Genome-wide association analysis of agronomic traits related to eggplant fruits: a review / 生物工程学报

Eggplant is an important horticultural crop and one of the most widely grown vegetables in the Solanaceae family. Eggplant fruit-related agronomic traits are complex quantitative traits with low efficiency and long cycle time for traditional breeding selection. With the rapid development of high-throughput sequencing technology and bioinformatics tools, genome-wide association study (GWAS) has shown great application potential in analyzing the genetic rules of complex agronomic traits related to eggplant fruits. This paper first reviews the progress of genome-wide association analysis in eggplant fruit shape, fruit color and other fruit-related agronomic traits. Subsequently, aiming at the problem of missing heritability, which is common in the genetic studies of eggplant quantitative traits, this paper puts forward the development strategies of eggplant GWAS in the future based on the hot spots of application of four GWAS strategies in the research of agronomics traits related to eggplant fruits. Lastly, the application of GWAS strategy in the field of eggplant molecular breeding is expected to provide a theoretical basis and reference for the future use of GWAS to analyze the genetic basis of various eggplant fruit-related traits and to select fruit materials that meet consumer needs.

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.

Exploration of transcriptome SSR markers and its application in genetic diversity assessment of Asarum sieboldii / 中国中药杂志

To explore the genetic diversity of Asarum sieboldii this study developed SSR markers based on transcriptome sequencing results and five populations of A.sieboldii from different regions were used as samples for genetic diversity assessment using software such as GenALEx 6.5, NTSYS 2.1, and Structure 2.3.4. The results showed that 16 SSR markers with high polymorphism and good repeatability were selected from the A.sieboldii transcriptome. Primers designed based on the flanking sequences of these markers successfully amplified 56 polymorphic fragments from 150 individual samples of the five A.sieboldii populations. On average, each primer amplified 3.5 polymorphic fragments, ranging from 2 to 8. The mean values of expected heterozygosity(H_e), Shannon's diversity index(I), Nei's gene diversity index(H), and the polymorphic information content(PIC) were 0.172, 0.281, 0.429, and 0.382, respectively. The mean population differentiation coefficient(F_(ST)) was 0.588, consistent with the analysis of molecular variance(AMOVA) results, which indicated greater genetic variation among A.sieboldii populations(69%) than that within populations(31%). The percentage of polymorphic loci(PPL) ranged from highest to lowest as SNJ>LN>SY>SZ>TB. Principal coordinate analysis(PCoA) and UPGMA clustering analysis further revealed genetic clustering of A.sieboldii individuals based on their geographical distribution, consistent with the results of the structure clustering analysis. In summary, the SSR markers developed from the transcriptome effectively assessed the genetic differentiation and population structure of natural A.sieboldii populations, revealing a relatively low genetic diversity in A.sieboldii, with genetic variation primarily observed at the population level and a correlation between population differentiation and geographic distance.

Variability of PDYN and OPRK1 genes in four argentinian populations and its genetic association with clinical variables related to acute postsurgical pain / Variabilidad de los genes PDYN y OPRK1 en cuatro poblaciones argentinas y su asociación con variables clínicas relacionadas al dolor agudo post-quirúrgico

ABSTRACT Several population studies showed an association between variation in pain sensitivity and genetic polymorphisms located in Prodynorphin (PDYN) and Kappa Opioid Receptor (OPRK1) human genes. We analysed polymorphisms of these two genes to characterise their variation in Argentinian populations, as well as to evaluate their association with acute pain sensitivity. We studied 11 genetic markers in individuals from four locations in Argentina (Ciudad Autónoma de Buenos Aires, La Plata, Resistencia, and Misión Nueva Pompeya), calculated the population parameters, and evaluated the possible association among pain sensitivity, clinical, and genetic variables through a Generalised Estimating Equation model. High linkage disequilibrium was observed in the four populations for both genes, and significant differences were found among frequencies of Argentinian populations and those from other continents reported in the 1000 Genomes Project. Four PDYN gene polymorphisms from 3´ untranslated region and exon 4 showed association with acute pain sensitivity. One genotype of each of these polymorphisms was associated with a higher pain sensitivity, probably related with the activation of the N-methyl-D-aspartate (NMDA) receptors. We found a strong association with acute pain for the following clinical variables: 1) time after surgery, 2) intravenous klosidol supplied every 8 h, and 3) type of incision. Our results highlight the importance of a regional study of genetic variants which influence pain sensitivity and analgesic response.

