Nei's Distance Research Articles

First report of bacteria associated with soft rot in yellow pitahaya (Selenicereus megalanthus haw.) in Colombia crops

Colombia is the ninth largest producer of dragon fruit in the world and the department of Boyacá is the largest with 440 hectares planted. Bacterial phytopathogens can cause pitahaya fruit losses and low yields by producing stem soft rot. This research aimed to study and identified possible agents of bacterial diseases of pitahaya in Boyacá, Colombia. Thirteen farms in the region were selected to take 20 samples by means of a targeted and random sampling of stem and fruit tissues with soft rot symptoms in the early stages of the disease. A process of microbiological isolation, biochemical and molecular taxonomic identification of the isolated bacteria. The 16s rRNA gene sequences of the V2-V5 region were edited by removing the primers, assembling and obtaining the consensus sequence of the primers 1100R-337F and 800R -518F. The phylogenetic analysis was performed by BLAST at NCBI, using the “Classifier” and “SeqMatch” tools from the RDP website, and phylogenetic trees were created by multiple alignment using the MUSCLE algorithm and the Tamura Nei distance method was performed. Signs like blisters and mucilaginous fluids, symptoms like yellow and brown chlorotic spots, soft rot, and liquefaction were identified, and possible vectors like flies and ants were report. Twenty-five bacterial morphotypes were identified classifieds in 4 phyla, 9 families and 13 genera. The analysis of the 16S rRNA gene sequences of the bacterial strains showed a 98 to 100% identity with Enterobacter cloacae, Pectobacterium carotovora and Paenibacillus glucanolyticus, reported in other studies as causing the soft rot of the pitahaya stem and fruit. New species were reported as possible pathogenic bacteria of pitahaya: Pantoea cypripedii, Kluyvera intermedia and Klebsiella oxytoca. Infectivity assays did not have positive results. The microbiota identified in the stages of the necrotrophic phase or final stage of soft rot of the stem belong to the genera Achromobacter, Sphingobacterium, Pseudomonas, Klebsiella, Paenibacillus, Bacillus, Stenotrophomonas and Microbacterium. In the fly Leptoglossus zonatus associated with the crop were identified Pseudomonas fulva and Lysinibacillus fusiformis were identified. This is also the first official report of a complex of possible phytopathogen bacteria of the order Enterobacterales (Enterobacteriacea, Erwiniaceae and Pectobacteriaceae family) in symptoms by bacterial disease on pitahaya Colombian crops. Identification of the bacteria in a pathogenic system can guide chemical and biological control practices in order to increase the productive and export potential of exotic and orphan crops from small local farmings.

Isolation and endemism in the subterranean aquatic snails of the genus Belgrandiella A. J. Wagner, 1928 (Caenogastropoda: Truncatelloidea: Hydrobiidae)

The Western Balkans hosts the richest subterranean aquatic gastropod fauna in the world. The main factors shaping intraspecies diversity are thought to be isolation and endemism. In the genus Belgrandiella, minute snails inhabiting subterranean waters and springs in Central Europe and Balkans, molecular studies have shown much fewer valid species than previously anticipated. The present study applies mitochondrial cytochrome c oxidase subunit I, histone 3, and RAPD analysis, to check the inter- and intraspecies genetic diversity in 36 Belgrandiella populations from caves, springs and interstitial aquifers. The level of gene flow is assessed to check if these snails form a widespread genetically uniform metapopulation or rather follow the highly endemic pattern. The studied populations have been assigned to six species. In the most widely distributed B. kusceri from 21 populations, 60 sequenced specimens represent 16 haplotypes. While the same haplotypes are present in distant populations, gene flow between the other populations is low. Nei distances for RAPD show no geographic pattern. The interspecies differences in COI evidently confirm the time of speciation in Pleistocene, before karstification, which rejects speciation within isolated caves. The pattern observed in Belgrandiella seems more similar to the one described in Montenegrospeum than in Kerkia.

Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms

Wallachian and Sumava sheep are autochthonous breeds that have undergone a significant bottleneck effect and subsequent restoration efforts. The first objective of this study was to evaluate the degree of genetic variability of both breeds and, therefore, the current management of the breeding. The second was to determine whether these two breeds still retain their genetic uniqueness in relation to each other and other breeds, despite regenerative interventions. Our data consisted of 48 individuals of Sumava and 37 individuals of Wallachian sheep. The comparison data contained 25 other breeds (primarily European) from the HapMap dataset generated by the International Sheep Genomics Consortium. When comparing all 27 breeds, the Czech breeds clustered with 15 other breeds and formed a single branch with them according to Nei's distances. At the same time, however, the clusters of both breeds were integral and easily distinguishable from the others when displayed with principal component analysis (PCA). Population substructure analysis did not show any common genetic ancestry of the Czech national breeds and breeds used for regeneration or, eventually, breeds whose ancestral population was used for regeneration. The average values of FST were higher in Wallachian sheep (FST = 0.14) than in Sumava sheep (FST = 0.08). The linkage disequilibrium (LD) extension per autosome was higher in Wallachian than in Sumava sheep. Consequently, the Ne estimates five generations ago were 68 for Sumava versus 34 for Wallachian sheep. Both native Czech breeds exhibit a wide range of inbreeding based on the excess of homozygosity (FHOM) among individuals, from −0.04 to 0.16 in Sumava and from −0.13 to 0.12 in Wallachian. Average inbreeding based on runs of homozygosity was 0.21 in Sumava and 0.27 in Wallachian. Most detected runs of homozygosity (ROH) were less than 5 Mb long for both breeds. ROH segments longer than 15 Mb were absent in Wallachian sheep. Concerning putative selection signatures, a total of 471 candidate genes in Wallachian sheep within 11 hotspots and 653 genes within 13 hotspots in Sumava sheep were identified. Czech breeds appear to be well differentiated from each other and other European breeds. Their genetic diversity is low, especially in the case of the Wallachian breed. Sumava is not so threatened by low diversity but has a larger share of the non-native gene pool.

Fingerprinting, structure, and genetic relationships among selected accessions of blue honeysuckle (Lonicera caerulea L.) from European collections

Due to its value and economic importance, the genome of Lonicera caerulea L. has been widely studied in various fields of science. In this study the genetic structure and relationships between 24 accessions of L. caerulea of different origins were assessed. A total of 692, 814, and 258 loci were amplified using 43 RAPD (random amplified polymorphic DNA), 40 ISSR (intersimple sequence repeat), and 20 R-ISSR (RAPD+ISSR) primers, respectively. Among the amplified loci, 66–78% were polymorphic and 12–20% were private. Selected R-ISSR sequences were detected in Lonicera japonica transcripts. Cluster and STRUCTURE analyses performed for each of the techniques revealed the existing differences and unknown similarities between the genotypes. The r-factor values calculated in the Mantel test indicated highly significant positive correlations between the Nei distance matrices, similar to the FST values (FST_RAPD = 0.223, FST_ISSR = 0.279, FST_R-ISSR = 0.363) determined in the analysis of molecular variance. It was found that 78%, 72%, and 64% of the genetic variations were related to the differences observed within the populations, which suggest that the variations are mainly reflected in the differences among the genotypes. The principal coordinate analysis showed greater differences between the mean distances of the Lonicera genotype pair and the actual distances of the same pairs on the Nei matrix compared to multidimensional scaling. These differences were 45%, 56%, and 42% higher for RAPD, ISSR and R-ISSR, respectively.

Genetic Relationship between Sweet Grain Sorghum and the Other Sorghum Types Cultivated in Burkina Faso Assessed with Nuclear Microsatellite Markers SSRs

In Burkina Faso, sweet grain sorghum [Sorghum bicolor (L.) Moench] is generally cultivated in association with several other types of sorghum. However, the lack of information on the genetic relationship between this sorghum and grain sorghum as well as sweet stalk sorghum hinders the efficient management of its genetic resources. Thus, 34 sorghum accessions consisting of 14-grain sorghum, 10-sweet stalk sorghum, and 10 sweet grain sorghum were evaluated using 15 nuclear microsatellites markers (SSRs) to determine their genetic relationship. Results revealed significant genetic diversity within each sorghum type and a significant index of genetic differentiation per pair of sorghum types (0.017) between sweet grain sorghum and sweet stalk sorghum. The minimum Nei distance was also high (0.12) between these two sorghum types. Sweet grain sorghum indeed showed the lowest values of theoretical heterozygosity (0.35), of observed heterozygosity (0.13). Structuring of the accessions of the three types of sorghum cultivated in two distinct groups, one of grain sorghum and sweet stalk sorghum and another consisting of accessions of grain sorghum and sweet grain sorghum was also obtained. The low differentiation observed would suggest greater genetic proximity between the three types of sorghum. The differences observed would be more of a physiological and biochemical nature. These results could contribute to better management of the genetic resources of sweet grain sorghum.

