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1.
Fa Yi Xue Za Zhi ; 35(3): 308-313, 2019 Jun.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-31282626

RESUMO

Abstract: Objective To explore the genetic polymorphism of Y chromosome D-M174 haplogroup and sub-haplogroups in East Asia. Methods The samples of 1 426 unrelated male individuals from East Asia were collected, and then 7 Y chromosome haplogroup D-M174 and the Y-SNP of its sub-haplogroups were detected with mini-sequencing. The 22 Y-STR genotypes were detected with DNA Typer™ Y26 kit. The haplogroup was analyzed using direct counting method, heatmap, phylogenetic cluster and network graph cluster, and then distribution of genetic polymorphism and the clustering relation between populations and samples of Y chromosome D haplogroup were discussed. Results Haplogroup D-M174 were distributed mostly among Tibetans (40.96%)and Japanese (35.71%), while less or none were distributed among the surrounding areas of Tibet and other areas. Conclusion The geographical distribution of Y chromosome D-M174 haplogroup in East Asian populations has significant characteristics.


Assuntos
Cromossomos Humanos Y , Genética Populacional , Extremo Oriente , Haplótipos , Humanos , Masculino , Filogenia , Polimorfismo Genético
2.
Fa Yi Xue Za Zhi ; 35(3): 314-318, 2019 Jun.
Artigo em Inglês, Chinês | MEDLINE | ID: mdl-31282627

RESUMO

Abstract: Objective To explore the distribution of genetic structure of Y-SNP and Y-STR genetic markers in different ethnic groups and its application in forensic science. Methods SNaPshot minisequencing was used to detect the polymorphisms of 12 Y-SNP loci in 439 males from 6 ethnic groups, including Guangxi Han, Guangxi Jing, Guangxi Miao, Guangxi Yao, Guangxi Zhuang and Guangxi Dong. DNATyperTM Y26 kit was used to multiplex-amplify 26 Y-STR loci. The PCR products were analyzed by 3130xl genetic analyzer. The network analysis of Y-STR haplotype under the same Y-SNP haplogroup was analyzed by Network 5.0 software. Results Six haplogroups defined by 12 Y-SNP loci were detected in 6 ethnic groups, and 362 haplotypes were detected in 26 Y-STR loci. The haplotype diversity was 0.996 6. In the C haplogroup, the samples from Guangxi Yao, Guangxi Zhuang and Guangxi Dong were clustered on different branches; in the O1 haplogroup, those from Guangxi Zhuang, Guangxi Miao and Guangxi Jing were relatively independent and clustered separately; in the O2 haplogroup, some samples from Guangxi Miao and Guangxi Yao were gathered in a cluster. Conclusion Based on the Y-STR network analysis of samples with identical haplogroup of Y-SNP, some ethnic groups can be preliminarily distinguished, which could be used to infer male suspects' ethnic group through detecting their genetic markers left in the crime scene.


Assuntos
Cromossomos Humanos Y , Grupos Étnicos , China , Genética Populacional , Haplótipos , Humanos , Masculino , Repetições de Microssatélites
3.
Nat Commun ; 10(1): 2405, 2019 06 03.
Artigo em Inglês | MEDLINE | ID: mdl-31160560

RESUMO

Culture (behaviour based on socially transmitted information) is present in diverse animal species, yet how it interacts with genetic evolution remains largely unexplored. Here, we review the evidence for gene-culture coevolution in animals, especially birds, cetaceans and primates. We describe how culture can relax or intensify selection under different circumstances, create new selection pressures by changing ecology or behaviour, and favour adaptations, including in other species. Finally, we illustrate how, through culturally mediated migration and assortative mating, culture can shape population genetic structure and diversity. This evidence suggests strongly that animal culture plays an important evolutionary role, and we encourage explicit analyses of gene-culture coevolution in nature.


