Study on the population genetic structure and phylogenetic relationship of the Han population in Dalian / 中国法医学杂志

Objective To study the population genetic structure and phylogenetic relationships by combining Y-STR haplotype genetic information from the Han population in Dalian with 32 domestic and foreign groups.Methods Blood samples of 958 Han male volunteers from Dalian were collected.Genetic typing of 42 genetic loci was completed using Y-STR fluorescent reagent kits and capillary electrophoresis.Related forensic parameters were calculated.Nei's standard genetic distances among 33 populations based on 17 Y-STR loci were computed,in order to create a principal coordinate analysis as well as construct a phylogenetic tree.Results The analysis of genetic polymorphisms at 42 Y-STR loci revealed 30 unconventional alleles at 10 loci.Genetic analysis of the population based on 17 Y-STR loci confirmed that Dalian's Han population had the closest genetic distance to the Anshan's Han population,followed by populations from Henan,Heilongjiang,Jilin,Shandong,and Chongqing.Furthermore,the genetic distances between the Han population in Dalian and the Qiang population in Beichuan or the Miao population in Guizhou were relatively closer than that to the Manchu population living in Liaoning.Conclusion The genetic distance between the Han population in Dalian and other groups is not entirely proportional to ethnicities and geographical proximity.Both population migration and ethnic assimilation or isolation may have influence on it.

Population genetics analysis of Oncomelania hupensis in Jiaxing， Zhejiang Province， 2022 / 上海预防医学

ObjectiveTo genotype Oncomelania hupensis， based on microsatellites， in different snail-bearing environments in Jiaxing City， Zhejiang Province， for population genetics analysis in order to explore the reasons and influencing factors for the existence or proliferation of snails and to provide scientific basis for effective monitoring and control of snails. MethodsA total of 90 snail samples from three populations were collected in Yaobang Village （YB） and Sanxing Village （SX） in Pinghu City， and Yunhe Farm （YH） in Xiuzhou District， all were selected for snail checking in key snail habitats of Jiaxing City in 2022. DNA of the snails was genotyped and analyzed for population genetics using nine microsatellite loci. ResultsA total of 84 alleles were observed， and the mean number of alleles （Na） was 7.889， 5.667， and 3.778 for YB， SX， and YH respectively； the number of effective alleles （NeA） was 4.807， 3.329， and 2.294， respectively； and the coefficients of inbreeding （FIS） were 0.400， 0.377， and 0.493， respectively. Under the Infinite Allele Model （IAM）， the SX and YH might have a recent bottleneck. The NEstimator and LDNe software calculated effective population sizes （Ne） were above 31.9. AMOVA analysis showed that the variation of snails in the three populations mainly existed among individuals， accounting for 41.4% of the total variation. The value of the index of genetic differentiation between populations （FST） was 0.286， indicating a high degree of genetic differentiation. The results of the principal component analysis and phylogenetic tree were consistent， and the three populations were divided into two lineages， YB and SX were one lineage， and YH belonged to another independent lineage. Population history and dynamics analysis showed that the gene flow of the three populations was insufficient， population divergence history indicated that YH might have diverged from SX first， and YB was produced by the contact fusion of SX and YH. ConclusionThe genetic diversity of snail populations in Jiaxing City is generally low， and the snail populations are unstable， with a great degree of genetic differentiation and insufficient gene flow among populations. This study can provide a basis for evaluating the effectiveness of the control of the snail as well as monitoring the trend of the spread of the snail.

Common but not connected: high genetic structure and cryptic genetic diversity in the ubiquitous biting midge Culicoides peregrinus Kieffer

@#The biting midge Culicoides peregrinus Kieffer is a significant pest and vector species, and knowledge of its genetic diversity and genetic structure is critically important for designing an effective control program. However, such information is limited to only small sample-size DNA barcoding studies. Therefore, in this study, we used mitochondrial cytochrome c oxidase I (COI) to examine genetic structure and diversity of C. peregrinus from northeastern Thailand. In addition, we also inferred genetic relationships between C. peregrinus from Thailand and those reported from other countries across the geographic range of the species. Maximum intraspecific genetic divergence (3.83%) within Thai specimens was relatively high compared to other Culicoides species. Genetic structure analysis revealed that 71% (32 from 45) of population comparisons were highly significantly different. A high level of genetic structure among populations, even between those in close geographic proximity (22 km geographic distance) suggested that there has been little or no movement between local populations. This is possibly due to the ability to exploit diverse types of breeding site and a generalist feeding habit which enables C. peregrinus to complete its life cycle within cattle pens. Genetic relationships between Thai C. peregrinus and those reported from other countries revealed three genetically divergent lineages (A, B and C) associated with geographic origins. Specimens from Thailand + China formed lineage A, those from Australia formed lineage B and India + Bangladesh belonged to lineage C. These genetically divergent lineages also agree with morphological variation of the wing pale marking spots. Further investigation using independent genetic loci from nuclear genes will be very useful to resolve taxonomic status of these divergent lineages.

