Principal Component Discriminant Analysis Research Articles

Molecular Epidemiology of Ralstonia pseudosolanacearum Phylotype I Strains in the Southwest Indian Ocean Region and Their Relatedness to African Strains.

The increasing requirement for developing tools enabling fine strain traceability responsible for epidemics is tightly linked with the need to understand factors shaping pathogen populations and their environmental interactions. Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is one of the most important plant diseases in tropical and subtropical regions. Sadly, little, outdated, or no information on its epidemiology is reported in the literature, although alarming outbreaks are regularly reported as disasters. A large set of phylotype I isolates (n = 2,608) was retrieved from diseased plants in fields across the Southwest Indian Ocean (SWIO) and Africa. This collection enabled further assessment of the epidemiological discriminating power of the previously published RS1-MLVA14 scheme. Thirteen markers were validated and characterized as not equally informative. Most had little infra-sequevar polymorphism, and their performance depended on the sequevar. Strong correlation was found with a previous multilocus sequence typing scheme. However, 2 to 3% of sequevars were not correctly assigned through endoglucanase gene sequence. Discriminant analysis of principal components (DAPC) revealed four groups with strong phylogenetic relatedness to sequevars 31, 33, and 18. Phylotype I-31 isolates were highly prevalent in the SWIO and Africa, but their dissemination pathways remain unclear. Tanzania and Mauritius showed the greatest diversity of RSSC strains, as the four DAPC groups were retrieved. Mauritius was the sole territory harboring a vast phylogenetic diversity and all DAPC groups. More research is still needed to understand the high prevalence of phylotype I-31 at such a large geographic scale.

Virulence Phenotyping and Molecular Genotyping Reveal High Diversity Within and Strong Gene Flow Between the Puccinia striiformis f. sp. tritici Populations Collected from Barberry and Wheat in Shaanxi Province of China.

Emergence of new Puccinia striiformis f. sp. tritici races that overcome resistance of wheat cultivars is a challenging issue for wheat production. Although sexual reproduction of the fungus on barberry plants under field conditions in the spring in China has been reported, the diversity of the pathogen on barberry plants and the relationship to the population in wheat fields have not been determined. In the present study, two P. striiformis f. sp. tritici populations collected in western Shaanxi Province in May 2016, one from barberry plants (103 isolates) and the other from nearby wheat crops (107 isolates), were phenotyped for virulence and genotyped with simple sequence repeat (SSR) markers. The phenotypic and genotypic data of the two populations were compared to determine their relationships. A total of 120 races, including 29 previously known races (seven were shared by the two populations) and 91 new races (35 from barberry and 56 from wheat), were identified. Similarly, a total of 132 multilocus genotypes, including 51 only from barberry, 77 only from wheat, and four from both, were detected using the SSR markers. Analyses of molecular variance identified high (93%) genetic variance within populations and low but still significant variance (7%) between the populations. Nonparametric multivariate discriminant analysis of principal components and STRUCTURE analysis showed that the two populations had a close relationship with little genetic differentiation (FST = 0.038) and strong gene flow (Nm = 6.34, P = 0.001) between them. Although the analysis of linkage disequilibrium indicated clonal populations, the isolation of P. striiformis f. sp. tritici from barberry plants and the high genetic diversities in the barberry and wheat populations suggest that barberry plants provide aeciospores to infect wheat crops in the area. The information is useful for understanding stripe rust epidemiology and management of the disease.

Investigating an Unknown Biodiversity: Evidence of Distinct Lineages of the Endemic Chola Guitarfish Pseudobatos percellens Walbaum, 1792 in the Western Atlantic Ocean