Assuntos
Migração Animal , Evolução Cultural , Evolução Molecular , Comportamento Sexual Animal , Animais , Comportamento Animal , Aves , Cetáceos , Ecologia , Variação Genética , Genética Populacional , Primatas
4.
Vet Microbiol ; 233: 61-67, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31176414

RESUMO

The incidence of infections with extended spectrum ß-lactamase producing Escherichia coli (ESBL-E) is increasing both in humans and animals. There is a paucity of data about the rate of faecal carriage of ESBL-E in pets. In this study, faecal swabs collected from 586 pets (225 cats; 361 dogs) in Auckland, New Zealand, were analysed for the presence of ESBL-E by culture, and a questionnaire was delivered to the owners. The ESBL-E were characterised and data elicited by the questionnaires were used for a multivariable analysis, to investigate the factors associated with faecal ESBL-E carriage. The prevalence of ESBL-E in faecal swabs was 6.4%. The ß-lactamase genes detected in the ESBL-E were the blaCTX-M-14 (n = 2) and blaCMY-2 (n = 34). Several isolates displayed multilocus sequence types (ST) associated with human and animal infections. Multiple isolates sharing the same ST displayed different antibiograms and ß-lactamase genes, reflecting horizontal gene transfer between and within ST. Variables independently associated with increased odds of ESBL-E carriage were: animal received systemic antimicrobial treatment in the six months before the sampling; presence of household members working in veterinary clinics; presence of household members travelling overseas in the six months before the sampling. We conclude that pets are colonised by ESBL-E which are genotypically similar to the bacteria found to infect humans and animals. The statistical analysis suggested a number of eco-epidemiological factors associated with ESBL-E carriage. In particular, they suggest veterinary clinics may represent hot-spots of antimicrobial resistance.


Assuntos
Portador Sadio/veterinária , Farmacorresistência Bacteriana Múltipla/genética , Infecções por Escherichia coli/veterinária , Escherichia coli/genética , Animais de Estimação/microbiologia , beta-Lactamases/genética , Animais , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Portador Sadio/epidemiologia , Gatos/microbiologia , Cães/microbiologia , Escherichia coli/enzimologia , Infecções por Escherichia coli/epidemiologia , Fezes/microbiologia , Feminino , Transferência Genética Horizontal , Genética Populacional , Genótipo , Hospitais Veterinários , Humanos , Masculino , Tipagem de Sequências Multilocus , Nova Zelândia/epidemiologia , Prevalência , beta-Lactamases/biossíntese
5.
Hum Genet ; 138(7): 739-748, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31154530

RESUMO

Metabolic syndrome is a complex human disorder characterized by a cluster of conditions (increased blood pressure, hyperglycemia, excessive body fat around the waist, and abnormal cholesterol or triglyceride levels). Any of these conditions increases the risk of serious disorders such as diabetes or cardiovascular disease. Currently, the degree of genetic regulation of this syndrome is under debate and partially unknown. The principal aim of this study was to estimate the genetic component and the common environmental effects in different populations using full pedigree and genomic information. We used three large populations (Gubbio, ARIC, and Ogliastra cohorts) to estimate the heritability of metabolic syndrome. Due to both pedigree and genotyped data, different approaches were applied to summarize relatedness conditions. Linear mixed models (LLM) using average information restricted maximum likelihood (AIREML) algorithm were applied to partition the variances and estimate heritability (h2) and common sib-household effect (c2). Globally, results obtained from pedigree information showed a significant heritability (h2: 0.286 and 0.271 in Gubbio and Ogliastra, respectively), whereas a lower, but still significant heritability was found using SNPs data ([Formula: see text]: 0.167 and 0.254 in ARIC and Ogliastra). The remaining heritability between h2 and [Formula: see text] ranged between 0.031 and 0.237. Finally, the common environmental c2 in Gubbio and Ogliastra were also significant accounting for about 11% of the phenotypic variance. Availability of different kinds of populations and data helped us to better understand what happened when heritability of metabolic syndrome is estimated and account for different possible confounding. Furthermore, the opportunity of comparing different results provided more precise and less biased estimation of heritability.


