinical strains and virulent strains. Therefore, these findings might indicate the risk of Vibrio infections for seafood consumers, especially in Yala province where seafood needs to be imported from other provinces. [ABSTRACT FROM AUTHOR]

Background: Mulberry (Morus spp.) is an economically important woody plant, which has been used for sericulture (silk farming) for thousands of years. The genetic background of mulberry is complex due to polyploidy and frequent hybridization events. Results: Comparative genomic in situ hybridization (cGISH) and self-GISH were performed to illustrate the chromosome constitution and genetic relationships of 40 mulberry accessions belonging to 12 species and three varietas in the Morus genus and containing eight different ploidy levels. We identified six homozygous cGISH signal patterns and one heterozygous cGISH signal pattern using four genomic DNA probes. Using cGISH and self-GISH data, we defined five mulberry sections (Notabilis, Nigra, Wittiorum, and Cathayana, all contained only one species; and Alba, which contained seven closely related species and three varietas, was further divided into two subsections) and proposed the genetic relationships among them. Differential cGISH signal patterns detected in section Alba allowed us to refine the genetic relationships among the closely related members of this section. Conclusions: We propose that GISH is an efficient tool to investigate the chromosome constitution and genetic relationships in mulberry. The results obtained here can be used to guide outbreeding of heterozygous perennial crops like mulberry. [ABSTRACT FROM AUTHOR]

Background: Coccidiosis caused by Eimeria zuernii (Eimeriidae: Coccidia) represents a significant economic threat to the bovine industry. Understanding the evolutionary and genetic biology of E. zuernii can assist in new interaction developments for the prevention and control of this protozoosis. Methods: We defined the evolutionary and genetic characteristics of E. zuernii by sequencing the complete mitogenome and analyzing the genetic diversity and population structure of 51 isolates collected from eight yak breeding parks in China. Results: The 6176-bp mitogenome of E. zuernii was linear and encoded typical mitochondrial contents of apicomplexan parasites, including three protein-coding genes [PCGs; cytochrome c oxidase subunits I and III (cox1 and cox3), and cytochrome b (cytb)], seven fragmented small subunit (SSU) and 12 fragmented large subunit (LSU) rRNAs. Genome-wide comparative and evolutionary analyses showed cytb and cox3 to be the most and least conserved Eimeria PCGs, respectively, and placed E. zuernii more closely related to Eimeria mephitidis than other Eimeria species. Furthermore, cox1-based genetic structure defined 24 haplotypes of E. zuernii with high haplotype diversities and low nucleotide diversities across eight geographic populations, supporting a low genetic structure and rapid evolutionary rate as well as a previous expansion event among E. zuernii populations. Conclusions: To our knowledge, this is the first study presenting the phylogeny, genetic diversity, and population structure of the yak E. zuernii, and such information, together with its mitogenomic data, should contribute to a better understanding of the genetic and evolutionary biological studies of apicomplexan parasites in bovines. [ABSTRACT FROM AUTHOR]

Nucleosynthetic isotope variations are powerful tools to investigate genetic relationships between meteorite groups and planets. They are instrumental to assess the early evolution of the solar system, including mixing and reservoir formation in the protoplanetary disk, as well as planet formation. To address these questions, we report high-precision nucleosynthetic Ti isotope compositions of a wide range of bulk meteorites, partially complemented with new Cr isotope data. New Ti isotope data confirm the first order dichotomy observed between carbonaceous chondrites (CC), representing outer solar system compositions, and non-carbonaceous (NC) meteorites from the inner solar system. The data in combination with nucleosynthetic isotope data of other elements (e.g., Cr, Ca) indicate that isotopically heterogeneous reservoirs were also present as sub-reservoirs in the inner disk (NC reservoir), generating two or more clusters i.e., (i) the Vesta-like howardites-eucrites-diogenites (HEDs), mesosiderites, angrites, acapulcoites, lodranites, and brachinites and (ii) the Earth-Mars-like ordinary chondrites (OC), aubrites, enstatite chondrites (EC), winonaites, IAB silicates, rumuruti chondrites (R), Martian and terrestrial samples. These reservoirs likely represent disk substructures such as secondary gaps and ring-structures, created by spiral arms, which were emitted from the growing Jupiter and/or Saturn. The distinct isotopic compositions of these reservoirs may reflect thermal processing of material within the disk in combination with temporal isotopic variations either due to isotopically variable infalling material from a heterogeneous molecular cloud and/or thermal processing during the infall that induced such heterogeneities. Such effects were likely reinforced by thermal processing of the material within the disk itself and by physical size- and density sorting of dust caused by the giant planets, creating gaps and pressure bumps in the disk. Genetic relationships of meteorite groups and their implications on parent body formation are evaluated. New high precision Ti isotope data are consistent with that (i) CH and CB meteorites derive from a common parent body, which most likely accreted material from the same isotopic reservoir as the parent body of CR chondrites, (ii) silicates of IAB irons and winonaites originate from the same parent body, and (iii) mesosiderites and HED meteorites have a common origin on Vesta. The indistinguishable Ti and Cr isotope compositions of HEDs/mesosiderites to acapulcoites are not attributed to a common parent body, because of petrologic and chemical differences in addition to their distinct O isotope compositions. Their parent bodies likely accreted in the same disk region, which showed a higher level of O isotope heterogeneity compared to that of Ti, Cr and other refractory nucleosynthetic tracers. The similarity in Ti isotope compositions of Martian meteorites and OCs indicates that OC-like material belongs to the main building blocks of Mars. [ABSTRACT FROM AUTHOR]