RESUMEN La asociación entre la sensibilidad al dolor y los polimorfismos que presentan los genes humanos de prodinorfina (PDYN) y receptor opioide kappa (OPRK1) se ha evidenciado en distintos estudios poblacionales. Con el objetivo de caracterizar la variación de estos genes y evaluar su asociación con dolor agudo en la población argentina, analizamos 11 polimorfismos en individuos provenientes de cuatro localidades argentinas (Ciudad Autónoma de Buenos Aires, La Plata, Resistencia, y Misión Nueva Pompeya). Calculamos los parámetros poblacionales y evaluamos la posible asociación entre sensibilidad al dolor, variables clínicas y variables genéticas a través de un modelo de ecuación generalizada de estimación. Se observó alto desequilibrio de ligamiento para ambos genes en las cuatro poblaciones analizadas, y se encontraron diferencias significativas entre las frecuencias de poblaciones argentinas y las reportadas en el Proyecto 1000 Genomes para poblaciones de otros continentes. Cuatro polimorfismos de la región 3´UTR y el exón 4 de PDYN mostraron asociación con la sensibilidad al dolor agudo. En cada uno de estos polimorfismos, un genotipo resultó asociado con alta sensibilidad al dolor, probablemente en relación con la activación de receptores N-metil-D-aspartato (NMDA). Encontramos una fuerte asociación con dolor agudo para las siguientes variables clínicas: 1) tiempo post-cirugía, 2) administración intravenosa de klosidol cada 8 h, y 3) tipo de incisión. Nuestros resultados resaltan la importancia de realizar estudios regionales de variables genéticas que influyen en la sensibilidad al dolor y la respuesta analgésica.

Analysis of the genetic diversity of Dragon fruit based on ISSR markers in Colombia / Análise da diversidade genética da fruta do dragão com base em marcadores ISSR na Colômbia

Selenicereus megalanthus H. is a tropical fruit belonging to the family Cactaceae, is rich in essential nutrients, antioxidants and bioactive components. It presents wide variability in different characteristics and a great demand in the market; however, genetic studies in Colombia are scarce. The main of this study was to characterize the genetic diversity of 76 yellow pitahaya genotypes with eight ISSR markers. Genetic parameters expected average heterozygosity (He), percentage of polymorphic loci, genetic distances and Fst were estimated with TFPGA. The analysis of the population genetic structure was carried out with the STRUCTURE 2.3.4. As a result, 225 alleles were generated and the number of polymorphic loci ranged 85 (CT, AG) to 90 (GT). High genetic diversity was found, with an average value of heterozygosity was 0.34 with a genetic differentiation coefficient (Fst) of 0.26, indicating that there was a great genetic diversity, similar values than those reported in other studies of pitahaya genetic diversity in Colombia. The 76 genotypes were grouped into K=3 according to geographic location, however, in some groups a mixture of individuals from different origins was observed. The analysis of molecular variance (AMOVA) showed higher variation (75%) within groups than among groups (25%). These results provide information that can be used to develop conservation strategies for dragon fruit and breeding programs to obtain more productive pitahaya genotypes with superior quality, high yield and with resistance to biotic and abiotic factors.

