RESUMEN

BACKGROUND: The genus Ternstroemia is associated with the vulnerable tropical montane cloud forest in Mexico and with other relevant vegetation types worldwide. It contains threatened and pharmacologically important species and has taxonomic issues regarding its species limits. This study describes 38 microsatellite markers generated using a genomic-based approach. METHODS AND RESULTS: We tested 23 of these markers in a natural population of Ternstroemia lineata. These markers are highly polymorphic (all loci polymorphic with 3-14 alleles per locus and expected heterozygosity between 0.202 and 0.908), most of them (19 out of 23) are in Hardy-Weinberg Equilibrium and free of null alleles (18 out of 23). Also we found no evidence of linkage among them. Finally, we tested the transferability to six other American species of Ternstroemia, two other Pentaphylacaceae species, and four species from different families within the order Ericales. CONCLUSIONS: These molecular resources are promising tools to investigate genetic diversity loss and as barcodes for ethnopharmacological applications and species delimitation in the family Pentaphylacaceae and some Ericales, among other applications.

Asunto(s)

Ericales , Humanos , Ericales/genética , Genoma , Genómica , Heterocigoto , Repeticiones de Microsatélite/genética , Alelos , Secuenciación de Nucleótidos de Alto Rendimiento , Sitios Genéticos/genética

RESUMEN

OBJECTIVE: This work was undertaken in order to identify Parkinson's disease (PD) risk variants in a Latino cohort, to describe the overlap in the genetic architecture of PD in Latinos compared to European-ancestry subjects, and to increase the diversity in PD genome-wide association (GWAS) data. METHODS: We genotyped and imputed 1,497 PD cases and controls recruited from nine clinical sites across South America. We performed a GWAS using logistic mixed models; variants with a p-value <1 × 10-5 were tested in a replication cohort of 1,234 self-reported Latino PD cases and 439,522 Latino controls from 23andMe, Inc. We also performed an admixture mapping analysis where local ancestry blocks were tested for association with PD status. RESULTS: One locus, SNCA, achieved genome-wide significance (p-value <5 × 10-8 ); rs356182 achieved genome-wide significance in both the discovery and the replication cohorts (discovery, G allele: 1.58 OR, 95% CI 1.35-1.86, p-value 2.48 × 10-8 ; 23andMe, G allele: 1.26 OR, 95% CI 1.16-1.37, p-value 4.55 × 10-8 ). In our admixture mapping analysis, a locus on chromosome 14, containing the gene STXBP6, achieved significance in a joint test of ancestries and in the Native American single-ancestry test (p-value <5 × 10-5 ). A second locus on chromosome 6, containing the gene RPS6KA2, achieved significance in the African single-ancestry test (p-value <5 × 10-5 ). INTERPRETATION: This study demonstrated the importance of the SNCA locus for the etiology of PD in Latinos. By leveraging the demographic history of our cohort via admixture mapping, we identified two potential PD risk loci that merit further study. ANN NEUROL 2021;90:353-365.

Asunto(s)

Sitios Genéticos/genética , Variación Genética/genética , Estudio de Asociación del Genoma Completo/métodos , Hispánicos o Latinos/genética , Enfermedad de Parkinson/etnología , Enfermedad de Parkinson/genética , Adulto , Anciano , Estudios de Cohortes , Femenino , Humanos , Masculino , Persona de Mediana Edad , Enfermedad de Parkinson/diagnóstico , Polimorfismo de Nucleótido Simple/genética , América del Sur/etnología