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Abstract Background Karyotype dynamics driven by chromosomal rearrangements has long been considered as a fundamental question in the evolutionary genetics. Saccharum spontaneum, the most primitive and complex species in the genus Saccharum, has reportedly undergone at least two major chromosomal rearrangements, however, its karyotypic evolution remains unclear. Results In this study, four representative accessions, i.e., hypothetical diploid sugarcane ancestor (sorghum, x = 10), Sa. spontaneum Np-X (x = 10, tetraploid), 2012–46 (x = 9, hexaploid) and AP85–441 (x = 8, tetraploid), were selected for karyotype evolution studies. A set of oligonucleotide (oligo)-based barcode probes was developed based on the sorghum genome, which allowed universal identification of all chromosomes from sorghum and Sa. spontaneum. By comparative FISH assays, we reconstructed the karyotype evolutionary history and discovered that although chromosomal rearrangements resulted in greater variation in relative lengths of some chromosomes, all chromosomes maintained a conserved metacentric structure. Additionally, we found that the barcode oligo probe was not applicable for chromosome identification in both Sa. robustum and Sa. officinarum species, suggesting that sorghum is more distantly related to Sa. robustum and Sa. officinarum compared with Sa. spontaneum species. Conclusions Our study demonstrated that the barcode oligo-FISH is an efficient tool for chromosome identification and karyotyping research, and expanded our understanding of the karyotypic and chromosomal evolution in the genus Saccharum.

Microsatellite loci represent prevalent molecular markers for assessing genetic diversity, phylogenetic and evolutionary relationships between different in origin broomrape taxon. In the present study, the genetic differences and relationships among 3 broomrape races from Bulgaria, Turkey, Moldova and Romania were identified by ISSR markers. The obtained results on genetic diversity parameters showed that race H is more variable than races G and E. However, the gene diversity within populations was the greatest in race G, followed by race H and E. The limited gene flow for races H and G determined significant genetic differentiation of populations. Conversely, a comparatively moderate gene flow for race E pointed to a little differentiation among populations. These findings were also corroborated by AMOVA, demonstrating high genetic diferences within (89%) and lower (11%) among races. The investigation also revealed the existence evolutionary differences between all races. This situation proves the action of evolutive molecular mechanisms which offered, in time, discrete genetic particularities at broomrape, indicating that the existing races are unstable over time and they are constantly adapting to the new more sunflower resistance hybrids. [ABSTRACT FROM AUTHOR]