Anthropogenic actions have affected marine species for a long time, through overexploitation of natural stocks and habitat degradation, influencing the life strategies of several taxa, especially rays and sharks, which have suffered significant population declines in recent years. Therefore, conservation actions and stock management have become paramount. In this regard, chola guitarfish, Pseudobatos percellens, distributed throughout the Brazilian coast, is often commercially fished by local artisanal fleets or as by-catch in shrimp trawl fisheries. Therefore, this study aimed to understand the genetic diversity of P. percellens throughout the Brazilian coast, using single nucleotide polymorphisms (SNPs). Genetic analyses employing 3329 SNPs revealed a hidden biodiversity within P. percellens, with at least one lineage occurring in the Northern and Northeastern regions and another distributed in the Southeastern/Southern Brazilian coast, with high genetic differentiation between them. However, the Discriminant Analysis of Principal Components (DAPC) indicated the presence of in fact three lineages distributed in these regions that must still be better investigated. Therefore, to ensure adequate conservation of chola guitarfish biodiversity, populations must be managed separately along the Brazilian coast. Furthermore, the need for a taxonomic review for this group is noted.

Inferring multilocal typologies of agrosystems and farmers’ practices: A methodological basis for the setting of participatory breeding designs

Family farms play an essential role in agroecological transition in Sahelian countries and worldwide. They present diversified features in terms of socio-economic organization, agrobiodiversity management and cropping systems diversity. Decentralized participatory breeding approaches aim to sustain the diversity of varieties adapted for such smallholder farmers' contexts. However the lack of clear target population of environments limits the focus and the efficiency of these approaches given the large diversification of the local contexts. In this study, we surveyed variables linked to agrosystems, crop management options and farmers’ criteria of varietal evaluation from 254 family farms sampled along 13 locations spanning the target area of a decentralized participatory breeding program of cowpea crop (Vigna unguiculata L. Walp) in Niger. The objective of our study was to infer typologies of family farms in the study area based on relevant variables supporting the setting of target population of environments (TPEs) to be considered in the breeding program. We used factorial analysis of mixed data (FAMD) and the Discriminant Analysis of Principal Components (DAPC) to infer the clusters. Chi square test, analysis of variance and generalized linear model were used to identify key variables discriminating the clusters. These clusters were geographically mapped to analyze their multilocal distribution. So, we identified and characterized four clusters structuring the diversity of the local agrosystems (Typologie G), five clusters structuring the diversity of cowpea cropping management options (Typologie C) and five clusters structuring the diversity of criteria used by farmers to evaluate the performance of cowpea varieties in the local contexts (Typologie P). Typology G distinguished farms based on discriminating variables linked for instance to secondary activities, cultivated species, soil fertility management practices and farm resources including land and livestock. Typology C distinguished farms based on cowpea management pratices including the secondary crop intercropped with cowpea (sorghum, Guinea sorrel, sesame or groundnut) and the use of cowpea harvest products (seeds, haulms, hulls). Typology P was based on discriminating performance criteria including cycle length, insect resistance, striga resistance, drought resistance, haulm production and economic value of cowpea variety. This methodology provides a robust and replicable way for the definition of clusters capturing the diversity of farms and local contexts. We discussed the perspective of using these clusters to set target population of environments for decentralized breeding programs.

Genetic diversity and population structure of Uganda's yam (Dioscorea spp.) genetic resource based on DArTseq.

Assessing the genetic diversity of yam germplasm from different geographical origins for cultivation and breeding purposes is an essential step for crop genetic resource conservation and genetic improvement, especially where the crop faces minimal attention. This study aimed to classify the population structure, and assess the extent of genetic diversity in 207 Dioscorea rotundata genotypes sourced from three different geographical origins. A total of 4,957 (16.2%) single nucleotide polymorphism markers were used to assess genetic diversity. The SNP markers were informative, with polymorphic information content ranging from 0.238 to 0.288 and a mean of 0.260 across all the genotypes. The observed and expected heterozygosity was 0.12 and 0.23, respectively while the minor allele frequency ranged from 0.093 to 0.124 with a mean of 0.109. The principal coordinate analysis, model-based structure and discriminant analysis of principal components, and the Euclidean distance matrix method grouped 207 yam genotypes into three main clusters. Genotypes from West Africa (Ghana and Nigeria) had significant similarities with those from Uganda. Analysis of molecular variance revealed that within-population variation across three different geographical origins accounted for 93% of the observed variation. This study, therefore, showed that yam improvement in Uganda is possible, and the outcome will constitute a foundation for the genetic improvement of yams in Uganda.

Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato (Ipomoea batatas) collection.

Sweetpotato (Ipomoea batatas) is the sixth most important food crop and plays a critical role in maintaining food security worldwide. Support for sweetpotato improvement research in breeding and genetics programs, and maintenance of sweetpotato germplasm collections is essential for preserving food security for future generations. Germplasm collections seek to preserve phenotypic and genotypic diversity through accession characterization. However, due to its genetic complexity, high heterogeneity, polyploid genome, phenotypic plasticity, and high flower production variability, sweetpotato genetic characterization is challenging. Here, we characterize the genetic diversity and population structure of 604 accessions from the sweetpotato germplasm collection maintained by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetic Resources Conservation Unit (PGRCU) in Griffin, Georgia, United States. Using the genotyping-by-sequencing platform (GBSpoly) and bioinformatic pipelines (ngsComposer and GBSapp), a total of 102,870 polymorphic SNPs with hexaploid dosage calls were identified from the 604 accessions. Discriminant analysis of principal components (DAPC) and Bayesian clustering identified six unique genetic groupings across seven broad geographic regions. Genetic diversity analyses using the hexaploid data set revealed ample genetic diversity among the analyzed collection in concordance with previous analyses. Following population structure and diversity analyses, breeder germplasm subsets of 24, 48, 96, and 384 accessions were established using K-means clustering with manual selection to maintain phenotypic and genotypic diversity. The genetic characterization of the PGRCU sweetpotato germplasm collection and breeder germplasm subsets developed in this study provide the foundation for future association studies and serve as precursors toward phenotyping studies aimed at linking genotype with phenotype.

Genetic diversity, population structure and parentage analysis of Brazilian grapevine hybrids after half a century of genetic breeding

In the 1940s, the Agronomic Institute of Campinas (IAC) started a grapevine breeding program to develop new cultivars adapted to the tropical and subtropical regions of Brazil. More than 2,000 crosses were carried out over 50 years, using 850 varieties as parents. However, among the thousands of hybrids developed by the program, only 130 are still maintained in the IAC grapevine germplasm collection. Little is known about their genetic makeup and usefulness for current breeding programs. In this study, we genotyped 130 Brazilian grape hybrids at 21 polymorphic microsatellite markers to evaluate the genetic diversity and population structure of the hybrids and verified their disclosed pedigrees. The results showed that the hybrid collection is highly diverse, with an expected heterozygosity (HE) of 0.80 and an observed heterozygosity (Ho) of 0.78. Strong structure in three subgroups based mainly on the usage and combination of parental groups was revealed by STRUCTURE software and confirmed by discriminant analysis of principal components (DAPC). Through molecular profiling analysis, fourteen synonyms, one homonym and one duplicate were identified. Parentage analysis confirmed 24 full parentages, as well as 33 half-kinships. In addition, 18 pedigrees were invalidated, and seven mislabeling events were identified. No compatible parent was identified for 33% of the IAC hybrids, highlighting severe genetic erosion in the IAC germplasm. The molecular characterization of the breeding hybrid bank collection contributes to our understanding of the genetic basis of the varieties, guiding the efficient utilization of available genetic diversity. Together, our results could be applied to other breeding programs and assist in the selection of parents, management of the breeding collection, and conservation of grapevine genetic resources.

A Possible Mixing Genetic Pool of Eastern Little Tuna Euthynnus affinis Cantor (1849) from the Western and Southern Part of Indonesian Waters

Eastern little tuna (Euthynnus affinis) is a commercially important species for coastal communities in the western and southern part of Indonesia. However, little is known about its characteristics. Therefore, a comprehensive and broader research of its population structure is imminent in response to conserve and manage the fishery sustainably. This study aimed to fill the gap of the lacking information on the stock separation of eastern little tuna within the Indonesian archipelagic waters and its Economic Exclusive Zone (EEZ). Population genetic approaches were used to examine population structure using the mitochondrial DNA (mtDNA) control region marker. A total of 94 samples were collected from nine landing sites between January to September 2020. Polymerase chain reaction (PCR) was used to amplify the samples, and Sanger sequencing was used to sequence them. The findings showed a mean value of 0.922 for genetic diversity (Hd) and 0.009 for nucleotide diversity (π). Both of these numbers pointed to a high level of genetic diversity. A further population analyses using Analysis of Molecular Variance (AMOVA) and Discriminant Analysis of Principal Component (DAPC) confirmed a mixing gene pool with no distinct population structure detected (ΦST value of 0.097 and p-value>0.05).