Assuntos
Predisposição Genética para Doença , Genética Populacional/métodos , Genoma Humano , Estudo de Associação Genômica Ampla , Genômica/métodos , Síndrome Metabólica/genética , Polimorfismo de Nucleotídeo Único , Estudos de Coortes , Feminino , Genótipo , Humanos , Masculino , Modelos Genéticos , Linhagem
6.
Hum Genet ; 138(7): 757-769, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31168775

RESUMO

An ethnicity is characterized by genomic fragments, single nucleotide polymorphisms (SNPs), and structural variations specific to it. However, the widely used 'standard human reference genome' GRCh37/38 is based on Caucasians. Therefore, de novo-assembled reference genomes for specific ethnicities would have advantages for genetics and precision medicine applications, especially with the long-read sequencing techniques that facilitate genome assembly. In this study, we assessed the de novo-assembled Chinese Han reference genome HX1 vis-à-vis the standard GRCh38 for improving the quality of assembly and for ethnicity-specific applications. Surprisingly, all genomic sequencing datasets mapped better to GRCh38 than to HX1, even for the datasets of the Chinese Han population. This gap was mainly due to the massive structural misassembly of the HX1 reference genome rather than the SNPs between the ethnicities, and this misassembly could not be corrected by short-read whole-genome sequencing (WGS). For example, HX1 and the other de novo-assembled personal genomes failed to assemble the mitochondrial genome as a contig. We mapped 97.1% of dbSNP, 98.8% of ClinVar, and 97.2% of COSMIC variants to HX1. HX1-absent, non-synonymous ClinVar SNPs were involved in 140 genes and many important functions in various diseases, most of which were due to the assembly failure of essential exons. In contrast, the HX1-specific regions were scantly expressible, as shown in the cell lines and clinical samples of Chinese patients. Our results demonstrated that the de novo-assembled individual genome such as HX1 did not have advantages against the standard GRCh38 genome due to insufficient assembly quality, and that it is, therefore, not recommended for common use.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Grupos Étnicos/genética , Genoma Humano , Genômica/normas , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Padrões de Referência , Análise de Sequência de DNA/normas , Algoritmos , Mapeamento de Sequências Contíguas , Genética Populacional , Humanos , Polimorfismo de Nucleotídeo Único , Transcriptoma
7.
Forensic Sci Int ; 301: 174-181, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31167154

RESUMO

Allele frequency data for 22 short tandem repeat loci; D18S1364, D1S1656, D13S325, D5S2800, D9S1122, D4S2366, D3S1744, D12S391, D11S2368, D21S2055, D20S482, D8S1132, D7S3048, D2S441, D19S253, D10S1248, D17S1301, D22-GATA198B05, D16S539, D6S474, D14S1434 and D15S659 from the SureID® 23comp Human DNA Identification Kit have been determined for unrelated individuals in European, South Asian and African populations. Deviations from Hardy-Weinberg equilibrium were observed in loci D1S1656 and D19S253 in European; D18S1364, D6S474 and D14S1434 in South Asian; and D9S1122 and D8S1132 in African populations (p-value <0.05). However, after Bonferroni correction no significant deviations were observed (p-value <0.002). The most discriminating loci were D1S1656 and D12S391 for European (PD=0.977), D21S2055 for South Asian (PD=0.980), and D21S2055 and D7S3048 for African (PD=0.972) populations. The match probabilities were 1 in 6.7×1025 for European, 1 in 1.4×1026 for South Asian and 1 in 1.6×1026 for African populations. These findings established the high discriminatory capacity and robustness of the tested STR loci for forensic identification and kinship testing.


Assuntos
Grupos de Populações Continentais/genética , Impressões Digitais de DNA/instrumentação , Genética Populacional , Repetições de Microssatélites , Frequência do Gene , Humanos , Reação em Cadeia da Polimerase
8.
Biol Bull ; 236(3): 199-206, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31167090

RESUMO

The barnacle Balanus glandula is a broadly distributed species in the temperate northeastern Pacific that is notable for a robust genetic cline between about 36° and 40° N latitude. Prior work established the evolutionary origins of this pattern and proposed that it is maintained by environmental selection. In recent years, "climate velocity" studies in marine habitats have shown dramatic distributional shifts for many species as they track their preferred temperature range in a warming ocean. We re-sampled B. glandula across its entire geographic range to determine whether there has been any shift in this genetic distribution, a development signaling that temperature or other climate factors are maintaining this genetic cline. Additionally, we asked whether the spatially distributed mitochondrial lineages also vary in reproductive output with latitude, using location as a proxy for temperature and other coastal environmental factors. Here we show that although the distribution of the genetic cline has not appreciably changed, there is a notable association of decreased reproductive output at lower latitudes of the distribution in the "northern" lineage of B. glandula.