RESUMEN

In a rapidly changing climate, flowering time (FL) adaptation is important to maximize seed yield in flax (Linum usitatissimum L.). However, our understanding of the genetic mechanism underlying FL in this multipurpose crop remains limited. With the aim of dissecting the genetic architecture of FL in flax, a genome-wide association study (GWAS) was performed on 200 accessions of the flax core collection evaluated in four environments. Two single-locus and six multi-locus models were applied using 70,935 curated single nucleotide polymorphism (SNP) markers. A total of 40 quantitative trait nucleotides (QTNs) associated with 27 quantitative trait loci (QTL) were identified in at least two environments. The number of QTL with positive-effect alleles in accessions was significantly correlated with FL (r = 0.77 to 0.82), indicating principally additive gene actions. Nine QTL were significant in at least three of the four environments accounting for 3.06-14.71% of FL variation. These stable QTL spanned regions that harbored 27 Arabidopsis thaliana and Oryza sativa FL-related orthologous genes including FLOWERING LOCUS T (Lus10013532), FLOWERING LOCUS D (Lus10028817), transcriptional regulator SUPERMAN (Lus10021215), and gibberellin 2-beta-dioxygenase 2 (Lus10037816). In silico gene expression analysis of the 27 FL candidate gene orthologous suggested that they might play roles in the transition from vegetative to reproductive phase, flower development and fertilization. Our results provide new insights into the QTL architecture of flowering time in flax, identify potential candidate genes for further studies, and demonstrate the effectiveness of combining different GWAS models for the genetic dissection of complex traits.

Asunto(s)

Lino , Copas de Floración/crecimiento & desarrollo , Copas de Floración/genética , Lino/genética , Lino/crecimiento & desarrollo , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Genes de Plantas , Sitios Genéticos/genética , Estudio de Asociación del Genoma Completo/métodos , Desequilibrio de Ligamiento , Sitios de Carácter Cuantitativo , Semillas/genética , Análisis de Secuencia de ADN , Factores de Tiempo

RESUMEN

Kisspeptin has been identified as a key regulatory protein in the release of gonadotropin-releasing hormone (GnRH), which subsequently increases gonadotropin secretion during puberty to establish reproductive function and regulate the hypothalamic-pituitary-gonadal axis. The effects of variants in the KISS1, KISS1R, and GNRHR genes and their possible association with assisted reproduction outcomes remain to be elucidated. In this study, we used next-generation sequencing to investigate the associations of the genetic diversity at the candidate loci for KISS1, KISS1R, and GNRHR with the hormonal profiles and reproductive outcomes in 86 women who underwent in vitro fertilization treatments. Variants in the KISS1 and KISS1R genes were associated with luteinizing hormone (rs35431622:T>C), anti-Mullerian hormone (rs71745629delT), follicle-stimulating hormone (rs73507529:C>A), and estradiol (rs73507527:G>A, rs350130:A>G, and rs73507529:C>A) levels, as well as with reproductive outcomes such as the number of oocytes retrieved (s35431622:T>C), metaphasis II oocytes (rs35431622:T>C), and embryos (rs1132506:G>C). Additionally, variants in the GNRHR UTR3' (rs1038426:C>A, rs12508464:A>C, rs13150734:C>A, rs17635850:A>G, rs35683646:G>A, rs35610027:C>G, rs35845954:T>C, rs17635749:C>T, and rs7666201:C>T) were associated with low prolactin levels. A conjoint analysis of clinical, hormonal, and genetic variables using a generalized linear model identified two variants of the KISS1 gene (rs71745629delT and rs1132506:G>C) that were significantly associated with hormonal variations and reproductive outcomes. The findings suggest that variants in KISS1, KISS1R, and GNRHR genes can modulate hormone levels and reproductive outcomes.