Genetic connectivity in the spotted rose snapper Lutjanus guttatus (Lutjaniformes: Lutjanidae) between Mexico and Panama throughout the Tropical Eastern Pacific

Abstract The spotted rose snapper, Lutjanus guttatus, is an important fishery species with high potential for aquaculture. Genetic characterization of its natural populations is necessary to avoid stock collapse and loss of genetic diversity. Previous studies carried out in the Tropical Eastern Pacific (TEP), however, have shown contrasting results in the genetic structure of fish populations, particularly in species of Lutjanidae. Therefore, to understand the genetic structure of spotted rose snapper in the TEP, twelve microsatellite loci were used to assess the genetic diversity and explore the hypothesis of population genetic structure in samples of the species collected throughout the TEP. Fin clips from 186 sampled individuals (27 to 49 per site) were analyzed from five sites in the three regional biogeographic provinces, delimited by shoreline reef habitat breaks: La Paz (Cortez province), Colima and Oaxaca (Mexican province), Chiriqui and Port of Panama (Panamic province). Results of global Analysis of Molecular Variance (AMOVA), population pairwise FST, hierarchical AMOVA, and a discriminant analysis of principal components (DAPC) reflected a panmictic population involving the entire set of sampled sites. The role of larval dispersal, post-recruitment migration, and marine current dynamics as drivers of genetic connectivity in this species is discussed.

Genetic Analysis of Colletotrichum siamense Populations from Different Hosts and Counties in Hainan, China, Using Microsatellite Markers.

Colletotrichum siamense was demonstrated as the dominant species among Colletotrichum spp. that infected rubber tree, areca palm, and coffee in Hainan, China. However, the extent of genetic differentiation within the species C. siamense in relation to geographical regions and host species is not known. In this study, 112 C. siamense isolates were genotyped with 12 microsatellite markers. In total, there were 99 multilocus genotypes. Results from permutational multivariate analysis of variance and analysis of molecular variance indicated that there was no significant genetic differentiation between fungal populations with respect to host, location (county), and year. Discriminant analysis of principal components and STRUCTURE analysis showed that C. siamense isolates grouped into three clusters; further analysis confirmed that there were significant (P < 0.001) genetic differences among the three clusters. However, each cluster had isolates from different hosts, counties, or years, supporting the lack of genetic differentiation with respect to host, county, and year. Statistical analyses of allelic associations indicated some evidence for recombination within the populations defined on the basis of host or county. The present findings provide insights into the genetic structure of C. siamense on the three perennial host species in Hainan and suggest that the disease on these three crops can be effectively considered as one disease and, hence, needs to be controlled simultaneously in mixed plantations.

Parasite communities and genetic structure of non-native pumpkinseed,Lepomis gibbosus, in different Black Sea drainages of Ukraine

In recent years, pumpkinseedLepomis gibbosus(Actinopterygii: Centrarchidae) have spread intensively to many parts of Europe, including Ukraine. In this study, we (1) assess intra-population genetic variability in five widely-spaced Ukrainian pumpkinseed populations and compare their population genetic structure with other European populations and (2) provide a comprehensive survey of pumpkinseed parasites across the region. Discriminant analysis of principal components and FSTanalyses based on microsatellites indicated that all five populations formed discrete clusters. Within Europe, Ukrainian populations were most closely associated with populations from the River Danube, suggesting that the Danube is the main source of all Ukrainian pumpkinseed populations. The parasite fauna comprised 15 taxa, most of which (92%) were native to North America (monogeneaOnchocleidus similisandO. dispar; myxozoanMyxobolus dechtiari). Parasites acquired in the species' new range occurred accidentally, with onlyTrichodinaciliates found relatively frequently and the eye flukesDiplostomum pseudospathaceumandTylodelphys clavataoccurring at higher prevalence. Absence of specific monogeneans in pumpkinseed from estuaries (Khadzhibey and Sukhyi Lymans) indicates low tolerance ofOnchocleidusspecies to salinity.