Ping'ou hybrid hazelnut is one of the most profitable tree nuts in China, but economically important cultivars must first be genetically validated to meet industrial demand. Traditional approaches used for cultivar identification are mainly trait-based and unreliable. Previous approaches at the DNA level, focusing on the identification of species or/and varieties that originated in China, were not used widely in hybrid hazelnut because there was no proper standard sample. In this research, a multiplexed fingerprinting test was conducted to allow for hazelnut cultivar identification using SSR markers derived from European hazelnut. Twenty-seven SSR markers were used to fingerprint 57 genetically unique Ping'ou hybrid hazelnut and related wild species. All markers showed a high level of polymorphism, as indicated by mean values for observed heterozygosity (Ho = 0.84), expected heterozygosity (He = 0.80), and polymorphism information content (PIC = 0.78). A total of 301 alleles were detected, and the number of effective alleles varied from 6 for KG817 and GB818 to 18 for B654, with an average of 11.2 alleles per locus. Moreover, the Shannon's information index (I) ranged from 1.293 for BR215 to 2.385 for B654, with an average of 1.908. The neighbor-joining tree, principal coordinate analysis, and Bayesian analysis revealed clear separation between hybrid cultivars and wild forms (Cluster/group I), as well as the differentiation within hybrid genotypes (Clusters/groups II and III). Additionally, the NJ dendrogram demonstrated a further split within Clusters/group III (III a and III b). Altogether, with the comparable SSR information of the European hazelnut cultivar 'Barcelona', the newly developed marker sets can assist in the germplasm identification of hazelnut cultivars and reproductive materials. Importantly, these combined SSR loci can be applied to characterize the genetic relationships and population structures among wild genotypes and hybrid cultivars, which will then provide information to guide hazelnut breeding based on their genetic background. [ABSTRACT FROM AUTHOR]

Copyright of Uranium Geology is the property of Uranium Geology Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

So far, there has been limited use of molecular markers in arabica coffee breeding program in Ethiopia. The objectives of this study were to explore the effectiveness of simple sequence repeats markers (SSRs) in detecting polymor- phism and to assess the extent of genetic diversity and relationships among ex-situ conserved Arabica coffee accessions. Sixty-two forest coffee accessions planted in the experimental plot of the Ethiopian coffee breeding program were evaluated using 14 SSR markers. These markers amplified a total of 100 alleles, varying from four to ten alleles per locus, with an average of 7.2 across all loci. The rate of polymorphism ranged from 75 to 100, with a mean value of 96.4 across the accessions. The polymorphic information content (PIC) varied from 0.26 to 0.92, with a mean value of 0.70. The genetic similarity coefficient values between 72% possible pair-wise combinations ranged from 0.18 to 0.50, with overall mean value of 0.44. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on Jaccard’s genetic similarity grouped the accessions into five main clusters and two singletons at

• The study evaluated the molecular characterization of 81 accessions, as well as ELISA analysis to estimate sanitary status. • The results can improve grapevines germplasm management and emphasizes the need to recover the endangered genetic diversity. • Autochthonous grapevines have shown a high incidence of certain viruses. The conservation of genetic variability and the preservation of vine biodiversity are critical, current objectives of viticultural research. Germplasm assessment is extremely difficult, particularly when many accessions are included. Microsatellite markers have become an essential tool for germplasm collection management and an approach to genetic diversity. This research reviews the molecular characterization of eighty-one accessions stored at the Skikda germplasm collection in Algeria, as well as ELISA analysis to detect viruses and estimate sanitary status. Accessions were genotyped with 12 highly polymorphic microsatellite markers, including the nine 'international' loci used for grapevine identity. Genetic diversity is affirmed by the high number (149) of different alleles (mean of 12,42 alleles per locus), the average expected heterozygosity and observed heterozygosity were determined to be 0,850 and 0,864, respectively and to uncover instances of synonymy, misnaming, and duplication. A total of 43 distinct genotypes were found and the genotypes of 30 accessions were validated according to the reference literature and Vitis public and private databases; most of autochthonous varieties that have been propagated for a long time in a small, closed and circle area have displayed a high incidence of GLRaV-3 and GVA, with 61.9% and 50%, respectively. A close relationship was demonstrated with certain grape varieties from the eastern and western areas of the Mediterranean basin, resulting from previous vine cultivar exchanges. Together, our results can improve grapevine germplasm management and emphasizes the need to recover the endangered genetic diversity that characterizes negligible and ignored vines or germplasm biotypes, and the need to reappraise and support the effective exploitation of variability resources to assist in the development of new grapes varieties and rootstocks which will then enhance the regional food and agriculture industry. [ABSTRACT FROM AUTHOR]