Asunto(s)

Variación Genética , Hormona Liberadora de Gonadotropina/metabolismo , Kisspeptinas/genética , Receptores de Kisspeptina-1/genética , Receptores LHRH/genética , Reproducción/genética , Adulto , Femenino , Sitios Genéticos/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Infertilidad/genética

RESUMEN

Microsatellite markers are a useful genetic tool to answer ecological and conservation genetics questions. Microsatellite primers were developed and characterized to evaluate forest fragmentation effects on genetic structure, diversity and gene flow patterns in the dioecious tropical tree Astroniumgraveolens (Anacardiaceae). Using genomic library enrichment, sixteen microsatellite loci were developed for A.graveolens. Polymorphism was evaluated in 80 individuals from four localities in Mexico. The overall number of alleles detected was 63, average alleles per locus 3.9 with a range from one to 11 per locus. Cross amplification trails on related species in the Anacardiaceae family: Spondiaspurpurea and Amphipterygiumadstringens, achieved successful amplification for all primers. Microsatellite markers described here are the first to be characterized for A.graveolens. These genetic markers will be a useful tool to assess the genetic consequences of habitat fragmentation and selective logging on A.graveolens populations. Cross amplification success on S.purpureaandA.adstringens suggest that they may be used for population genetic studies in other species within the family.

Asunto(s)

Anacardiaceae/genética , Repeticiones de Microsatélite/genética , Alelos , Anacardiaceae/metabolismo , Cartilla de ADN/genética , ADN de Plantas/genética , Flujo Génico/genética , Frecuencia de los Genes/genética , Sitios Genéticos/genética , Marcadores Genéticos/genética , Biblioteca Genómica , Genotipo , Heterocigoto , Desequilibrio de Ligamiento/genética , México , Polimorfismo Genético/genética , Especificidad de la Especie , Árboles/genética , Árboles/metabolismo

RESUMEN

The Thraupidae family is one of the most wanted by bird breeders in Brazil because it is represented by its diverse, colorful and melodious singers. The Great-billed Seed-finch, Sporophila maximiliani, is the only representative of the genus Sporophila considered critically endangered in Brazil. Due to the demands of environmental agencies and of conservation programs, there is a need to increase the number of molecular markers available for the genus and specially for S. maximiliani. Therefore, this work aimed to provide a new set of microsatellite markers for S. maximiliani in order to help bird breeders and environmental agencies on fulfilling its demands as well as contributing with extra genetics tools for conservation programs of the S. maximiliani. Of the 30 markers developed, 25 successfully amplified, and 22 were polymorphic. Annealing temperature varied from 52 to 64 °C, number of alleles from 2 to 13, and the medium allele richness was 7.25 and medium expected, observed heterozygosity and PIC were, respectively, 0.812, 0.661 and 0.752. The probability of identity estimate was 8.54 × 10-27 and all the other probabilities of non-exclusion (sib-identity, parent pair and first-parent) were < 0.001, indicating that this set of microsatellite markers have high genetic variability and high power of individual genetic differentiation for S. maximiliani. Therefore, this work increases the options of molecular markers to be used on inspection for environmental agencies and for conservation programs on analyzing genetic variability and population studies for S. maximiliani.

Asunto(s)

Pinzones/genética , Repeticiones de Microsatélite/genética , Alelos , Animales , Conservación de los Recursos Naturales/métodos , Cartilla de ADN/genética , Especies en Peligro de Extinción , Sitios Genéticos/genética , Variación Genética/genética , Heterocigoto , Passeriformes/genética , Reacción en Cadena de la Polimerasa/métodos , Polimorfismo Genético/genética , Análisis de Secuencia de ADN/métodos

RESUMEN

It is believed that genetic factors play a large role in the development of many cognitive and neurological processes; however, epidemiological evidence for the genetic basis of childhood neurodevelopment is very limited. Identification of the genetic polymorphisms associated with early-stage neurodevelopment will help elucidate biological mechanisms involved in neuro-behavior and provide a better understanding of the developing brain. To search for such variants, we performed a genome-wide association study (GWAS) for infant mental and motor ability at two years of age with mothers and children recruited from cohorts in Bangladesh and Mexico. Infant ability was assessed using mental and motor composite scores calculated with country-specific versions of the Bayley Scales of Infant Development. A missense variant (rs1055153) located in the gene WWTR1 reached genome-wide significance in association with mental composite score (meta-analysis effect size of minor allele ßmeta = -6.04; 95% CI: -8.13 to -3.94; P = 1.56×10-8). Infants carrying the minor allele reported substantially lower cognitive scores in both cohorts, and this variant is predicted to be in the top 0.3% of most deleterious substitutions in the human genome. Fine mapping and region-based association testing provided additional suggestive evidence that both WWTR1 and a second gene, LRP1B, were associated with infant cognitive ability. Comparisons with recently conducted GWAS in intelligence and educational attainment indicate that our phenotypes do not possess a high genetic correlation with either adolescent or adult cognitive traits, suggesting that infant neurological assessments should be treated as an independent outcome of interest. Additional functional studies and replication efforts in other cohorts may help uncover new biological pathways and genetic architectures that are crucial to the developing brain.