Genetic diversity and spatial structure of indigenous sheep population of Benin revealed by microsatellite markers

This study investigated the genetic variability existing within the indigenous sheep population of Benin. Hair samples from 681 unrelated sheep collected across the 10 phytogeographic zones of Benin were genotyped using a set of 12 microsatellite markers. Genetic diversity indices, Bayesian ancestral admixture model, Self-Organizing Map (SOM), and Discriminant Analysis of Principal Components (DAPC), were performed to assess both the genetic diversity and spatial structure of the population under study. The polymorphism information content (PIC) recorded for each microsatellite marker used was greater than 0.50 with an average value of 0.70. The average number of alleles (12.17) and heterozygosity values (He = 0.73; Ho = 0.68) obtained suggest high genetic diversity within the Beninese sheep population. The population genetic structure analysis revealed two ancestral sheep populations in Benin, namely, the Djallonké and Sahelian sheep. Furthermore, SOM and DAPC identified four clusters of sheep within the 10 phytogeographic zones, including two Djallonké and two Sahelian subpopulations with some admixture. Djallonké sheep were predominant in the humid zones of southern Benin, with one subpopulation mainly present in the Pobè and Oueme Valley zones, and the second in Coastal, Plateau, and Zou zones. The latter subpopulation seemed the most admixed, with a mean Djallonké ancestral proportion of 86.15%. Sahelian sheep were predominant in the phytogeographic zones of northern Benin. Sheep from the driest North zone consisted the first Sahelian subpopulation and had a higher Sahelian ancestry proportion (89.81%) compared to the second subpopulation (69.29%) that most consisted of sheep from the other phytogeographic zones of the North.

Impact of cultural and genetic structure on food choices along the Silk Road

The complex interplay between genetics, culture, and environment forms an individual's biology, influencing their behavior, choices, and health. However, to what extent information derived from this intertwined network could be quantitatively summarized to provide a glance at an individual's lifestyle is difficult to say. Here, we focused on dietary preferences as cultural proxies and genome-wide data of 543 individuals from six historical Silk Road countries: Georgia, Armenia, Azerbaijan, Uzbekistan, Kazakhstan, and Tajikistan. These lands favored the dispersal of innovations, foods, and DNA halfway across Eurasia, thus representing an ideal subject to explore interactions of cultural factors and genetic ancestry. We used discriminant analysis of principal components to infer cultural clusters, where mixed memberships are allowed. Five different clusters emerged. Of these, clusters 1 and 3, driven by aversion to pork and alcoholic beverages, mirrored genetic admixture patterns with the exception of Azerbaijan, which shares preferences supported by Islamic culture with Eastern countries. Cluster 3 was driven by protein-rich foods, whose preference was significantly related to steppe pastoralist ancestry. Sex and age were secondary clustering factors, with clusters formed by male and young individuals being related to alcohol preference and a reduced liking for vegetables. The soft clustering approach enabled us to model and summarize the individual's dietary information in short and informative vectors, which show meaningful interaction with other nondietary attributes of the studied individuals. Encoding other cultural variables would help summarize an individual's culture quantitatively, thus ultimately supporting its inclusion as a covariate in future association studies.