Population structure and pattern of geographic differentiation of Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae) in Turkey.

The Colorado potato beetle (CPB) is the most harmful pest of potato in potato cultivation regions globally. Although it is an economically important agricultural pest, the population structure and colonization route of this species in Turkey are uncertain. We used microsatellite and mitochondrial DNA (mtDNA) markers to obtain information about the population source, structure and bio-invasion route of CPB populations in Turkey. The common single mtDNA haplotype in European CPB populations was obtained in all Turkish CPB populations based on mtDNA data analysis. However, microsatellites revealed a low level of genetic variation in CPB populations. The results of microsatellite analysis [factorial correspondence analysis (FCA), Bayesian analysis of genetic population structure (BAPS), unweighted pair group method with arithmetic mean (UPGMA) dendrogram, F-statistics and Nei's distances] indicated three groups for invasive CPB: Thrace-Marmara and Aegean; Black Sea, Central Anatolia and Mediterranean; Northeastern Anatolia. Region-specific alleles have been identified in regions, where commercial potato cultivation and insecticide use are intensive. The detection of a single fixed European haplotype in all Turkish populations has proved that CPB in Turkey originated from Europe as a result of a founder event occurred in European populations. Low genetic variation was due to the short time period since the spread of CPB from America to Europe. The highest number of private alleles were found in the top commercial potato cultivation region-Central Anatolia from where the CPB populations spread to other parts of Turkey. © 2021 Society of Chemical Industry.

Genetic diversity evolution of a sheep breed reintroduced after extinction: Tracing back Christopher Columbus' first imported sheep

New World's hair sheep breeds may genetically stem from West African introgression into established ecotypes of Spanish descent presumably extinct in the XIX Century. However, present Canary non-wooled breeds have presumably regressively resulted from the absorption of primitive individuals through Venezuelan descendants. We studied genetic diversity, structure, and evolution of the Canary hair sheep since its reintroduction in the 1950s. Demographic and genetic variability were evaluated using ENDOG (v4.8). Effective population size based on individual inbreeding rate was around one third higher than when based on individual coancestry rate. Nei's distances and equivalent subpopulations number indicated a highly-structured population. Although genetic diversity loss since the founder generations could be considered small, narrower pedigree bottlenecks could result from intraflock breeding policies and excessive contribution of few ancestors. Long generation intervals could be considered when reducing inbreeding. Wright's fixation statistics indicated slight interflock inbreeding. Pedigree completeness suggested genetic parameters were reliable, hence controlling inbreeding negative effects, could indeed, be crucial preserving these animal resources, consolidating the population in the archipelago after reintroduction.

Genetic diversity and structure of Buxus hyrcana (Pojark) populations in the Caspian forests of northern Iran revealed by ISSR markers

The Caspian boxwood (Buxus hyrcana) is an endangered, evergreen species in the Hyrcanian forests. The prevalence of pests and boxwood blight disease are bound to reduce the genetic diversity of this species in the near future. Accordingly, the current study considered habitat conservation and restoration by evaluating the genetic diversity of different Caspian boxwood populations. Ninety-seven accessions from seven geographic regions of Hyrcanian forests in Iran were investigated to determine genetic diversity and differentiation among and between populations using 10 ISSR primers. Results showed that the inter-population genetic diversity in B. hyrcana was estimated to be higher than intra-population genetic diversity. Principal coordinates analysis was performed on the populations, along with cluster (based on the Nei distance) and Bayesian structure analysis which classified the populations based on their distance from the sea and their altitude above sea level. Our findings suggest that geographic and environmental factors have an essential role in shaping regional gene flow and influence the genetic structure of B. hyrcana populations in the Hyrcanian forests.