Asunto(s)

Cognición , Sitios Genéticos/genética , Genoma Humano/genética , Adulto , Alelos , Bangladesh , Preescolar , Estudios de Cohortes , Femenino , Estudio de Asociación del Genoma Completo , Humanos , Masculino , México , Madres , Destreza Motora , Fenotipo

RESUMEN

BACKGROUND: Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs. RESULTS: We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency. CONCLUSIONS: Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.

Asunto(s)

Ascomicetos/fisiología , Mapeo Cromosómico , Resistencia a la Enfermedad/genética , Sitios Genéticos/genética , Glycine max/genética , Enfermedades de las Plantas/microbiología , Polimorfismo de Nucleótido Simple , Alelos , Marcadores Genéticos/genética , Fenotipo , Enfermedades de las Plantas/inmunología , Glycine max/inmunología , Glycine max/microbiología

RESUMEN

Microsatellite markers provide high polymorphism levels, useful to study genetic diversity and gene flow patterns in plant populations. Here we develop and characterize microsatellite primers to evaluate patterns of genetic structure and diversity, and gene flow levels in the dioecious tropical tree Spondias purpurea (Anacardiaceae). Twenty-four microsatellite primers were developed for Spondias purpurea. Polymorphism was evaluated in 139 individuals from three localities in Mexico. Ten loci were polymorphic. The number of alleles ranged between two and 21, the average number of alleles was 5.88. Cross-amplification trials on S. mombin, S. radlkoferi, Astronium graveolens and Amphipterygium adstringens achieved successful amplification for only six microsatellites in S. mombin and S. radlkoferi. Microsatellites developed for S. purpurea will be a useful tool to estimate genetic diversity within and among populations, as well as to assess the consequences of habitat fragmentation on gene flow patterns of this species.

Asunto(s)

Anacardiaceae/genética , Repeticiones de Microsatélite/genética , Alelos , Animales , Cartilla de ADN/genética , ADN de Plantas/genética , Flujo Génico/genética , Sitios Genéticos/genética , Heterocigoto , Desequilibrio de Ligamiento/genética , México , Polimorfismo Genético/genética , Especificidad de la Especie , Árboles/genética

RESUMEN

Ten microsatellite markers were developed using next-generation sequencing data for Alibertia edulis (Rubiaceae), a widely distributed species typical of Cerrado (Brazilian savanna) vegetation. The markers were polymorphic in the two populations analyzed. The numbers of alleles, and observed (HO) and expected (HE) heterozygosities per polymorphic locus ranged from 2 to 11, 0.091 to 1.0, and 0.100 to 0.937 respectively. The SSR loci demonstrated moderate to high polymorphism values in both populations analyzed, with PIC values ranging from 0.26 to 0.91, and total allele numbers ranging from three to 16. The inbreeding coefficient values were generally higher in the Piauí population (ranging from - 0.593 to 0.762) than in the Mato Grosso population (ranging from - 1 to 0.575). The differences observed between those disjunct populations suggest they harbor different alleles, which has implications for Cerrado conservation strategies. Those loci will be useful for population studies of A. edulis.