Genetic structure of Plasmopara halstedii populations across Europe and South Russia

AbstractPlasmopara halstedii is a biotrophic parasite of sunflower (Helianthus annuus). We genetically analysed 162 P. halstedii samples collected between 1982 and 2018, representing a 3500 km west–east transect across Europe, from France to the Krasnodar region in southern Russia. To assess the population genetic structure among P. halstedii isolates, we sequenced two mitochondrial regions (cox1 and cox2), in addition to analysing eight polymorphic simple sequence repeat (SSR, microsatellite) markers. Sequencing of cox2 enabled comparison of our data with recent SSR‐based studies to provide further evidence for differences among P. halstedii strains infecting different hosts (H. annuus, H. × laetiflorus, Rudbeckia spp.). There are two different lineages infecting H. annuus that we resolved on a neighbour‐joining tree, which also corresponded to a discriminant analysis of principal components. This suggests at least two independent introductions of P. halstedii on sunflower. We observed no relationship between the phylogenetic placement of the individual samples and virulence characteristics, indicating independent evolution of virulence phenotypes. Both genetic markers clearly separated P. halstedii samples originating from H. annuus and H. × laetiflorus, suggesting these might represent distinct species.

An isolated population reveals greater genetic structuring of the Australian dingo

The Australian dingo is a recent anthropogenic addition to the Australian fauna, which spread rapidly across the continent and has since widely interbred with modern dogs. Genetic studies of dingoes have given rise to speculation about their entry to the continent and subsequent biogeographic effects, but few studies of their contemporary population structure have been conducted. Here we investigated the dingo ancestry and population structure of free-living dogs in western Victoria and contrasted it with a wider southern Australian sample. We wished to determine whether their geographic isolation was mirrored in genetic isolation. To address this question, we analysed 34 microsatellite markers using Bayesian clustering and discriminant analysis of principal components, and summarised genetic diversity at the population and individual level. The broader southern Australia sample (n = 1138) comprised mostly hybrid animals, with 30% considered pure dingoes. All western Victorian individuals (n = 59) appeared to be hybrids with high dingo ancestry. The population showed no evidence of admixture with other populations and low genetic diversity on all measures tested. Based upon our characterisation of this unusual mainland population, we advise against assuming homogeneity of dingoes across the continent.

A roadmap to robust discriminant analysis of principal components.

Identification of population structure is a common goal for a variety of applications, including conservation, wildlife management, and medical genetics. The outcome of these analyses can have far reaching implications; therefore, it is important to ensure an understanding of the strengths and weaknesses of the methodologies used. Increasing in popularity, the discriminant analysis of principal components (DAPC) method incorporates combinations of genetic variables (alleles) into a model that differentiates individuals into genetic clusters. However, users may not have a full understanding of how to best parameterize the model. In this issue of Thia (Molecular Ecology Resources, 2022) looks under the hood of the DAPC. Using simulated data, he demonstrates the importance of careful parameter selection in developing a DAPC model, what the implications are for over-fitting the model, and finally, how best to evaluate the results of DAPC models. This work highlights the issues that can arise when over-parameterizing the DAPC model when gene flow is high among clusters and provides important guidelines to ensure researchers are making conclusions that are biologically relevant.

Population genomics of the neotropical palm Copernicia prunifera (Miller) H. E. Moore: Implications for conservation.

Copernicia prunifera (Miller) H. E. Moore is a palm tree native to Brazil. The products obtained from its leaf extracts are a source of income for local families and the agroindustry. Owing to the reduction of natural habitats and the absence of a sustainable management plan, the maintenance of the natural populations of this palm tree has been compromised. Therefore, this study aimed to evaluate the diversity and genetic structure of 14 C. prunifera populations using single nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing (GBS) to provide information that contributes to the conservation of this species. A total of 1,013 SNP markers were identified, of which 84 loci showed outlier behavior and may reflect responses to natural selection. Overall, the level of genomic diversity was compatible with the biological aspects of this species. The inbreeding coefficient (f) was negative for all populations, indicating excess heterozygotes. Most genetic variations occurred within populations (77.26%), and a positive correlation existed between genetic and geographic distances. The population structure evaluated through discriminant analysis of principal components (DAPC) revealed low genetic differentiation between populations. The results highlight the need for efforts to conserve C. prunifera as well as its distribution range to preserve its global genetic diversity and evolutionary potential.

Elucidating the Genetic Relationships on the Original Old Sicilian Triticum Spp. Collection by SNP Genotyping.