Assuntos
Distribuição Animal/fisiologia , Thoracica/genética , Animais , Mudança Climática , DNA Mitocondrial/genética , Ecossistema , Complexo IV da Cadeia de Transporte de Elétrons/genética , Genética Populacional , Oceano Pacífico , Reprodução/fisiologia , Temperatura Ambiente , Thoracica/fisiologia
9.
Anim Genet ; 50(4): 391-394, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31179556

RESUMO

In this study, we conducted genomic prediction for two Yorkshire purebred populations (Yichun and Chifeng) from two different provinces of China that both had a limited population size. Two growth traits (age adjusted to 100 kg weight, AGE; back-fat thickness adjusted to 100 kg weight, BF) and one reproduction trait (total number of piglets born, TNB) were analyzed with four prediction strategies: one-population BLUP, joint two-population BLUP, one-population single-step BLUP (SSBLUP) and joint two-population SSBLUP. Our results illustrate that accuracies of genomic estimated breeding values were improved for BF and TNB for the Yichun population and for BF for the Chifeng population by genomic prediction (one-population SSBLUP and joint two-population SSBLUP). The accuracy of TNB for the Yichun population was increased two fold when comparing the one-population SSBLUP to the one-population BLUP prediction. Meanwhile, prediction biases were dramatically reduced for AGE for the Yichun population and for TNB for the Chifeng population. The conclusions of this study are as follows: first, genomic prediction is useful for improving prediction accuracy for purebred pig breeding farms with a limited population size; second, joint genomic prediction for different populations of the same breed with certain genetic links has the trend to further improve prediction accuracy.


Assuntos
Sus scrofa/genética , Animais , China , Genética Populacional , Genoma , Modelos Biológicos , Análise de Regressão , Sus scrofa/classificação
10.
Croat Med J ; 60(3): 191-200, 2019 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-31187946

RESUMO

AIM: To determine allele frequencies and forensic statistics of 22 autosomal short tandem repeat loci in Chinese Mongolian population. METHODS: Blood specimens were collected from 134 unrelated healthy Mongolian individuals, and 22 short tandem repeat loci were co-amplified and genotyped. Allele frequencies and forensic parameters were calculated, and population genetic differences were analyzed among Mongolian population and other eight Chinese populations: Northern Han, Guangdong Han, Chengdu Han, Xinjiang Hui, Xinjiang Uygur, Hainan Li, Qinghai Tibetan, and Hainan Han. RESULTS: All the loci were in the Hardy-Weinberg equilibrium, and after Bonferroni correction there was no linkage disequilibrium between them. The allele frequencies of these 22 loci were between 0.0037 and 0.3657. This panel had high discriminating power and genetic polymorphism in the Mongolian population, with combined power of discrimination of 0.999999999999999999999999998399 and combined probability of exclusion of 0.9999999999566925. Structure analysis showed no evidence that these nine Chinese populations had different component distribution. However, genetic distance analysis showed significant differences among them (P<0.05). CONCLUSION: The combined application of these 22 loci could be useful for forensic purposes in the Mongolian population. Mongolian population had smaller genetic distances from the populations in northern China (Northern Han, Xinjiang Uygur, and Xinjiang Hui) than from the populations in Hainan province (Hainan Han and Hainan Li populations).