Morphological and genetic diversity of Pura Raza Español horse with regard to the coat colour.

Gene mutations influencing melanocytes also impact on physiological and behavioural functions. In this study, we investigated their association with four different coat colours in the Pura Raza Español (PRE) horse using morphological traits and molecular datasets. Four different subpopulations were identified according to individual coat colour: grey, bay, chestnut and black. Coat colour significantly associated with morphological measurements. Observed and expected heterozygosity values were low in grey compared with the other three subpopulations, suggesting the presence of unique ancestral alleles probably arisen by genetic drift and selection mechanism effects. Nei's distance demonstrated a clear division among subpopulations, the grey being the most divergent group. Gene flow estimates were similar, showing the lowest values in grey. Divergence times among subpopulations assessed with the average square distance suggested that grey was the original PRE population which diverged from bay, chestnut and black. Our results also demonstrated a clear morphological differentiation according to coat colour. The close genetic structure of bay and chestnut PRE subpopulations and the clear differences in most morphological traits of grey and chestnut PRE mares would suggest the pleiotropic effect of genomic regions determining coat colour in horses. However, further analysis including genomic information would be necessary to elucidate the mechanisms involved.

Reliability and Construct Validity of the NEI VFQ-25 in a Subset of Patients With Geographic Atrophy From the Phase 2 Mahalo Study

Geographic atrophy (GA) is an advanced form of age-related macular degeneration characterized by progressive, irreversible visual function loss. This analysis evaluates the psychometric properties of the 25-Item National Eye Institute Visual Function Questionnaire (NEI VFQ-25) composite, near activity, and distance activity scores in patients with GA. Reliability and validity study. Reliability and validity were tested with NEI VFQ-25 data collected from 100 subjects with GA from United States' sites of the phase 2 Mahalo study of lampalizumab (ClinicalTrials.gov identifier: NCT01229215). Strong internal consistency and reproducibility were demonstrated for the NEI VFQ-25 composite (Cronbach's α, 0.95; intraclass correlation coefficient [ICC], 0.86), near activity (Cronbach's α, 0.84; ICC, 0.80), and distance activity (Cronbach's α, 0.84; ICC, 0.84) scores. Convergent validity with the binocular measures, Minnesota Low-Vision Reading Test (MNRead) reading speed and Functional Reading Independence (FRI) index score, was demonstrated for baseline NEI VFQ-25 composite (Pearson correlation [r]= 0.61 and 0.69, respectively), near activities (r=0.69 and 0.73), and distance activities (r= 0.57 and 0.64) scores. Known-group validity testing for baseline mean NEI VFQ-25 scores (composite, near activities, and distance activities) showed differences between patients with mean maximum MNRead reading speed ≥ 80 vs < 80 words per minute, and between mean FRI index score ≥ 2.5 vs < 2.5 (all P < .0001). Psychometric evidence supports the NEI VFQ-25 as a reliable and valid cross-sectional measure of the impact of GA on patient visual function and vision-related quality of life.

The genetic diversity and applicability assessment of autosomal STRs among Chinese populations by a novel Fixation Index and Nei's index.

The population-specific FST in STR loci of Chinese populations has not been focused on. Here, we genotyped 19 STRs in 530 unrelated healthy individuals of Xuzhou Han population, and collected data of 30,308 samples from 32 Hans and 50 minorities nationwide. The population-specific βi and locus-specific βil were calculated to evaluate the applicable value of STRs. Next, we generated the genetic structure of various ethnic populations by Neighbor-Joining tree and Multidimensional Scaling plot based on pairwise Nei's distances. We found that TH01 and TPOX possessed high ability in discriminating populations which may be reled to the mutation rate of these STRs. Additionally, our data indicated that Chinese Han was homogenous and the population-specific βis of northern Hans were generally smaller than southern Hans (p > 0.05). We concluded that population-specific FST for autosomal STR loci could be used to reveal the unique genetic characteristics and thus uncover the genetic relationship among Chinese populations.