Asunto(s)

Rubiaceae/genética , Alelos , Brasil , ADN de Plantas/genética , Sitios Genéticos/genética , Pradera , Repeticiones de Microsatélite/genética , Polimorfismo Genético/genética , Árboles/genética

RESUMEN

Traits related to plant lodging and architecture are important determinants of plant productivity in intensive maize cultivation systems. Motivated by the identification of genomic associations with the leaf angle, plant height (PH), ear height (EH) and the EH/PH ratio, we characterized approximately 7,800 haplotypes from a set of high-quality single nucleotide polymorphisms (SNPs), in an association panel consisting of tropical maize inbred lines. The proportion of the phenotypic variations explained by the individual SNPs varied between 7%, for the SNP S1_285330124 (located on chromosome 9 and associated with the EH/PH ratio), and 22%, for the SNP S1_317085830 (located on chromosome 6 and associated with the leaf angle). A total of 40 haplotype blocks were significantly associated with the traits of interest, explaining up to 29% of the phenotypic variation for the leaf angle, corresponding to the haplotype hapLA4.04, which was stable over two growing seasons. Overall, the associations for PH, EH and the EH/PH ratio were environment-specific, which was confirmed by performing a model comparison analysis using the information criteria of Akaike and Schwarz. In addition, five stable haplotypes (83%) and 15 SNPs (75%) were identified for the leaf angle. Finally, approximately 62% of the associated haplotypes (25/40) did not contain SNPs detected in the association study using individual SNP markers. This result confirms the advantage of haplotype-based genome-wide association studies for examining genomic regions that control the determining traits for architecture and lodging in maize plants.

Asunto(s)

Haplotipos , Fenotipo , Hojas de la Planta/anatomía & histología , Zea mays/fisiología , Cromosomas de las Plantas/genética , Sitios Genéticos/genética , Estudio de Asociación del Genoma Completo , Polimorfismo de Nucleótido Simple

RESUMEN

Spondias tuberosa Arr. Cam belongs to the Anacardiaceae family, an economically important family of plants whose fruits are consumed by humans and animals. The aim of this study was to develop microsatellite markers using sequences from high-throughput sequencing and a magnetic bead enrichment method. The sequences were used to obtain contigs with a minimum of 500 nucleotides using Ray software and the mining of the simple sequence repeats (SSR) was performed with Phobos software, while the primers were designed by Primer3. We developed 18 polymorphic nuclear microsatellite markers and successfully cross-amplified them to three Spondias species. In S. tuberosa, the alleles ranged from 2 to 5 for each locus and Hardy-Weinberg equilibrium was found for 16 loci, with an expected and observed heterozygosity at 0.095-0.755 and 0.1-0.75, respectively. Cross-transferability was obtained for all loci in S. bahiensis, S. dulcis and S. purpurea. We concluded that the microsatellite markers developed in this study are useful in genetic population and conservation studies, as well as for investigating the hybrid origins of Spondias species.

Asunto(s)

Anacardiaceae/genética , Frecuencia de los Genes , Sitios Genéticos/genética , Genética de Población/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Desequilibrio de Ligamiento , Repeticiones de Microsatélite , Reacción en Cadena de la Polimerasa/métodos , Polimorfismo Genético/genética

RESUMEN

Many genetic loci affect circulating lipid levels, but it remains unknown whether lifestyle factors, such as physical activity, modify these genetic effects. To identify lipid loci interacting with physical activity, we performed genome-wide analyses of circulating HDL cholesterol, LDL cholesterol, and triglyceride levels in up to 120,979 individuals of European, African, Asian, Hispanic, and Brazilian ancestry, with follow-up of suggestive associations in an additional 131,012 individuals. We find four loci, in/near CLASP1, LHX1, SNTA1, and CNTNAP2, that are associated with circulating lipid levels through interaction with physical activity; higher levels of physical activity enhance the HDL cholesterol-increasing effects of the CLASP1, LHX1, and SNTA1 loci and attenuate the LDL cholesterol-increasing effect of the CNTNAP2 locus. The CLASP1, LHX1, and SNTA1 regions harbor genes linked to muscle function and lipid metabolism. Our results elucidate the role of physical activity interactions in the genetic contribution to blood lipid levels.