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Grupos Étnicos/genética , Repetições de Microssatélites , Polimorfismo Genético , China , Feminino , Genética Forense , Frequência do Gene , Loci Gênicos , Testes Genéticos , Genética Populacional , Genótipo , Humanos , Masculino
11.
Anim Genet ; 50(4): 334-346, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31199540

RESUMO

Overlapping runs of homozygosity (ROH islands) shared by the majority of a population are hypothesized to be the result of selection around a target locus. In this study we investigated the impact of selection for coat color within the Noriker horse on autozygosity and ROH patterns. We analyzed overlapping homozygous regions (ROH islands) for gene content in fragments shared by more than 50% of horses. Long-term assortative mating of chestnut horses and the small effective population size of leopard spotted and tobiano horses resulted in higher mean genome-wide ROH coverage (SROH ) within the range of 237.4-284.2 Mb, whereas for bay, black and roan horses, where rotation mating is commonly applied, lower autozygosity (SROH from 176.4-180.0 Mb) was determined. We identified seven common ROH islands considering all Noriker horses from our dataset. Specific islands were documented for chestnut, leopard spotted, roan and bay horses. The ROH islands contained, among others, genes associated with body size (ZFAT, LASP1 and LCORL/NCAPG), coat color (MC1R in chestnut and the factor PATN1 in leopard spotted horses) and morphogenesis (HOXB cluster in all color strains except leopard spotted horses). This study demonstrates that within a closed population sharing the same founders and ancestors, selection on a single phenotypic trait, in this case coat color, can result in genetic fragmentation affecting levels of autozygosity and distribution of ROH islands and enclosed gene content.


Assuntos
Tamanho Corporal , Cor de Cabelo , Cavalos/genética , Animais , Genética Populacional , Técnicas de Genotipagem , Homozigoto , Cavalos/classificação , Polimorfismo de Nucleotídeo Único
12.
Genet Sel Evol ; 51(1): 17, 2019 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-31035934

RESUMO

Catla catla (Hamilton) fertilised spawn was collected from the Halda, Jamuna and Padma rivers in Bangladesh from which approximately 900 individuals were retained as 'candidate founders' of a breeding population. These fish were fin-clipped and genotyped using the DArTseq platform to obtain, 3048 single nucleotide polymorphisms (SNPs) and 4726 silicoDArT markers. Using SNP data, individuals that shared no putative parents were identified using the program COLONY, i.e. 140, 47 and 23 from the Halda, Jamuna and Padma rivers, respectively. Allele frequencies from these individuals were considered as representative of those of the river populations, and genomic relationship matrices were generated. Then, half-sibling and full-sibling relationships between individuals were assigned manually based on the genomic relationship matrices. Many putative half-sibling and full-sibling relationships were found between individuals from the Halda and Jamuna rivers, which suggests that catla sampled from rivers as spawn are not necessarily representative of river populations. This has implications for the interpretation of past population genetics studies, the sampling strategies to be adopted in future studies and the management of broodstock sourced as river spawn in commercial hatcheries. Using data from individuals that shared no putative parents, overall multi-locus pairwise estimates of Wright's fixation index (FST) were low (≤ 0.013) and the optimum number of clusters using unsupervised K-means clustering was equal to 1, which indicates little genetic divergence among the SNPs included in our study within and among river populations.


Assuntos
Carpas/genética , Genética Populacional/métodos , Alelos , Criação de Animais Domésticos , Animais , Ásia Sudeste , Cruzamento/métodos , Cyprinidae/genética , Frequência do Gene/genética , Genômica , Genótipo , Polimorfismo de Nucleotídeo Único/genética , Rios , Irmãos
13.
BMC Plant Biol ; 19(1): 187, 2019 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-31064322

RESUMO

BACKGROUND: It is important to explore renewable alternatives (e.g. biofuels) that can produce energy sources to help reduce reliance on fossil oils, and reduce greenhouse gases and waste solids resulted from fossil oils consumption. Camelina sativa is an oilseed crop which has received increasing attention due to its short life cycle, broader adaptation regions, high oil content, high level of omega-3 unsaturated fatty acids, and low-input requirements in agriculture practices. To expand its Camelina production areas into arid regions, there is a need to breed for new drought-tolerant cultivars. Leaf cuticular wax is known to facilitate plant development and growth under water-limited conditions. Dissecting the genetic loci underlying leaf cuticular waxes is important to breed for cultivars with improved drought tolerance. RESULTS: Here we combined phenotypic data and single nucleotide polymorphism (SNP) data from a spring C. sativa diversity panel using genotyping-by-sequencing (GBS) technology, to perform a large-scale genome-wide association study (GWAS) on leaf wax compositions. A total of 42 SNP markers were significantly associated with 15 leaf wax traits including major wax components such as total primary alcohols, total alkanes, and total wax esters as well as their constituents. The vast majority of significant SNPs were associated with long-chain carbon monomers (carbon chain length longer than C28), indicating the important effects of long-chain carbon monomers on leaf total wax biosynthesis. These SNP markers are located on genes directly or indirectly related to wax biosynthesis such as maintaining endoplasmic reticulum (ER) morphology and enabling normal wax secretion from ER to plasma membrane or Golgi network-mediated transport. CONCLUSIONS: These loci could potentially serve as candidates for the genetic control involved in intracellular wax transport that might directly or indirectly facilitate leaf wax accumulation in C. sativa and can be used in future marker-assisted selection (MAS) to breed for the cultivars with high wax content to improve drought tolerance.