Preliminary study on the mechanism underlying the ecological isolation of Oncomelania hupensis populations in Changde City / 中国血吸虫病防治杂志

Objective To investigate ecological isolation between Oncomelania hupensis snail populations in hilly regions and marshland and lake regions in Yuanjiang valley, Changde City, Hunan Province, and to unravel its underlying mechanisms. Methods Taoyuan County, Shimen County, Linli County and Lixian County in Changde City were selected as snail sampling sites in hilly regions, and Lixian County, Jinshi City, West Lake Administration District, Hanshou County and Dingcheng District were selected as snail sampling sites in marshland and lake areas. Cytochrome C oxidase 1 (cox 1) gene was amplified in snail samples and sequenced. The genetic sequences of O. hupensis snails were aligned using the software MEGA 11, and the haplotypes of O. hupensis snails were determined using the software DNASP 5.10.01. The phylogenetic tree was generated using Bayesian inference with the software MrBayes 3.2, and analysis of molecular variance (AMOVA) was performed to analyze the source of genetic divergence and estimate the genetic divergence index (FST) among snail populations with the software Arlequin 3.5.2.2. The genetic barrier among 11 O. hupensis snail populations was estimated using the Monmonier algorithm of adegenet toolkit in R package. The settings with “land in winter and water in summer” in the Yuanjian River section were divided into two categories according to the upstream and downstream, and the areas with “land in winter and water in summer” in the upstream and downstream were transformed into raster data, and then loaded into the software Fragstats 4 for analysis of landscape indicators. The trends in changes of digital elevation were extracted from the Yuanjiang River section based on the digital elevation model, and made three-dimensional visualization using the R package. Results The mitochondrial cox 1 gene were amplified in 165 O. hupensis snais from 11 sampling sites and sequenced, and a total of 152 valid gene sequences were obtained, with 46 haplotypes or 9 populations determined. No haplotype was shared in snails between Taoyuan County and Dingcheng District and Hanshou County along the downstream of the Yuanjiang River. The total area of settings with “land in winter and water in summer” was 617.66 hm2 in the upsteram of the Yuanjiang River, which consisted of 473 patches, with each patch measuring 1.31 hm2, the largest area index of 0.735 2, the landscape division index of 0.999 9, and the landscape shape index of 45.293 7. The total area of settings with “land in winter and water in summer” was 9 956.92 hm2 in the downstream of the Yuanjiang River, which consisted of 771 patches, with each patch measuring 12.91 hm2, the largest area index of 97.839 9, the landscape division index of 0.042 7, and the landscape shape index of 7.249 6. The area of settings with “land in winter and water in summer” was much larger in the downstream than that in the upstream of the Yuanjiang River, and the stronger landscape connectivity and non-remarkable alteration of riverbed elevation provided suitable habitats for snail breeding. Conclusion The hydrological and environmental characteristics of the upstream of the Yuanjiang River restrain the breeding and spread of O. hupensis, resulting in ecological isolation between Oncomelania hupensis in Taoyuan County and those in the downstream of Yuanjiang River.

Molecular diversity of genes related to biological rhythms (period and timeless) and insecticide resistance (Na V and ace-1) in Anopheles darlingi

BACKGROUND Malaria is a public health concern in the Amazonian Region, where Anopheles darlingi is the main vector of Plasmodium spp. Several studies hypothesised the existence of cryptic species in An. darlingi, considering variations in behaviour, morphological and genetic aspects. Determining their overall genetic background for vector competence, insecticide resistance, and other elements is essential to better guide strategies for malaria control. OBJECTIVES This study aimed to evaluate the molecular diversity in genes related to behaviour and insecticide resistance, estimating genetic differentiation in An. darlingi populations from Amazonian localities in Brazil and Pacific Colombian region. METHODS We amplified, cloned and sequenced fragments of genes related to behaviour: timeless (tim) and period (per), and to insecticide resistance: voltage-gated sodium channel (Na V ) and acetylcholinesterase (ace-1) from 516 An. darlingi DNA samples from Manaus, Unini River, Jaú River and Porto Velho - Brazil, and Chocó - Colombia. We discriminated single nucleotide polymorphisms (SNPs), determined haplotypes and evaluate the phylogenetic relationship among the populations. FINDINGS The genes per, tim and ace-1 were more polymorphic than Na V . The classical kdr and ace-1 R mutations were not observed. Phylogenetic analyses suggested a significant differentiation between An. darlingi populations from Brazil and Colombia, except for the Na V gene. There was a geographic differentiation within Brazilian populations considering per and ace-1. CONCLUSIONS Our results add genetic data to the discussion about polymorphisms at population levels in An. darlingi. The search for insecticide resistance-related mechanisms should be extended to more populations, especially from localities with a vector control failure scenario.

Genetic diversity analysis of forty-three insertion/deletion loci for forensic individual identification in Han Chinese from Beijing based on a novel panel / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Due to the virtues of no stutter peaks, low rates of mutation, and short amplicon sizes, insertion/deletion (InDel) polymorphism is an indispensable tool for analyzing degraded DNA samples from crime scenes for human identifications (Wang et al., 2021). Herein, a self-developed panel of 43 InDel loci constructed previously by our group was utilized to evaluate the genetic diversities and explore the genetic background of the Han Chinese from Beijing (HCB) including 301 random healthy individuals. The lengths of amplicons at 43 InDel loci in this panel ranged from 87 to 199 bp, which indicated that the panel could be used as an effective tool to utilize highly degraded DNA samples for human identity testing. The loci in this panel were validated and performed well for forensic degraded DNA samples (Jin et al., 2021). The combined discrimination power (PD) and combined probability of exclusion (PE) values in this panel indicated that the 43 InDel loci could be used as the candidate markers in personal identification and parentage testing of HCB. In addition, population genetic relationships between the HCB and 26 reference populations from five continents based on 19 overlapped InDel loci were displayed by constructing a phylogenetic tree, principal component analysis (PCA), and population genetic structure analysis. The results illustrated that the HCB had closer genetic relationships with the Han populations from Chinese different regions.