Selenicereus megalanthus H. é uma fruta tropical pertencente à família Cactaceae, rica em nutrientes essenciais, antioxidantes e componentes bioativos. Apresenta grande variabilidade em diferentes características e uma grande demanda no mercado; no entanto, os estudos genéticos na Colômbia são escassos. O principal deste estudo foi caracterizar a diversidade genética de 76 genótipos de pitahaya amarela com oito marcadores ISSR. Parâmetros genéticos esperados de heterozigosidade média (He), porcentagem de locos polimórficos, distâncias genéticas e Fst foram estimados com TFPGA. A análise da estrutura genética da população foi realizada com a ESTRUTURA 2.3.4. Como resultado, 225 alelos foram gerados e o número de loci polimórficos variou de 85 (CT, AG) a 90 (GT). Foi encontrada alta diversidade genética, com um valor médio de heterozigosidade de 0,34 com coeficiente de diferenciação genética (Fst) de 0,26, indicando que havia uma grande diversidade genética, valores semelhantes aos relatados em outros estudos de diversidade genética de pitahaya na Colômbia. Os 76 genótipos foram agrupados em K = 3 de acordo com a localização geográfica, porém, em alguns grupos foi observada uma mistura de indivíduos de diferentes origens. A análise de variância molecular (AMOVA) mostrou maior variação (75%) dentro dos grupos do que entre os grupos (25%). Esses resultados fornecem informações que podem ser utilizadas para desenvolver estratégias de conservação da fruta do dragão e programas de melhoramento para a obtenção de genótipos de pitahaya mais produtivos, com qualidade superior, alto rendimento e com resistência a fatores bióticos e abióticos.

Analysis of the genetic diversity of Dragon fruit based on ISSR markers in Colombia

Abstract Selenicereus megalanthus H. is a tropical fruit belonging to the family Cactaceae, is rich in essential nutrients, antioxidants and bioactive components. It presents wide variability in different characteristics and a great demand in the market; however, genetic studies in Colombia are scarce. The main of this study was to characterize the genetic diversity of 76 yellow pitahaya genotypes with eight ISSR markers. Genetic parameters expected average heterozygosity (He), percentage of polymorphic loci, genetic distances and Fst were estimated with TFPGA. The analysis of the population genetic structure was carried out with the STRUCTURE 2.3.4. As a result, 225 alleles were generated and the number of polymorphic loci ranged 85 (CT, AG) to 90 (GT). High genetic diversity was found, with an average value of heterozygosity was 0.34 with a genetic differentiation coefficient (Fst) of 0.26, indicating that there was a great genetic diversity, similar values than those reported in other studies of pitahaya genetic diversity in Colombia. The 76 genotypes were grouped into K=3 according to geographic location, however, in some groups a mixture of individuals from different origins was observed. The analysis of molecular variance (AMOVA) showed higher variation (75%) within groups than among groups (25%). These results provide information that can be used to develop conservation strategies for dragon fruit and breeding programs to obtain more productive pitahaya genotypes with superior quality, high yield and with resistance to biotic and abiotic factors.

Resumo Selenicereus megalanthus H. é uma fruta tropical pertencente à família Cactaceae, rica em nutrientes essenciais, antioxidantes e componentes bioativos. Apresenta grande variabilidade em diferentes características e uma grande demanda no mercado; no entanto, os estudos genéticos na Colômbia são escassos. O principal deste estudo foi caracterizar a diversidade genética de 76 genótipos de pitahaya amarela com oito marcadores ISSR. Parâmetros genéticos esperados de heterozigosidade média (He), porcentagem de locos polimórficos, distâncias genéticas e Fst foram estimados com TFPGA. A análise da estrutura genética da população foi realizada com a ESTRUTURA 2.3.4. Como resultado, 225 alelos foram gerados e o número de loci polimórficos variou de 85 (CT, AG) a 90 (GT). Foi encontrada alta diversidade genética, com um valor médio de heterozigosidade de 0,34 com coeficiente de diferenciação genética (Fst) de 0,26, indicando que havia uma grande diversidade genética, valores semelhantes aos relatados em outros estudos de diversidade genética de pitahaya na Colômbia. Os 76 genótipos foram agrupados em K = 3 de acordo com a localização geográfica, porém, em alguns grupos foi observada uma mistura de indivíduos de diferentes origens. A análise de variância molecular (AMOVA) mostrou maior variação (75%) dentro dos grupos do que entre os grupos (25%). Esses resultados fornecem informações que podem ser utilizadas para desenvolver estratégias de conservação da fruta do dragão e programas de melhoramento para a obtenção de genótipos de pitahaya mais produtivos, com qualidade superior, alto rendimento e com resistência a fatores bióticos e abióticos.