Assuntos
Brassicaceae/genética , Folhas de Planta/química , Polimorfismo de Nucleotídeo Único , Ceras/química , Ceras/metabolismo , Álcoois/metabolismo , Aldeídos/metabolismo , Algoritmos , Alcanos/metabolismo , Transporte Biológico/genética , Genética Populacional , Estudo de Associação Genômica Ampla , Desequilíbrio de Ligação , Fenótipo , Folhas de Planta/genética
14.
An Acad Bras Cienc ; 91(2): e20180179, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31038531

RESUMO

Expanding populations may loss genetic diversity because sequential founder events throughout a wave of demographic expansion may cause "allele surfing", as the alleles of founder individuals may propagate rapidly through space. The spatial components of allele surfing have been studied by geneticists, but have never been investigate on dynamic and shifting habitats. Here we used an individual-based-model (IBM) to study how interactions between different habitat restoration scenarios and biological characteristics (dispersal capacity) affect the spatial patterns of the genetic structure of a population during demographic expansion. We found that both habitat dynamics and dispersal capacity, as well as their interaction, were the drivers of emergent pattern of genetic diversity and allele surfing. Specifically, allele surfing is more common when a species with low dispersal capacity colonizes a large geographic area with slow restoration (low carrying capacity). Despite this, we showed that allele surfing can be reduced, or even avoided, by dispersal management through suitable habitat restoration. Thus, investigating how colonization generates a spatial variation in genetic diversity, and which parameters control the emergent genetic pattern, are essential steps to planning assisted gene flow, which is fundamental for an effective planning of habitat restoration.


Assuntos
Alelos , Evolução Biológica , Ecossistema , Genética Populacional/métodos , Dinâmica Populacional , Humanos , Análise Espaço-Temporal , Especificidade da Espécie
15.
Forensic Sci Int Genet ; 41: 159-167, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31136932

RESUMO

At present, several mature ancestry informative SNP (AISNP) panels are used to distinguish between continental regions of the world, but a more accurate division within the continent requires a secondary panel to complete. However, many AISNPs for the subgroup ancestry inference are selected from the Kidd Lab panel of 55 AISNPs or other published papers. These panels inevitably lack valuable markers for subgroup ancestry inference. Therefore, instead of choosing from the published panels, we used the 1000 Genomes Project to screen potentially informational markers in Asian populations, including single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (InDels). The allele frequencies of all autosomal SNPs and InDels of the 1000 Genomes Project were compared between 10 populations in Asia to identify markers with the largest pairwise allele frequency differences. Finally, we established a second-tier panel of 18 AIMs in this study, which not only divided the 26 populations of the 1000 Genomes Project into six clusters, but also divided the Asia subgroup into four clusters: Gujarati, East Asia, Southeast Asia and South Asia.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Marcadores Genéticos , Genética Populacional , Ásia , Frequência do Gene , Genótipo , Humanos , Mutação INDEL , Reação em Cadeia da Polimerase , Polimorfismo de Nucleotídeo Único
16.
BMC Genomics ; 20(1): 334, 2019 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-31053061

RESUMO

BACKGROUND: Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns. RESULTS: We sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male-biased gene flow. CONCLUSIONS: Our results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by widespread breeding practices associated with male-biased gene flow.