The Mexican Tropical Pacific (MTP) is rich in chitons, mainly represented by the genera Callistochiton Carpenter in Dall, 1879 and Stenoplax Dall, 1879. Despite the widespread presence of these genera in the region, few species have been studied at a molecular level. Using partial cytochrome oxidase I (cox1) gene sequences, we analyzed the genetic relationships of four Callistochiton and four Stenoplax species (including Caribbean species), along with two putative new species. Each genus was analyzed separately. The Bayesian Inference (BI) and neighbor-joining analyses recovered two main clades in both genera and support the existence of two new species. Stenoplax quetzalcoatli sp. nov. was recovered sister to Stenoplax petaloides Gould, 1846 and this clade was recovered sisters to Stenoplax mariposa (Dall, 1919). Stenoplax limaciformis (Sowerby in Broderip and Sowerby, 1832) was recovered sister to Stenoplax purpurascens C.B. Adams, 1845 and both nested with Stenoplax floridana Pilsbry, 1892. Callistochiton guerreroensis sp. nov. and Callistochiton cf. expressus are sister species of Callistochiton colimensis (A.G. Smith, 1961). In addition, to solve the identity of two new taxa, we inspected various morphological characters using scanning electron microscopy (SEM). We identified differences between Stenoplax quetzalcoatli sp. nov. and species of the Stenoplax rugulata (Sowerby, 1832) complex characterized by small size and irregular sculpturing. Moreover, Callistochiton guerreroensis sp. nov. differs from Callistochiton expressuss (Carpenter, 1865) by a higher number of ribs in the head valve, minor lateral teeth with a bilobed blade directed inwards, and dorsal girdle scales with rounded spherules. [ABSTRACT FROM AUTHOR]

The sweet cherry is an important fruit species that is widespread globally. In addition to the well-known traditional and modern varieties, a myriad of landraces is present in Europe, as well as in southern Italy. This study aims to evaluate the population structure, genetic relationships, and cases of duplicate samples in a collection of 143 accessions using GBS-derived SNP markers. The genetic material under investigation includes modern commercial varieties, ancient European and American varieties, landraces, and individuals retrieved from small orchards. Some of the known varieties were genetically analyzed here for the first time. In addition, several genotypes were collected from the Basilicata region (southern Italy), an area largely unexplored for sweet cherry genetic resources. The relationships among genotypes were assessed using four different methods: allele frequency and ancestry estimation, principal component analysis, Neighbor-Joining tree, and identity-by-state estimation. The analyses returned quite congruent results and highlighted the presence of four main genetic groups, namely: (i) American varieties, (ii) the 'Germersdorfer-Ferrovia' cluster, (iii) the 'Burlat' group, and (iv) the group of Italian landraces. The main drivers of clustering were ancestry, geographical distribution, and some important traits such as self-compatibility. The sweet cherries from Basilicata, herewith examined for the first time, were mostly distributed within the group of Italian landraces, being particularly linked to the autochthonous varieties of the Campania region. However, some genotypes were outside this group, thus suggesting the introduction of genetic material from other Italian regions or from European countries. The considerable amount of American and European modern varieties analyzed are genetically very closely related, suggesting a reduced genetic basis. In addition, we highlighted the discriminating ability of SNP markers to distinguish between an original variety and its mutant. Overall, our results may be useful in defining conservation strategies for sweet cherry germplasm and developing future breeding programs to enlarge the genetic basis of commercial varieties. [ABSTRACT FROM AUTHOR]

Background: Karyotype dynamics driven by chromosomal rearrangements has long been considered as a fundamental question in the evolutionary genetics. Saccharum spontaneum, the most primitive and complex species in the genus Saccharum, has reportedly undergone at least two major chromosomal rearrangements, however, its karyotypic evolution remains unclear. Results: In this study, four representative accessions, i.e., hypothetical diploid sugarcane ancestor (sorghum, x = 10), Sa. spontaneum Np-X (x = 10, tetraploid), 2012–46 (x = 9, hexaploid) and AP85–441 (x = 8, tetraploid), were selected for karyotype evolution studies. A set of oligonucleotide (oligo)-based barcode probes was developed based on the sorghum genome, which allowed universal identification of all chromosomes from sorghum and Sa. spontaneum. By comparative FISH assays, we reconstructed the karyotype evolutionary history and discovered that although chromosomal rearrangements resulted in greater variation in relative lengths of some chromosomes, all chromosomes maintained a conserved metacentric structure. Additionally, we found that the barcode oligo probe was not applicable for chromosome identification in both Sa. robustum and Sa. officinarum species, suggesting that sorghum is more distantly related to Sa. robustum and Sa. officinarum compared with Sa. spontaneum species. Conclusions: Our study demonstrated that the barcode oligo-FISH is an efficient tool for chromosome identification and karyotyping research, and expanded our understanding of the karyotypic and chromosomal evolution in the genus Saccharum. [ABSTRACT FROM AUTHOR]