Phylogeography of the white-crowned parrot (Pionus senilis) / Filogeografia do maitaca-de-testa-branca (Pionus senilis)

Abstract The white-crowned parrot Pionus senilis (von Spix, 1824) is distributed throughout Middle America, inhabiting the Gulf of Mexico coastal area from Tamaulipas (Mexico) to northern Panama. We used mitochondrial data (COI, ND2 and ND4) from 55 specimens to infer phylogenetic relationships, and analyzed the phylogeographic structure, genetic diversity, divergence periods, and historical demography to explore phylogeographic patterns. We found three divergent lineages: two geographically separated by the Isthmus of Tehuantepec, and the third, in Costa Rica by the Nicaragua Depression. The analysis of molecular variance and statistical analyses were consistent with genetically distinct populations. The Central American lineage diverged 1.33 million years ago, whereas the other two lines branched off 1.19 million years ago. This phylogenetic pattern has been reported in other species of Middle American birds.

Resumo A curica-de-testa-branca Pionus senilis (von Spix, 1824) está distribuída por toda a América Central, habitando a área costeira do Golfo do México de Tamaulipas (México) ao norte do Panamá. Usamos dados mitocondriais (COI, ND2 e ND4) de 55 espécimes para inferir relações filogenéticas e analisamos a estrutura filogeográfica, diversidade genética, períodos de divergência e demografia histórica para explorar padrões filogeográficos. Encontramos três linhagens divergentes: duas geograficamente separadas pelo Istmo de Tehuantepec, e a terceira, na Costa Rica pela Depressão da Nicarágua. A análise de variância molecular e as análises estatísticas foram consistentes com populações geneticamente distintas. A linhagem da América Central divergiu há 1.33 milhão de anos, enquanto as outras duas linhas se ramificaram há 1.19 milhão de anos. Este padrão filogenético foi relatado em outras espécies de aves da América Central.

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.

Genetic Diversity Analysis of Erigeron breviscapus Based on SSR Markers / 中国实验方剂学杂志

Objective:To explore the genetic diversity and population structure of <italic>Erigeron breviscapus</italic>， so as to provide a scientific basis for its resource protection and rational utilization. Method:Twelve pairs of simple sequence repeat（SSR） primers were screened out from 243 individuals in 16 natural populations to calculate the genetic diversity parameters of <italic>E. breviscapus</italic>， which were then subjected to principal coordinate analysis and cluster analysis. Result:Twelve SSR markers generated 209 alleles， with an average of 17.417 alleles per locus. Based on 12 SSR markers and 16 populations of <italic>E. breviscapus</italic>， the observed heterozygosity （<italic>H</italic>₀） values were determined to be 0.603 and 0.613， the expected heterozygosity （<italic>H</italic>_e）to be 0.658 and 0.659， and the Shannon's information index （<italic>I</italic>） to be 1.443 and 1.446， respectively. The Wright's fixation index （<italic>F</italic>_st） was 0.123 and gene flow （<italic>N</italic>_m） was 2.077. Analysis of molecular variance （AMOVA） and genetic differentiation revealed that genetic variation within populations was the main source of total variation. The Nei's genetic distance and genetic identity coefficients were within the ranges of 0.107 （YA and XY）-0.713 （SZ and XZD） and 0.490 （SZ and XZD）-0.899 （YA and XY）， respectively. As demonstrated by the principal coordinate analysis and cluster analysis， the 16 populations of <italic>breviscapus </italic>were divided into two clusters. Conclusion:The genetic diversity of <italic>E. breviscapus</italic> was relatively high and there existed certain genetic differentiation and gene flow within and among populations. The genetic variation was mainly present within populations. All these have provided reference for subsequent study on good germplasm selection of <italic>E. breviscapus.</italic>