Assuntos
Cruzamento , Bovinos/genética , Variação Genética , Genética Populacional , Genoma , Genômica/métodos , Animais , Bovinos/classificação , Cromossomos de Mamíferos , DNA Mitocondrial/genética , Europa (Continente) , Feminino , Fluxo Gênico , Genótipo , Haplótipos , Masculino , Repetições de Microssatélites , Filogenia , Cromossomo Y
17.
MBio ; 10(2)2019 04 30.
Artigo em Inglês | MEDLINE | ID: mdl-31040246

RESUMO

The global spread of Plasmodium falciparum chloroquine resistance transporter (PfCRT) variant haplotypes earlier caused the widespread loss of chloroquine (CQ) efficacy. In Asia, novel PfCRT mutations that emerged on the Dd2 allelic background have recently been implicated in high-level resistance to piperaquine, and N326S and I356T have been associated with genetic backgrounds in which resistance emerged to artemisinin derivatives. By analyzing large-scale genome sequencing data, we report that the predominant Asian CQ-resistant Dd2 haplotype is undetectable in Africa. Instead, the GB4 and previously unexplored Cam783 haplotypes predominate, along with wild-type, drug-sensitive PfCRT that has reemerged as the major haplotype. To interrogate how these alleles impact drug susceptibility, we generated pfcrt-modified isogenic parasite lines spanning the mutational interval between GB4 and Dd2, which includes Cam783 and involves amino acid substitutions at residues 326 and 356. Relative to Dd2, the GB4 and Cam783 alleles were observed to mediate lower degrees of resistance to CQ and the first-line drug amodiaquine, while resulting in higher growth rates. These findings suggest that differences in growth rates, a surrogate of parasite fitness, influence selection in the context of African infections that are frequently characterized by high transmission rates, mixed infections, increased immunity, and less recourse to treatment. We also observe that the Asian Dd2 allele affords partial protection against piperaquine yet does not directly impact artemisinin efficacy. Our results can help inform the regional recommendations of antimalarials, whose activity is influenced by and, in certain cases, enhanced against select PfCRT variant haplotypes.IMPORTANCE Our study defines the allelic distribution of pfcrt, an important mediator of multidrug resistance in Plasmodium falciparum, in Africa and Asia. We leveraged whole-genome sequence analysis and gene editing to demonstrate how current drug combinations can select different allelic variants of this gene and shape region-specific parasite population structures. We document the ability of PfCRT mutations to modulate parasite susceptibility to current antimalarials in dissimilar, pfcrt allele-specific ways. This study underscores the importance of actively monitoring pfcrt genotypes to identify emerging patterns of multidrug resistance and help guide region-specific treatment options.


Assuntos
Resistência a Múltiplos Medicamentos , Aptidão Genética , Genótipo , Malária Falciparum/parasitologia , Proteínas de Membrana Transportadoras/genética , Plasmodium falciparum/crescimento & desenvolvimento , Proteínas de Protozoários/genética , África/epidemiologia , Ásia/epidemiologia , Frequência do Gene , Genética Populacional , Malária Falciparum/epidemiologia , Proteínas Mutantes/genética , Plasmodium falciparum/classificação , Plasmodium falciparum/genética , Plasmodium falciparum/isolamento & purificação
18.
Forensic Sci Int Genet ; 41: 128-136, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31079022