Asunto(s)

Ejercicio Físico , Sitios Genéticos/genética , Lípidos/sangre , Lípidos/genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Pueblo Asiatico/genética , Población Negra/genética , Brasil , Proteínas de Unión al Calcio/genética , Colesterol/sangre , HDL-Colesterol/sangre , HDL-Colesterol/genética , LDL-Colesterol/sangre , LDL-Colesterol/genética , Femenino , Estudio de Asociación del Genoma Completo , Genotipo , Hispánicos o Latinos/genética , Humanos , Proteínas con Homeodominio LIM/genética , Metabolismo de los Lípidos/genética , Masculino , Proteínas de la Membrana/genética , Proteínas Asociadas a Microtúbulos/genética , Persona de Mediana Edad , Proteínas Musculares/genética , Proteínas del Tejido Nervioso/genética , Factores de Transcripción/genética , Triglicéridos/sangre , Triglicéridos/genética , Población Blanca/genética , Adulto Joven

RESUMEN

Microsatellites markers were developed for Paypayrola blanchetiana (Violaceae), a near-dispersing forest tree forming aggregated populations, to investigate genetic diversity and gene flow among subpopulations in a fragmented environment. Next generation sequencing (Illumina platform) was used to develop ten nuclear microsatellite loci and one plastid microsatellite locus that amplify in P. blanchetiana. Polymorphism was tested in two subpopulations separated by a distance of approximately 11 km. The identified loci contained between two and five alleles per locus. Observed heterozygosity ranged between 0.063 and 0.563 in both subpopulations, while expected heterozygosity ranged from 0.063 to 0.567 in the first, and 0.063-0.627 in the second subpopulation. The microsatellites are among the first in the family Violaceae and will be useful for population genetic studies in this species. Amplification was successful in one further Paypayrola species from Amazonia, which suggest a wider usefulness of the present markers.

Asunto(s)

Repeticiones de Microsatélite/genética , Violaceae/genética , Alelos , Brasil , Mapeo Cromosómico/métodos , Cartilla de ADN , Sitios Genéticos/genética , Genética de Población/métodos , Genotipo , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Polimorfismo Genético/genética , Especificidad de la Especie , Árboles/genética

RESUMEN

The population of Guatemala includes Mestizos (admixed) and different Mayan groups (Native Americans), which have been poorly studied in regards to short tandem repeat (STR) loci used for human identification (HID) purposes. Therefore, 483 unrelated Guatemalan volunteers from one Mestizo and three Mayan populations (Poqomchi, Ixil, and Achi) were analyzed with an AmpFlSTR Identifiler™ kit. Allele frequencies and forensic parameters were obtained for 15 autosomal STRs in these populations. Hardy-Weinberg equilibrium by locus and equilibrium linkage between pair of loci were demonstrated by exact tests in all the studied populations. Larger genetic differentiation probably due to genetic drift effects was observed among the studied Guatemalan Mayan groups than the neighboring Mexican Mayas. In brief, our results validate to use the Identifiler™ kit for HID in three non-previously studied Mayan groups, and one Mestizo population from Guatemala.

Asunto(s)

Genética Forense/métodos , Técnicas de Genotipaje/métodos , Repeticiones de Microsatélite/genética , Juego de Reactivos para Diagnóstico , Femenino , Frecuencia de los Genes , Flujo Genético , Ligamiento Genético , Sitios Genéticos/genética , Guatemala/etnología , Humanos , Desequilibrio de Ligamiento , Masculino