Population genetics of three threatened catfish species in heterogeneous environments of the Cauca River, Colombia

Neotropical catfishes Ageneiosus pardalis, Pimelodus grosskopfii and Sorubim cuspicaudus are migratory fishes of commercial importance that exhibit decreasing populations due to overfishing and other anthropic interventions. This study used species-specific microsatellite loci to test the hypothesis that threatened fish populations show genetic vulnerability signs and are genetically structured in the middle and lower sections of the Cauca River. The studied species exhibit genetic diversity levels higher than the average values reported for Neotropical Siluriformes; however, they seem to have suffered recent bottlenecks and they present significant endogamy levels that are higher for the critically endangered catfish P. grosskopfii. Furthermore, both Ageneiosus pardalis and S. cuspicaudus are each formed by one genetic group, while Pimelodus grosskopfii comprises two coexisting genetic groups. The information obtained in this study is useful for the decision making in management plans that are appropriate for the sustainability of these three species populations within the proposal for the expansion of the hydroelectric development and other anthropic activities.(AU)

Los bagres Neotropicales Ageneiosus pardalis, Pimelodus grosskopfii y Sorubim cuspicaudus, son peces migratorios de importancia comercial cuyas poblaciones han disminuido debido a la sobrepesca y otras intervenciones antrópicas. En este trabajo, se utilizaron loci microsatélites especie-específicos para contrastar la hipótesis de que las poblaciones de peces amenazadas muestran señales de vulnerabilidad genética y están genéticamente estructuradas en los sectores medio y bajo del río Cauca. Las especies estudiadas exhiben niveles de diversidad genética superiores a los promedios reportados para Siluriformes Neotropicales; sin embargo, parecen haber sufrido cuellos de botella recientes y presentan niveles significativos de endogamia que son más altos para el bagre en peligro crítico, P. grosskopfii. Además, Ageneiosus pardalis y S. cuspicaudus están conformados cada uno por un solo grupo genético, mientras que Pimelodus grosskopfii comprende dos grupos genéticos que coexisten. La información obtenida en este estudio es útil para la toma de decisiones en planes de manejo que sean adecuados para la sostenibilidad de las poblaciones de estas tres especies de bagre dentro de las propuestas para la expansión de desarrollo hidroeléctrico y otras actividades antrópicas.(AU)

Analysis of the population structure and genetic diversity of the red swamp crayfish (Procambarus clarkii) in China using SSR markers

BACKGROUND: Procambarus clarkii produces high-quality, delicious meat that is high in protein, low in fat, and rich in calcium and phosphorus. It has become an important aquatic resource in China. Our objectives are (i) to analyze the level of genetic diversity of P. clarkii populations; (ii) to explore the genetic differentiation (Gst); and (iii) to propose appropriate strategies for the conservation. RESULTS: In this study, Shannon's index (I) and Nei's gene diversity index (H) for P. clarkii were high (I = 0.3462 and H = 0.2325 on average and I = 0.6264, H = 0.4377 at the species level) based on the SSR markers. The expected heterozygosity value of 17 microsatellite loci in 25 crayfish populations was 0.9317, the observed heterozygosity value was 0.9121, and the observed number of alleles per locus was 2.000; and the effective number of alleles per locus was 1.8075. Among the P. clarkii populations, the inbreeding coefficient within populations (Fis) was 0.2315, overall inbreeding coefficient (Fit) was 0.4438, genetic differentiation coefficient among populations (Fst) was 0.3145 and gene differentiation (Gst) was 0.4785 based on SSR analyses. The cluster analysis results obtained by unweighted pair-group method with arithmetic mean (UPGMA) analysis, principal coordinate analysis (PCoA) and STRUCTURE analysis were similar. A mantel test showed that the isolation-by-distance pattern was not significant. CONCLUSIONS: The high Gst among P. clarkii populations is attributed to genetic drift and geographic isolation. The results indicated that more P. clarkii populations should be collected when formulating conservation and aquaculture strategies.