RESUMO

In addition to commonly used short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), insertion and deletion polymorphisms (InDels) have considerable potential in the field of forensic genetics because they combine desirable characteristics of both STRs and SNPs. In the present study, the SifaInDel 45plex system was designed to amplify 45 InDel markers, including 27 autosomal InDels (A-InDels), 16 X chromosome InDels (X-InDels) and two Y chromosome InDels (Y-InDels), simultaneously in a single PCR procedure and then detect products by capillary electrophoresis (CE). We also optimized the PCR conditions for the novel panel and performed several validation studies including repeatability/reproducibility, concordance, accuracy, sensitivity, stability, species specificity and population genetics. The results confirmed that full profiles could be obtained from ≥62.5 pg of input DNA and from a series of challenging samples encountered in routine casework. The SifaInDel 45plex panel could tolerate different concentrations of inhibitors, such as ≤50 µM hematin, ≤20 ng/µL nigrosine and ≤8000 ng/µL urea. In a population investigation, for the 27 A-InDels, the combined power of discrimination (CPD) exceeded 0.999999, and the combined power of exclusion in duos (CPED) and trios (CPET) was 0.955118 and 0.997754, respectively. For the 16 X-InDels, the combined PDMale and PDFemale was computed as 0.999845 and 0.999998, respectively, and the combined mean exclusion chance in father/daughter or mother/son duos (MECDuo) and mean exclusion chance in standard trios involving daughters (MECTrio) was 0.976220 and 0.998163, respectively. In addition, the two Y-InDels could play a role in correctly determining gender. Overall, the established SifaInDel 45plex panel is a well-performing, reliable and robust multiplex system that stands out for combining a considerable number of A-indels, X-indels and Y-indels based on a CE platform. The population study results also demonstrated that the SifaInDel 45plex panel could be a valid complementary approach for human identification and complex kinship analysis.


Assuntos
Cromossomos Humanos X , Cromossomos Humanos Y , Genética Forense , Marcadores Genéticos , Mutação INDEL , Polimorfismo Genético , Animais , Eletroforese Capilar , Feminino , Frequência do Gene , Genética Populacional , Genótipo , Humanos , Masculino , Reação em Cadeia da Polimerase , Especificidade da Espécie
19.
Forensic Sci Int Genet ; 41: e8-e13, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31085140

RESUMO

The analysis of X-chromosome STRs is useful in certain kinship cases for which autosomal markers provide insufficient statistical power. Particularly, powerful results are achieved in paternity cases with a daughter, when the alleged father is not accessible for analysis, contrarily to his unquestioned mother or daughter. However, representative haplotype frequencies for this type of markers are not available for some populations, as is the case of Argentina, which prevents the quantification of the proof in routine forensic analyses. In this work we present haplotype frequencies for the 12 X-chromosome STRs included in the Investigator Argus X-12 kit, as well as segregation data, obtained from the analysis of the genetic profiles of 457 father-daughter duos, which gave us information on 914 (unrelated) haplotypes from residents of all Argentinian provinces.


Assuntos
Cromossomos Humanos X , Genética Populacional , Haplótipos , Repetições de Microssatélites , Argentina , Impressões Digitais de DNA , Feminino , Frequência do Gene , Humanos , Desequilíbrio de Ligação , Masculino
20.
Forensic Sci Int Genet ; 41: 145-151, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31103798

RESUMO

In forensics, ancestry inference can provide leads for criminal investigation. Therefore, the time needed to generate results is the first priority. Single nucleotide polymorphisms (SNPs) are widely used genetic markers for ancestry inference. In this study, a rapid microfluidic-based SNP genotyping (MSG) chip was established to detect 72 autosomal SNPs for ancestry inference of East Asian populations. The DNA template was infused into the chip and distributed into reaction chambers with pre-spotted primer pairs under centrifugation. After sealing the inlets/outlets and the connections among adjacent reaction chambers, the chip was placed onto a plate thermocycler for competitive allele-specific PCR. The SNP genotyping results were generated by analyzing the extracted fluorescence signal of each reaction chamber after PCR was completed. The detection process took less time (2.5 h) and was simpler than other SNP genotyping methods, such as SNaPshot and MassArray. To assess the performance of the chip, its accuracy, specificity, and sensitivity were evaluated. A total of 50 samples were genotyped using the chip, and the consistency of all of the typing and sequencing results was 100%. For ancestry inference of unknown individuals, a reference database of 3628 individuals from 57 populations was employed, and the ancestry origin of 110 test samples was inferred, demonstrating that the differentiation of East Asian subpopulations can be achieved through the MSG chip method. Overall, the MSG chip method established in this study can effectively be used for rapid and accurate ancestry inference.


Assuntos
Grupo com Ancestrais do Continente Asiático/genética , Genótipo , Dispositivos Lab-On-A-Chip , Polimorfismo de Nucleotídeo Único , China , Genética Populacional , Humanos , Reação em Cadeia da Polimerase , Sensibilidade e Especificidade
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