HBV genotyping and population genetics analysis of voluntary blood donors in five regions of China / 中国输血杂志

【Objective】 To investigate the distribution of Hepatitis B virus(HBV)genotypes and the genetic characteristics of genotype B HBV populations among voluntary blood donors in five regions of China. 【Methods】 A total number of 630 plasma samples from blood donors with positive HBV HBsAg neutralization test from 2014 to 2016 in Guangxi Blood Center, Chongqing Blood Center, Urumqi Blood Center, Mianyang Central Blood Station and Luoyang Central Blood Station were collected. The S-region sequence of the HBV genome was amplified by semi-nested PCR and followed with Sanger sequencing in order to investigate the HBV genotype distribution and population genetics. 【Results】 Among the voluntary blood donors in five regions, 55 cases of HBV S gene fragments were successfully amplified. Three genotypes were found in HBV typing, including 46 cases of type B(83.64%), 7 cases of type C(12.73%) and 2 cases of type D(3.63%). There were 15 cases of type B and 3 cases of type C in Guangxi; 10 cases of type B and 1 case of type C in Chongqing; 3 cases of type B, 1 case of type C and 1 case of type D in Luoyang; 15 cases of type B in Mianyang; 3 cases of type B, 2 cases of type C and 1 case of type D in Urumqi. The mismatch distribution of the HBVB type population with the largest population number showed a unimodal distribution, and the results of Tajima′s D test and Fu′s Fs test were both negative, indicating that the HBV population in these five regions was expanding. 【Conclusion】 The prevalent genotype of HBV in voluntary blood donors is type B, and the type B HBV population is experiencing a slow expansion, which should attract our attention. In the future, a thorough molecular epidemiological investigation of HBV should be carried out to ensure blood safety.

Aedes aegypti queenslandensis: first geographic occurrence in Brazil and epidemiological implications

ABSTRACT Aedes aegypti is the mosquito that has been most successful in adapting to the anthropic environment and transmitting several viruses to humans as well. The species has three subspecies that can identified by the variations in the color of the abdominal scales. Each subspecies possesses a distinct scale color pattern. Herein, it is described the first register of Ae. aegypti queenslandensis in São Paulo State, Brazil. Both the scale color pattern, and factor involved in the emergence of the local population are discussed, as well as possible epidemiological implications.

Dinâmica das populações de Triatoma infestans no Chaco Paraguaio: Análise genética populacional da reinfestação domiciliar após controle vetorial / Dynamics of Triatoma infestans populations in the Paraguayan Chaco: Population genetic analysis of household reinfestation following vector control

Background Although domestic infestations by Triatoma infestans have been successfully controlled across Latin America, in areas of the Gran Chaco region, recurrent post-spraying house colonization continues to be a significant challenge, jeopardizing Chagas disease vector control and maintaining active Trypanosoma cruzi transmission. Methodology/Principal findings To investigate the dynamics of triatomine reinfestation in a rural area of the Paraguayan Chaco, genetic characterization (based on 10 microsatellite loci and cytochrome B sequence polymorphisms) was performed on baseline and reinfestant T. infestans (n = 138) from four indigenous communities and adjacent sylvatic sites. House quality and basic economic activities were assessed across the four communities. Significant genetic differentiation was detected among all baseline triatomine populations. Faster reinfestation was observed in the communities with higher infestation rates pre-spraying. Baseline and reinfestant populations from the same communities were not genetically different, but two potentially distinct processes of reinfestation were evident. In Campo Largo, the reinfestant population was likely founded by domestic survivor foci, with reduced genetic diversity relative to the baseline population. However, in 12 de Junio, reinfestant bugs were likely derived from different sources, including survivors from the pre-spraying population and sympatric sylvatic bugs, indicative of gene-flow between these habitats, likely driven by high human mobility and economic activities in adjacent sylvatic areas. Conclusions/Significance Our results demonstrate that sylvatic T. infestans threatens vector control strategies, either as a reinfestation source or by providing a temporary refuge during insecticide spraying. Passive anthropogenic importation of T. infestans and active human interactions with neighboring forested areas also played a role in recolonization. Optimization of spraying, integrated community development and close monitoring of sylvatic areas should be considered when implementing vector control activities in the Gran Chaco.