Genetic characteristics of Kodar snow sheep using SNP markers

For the first time nuclear DNA polymorphisms were studied in Kodar snow sheep (Ovis nivicola kodarensis, KOD). KOD is a representative of a small isolated population of Asian snow sheep (Ovis nivicola Eschscholtz, 1829) inhabiting the Kodar Ridge (Irkutsk oblast, Transbaikal krai). We compared KOD with the geographically closest Yakut subspecies (Ovis nivicola lydekkeri). Genome-wide study of single-nucleotide polymorphisms (SNPs) was performed using the Illumina OvineSNP50 BeadChip (Illumina, United States). The final set of markers for analysis included 1030 SNPs. We found that Kodar snow sheep had almost 10 times lower level of genetic diversity evaluated by multilocus heterozygosity—MLH (0.027 for KOD vs 0.215–0.270 for individuals of Yakut subspecies) and standardized MLH—stMLH (0.116 against 0.910–1.147). The results of multidimensional scaling (MDS), Nei distances calculations (DN) and STRUCTURE analysis showed a clear genetic differentiation of Kodar snow sheep from Yakut subspecies. Our data is the first step to understanding the demographic history of the original Kodar population of snow sheep.

The low level of differences between mitogenomes of the Sakhalin sturgeon Acipenser mikadoi Hilgendorf, 1892 and the green sturgeon A. medirostris Ayeres, 1854 (Acipenseridae) indicates their recent divergence

The complete mitochondrial genome of the Sakhalin sturgeon Acipenser mikadoi and two mitogenomes of the Amur sturgeon A. schrenckii were sequenced using Roche 454 technology. The mitogenomes of the green sturgeon A. medirostris (obtained from GenBank) and the Sakhalin sturgeon differ as much as the mitogenomes of two mtDNA haplogroups (SM and BG) found in the same population of the Amur sturgeon: 0.0042 ± 0.0006 and 0.0036 ± 0.0005 substitutions per site (Tamura–Nei distance, TrN), respectively. The differences of these mitogenome pairs from mitogenomes of sister species (kaluga A. dauricus and white sturgeon A. transmontanus) are 3–6 times larger: 0.0260 ± 0.0015 and 0.0102 ± 0.0008, respectively. Thus, the differences between the mitogenomes of the Sakhalin and green sturgeons can be attributed to the variability at the intraspecific level. The time that has passed since the divergence of the Sakhalin and green sturgeons is considered to be much shorter than was previously believed: approximately 0.16 rather than 9.60 million years.

Geographic Differentiation and Population Genetic Structure of Moniliophthora roreri in the Principal Cocoa Production Areas in Colombia.

Frosty pod rot (FPR) disease on cocoa, caused by Moniliophthora roreri, is one of the most devastating cocoa disease in the Western Hemisphere. In Colombia, the disease is particularly severe in the Magdalena Valley, which is considered the possible center of origin for the pathogen species. We analyzed the genetic diversity of isolates from the departments of Santander, Antioquia, Tolima, and Huila in Colombia using 23 simple-sequence repeats (SSR) markers. In total, 117 different multilocus genotypes were found among 120 isolates, each one representing a unique haplotype. High mutation rates in the SSR and gene flow can explain the high levels of diversity. Also, the observed and standardized indexes of association (IA and řd) indicate that the populations of M. roreri are clonal. Furthermore, given the high haplotype diversity and the significant linkage disequilibrium observed, we hypothesize that M. roreri could be a primarily asexual species undergoing sporadic recombination or partial recombination through parasexuality. A Bayesian clustering analysis implemented by STRUCTURE showed that the most probable number of genetic groups in the data was three, confirming the geographical differentiation among isolates. Similar results were obtained by a discriminant analysis of principal components, a principal coordinate analysis, and a neighbor-joining tree from microsatellite loci base on Nei distance. Cacao genotypes and environmental variables did contribute to the genetic differentiation of the groups. We discuss how this information could be used to improve the management of FPR at the regional level.