Nontyphoidal Salmonella strains are among the major foodborne pathogens with emerging multidrug-resistant phenotypes. In this study, antimicrobial susceptibility testing of a collection of Salmonella isolates (n ¼ 54) recovered from poultry and bivalve molluscs was performed. The study also investigated profiling of virulence and resistance genes as well as phylogenetic relationships through pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus (ERIC)–PCR fingerprinting. Results revealed the presence of multiple virulence genes among Salmonella isolates. Salmonella intestinal infection A (siiA), Salmonella outer protein (sopB and sopE), putative 4-hydroxybutyrate coenzyme A transferase (cat2), Salmonella atypical fimbria C (safC), and Salmonella Enteritidis fimbria B (sefB) were present in most (83.32 to 100%) of the isolates, whereas the remaining tested genes (Salmonella plasmid virulence [spvC and spvB]), and the sopE gene, were exclusively detected within the serotype Enteritidis. The highest resistance rates were observed for oxacillin (94.4%), ampicillin (37%), and nalidixic acid (27.7%), followed by cefotaxime and amoxicillin– clavulanic acid (14.8%), trimethoprim-sulfamethoxazole (9.3%), and ciprofloxacin (5.5%). The results indicate that the Salmonella Enteritidis serotype possessed the widest range of virulence determinants and increasing levels of resistance. Such high-risk clones should be particularly controlled in Tunisia. Overall, increased resistance and virulence confer a selective advantage for the evolution of these bacteria and represent an alarming problem for global public health. The genetic study via PFGE and ERIC-PCR showed the high diversity of the clonal origins of these bacteria and the sources of contamination and revealed the great capacity of Salmonella to diversify within food-producing animals. [ABSTRACT FROM AUTHOR]

Abstract Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r 2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV.

Single-step genomic prediction models became the prevailing tool in genetic evaluations of livestock due to high genomic performance, high genotyping costs for some animals, and utilizing both genotyped and un-genotyped animals. The objective of the current study was to investigate the effect of genetic relationships between the training and validation populations on the performance of single and multi-step GBLUP and BayesB, which in this regard the importance of un-genotyped individuals in generations after genomic selection and their roles on the necessity of reusing genomic selection in binary threshold traits was investigated. For this purpose, genomic populations were simulated to reflect the different number of QTL (33 and 534) with two different distributions of QTL (normal and gamma) on 29 chromosomes. Four statistical models (GBLUP, SS-GBLUP, BayesB and SS-BayesB) were implemented to analyze the simulated data. According to the results, GEBV accuracy was influenced by the relationships between the training and validation populations more significantly for multi-step models than for single-step models. Multi-step and single-step BayesB methods showed an obvious advantage over GBLUP and SSGBLUP when the trait is controlled by fewer QTLs. For the normal QTL effects distribution, BayesB methods (especially multi-step BayesB) obtained the lower accuracy than that of if more QTLs affecting the trait. Generally, since the increasing generation distance is a major challenge in the genomic selection of threshold traits, therefore the use of single-step methods makes possible reuse of genomic selection during the early generations of selection unnecessary. However, using single-step BayesB methods and its advantages in genomic evaluation depends on the identification of trait genetic architecture. [ABSTRACT FROM AUTHOR]