Several Triticum species spread in cultivation in Sicily and neighboring regions over the centuries, which led to the establishment of a large genetic diversity. Many ancient varieties were widely cultivated until the beginning of the last century before being replaced by modern varieties. Recently, they have been reintroduced in cultivation in Sicily. Here, the genetic diversity of 115 and 11 accessions from Sicily and Calabria, respectively, belonging to Triticum species was evaluated using a high-density SNP array. Einkorn, emmer, and spelta wheat genotypes were used as outgroups for species and subspecies; five modern varieties of durum and bread wheat were used as references. A principal coordinates analysis (PCoA) and an unweighted pair group method with arithmetic mean (UPGMA) showed four distinct groups among Triticum species and T. turgidum subspecies. The population structure analysis distinguished five gene pools, among which three appeared private to the T. aestivum, T. turgidum subsp. Turgidum, and 'Timilia' group. The principal component analysis (PCA) displayed a bio-morphological trait relationship of a subset (110) of ancient wheat varieties and their wide variability within the T. turgidum subsp. durum subgroups. A discriminant analysis of principal components (DAPC) and phylogenetic analyses applied to the four durum wheat subgroups revealed that the improved varieties harbored a different gene pool compared to the most ancient varieties. The 'Russello' and 'Russello Ibleo' groups were distinguished; both displayed higher genetic variability compared to the 'Timilia' group accessions. This research represents a comprehensive approach to fingerprinting the old wheat Sicilian germplasm, which is useful in avoiding commercial fraud and sustaining the cultivation of landraces and ancient varieties.

Changes of Barley Stripe Rust Populations in the United States from 1993 to 2017.

Barley stripe rust is a relatively new disease in the United States. The pathogen, Puccinia striiformis f. sp. hordei (Psh), was first observed in Texas in 1991 and has spread north and westwards and mainly caused epidemics in the western United States. A total of 447 isolates collected from 1993 to 2017 were identified as 382 multilocus genotypes (MLGs) using 14 simple sequence repeat markers. The MLGs were clustered into six molecular groups (MGs) using the discriminant analysis of principal components and the hierarchical cluster analysis, and the MGs had significant differences in frequency in different years. MG1 was present in the population prior to the year 2000. MG2, MG3, and MG4 became predominate after 2000. MG5 was detected in all 24 years but more frequent from 2010 to 2017. MG6 was the most recent group detected mainly from 2011 to 2017 and had the highest correlation coefficient with the virulence phenotypes among the MGs. The heterozygosity and genotypic diversity of the Psh populations increased from 2000 to 2017, even more from 2010 to 2017. The results indicate rapid genetic changes from year to year, with major molecular group changes around 2000 and 2010. The possible mechanisms underlying the population changes are discussed.

Application of MaxEnt Modeling and HRM Analysis to Support the Conservation and Domestication of Gevuina avellana Mol. in Central Chile.

The Chilean hazelnut (Gevuina avellana Mol., Proteaceae) is a native tree of Chile and Argentina of edible fruit-type nut. We applied two approaches to contribute to the development of strategies for mitigation of the effects of climate change and anthropic activities in G. avellana. It corresponds to the first report where both tools are integrated, the MaxEnt model to predict the current and future potential distribution coupled with High-Resolution Melting Analysis (HRM) to assess its genetic diversity and understand how the species would respond to these changes. Two global climate models: CNRM-CM6-1 and MIROC-ES2L for four Shared Socioeconomic Pathways: 126, 245, 370, and 585 (2021–2040; 2061–2080) were evaluated. The annual mean temperature (43.7%) and water steam (23.4%) were the key factors for the distribution current of G. avellana (AUC = 0.953). The future prediction model shows to the year 2040 those habitat range decreases at 50% (AUC = 0.918). The genetic structure was investigated in seven natural populations using eight EST-SSR markers, showing a percentage of polymorphic loci between 18.69 and 55.14% and low genetic differentiation between populations (Fst = 0.052; p < 0.001). According to the discriminant analysis of principal components (DAPC) we identified 10 genetic populations. We conclude that high-priority areas for protection correspond to Los Avellanos and Punta de Águila populations due to their greater genetic diversity and allelic richness.