GENETIC DIVERSITY AND STRUCTURE OF Oenocarpus mapora GERMPLASM CONSERVED AT EASTERN AMAZON

ABSTRACT The aim of this study was to evaluate the genetic diversity and structure in the germoplasm of Oenocarpus mapora conserved at Eastern Amazon. Thus, 88 individuals were genotyped with five microsatellite loci. These individuals belong to 24 accessions that were sampled in eight sample places of three Brazilian Amazon states conserved at the Active Germplasm Bank (AGB) of Embrapa Eastern Amazon. All loci were polymorphic and they generated 85 alleles with an average of 17 alleles per loci. Total genetic diversity (HE) was 0.48. Sample places were considered genetically distinct, with ?p = 0.354. The analysis of molecular variance (AMOVA) identified that the genetic portion among areas was of 36.14% and within 63.86%. The Nei distances varied from 0.091 between Abaetetuba and Santo Antônio do Tauá, both in the state of Pará (PA), to 4.18, between Parintins, AM and Rio Branco, AC. By means of Bayesian analysis, it was identified nine clusters that compose the accessions of the germplasm bank, with different distributions among individuals. The study showed high fixation rates per sample area, which indicates that there may have been significant inbreeding or crossing among parental individuals. It suggests that future samples should be made of different plants in natural populations. Even though, it was verified that there is considerable genetic variation in the germplasm of O. mapora.

Does phylogeographical structure relate to climatic niche divergence? A test using maritime pine (Pinus pinaster Ait.)

AbstractAimTo disentangle the effects of environmental and geographical processes driving phylogenetic distances among clades of maritime pine (Pinus pinaster). To assess the implications for conservation management of combining molecular information with species distribution models (SDMs; which predict species distribution based on known occurrence records and on environmental variables).LocationWestern Mediterranean Basin and European Atlantic coast.MethodsWe undertook two cluster analyses for eight genetically defined pine clades based on climatic niche and genetic similarities. We assessed niche similarity by means of a principal component analysis and Schoener's D metric. To calculate genetic similarity, we used the unweighted pair group method with arithmetic mean based on Nei's distance using 266 single nucleotide polymorphisms. We then assessed the contribution of environmental and geographical distances to phylogenetic distance by means of Mantel regression with variance partitioning. Finally, we compared the projection obtained from SDMs fitted from the species level (SDMsp) and composed from the eight clade‐level models (SDMcm).ResultsGenetically and environmentally defined clusters were identical. Environmental and geographical distances explained 12.6% of the phylogenetic distance variation and, overall, geographical and environmental overlap among clades was low. Large differences were detected between SDMsp and SDMcm (57.75% of disagreement in the areas predicted as suitable).Main conclusionsThe genetic structure within the maritime pine subspecies complex is primarily a consequence of its demographic history, as seen by the high proportion of unexplained variation in phylogenetic distances. Nevertheless, our results highlight the contribution of local environmental adaptation in shaping the lower‐order, phylogeographical distribution patterns and spatial genetic structure of maritime pine: (1) genetically and environmentally defined clusters are consistent, and (2) environment, rather than geography, explained a higher proportion of variation in phylogenetic distance. SDMs, key tools in conservation management, better characterize the fundamental niche of the species when they include molecular information.

Variability and interpopulation differentiation of rare species Gueldenstaedtia monophylla Fisch. (Fabaceae)

Genetic variability of rare species G. monophylla of 7 natural populations in the central part of its range (Ongudai district of the Altai Republic) was studied. To characterize the genetic diversity that rare relict species as the species and on the population level SDS-electrophoresis seed storage protein was used. Polypeptide spectra seeds contain from 17 to 32 protein components, of which 28 were polymorphic. The populations of G. monophylla was revealed sufficiently high level of genetic polymorphism, genetic similarity index within populations studied ranged from 0.673- 0,813. The highest variability of seed storage proteins found in populations Inegen (S = 0,673) and Small Yin (S = 0,734). The lowest level of variability of the spectra of the polypeptide identified in a population of Big Yaloman S = 0,813. The genetic distance of Nei (D) between the studied populations was 0,018-0,215, the greatest distance in the protein spectra was found between populations Inegen and M. Yin – 0,215. Population Inegen most geographically isolated from other populations we studied, Nei distance between this population and all other populations varied from 0,113 to 0,215. With AMOVA was found that the share of intra-population variability account for 53 % and inter-population – 47 %. Perhaps quite high genetic diversity in populations of G. monophylla is provided and maintained by such biological characteristics of the species, as the cross-pollination, most of the life expectancy and long reproductive period. The results of our study suggest that some rare species are able to maintain high levels of genetic diversity, even with a small amount of the population. The relatively high level of genetic variability indicates that the current genetic drift and inbreeding does not pose a threat to the survival of the species.