RESUMEN

The sea cucumber Holothuria grisea has become the subject of intense and unregulated fishing in northeastern Brazil due to their growing demand in Asian market. However, there is little knowledge about the dynamics and genetics of H. grisea wild populations on the South American coast. In this study, we present the first set of H. grisea microsatellite markers, identified and characterized using Illumina paired-end reads of whole genome shotgun sequencing. From 50 strictly selected candidates, eight novel microsatellite markers were successfully developed. We then genotyped 30 individuals to evaluate the degree of polymorphism and validate the markers. The number of alleles ranged from three to 14, while observed and expected heterozygotes ranged from 0.156 to 0.906 and from 0.283 to 0.774, respectively. After correcting for multiple tests,we found no evidence of linkage disequilibrium in all pairwise combinations between the loci. One locus (Hgr15607) revealed deviation from the Hardy-Weinberg equilibrium, as well as the presence of null alleles. However, we observed significant differences in frequency distribution between males and females at locus Hgr15607. We believe that the markers describedhere will be useful for conservation efforts and management of H. grisea fisheries and for prospective aquaculture of these organisms.

Asunto(s)

Holothuria/genética , Repeticiones de Microsatélite/genética , Polimorfismo Genético , Secuenciación Completa del Genoma/métodos , Alelos , Animales , Brasil , Femenino , Frecuencia de los Genes , Sitios Genéticos/genética , Genotipo , Masculino

RESUMEN

The Hospital Infantil de México Federico Gómez (HIMFG) is a tertiary care hospital in Mexico City where Escherichia coli is frequently isolated from the urine samples of pediatric patients with urinary tract infections. A collection of 178 urinary Escherichia coli (UEc) isolates associated with complicated and uncomplicated urinary tract infections were evaluated in this study. The patterns of resistance to 9 antibiotic classes showed that 60.7% of the UEc isolates had a highly multidrug-resistant (MDR) profile. Genetic diversity analyses of the UEc isolates showed a high variability and revealed 16 clusters associated with four phylogenetic groups, namely, groups A, B1, B2, and D. Phylogenetic group B2 was widely associated with the 16 clusters as well as with virulence and fitness genes. The virulence and fitness genes in the UEc isolates, which included fimbriae-, siderophore-, toxin-, and mobility-associated genes, were grouped as occurring at a low, variable, or high frequency. Interestingly, only the papF gene could be amplified from some UEc isolates, and the sequence analysis of the pap operon identified an insertion sequence (IS) element and gene loss. These data suggested pathoadaptability and the development of immune system evasion, which was confirmed by the loss of P fimbriae-associated agglutination in the UEc isolates. E. coli clone O25-ST131 had a prevalence of 20.2% among the UEc isolates; these isolates displayed both a highly MDR profile and the presence of the papGII, fimH, papGIII, iutD, sat, hlyA, and motA genes. In conclusion, the UEc isolates from complicated urinary tract infection (cUTI) were characterized as being MDR, highly genetically diverse, and associated with phylogenetic group B2 and many virulence and fitness genes. Additionally, gene loss and IS elements were identified in some UEc isolates identified as clone O25-ST131.

Asunto(s)

Escherichia coli/aislamiento & purificación , Escherichia coli/fisiología , Infecciones Urinarias/complicaciones , Infecciones Urinarias/microbiología , Antibacterianos/farmacología , Niño , Farmacorresistencia Bacteriana/efectos de los fármacos , Escherichia coli/efectos de los fármacos , Escherichia coli/genética , Femenino , Sitios Genéticos/genética , Variación Genética , Humanos , Mutación INDEL , Masculino , México , Filogenia , Virulencia

RESUMEN

The Great-billed Seed-finch, Sporophila maximiliani, is a threatened neotropical bird that has declined mainly due to illegal trapping, with very few records in the wild in the last two decades. Despite the existence of a considerable captive population that could be used for reintroductions into the wild, many individuals are known to be hybrids either with other species or subspecies of the genus. Forensic investigations are urgently needed to distinguish between birds born in captivity from those from illegal trade. Microsatellites can be useful tools to assess individual admixture levels and to perform parentage tests that may confirm the origin of animals, but only a few loci are available for this group of birds. Here, we provide a set of 14 microsatellite loci isolated from the S. maximiliani, many of which also amplified and were polymorphic in the Pearly-bellied Seedeater, S. pileata, and in the Copper Seedeater, S. bouvreuil. In ten loci selected for the S. maximiliani, the number of alleles per locus varied from four to nine and observed and expected heterozygosities ranged from 0.13 to 1 and 0.56 to 0.83, respectively. These loci proved to be highly informative for forensic analyses, indicating that they may be useful for conservation management plans in these endangered tropical birds.