Population genetic structure of two herds of Aberdeen Angus cattle breed in Colombia / Estructura genética poblacional de dos hatos de ganado bovino Aberdeen Angus en Colombia / Estrutura genética da população de dois rebanhos da raça Aberdeen Angus na Colômbia

Abstract Background: Two biotypes of Aberdeen Angus cattle breed, known as Old Type and New Type, that differ in their origin and beef production are formally recognized. In Colombia, this breed has been commercialized for approximately 80 years. Studies on the origin, kinship and levels of genetic diversity of this breed in Colombian herds are scarce, yet important for planning crossing and management strategies. Objective: To measure the genetic diversity and structure of two Colombian herds of Old Type and New Type biotypes of Aberdeen Angus from Huila and Cundinamarca provinces and assess mitochondrial introgression with other breeds. Methods: A set of ten microsatellites and sequences of the Mitochondrial Control Region were characterized. Estimators of genetic diversity and population differentiation along with tests of population assignment were applied. Results: Nuclear loci were highly polymorphic as shown by the Polymorphic Information Content (0.599) and the Probability of Identity (1.896 10-08). Both populations were highly diverse and clearly differentiated into two groups corresponding to the Old Type and New Type phenotypes. In contrast, mitochondrial data failed to distinguish these two groups and showed extensive admixture. Conclusions: This study optimized a set of ten highly polymorphic nuclear markers that may be used for parentage and population genetic studies of Aberdeen Angus. Genetic differentiation in these loci agreed with phenotypic differences of the Old and New Types. However, mitochondrial data indicated ancestry of multiple European breeds in the origin of Colombian Aberdeen Angus.

Resumen Antecedentes: Dentro de la raza Aberdeen Angus existen dos biotipos conocidos como Old Type y New Type, las cuales difieren en su origen y producción de carne. En Colombia, esta raza se ha venido comercializando desde hace aproximadamente 80 años. No obstante, aún no se han realizado estudios sobre su origen, parentesco y niveles de diversidad genética de esta raza en hatos colombianos, lo cual es importante para planear estrategias de cruce y manejo. Objetivo: Medir la diversidad y estructura genética de dos hatos colombianos de Aberdeen Angus Old Type y New Type de Huila y Cundinamarca y evaluar la introgresión mitocondrial con otras razas. Métodos: Se caracterizó un grupo de diez loci microsatélite y se secuenció la Región Control Mitocondrial. Se aplicaron estimadores de diversidad genética y diferenciación poblacional, junto con pruebas de asignación poblacional. Resultados: Los loci microsatélite fueron altamente polimórficos, tal como lo indicaron el Contenido de Información Polimórfica (0,599) y la Probabilidad de Identidad (1,896 10-08). Las poblaciones evaluadas de Aberdeen Angus en Colombia fueron altamente diversas y se diferenciaron claramente en dos grupos correspondientes a los fenotipos Old Type y New Type. En contraste, los datos mitocondriales no recobraron estos dos grupos y mostraron una amplia mezcla genética. Conclusiones: Este estudio optimizó un grupo de diez marcadores altamente polimórficos que pueden ser usados para estudios de parentesco y genética poblacional de Aberdeen Angus. La diferenciación genética en loci nucleares concordó con las diferencias fenotípicas entre Old y New Types, pero los datos mitocondriales indicaron ancestría de múltiples razas europeas en el origen del Aberdeen Angus colombiano.

Resumo Antecedentes: Dentro da raça Aberdeen Angus há dois biótipos conhecidos como Old Type e New Type, que diferem em sua origem e produção de carne. Na Colômbia, esta raça é comercializada há aproximadamente 80 anos. Entretanto, estudos sobre a origem, o parentesco e os níveis de diversidade genética desta raça em rebanhos colombianos ainda não foram realizados, o que é importante para o planejamento de cruzamentos e estratégias de manejo. Objetivo: Medir a diversidade genética e a estrutura de dois rebanhos colombianos de biótipos de Old Type e New Type de Aberdeen Angus de Huila e Cundinamarca e avaliar a introgressão mitocondrial com outras raças. Métodos: Um grupo de dez loci de microssatélites foi caracterizado e a Região de Controle Mitocondrial foi sequenciada. As estimativas de diversidade genética e diferenciação populacional foram aplicadas, juntamente com testes de designação populacional. Resultados: Os locus microssatélites foram altamente polimórficos, conforme indicado pelo Conteúdo de Infomação Polimórfica (0,599) e Probabilidade de Identidade (1,896 10-08). As populações avaliadas de Aberden Angus na Colômbia eram altamente diversificadas e claramente diferenciadas em dois grupos correspondentes aos fenótipos do Old Type e New Type. Em contraste, os dados mitocondriais não recuperaram esses dois grupos e mostraram um amplo mix genético. Conclusões: Este estudo otimizou um grupo de dez marcadores altamente polimórficos que podem ser usados para estudos genéticos de parentesco e população de Aberdeen Angus. A diferenciação genética nos loci nucleares concordou com as diferenças fenotípicas entre os Old e New Types, mas os dados mitocondriais indicam ancestralidade de várias raças européias na origem do Aberdeen Angus colombiano.

CO1-Based DNA barcoding for assessing diversity of Pteropus giganteus from the state of Azad Jammu Kashmir, Pakistan / Código de barras de DNA à base de CO1 para avaliar a diversidade de Pteropus giganteus do estado de Azad Jammu e Caxemira, Paquistão

Abstract The flying fox (Pteropus giganteus) also familiar with the name of the greater Indian fruit Bat belongs to the order Chiroptera and family Pteropodidae. Current research emphasis on the DNA barcoding of P. giganteus in Azad Jammu Kashmir. Bat sequences were amplified and PCR products were sequenced and examined by bioinformatics software. Congeneric and conspecific, nucleotide composition and K2P nucleotide deviation, haplotype diversity and the number of haplotypes were estimated. The analysis showed that all of the five studied samples of P. giganteus had low G contents (G 19.8%) than C (27.8%), A (25.1%) and T (27.3%) contents. The calculated haplotype diversity was 0.60% and the mean intraspecific K2P distance was 0.001% having a high number of transitional substitutions. The study suggested that P. giganteus (R=0.00) do not deviate from the neutral evolution. It was determined from the conclusion that this mtDNA gene is a better marker for identification of Bat species than nuclear genes due to its distinctive characteristics and may serve as a landmark for the identification of interconnected species at the molecular level and in the determination of population genetics.