Analysis of genetic variability of Fasciola hepatica populations from different geographical locations by ISSR-PCR.

Inter-simple sequence repeats markers were used to determinate the genetic variability of Fasciola hepatica populations recovered from sheep and cattle from Spain (Sp1, Sp2, Sp3 and Sp4), UK (Eng), Ireland (Ir) and Mexico (Mex). Twenty five primers were tested but only five produced 39 reproducible bands, being 71.79% polymorphic bands. This percentage ranged from 10.26% in Sp4 to 48.72% in Sp1, and per host between 28.21 and 48.72% in sheep and between 10.26 and 38.46% in cattle. This relatively low range of genetic diversity within populations, with a mean of 34.40%, implies that a large proportion of variation resided among populations. The population differentiation (Gst = 0.547) indicated that 54.7% of variation is due to differences between populations and 45.3% due to differences within population. The Nei's distance ranged between 0.091 and 0.230 in sheep and between 0.150 and 0.337 in cattle. The genetic relationships between populations and individuals were shown by a UPGMA dendrogram and a principal coordinate analysis; both grouped all populations separately from Sp4, a population of from the Midwest of Spain with the lowest level of diversity. Small genetic distances were observed between Eng and Ir, on the one hand, and Sp1, Sp2, Sp3, from the Northwest of Spain, together with Mex, on the other.

&lt;b&gt;Use of microsatellite markers to assess the identity and genetic diversity of &lt;i&gt;Vitis labrusca&lt;/i&gt; and &lt;i&gt;Vitis rotundifolia&lt;/i&gt; cultivars

Ten grapevine cultivars were genotyped at eight microsatellite loci to characterize their identity and genetic diversity. Of these, nine cultivar profiles matched with those of databases and ‘Magoon’ matched with ‘Regale’ in the present study and ‘Regale’ in the University of California (Davis) database, implicating a likely error in planting. The number of alleles ranged from 5 (VVM5) to 9 (VVMD31), and the observed heterozygosity ranged from 37.14 (VVMD5) to 97.14% (VVMD27), with no significant differences in relation to the expected values for any of the loci, with the exception of VVMD5. The polymorphism information content values were observed to be above 0.25 in more than 85% of the loci analyzed, and VVMD31 was the most informative. The UPGMA analysis clustered the cultivars into two distinct groups. Within each group, the most divergent cultivars were ‘Bountiful’ (V. rotundifolia) and ‘Goethe’ (V. labrusca), also exhibiting the largest number of private alleles, 4 and 7, respectively. When comparing the two groups, the most divergent accessions were ‘Bountiful’ and ‘Bordo’, with the highest Nei distance. It was demonstrated that there is sufficient genetic variability in the cultivars used in this study to support breeding programs.

Vascular endothelial growth factor-A is associated with chronic mountain sickness in the Andean population.

A study of chronic mountain sickness (CMS) with a candidate gene--vascular endothelial growth factor A (VEGFA)--was carried out in a Peruvian population living at high altitude in Cerro de Pasco (4380 m). The study was performed by genotyping of 11 tag SNPs encompassing 2.2 kb of region of VEGFA gene in patients with a diagnosis of CMS (n = 131; 49.1 ± 12.7 years old) and unrelated healthy controls (n = 84; 47.2 ± 13.4 years old). The VEGFA tag SNP rs3025033 was found associated with CMS (p < 0.05), individuals with AG genotype have 2.5 more risk of CMS compared to those with GG genotype (p < 0.02; OR, 2.54; 95% CI: 1.10-5.88). Pairwise Fst and Nei's distance indicate genetic differentiation between Cerro de Pasco population and HapMap3 population (Fst > 0.36, p < 0.01), suggesting selection is operating on the VEGF gene. Our results suggest that VEGFA is associated with CMS in long-term residents at high altitude in the Peruvian Andes.