ABSTRACT Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a crucial disease for wheat worldwide and constantly threatens wheat production in southwestern and northwestern China, where the environment is a good fit for Pst oversummering and overwintering. However, the underlying genetic dynamics of spring epidemic Pst populations across large areas of continuous planting in the southwestern and northwestern regions are poorly understood. A total of 2,103 Pst isolates were sampled in the spring of 2019 from the two agroecosystems and grouped into three horizontal spatial scales (countywide, provincial, and regional subpopulations) and two vertical spatial scales that consisted of elevational and geomorphic subpopulations. A total of 776 multilocus genotypes were identified, with the highest genetic diversity found in the northern and Sichuan populations, particularly in the Ningxia and Sichuan Basins, while the lowest genetic diversity was found in the Yunnan and Guizhou populations. Multivariate discriminant analysis of principal components (DAPC) and STRUCTURE (STRUCTURE 2.3.4) analyses revealed variation in the genotypic compositions of the molecular groups on horizontal and vertical dimensions from north to south or vice versa and from low to high or vice versa, respectively. The regional neighbor-joining tree revealed three large spatial structures consisting of the southwestern, the northwestern, and the Xinjiang regions, while the Tibetan population connected the southwestern and northwestern regions. The isolates of the Sichuan Basin were scattered over the four quartiles by principal coordinate analysis, which indicated frequent genotype interchange with others. Greater genetic differentiation was observed between the southwestern and northwestern regions. Linkage equilibrium (P ≥ 0.05) was detected on different spatial scales, suggesting that Pst populations are using sexual reproduction or mixed reproduction (sexual and clonal reproduction) in southwestern and northwestern China. IMPORTANCE Understanding the epidemiology and population genetics of plant pathogens is crucial to formulate efficient predictions of disease outbreaks and achieve sustainable integrated disease management, especially for pathogens with migratory capability. Here, this study covers the genetic homogeneity and heterogeneity of different geographical Pst populations on broad to fine spatial scales from the key epidemic regions of the two agroecosystems in China, where wheat stripe rust occurs annually. We provide knowledge of the population genetics of Pst and reveal that, for instance, there is greater genetic diversity in northwestern China, there are close genetic relationships between Yunnan and Guizhou and between Gansu-Ningxia and Qinghai, and there are effects of altitude on genetic compositions, etc. All of these findings clarify the genetic relationships and expand the insights into the population dynamics and evolutionary mechanisms of Pst in southwestern and northwestern China, providing a theoretical basis for achieving sustainable control of wheat stripe rust in key epidemic regions.

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Background: The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results: Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions: Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV. [ABSTRACT FROM AUTHOR]

The sweet cherry is an important fruit species that is widespread globally. In addition to the well-known traditional and modern varieties, a myriad of landraces is present in Europe, as well as in southern Italy. This study aims to evaluate the population structure, genetic relationships, and cases of duplicate samples in a collection of 143 accessions using GBS-derived SNP markers. The genetic material under investigation includes modern commercial varieties, ancient European and American varieties, landraces, and individuals retrieved from small orchards. Some of the known varieties were genetically analyzed here for the first time. In addition, several genotypes were collected from the Basilicata region (southern Italy), an area largely unexplored for sweet cherry genetic resources. The relationships among genotypes were assessed using four different methods: allele frequency and ancestry estimation, principal component analysis, Neighbor-Joining tree, and identity-by-state estimation. The analyses returned quite congruent results and highlighted the presence of four main genetic groups, namely: (i) American varieties, (ii) the ‘Germersdorfer-Ferrovia’ cluster, (iii) the ‘Burlat’ group, and (iv) the group of Italian landraces. The main drivers of clustering were ancestry, geographical distribution, and some important traits such as self-compatibility. The sweet cherries from Basilicata, herewith examined for the first time, were mostly distributed within the group of Italian landraces, being particularly linked to the autochthonous varieties of the Campania region. However, some genotypes were outside this group, thus suggesting the introduction of genetic material from other Italian regions or from European countries. The considerable amount of American and European modern varieties analyzed are genetically very closely related, suggesting a reduced genetic basis. In addition, we highlighted the discriminating ability of SNP markers to distinguish between an original variety and its mutant. Overall, our results may be useful in defining conservation strategies for sweet cherry germplasm and developing future breeding programs to enlarge the genetic basis of commercial varieties.

Background: The correlation between gut microbiota and infections has garnered significant attention in previous studies; nevertheless, our understanding of the causal relationships and mechanisms between specific microbial species and infections remains limited., Methods: This study aimed to employ Mendelian randomization (MR) using single-nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) data of European ancestry to explore the genetic-level relationships between distinct types of gut microbiota and susceptibility to infections. Our analysis encompassed three prevalent infections: intestinal infections, pneumonia, and urinary tract infections, while concurrently examining various types of gut microbiota., Results: We identified 18 protective gut microbiotas alongside 13 associated with increased infection risk. Particularly noteworthy are certain microbial communities capable of producing butyrate, such as the Ruminococcaceae and Lachnospiraceae families, which exhibited both favorable and unfavorable effects. Additionally, we observed a few certain communities linked to infection susceptibility, including ErysipelotrichaceaeUCG003 (OR = 0.13, 95% CI: 0.054-0.33, p  = 1.24E-05), Collinsella (OR = 3.25, 95% CI: 2.00-5.27, p  = 1.87E-06), and NB1n (OR = 1.24, 95% CI: 1.09-1.40, p  = 1.12E-03)., Conclusion: This study reveals complex relationships between gut microbiota and various infections. Our findings could potentially offer new avenues for exploring prevention and treatment strategies for infectious diseases., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Lyu, Ma, Bai and Feng.)