Resumo A raposa-voadora (Pteropus giganteus), também conhecida como morcego indiano, pertence à ordem dos Chiroptera e à família Pteropodidae. A presente pesquisa dá ênfase ao código de barras de DNA de P. giganteus em Azad Jammu e Caxemira. Sequências genéticas dos morcegos foram amplificadas, e os produtos de PCR foram sequenciados e examinados por software de bioinformática. De espécies congenérica e coespecífica, foram estimados composição nucleotídica e desvio de nucleotídeos K2P, diversidade de haplótipos e número de haplótipos. A análise mostrou que todas as cinco amostras estudadas de P. giganteus apresentaram baixos teores de G (19,8%) em comparação com C (27,8%), A (25,1%) e T (27,3%). A diversidade de haplótipos calculada foi de 0,60%, e a distância média intraespecífica de K2P foi de 0,001%, com um elevado número de substituições transicionais. O estudo sugeriu que P. giganteus (R = 0,00) não se desviou da evolução neutra. É possível concluir que o gene mtDNA é um marcador favorável para identificação de espécies de morcegos do que genes nucleares por causa de suas características distintivas e pode servir como um marco para a identificação de espécies interconectadas em nível molecular e para a determinação genética de populações.

Ex situ plant germplasm conservation revised at the light of mechanisms and methods of genetics / Conservación de germplasma Ex situ revisada a la luz de mecanismos y métodos de genética

ABSTRACT Plant genetic resources for food and agriculture are ex situ conserved in germplasm banks as samples (accessions) of natural or naturalized populations, either as the originally sampled propagules (mainly seeds) or their multiplications. The premises underlying ex situ conservation are that (a) it is the safest and cheapest alternative for germplasm preservation for future generations and (b) accessions are representative of the genetic diversity encountered in nature. In the past decades, ideas, alternatives and considerations have been put forward on the topic, and protocols have been devised for plant germplasm sampling, conservation and multiplication. However, limitations in the management efficiency of germplasm banks have been pointed out by international organizations. In our opinion, germplasm banks in general need to revise their functioning and management at the light of principles and methods of Genetics. To that end, it is necessary to consider the reproductive biology of higher plants -whose genetic consequences at both the individual plant and the population levels are not always either fully understood or taken into account in devising the protocols-, the genetic structures of wild and cultivated populations, and the course of the genetic material in the populations. In this paper, we discuss the three topics and provide an example of a national forage breeding program, from germplasm bank accessions as the germplasm of origin to the obtainment of commercial cultivars. Finally, we present a proposal as a base for discussion among curators, researchers and breeders.

RESUMEN Los recursos genéticos vegetales para la alimentación y la agricultura se conservan ex situ en bancos de germoplasma como muestras (introducciones) de poblaciones naturales o naturalizadas ya sea como propágulos originales (mayoritariamente semillas) o sus multiplicaciones. Las premisas subyacentes son que (a) es la alternativa más segura y barata de preservación de germoplasma para futuras generaciones y (b) las introducciones son representativas de la diversidad genética que se encuentra en la naturaleza En las últimas décadas, se han presentado ideas, alternativas y consideraciones sobre el tema y se han elaborado protocolos para el muestreo, conservación y multiplicación de germoplasma. Sin embargo, organizaciones internacionales han señalado limitaciones en la eficiencia del manejo de los bancos de germoplasma. En nuestra opinión, se necesita revisar el funcionamiento y manejo de dichos bancos en general a la luz de los principios y métodos de Genética. Para tal fin, es necesario considerar la biología reproductiva de las plantas superiores -cuyas consecuencias genéticas a nivel de planta individual y de población no se comprenden en su totalidad o no se consideran al idear los protocolos -, las estructuras genéticas de poblaciones naturales y cultivadas, y el curso del material genético en las poblaciones. En este trabajo discutimos los tres temas y proveemos un ejemplo de un programa nacional de mejoramiento de forrajeras, desde las introducciones como germoplasma de origen hasta la obtención de cultivares comerciales. Finalmente, presentamos una propuesta como base de discusión entre curadores, investigadores y mejoradores.