Asunto(s)

Pinzones/genética , Repeticiones de Microsatélite/genética , Alelos , Animales , Conservación de los Recursos Naturales , Especies en Peligro de Extinción , Sitios Genéticos/genética , Heterocigoto , Passeriformes/genética

RESUMEN

Type 2 diabetes mellitus (T2D) is one of the two leading causes of mortality in Mexico. However, most studies have focused on Caucasians or Asians, and there are a small number of studies investigating Maya populations. Furthermore, to the best of our knowledge, there is no information on isolated Maya communities with T2D frequencies of 20% that are primarily attributed to ethnicity. Consequently, this study focused on assessing which genetic risk variants could be involved in the high rates of T2D in 92 individuals with Maya ancestry; 47 were diagnosed with T2D, and 45 were classified as healthy individuals. A pilot genome-wide association study was performed using the Affymetrix Axiom Genome-wide LAT1 array. The population structure was determined with the ADMIXTURE software using 1289 Latin American selected polymorphisms, and 39 polymorphisms associated with T2D were included for replication. Association tests were performed using the Statistical Analysis System (SAS) using the allelic, genotype and Armitage trend tests. The results indicated that population structure analysis displayed no differences between T2D patients and healthy individuals; 24 loci located were identified for probable association with T2D (p > 1.288 × 10-7 and p < 1.348 × 10-4); the polymorphism AGTR2 rs1914711 in chromosome X was identified by the allele test (OR = 6.824; p = 1.448 × 10-9) as a candidate gene for association with T2D; and ARL15 rs4311394 was associated as a T2D protector by genotype and the Armitage trend test (OR = 0.318; p = 0.001). In conclusion, this study proposes 24 candidate SNPs associated with T2D for replication studies and one for protective association with T2D.

Asunto(s)

Diabetes Mellitus Tipo 2/genética , Sitios Genéticos/genética , Predisposición Genética a la Enfermedad/genética , Alelos , Estudios de Casos y Controles , Etnicidad/genética , Femenino , Estudio de Asociación del Genoma Completo/métodos , Genotipo , Humanos , Masculino , México , Persona de Mediana Edad , Proyectos Piloto , Polimorfismo de Nucleótido Simple/genética , Riesgo , Población Blanca/genética

RESUMEN

Eleven microsatellite loci were developed and characterized for the sablefish, Anoplopoma fimbria. The markers were identified from sequences obtained by next generation sequencing. Thirty samples from Aleutians Islands were genotyped. The amplifications were performed with three different annealing temperature and amplification products were visualized in ABI 3500 Genetic Analyzer. No evidence for scoring errors was detected by stuttering or due large allele dropout and neither of the loci presented a high null allele frequency (> 0.2). The number means of alleles per locus was of 12.21 and mean of observed and expected heterozygosity were of 0.60 and 0.75 respectively. The sablefish represents a resource of high commercial value on the coasts of Japan, Russia, Canada and west coast of the United States and these new primers could be useful to future diversity and structure population studies.

Asunto(s)

Repeticiones de Microsatélite/genética , Perciformes/genética , Alelos , Animales , Cartilla de ADN , Frecuencia de los Genes/genética , Sitios Genéticos/genética , Variación Genética/genética , Heterocigoto , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Reacción en Cadena de la Polimerasa/métodos , Polimorfismo Genético/genética , Análisis de Secuencia de ADN/métodos