The sweet cherry is an important fruit species that is widespread globally. In addition to the well-known traditional and modern varieties, a myriad of landraces is present in Europe, as well as in southern Italy. This study aims to evaluate the population structure, genetic relationships, and cases of duplicate samples in a collection of 143 accessions using GBS-derived SNP markers. The genetic material under investigation includes modern commercial varieties, ancient European and American varieties, landraces, and individuals retrieved from small orchards. Some of the known varieties were genetically analyzed here for the first time. In addition, several genotypes were collected from the Basilicata region (southern Italy), an area largely unexplored for sweet cherry genetic resources. The relationships among genotypes were assessed using four different methods: allele frequency and ancestry estimation, principal component analysis, Neighbor-Joining tree, and identity-by-state estimation. The analyses returned quite congruent results and highlighted the presence of four main genetic groups, namely: (i) American varieties, (ii) the 'Germersdorfer-Ferrovia' cluster, (iii) the 'Burlat' group, and (iv) the group of Italian landraces. The main drivers of clustering were ancestry, geographical distribution, and some important traits such as self-compatibility. The sweet cherries from Basilicata, herewith examined for the first time, were mostly distributed within the group of Italian landraces, being particularly linked to the autochthonous varieties of the Campania region. However, some genotypes were outside this group, thus suggesting the introduction of genetic material from other Italian regions or from European countries. The considerable amount of American and European modern varieties analyzed are genetically very closely related, suggesting a reduced genetic basis. In addition, we highlighted the discriminating ability of SNP markers to distinguish between an original variety and its mutant. Overall, our results may be useful in defining conservation strategies for sweet cherry germplasm and developing future breeding programs to enlarge the genetic basis of commercial varieties.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), is a crucial disease for wheat worldwide and constantly threatens wheat production in southwestern and northwestern China, where the environment is a good fit for Pst oversummering and overwintering. However, the underlying genetic dynamics of spring epidemic Pst populations across large areas of continuous planting in the southwestern and northwestern regions are poorly understood. A total of 2,103 Pst isolates were sampled in the spring of 2019 from the two agroecosystems and grouped into three horizontal spatial scales (countywide, provincial, and regional subpopulations) and two vertical spatial scales that consisted of elevational and geomorphic subpopulations. A total of 776 multilocus genotypes were identified, with the highest genetic diversity found in the northern and Sichuan populations, particularly in the Ningxia and Sichuan Basins, while the lowest genetic diversity was found in the Yunnan and Guizhou populations. Multivariate discriminant analysis of principal components (DAPC) and STRUCTURE (STRUCTURE 2.3.4) analyses revealed variation in the genotypic compositions of the molecular groups on horizontal and vertical dimensions from north to south or vice versa and from low to high or vice versa, respectively. The regional neighbor-joining tree revealed three large spatial structures consisting of the southwestern, the northwestern, and the Xinjiang regions, while the Tibetan population connected the southwestern and northwestern regions. The isolates of the Sichuan Basin were scattered over the four quartiles by principal coordinate analysis, which indicated frequent genotype interchange with others. Greater genetic differentiation was observed between the southwestern and northwestern regions. Linkage equilibrium ( P ≥  0.05) was detected on different spatial scales, suggesting that Pst populations are using sexual reproduction or mixed reproduction (sexual and clonal reproduction) in southwestern and northwestern China. IMPORTANCE Understanding the epidemiology and population genetics of plant pathogens is crucial to formulate efficient predictions of disease outbreaks and achieve sustainable integrated disease management, especially for pathogens with migratory capability. Here, this study covers the genetic homogeneity and heterogeneity of different geographical Pst populations on broad to fine spatial scales from the key epidemic regions of the two agroecosystems in China, where wheat stripe rust occurs annually. We provide knowledge of the population genetics of Pst and reveal that, for instance, there is greater genetic diversity in northwestern China, there are close genetic relationships between Yunnan and Guizhou and between Gansu-Ningxia and Qinghai, and there are effects of altitude on genetic compositions, etc. All of these findings clarify the genetic relationships and expand the insights into the population dynamics and evolutionary mechanisms of Pst in southwestern and northwestern China, providing a theoretical basis for achieving sustainable control of wheat stripe rust in key epidemic regions.