The most important fishery resource in the Amazon, the migratory catfish Brachyplatystoma vaillantii (Siluriformes: Pimelodidae), is composed by an unique and genetically diverse population in the Solimões-Amazonas River System

The migratory catfish Brachyplatystoma vaillantii is one of the most important fishery resources in the Amazon. Intense capture occurs associated to its life cycle. In order to know the genetic status, we sequenced the mitochondrial DNA control region from 150 individuals of B. vaillantii, collected in five fishing landing locations, covering the length of the Solimões-Amazonas River in Brazil. Genetic diversity parameters suggest there is no genetic differentiation between the five localities. Population's expansion indicated by R 2 and Fu's Fs tests was also confirmed by the high number of unique haplotypes found. The Analyses of molecular variance indicated that nearly all variability was contained within locations (99.86%), and estimates of gene flow among B. vaillantii were high (F ST = 0.0014). These results suggest that Brachyplatystoma vaillantii forms a panmitic population along the Solimões-Amazonas River and, has greater genetic variability than other species of the Brachyplatystoma genus available so far. Although the influence of different tributaries on B. vaillantii migration patterns remains uncertain, a single population in the main channel should be consider in future policies for management of this resource. However, since the species' life cycle uses habitats in several countries, its management and conservation depend greatly of internationally joined efforts.(AU)

O bagre migrador, Brachyplatystoma vaillantii, é um dos mais importantes recursos pesqueiros da Amazônia. Intensa captura ocorre associada ao seu ciclo de vida. Para conhecer seu status genético, sequenciamos a região de controle do DNA mitocondrial de 150 indivíduos, coletados em cinco locais de desembarque pesqueiro, abrangendo toda a extensão do rio Solimões-Amazonas no Brasil. Os parâmetros de diversidade genética sugerem que não existe diferenciação genética entre as cinco localidades amostradas. A expansão populacional indicada pelos testes R 2 e Fs de Fu, também foi confirmada pelo elevado número de haplótipos únicos encontrados. A análise de variância molecular indicou que quase toda a variabilidade estava contida nas localidades (99,86%), e as estimativas de fluxo gênico desta espécie eram altas (F ST = 0,0014). Esses resultados sugerem que Brachyplatystoma vaillantii forma uma população panmítica ao longo do rio Solimões-Amazonas com maior variabilidade genética que outras espécies do gênero Brachyplatystoma disponíveis no momento. Embora a influência dos diferentes afluentes na migração de B. vaillantii permaneça incerta, em futuras políticas de gestão deste recurso deve-se considerá-lo como uma única população no canal principal. Entretanto, uma vez que seu ciclo de vida abrange habitats em vários países, seu manejo e conservação dependem muito de esforços internacionais em conjunto.(AU)

Variability and genetic structure in fragments of Eugenia involucrata De Candolle established through microsatellite markers / Variabilidade e estruturação genética em fragmentos de Eugenia involucrata de Candolle utilizando marcadores microssatélites

ABSCTRACT: Eugenia involucrata DC. is a forest species with high environmental and economic potential. The objective of this study was to quantify the genetic variability and analyzed the genetic structure of three natural fragments located in the central region of the Rio Grande do Sul state, Brazil. We used four microsatellite loci developed for the congener species Eugenia uniflora and using GenAlEx 6.5 software, parameters of genetic variability and its partition among and within fragments were estimated for each locus. We observed high levels of genetic variability (3.67 alleles per locus; HO = 0.815; HE = 0.625; FIS = −0.294), most of which (93%) were distributed within the fragments, suggesting that these individuals came from a single original population. Gene flow between fragments was high (2.35 to 4.56 migrants per generation), resulting in low genetic differentiation indexes (FST values ranging from 0.052 to 0.096). The fragments showed high genetic variability, distributed within the remnants themselves, and low genetic differentiation. Our results have repercussions for planning locally adapted germplasm collections for forest restoration programs, thereby avoiding the implantation of populations with an exogamous depression.

RESUMO: Eugenia involucrata DC. é uma espécie florestal com elevado potencial ambiental e econômico. O presente trabalho teve por objetivo quantificar a variabilidade e analisar a estruturação genética em três fragmentos naturais localizados na região central do estado do Rio Grande do Sul, Brasil. Com o emprego de quatro locos microssatélites desenvolvidos para a espécie congênere Eugenia uniflora e usando-se o software GenAlEx 6.5, foram estimados parâmetros de variabilidade genética, para cada loco, e sua partição entre e dentro dos fragmentos. Foram observados altos índices de variabilidade genética (3,67 alelos por loco; HO = 0,815; HE = 0,625; FIS = -0,294), com a maior proporção (93%) distribuída dentro dos fragmentos, sugerindo que os indivíduos estudados são provenientes de uma única população original. O fluxo gênico foi elevado entre os fragmentos, variando de 2,35 a 4,56 migrantes por geração, resultando em baixo índice de diferenciação genética (FST), entre 0,052 a 0,096. Os fragmentos estudados apresentam elevada variabilidade genética, a maior parte distribuída dentro dos próprios remanescentes, e baixa diferenciação genética. Os resultados observados têm repercussões no planejamento de coleta de germoplasma com adaptação local para programas de restauração florestal, assim evitando a implantação de populações com depressão exogâmica.

Genetic diversity of Euterpe edulis martius based on fruit traits / Diversidade genética de Euterpe edulis martius com base em características de frutos

Juçara (Euterpe edulis Martius) is a palm species from the Atlantic Forest whose fruits are important as a source of food to several individuals from the fauna of the region. Despite its ecological importance, juçara is found in the list of endangered species, due to the fragmentation of the forests and the illegal extraction of the heart of palm. We aimed to evaluate the inter- and intra-populational genetic diversity of E. edulis based on fruit and seed traits in forest fragments of the Espírito Santo State in Brazil. The aim was to generate information to be used in E. edulis breeding programs, or in the delineation of more efficient management and reforestation strategies. The study was carried out in 20 forest fragments and 198 fruit plants were sampled. Positive genetic association was observed between the evaluated traits, with the longitudinal diameter of the fruit (LDF) and the seed mass (SM) greatly affecting fruit mass (FM). The existence of inter- and intra-populational genetic divergence was proved. The genetic divergence found in E. edulis suggests that there is genetic material that can be explored in breeding programs and this information may also contribute to management strategies that can increase the species genetic diversity

Juçara (Euterpe edulis Martius) é uma espécie de palmeira da Mata Atlântica, que é importante como fonte de alimento para vários indivíduos da fauna. Apesar de sua importância ecológica, juçara é encontrada na lista de espécies ameaçadas à extinção, devido à fragmentação florestal e à extração ilegal do palmito. Nós tivemos como objetivo avaliar a diversidade genética inter e intra populacional de E. edulis com base em caracteres de frutos e sementes, em fragmentos florestais do Estado do Espírito Santo no Brasil, com o objetivo de gerar informações a serem utilizadas nos programas de melhoramento de E. edulis ou na delimitação de estratégias de manejo e reflorestamento mais eficientes. O estudo foi realizado em 20 fragmentos florestais e 198 plantas frutíferas foram amostradas. Foi observada uma grande associação genética positiva entre os caracteres avaliados, com as características diâmetro longitudinal dos frutos (LDF) e massa de sementes (SM) apresentando efeitos maiores do que a massa característica da fruta (FM). A existência de divergência genética inter e intrapopulacional foi comprovada. A divergência genética encontrada neste trabalho para E. edulis sugere a presença de material genético que vale a pena ser explorado em programas de melhoramento e essa informação também pode contribuir com estratégias de manejo para aumentar a diversidade genética das espécies.

Polimorfismo +405G> C del gen del factor de crecimiento de endotelio vascular en población cubana / Vascular Endothelial Growth Factor gene +405G> C polymorphism in the Cuban population

Introducción: El factor de crecimiento endotelial vascular (VEGF) es una proteína involucrada en la proliferación y migración celular del endotelio vascular, en cuyo gen se ha reportado el polimorfismo +405G>C. Se reconoce que no existen reportes genéticos poblacionales de esta variante en Cuba, que permitan caracterizar los perfiles inmunogenéticos a nivel molecular, para su aplicación en estudios de asociación alélica. Objetivo: Describir las frecuencias génicas y genotípicas del polimorfismo VEGF (+405 G>C) en la población cubana. Material y Métodos: Se realizó un estudio observacional, descriptivo, transversal, entre octubre de 2017 y marzo de 2018 en 162 neonatos cubanos, de ambos sexos y sanos, para el pesquisaje neonatal de enfermedades metabólicas, cuyas muestras biológicas se conservaban en el banco de ADN del Centro Nacional de Genética Médica. La caracterización molecular de los genotipos fue realizada mediante un PCR-ARMS. Se utilizó el software GENEPOP 4.4 y el paquete estadístico STATISTICA 8.0 para los cálculos de las frecuencias génicas y genotípicas. Resultados: La población no se ajustó al modelo de equilibrio de Hardy Weinberg para el gen evaluado. Las frecuencias génicas estimadas para el polimorfismo VEGF (+405 G>C) fueron de 0,33 para el alelo G y de 0,67 para el alelo C. El cálculo de las frecuencias genotípicas resultó en 0,14, 0,37 y 0,49, para las variantes GG, GC y CC, respectivamente. Conclusiones: Las frecuencias alélicas VEGF.C fueron superiores a la del alelo VEGF.G, siendo el genotipo VEGF.GG el de menor representación en el conjunto estudiado(AU)

Introduction: The vascular endothelial growth factor (VEGF) is a protein involved in the proliferation and cell migration of the vascular endothelium. In its gene, +405G>C Polymorphism has been reported. There are no population genetic reports of this variant in Cuba that allow the characterization of immunogenetic profiles at a molecular level for its application to allelic association studies. Objectives: To describe the genic and genotypic frequencies of the VEGF (+405 G>C) polymorphism in the Cuban population. Material and Methods: A descriptive cross-sectional observational study was carried out from October 2017 to March 2018 in 162 Cuban healthy newborns of both sexes for the neonatal screening for metabolic diseases, whose biological samples were conserved in the DNA bank of the National Center for Medical Genetics. The molecular characterization of the genotypes was carried out using a PCR-ARMS. The GENEPOP 4.4 software and the statistical software package STATISTICA 8.0 were used for the analysis of genic and genotypic frequencies. Results: The population did not adjust to the Hardy-Weinberg equilibrium model for the gene evaluated. The estimated gene frequencies of VEGF +405 G> C polymorphism were 0.33 for the G allele and 0.67 for the C allele. The calculation of the genotypic frequencies resulted in 0.14, 0.37 and 0.49, for the variants GG, GC and CC, respectively. Conclusions: The allelic frequencies of VEGF.C were higher than the frequencies of the VEGF.G allele, being the VEGF GG the least represented genotype in the group studied(AU)

Population genetics of invasive Pomacea spp. in Hangzhou City, Zhejiang Province / 中国血吸虫病防治杂志

Objective To investigate the distribution and identify the genetic genetics of invasive Pomacea species in Xihu District, Hangzhou City, so as to understand the spread tendency of Pomacea species. Methods The specimens of Pomacea species were collected from five sites in water systems (lakes, rivers and wetlands) and its costal lands in Xihu District, Hangzhou City in 2017 for morphological identification. Total DNA was isolated from the foot tissues of adult snails for amplification of the COI gene, and haplotype diversity and nucleic acid diversity analyses were performed. In addition, a phylogenetic tree was created based on the haplotype captured from GenBank and those from this study to investigate the phylogenetic relationships. Results Pomacea specimens, which were preliminarily characterized as Pomacea, were found in ponds, rivers and wetlands in Xihu District of Hangzhou City. A total of 16 sequences were captured from the DNA samples of Pomacea specimens, which belonged to 3 haplotypes, including Hap1, Hap2 and Hap3. A high frequency was seen in Hap1 and Hap3, and a low frequency was found in Hap2. The Pomacea specimens collected from the 5 sites in Xihu Districts included P. canaliculata and P. maculate. The Pomacea specimens with a Hap1 had a close genetic relationship with the P. canaliculata from Argentina, Guangdong Province and Hong Kong Special Administrative Region of China, and the Pomacea specimens with a Hap2 had a close genetic relationship with the P. canaliculata from Argentina, Japan and Guangzhou City of Guangdong Province, China, while the Pomacea specimens with a Hap2 had a close genetic relationship with the P. maculate from Argentina and Brazil. Conclusions P. canaliculata and P. maculata are present in Xihu District of Hangzhou City. P. maculata may spread to Xihu District through multiple introductions or water flow.

Molecular genetics of medicinal plants, past achievement, and new era / 中国中药杂志

Unraveling the genetic basis of medicinal plant metabolism and developmental traits is a long-standing goal for pharmacologists and plant biologists. This paper discusses the definition of molecular genetics of medicinal plants, which is an integrative discipline with medicinal plants as the research object. This discipline focuses on the heredity and variation of medicinal plants, and elucidates the relationship between the key traits of medicinal plants(active compounds, yield, resistance, etc.) and genotype, studies the structure and function, heredity and variation of medicinal plant genes mainly at molecular level, so as to reveal the molecular mechanisms of transmission, expression and regulation of genetic information of medicinal plants. Specifically, we emphasize on three major aspects of this discipline.(1)Individual and population genetics of medicinal plants, this part mainly highlights the genetic mechanism of the domestication, the individual genomics at the species level, and the formation of genetic diversity of medicinal plants.(2)Elucidation of biosynthetic pathways of active compounds and their evolutionary significance. This part summarizes the biosynthesis, diversity and molecular evolution of active compounds in medicinal plants.(3) Molecular mechanisms that shaping the key agronomic traits by internal and external factors. This part focuses on the accumulation and distribution of active compounds within plants and the regulation of metabolic network by environmental factors. Finally, we prospect the future direction of molecular genetics of medicinal plants based on the rapid development of multi-omics technology, as well as the application of molecular genetics in the future strategies to achieve conservation and breeding of medicinal plants and efficient biosynthesis of active compounds.

SELAdb: A database of exonic variants in a Brazilian population referred to a quaternary medical center in São Paulo

OBJECTIVES: High-throughput sequencing of genomes, exomes, and disease-focused gene panels is becoming increasingly common for molecular diagnostics. However, identifying a single clinically relevant pathogenic variant among thousands of genetic polymorphisms is a challenging task. Publicly available genomic databases are useful resources to filter out common genetic variants present in the population and enable the identification of each disease-causing variant. Based on our experience applying these technologies at Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, Brazil, we recognized that the Brazilian population is not adequately represented in widely available genomic databases. METHODS: Here, we took advantage of our 5-year experience as a high-throughput sequencing core facility focused on individuals with putative genetic disorders to build a genomic database that may serve as a more accurate reference for our patient population: SELAdb. RESULTS/CONCLUSIONS: Currently, our database comprises a final cohort of 523 unrelated individuals, including patients or family members managed by different clinics of HCFMUSP. We compared SELAdb with other publicly available genomic databases and demonstrated that this population is very heterogeneous, largely resembling Latin American individuals of mixed origin, rather than individuals of pure European ancestry. Interestingly, exclusively through SELAdb, we identified a spectrum of known and potentially novel pathogenic variants in genes associated with highly penetrant Mendelian disorders, illustrating that pathogenic variants circulating in the Brazilian population that is treated in our clinics are underrepresented in other population databases. SELAdb is freely available for public consultation at: http://intranet.fm.usp.br/sela

A review on the conservation genetic studies of Indian amphibians and their implications on developing strategies for conservation

Amphibians show a very high level of diversity and endemism and are facing global declines from the past few decades. Studies have shown that the molecular tools can be helpful in their conservation efforts. In India, more than 80% of amphibians are endemic and most show a narrow range of distribution. Most of the Indian amphibians lack information on their genetic diversity. In this study, were view the overall trend on amphibian studies in India with the specific focus on conservation genetics. Overall, of the 173 studies, only 14 dealt with the conservation of amphibians through genetic tools and five studies estimated the genetic diversity or gene structure. Here, we discuss the gaps and provide future directions on how genetic studies can be helpful in Indian amphibian conservation.