Population genetics of the fish Brycon henni (Characiformes: Bryconidae) using species-specific polymorphic microsatellite loci

Introduction: The freshwater fish Brycon henni (Characiformes: Bryconidae) is endemic to Colombia and currently considered as a "least concern" species according to the International Union for Conservation of Nature (IUCN). Objective: To develop microsatellite markers to examine population genetics in B. henni. Methods: Using a low-coverage sequencing genomic library, this study developed the first set of microsatellite loci to study the population genetics of this Neotropical species. These loci were used to evaluate the genetic diversity and structure of B. henni from three sites of the Magdalena-Cauca Basin (Colombia). Results: A set of 21 polymorphic microsatellite loci was highly informative and revealed that B. henni exhibits genetic diversity (5.143-5.619 alleles/locus, observed and expected heterozygosity = 0.461-0.645 and 0.604-0.662, respectively) and is evenly genetically structured between two tributaries of the Cauca River separated by only 30 km (F'ST = 0.093, Jost's DEST = 0.311, P < 0.001) a finding that indicates these may be reproductively isolated groups. Conclusions: We reported a set of 21 polymorphic microsatellite loci that allowed the detection of genetic structure at local and regional scales. This population genetic structure, concordant with that found in eight congeners, is relevant when determining the risk categorization of B. henni, as well as management, conservation, and restocking programs for this species.

Introducción: El pez de agua dulce Brycon henni (Characiformes: Bryconidae) es una especie endémica de Colombia que actualmente está catalogada como de "menor preocupación" por la Unión Internacional para la Conservación de la Naturaleza (UICN). Objetivo: Desarrollar marcadores microsatélites para estudiar la genética poblacional de Brycon henni. Métodos: Usando una biblioteca genómica de secuenciación de baja cobertura, este estudio desarrolló el primer grupo de loci microsatélites para el estudio de la genética poblacional de esta especie neotropical. Estos loci fueron usados para evaluar la diversidad genética y estructura de B. henni en tres sitios de la cuenca Magdalena-Cauca (Colombia). Resultados: Un grupo de 21 loci polimórficos tipo microsatélite fueron altamente informativos y revelaron que B. henni exhibe diversidad genética (5.143-5.619 alelos/locus, heterocigosidad observada y esperada = 0.461-0.645 y 0.604-0.662, respectivamente) y se encuentra genéticamente estructurado entre dos tributarios del río Cauca separados únicamente por 30 km (F'ST = 0.093, Jost's DEST = 0.311, P < 0.001), un resultado que indica que puede existir aislamiento reproductivo entre dichos grupos. Conclusiones: Reportamos un grupo de 21 loci polimórficos tipo microsatélite que permitieron la detección de la estructura genética a escala local y regional. Esta estructura genética poblacional, concordante con lo que se reporta para otros ocho congéneres, es relevante al determinar la categorización de riesgo de B. henni, así como los programas de manejo, conservación y repoblamiento para esta especie.

Caracterización genética de reproductores de Prochilodus magdalenae (pisces: prochilodontidae) usados en programas de repoblamiento en Colombia / Genetic characterization the stocks of Prochilodus magdalenae (pisces: prochilodontidae) used in stocking programs in Colombia

Prochilodus magdalenae es una especie de pez endémico de Colombia conocido por ser un importante recurso de interés comercial y para muchas comunidades relacionadas a las actividades pesqueras como actividad de sustento. No obstante, se ha observado un deterioro poblacional en ambientes naturales debido a factores tales como sobrepesca, fragmentación de ecosistemas, entre otros. Esto hace necesario caracterizar la diversidad genética de P. magdalenae en los sistemas reproductores de algunos centros piscícolas, que son usados para hacer repoblamientos en otras cuencas de Colombia y así proponer criterios técnicos y científicos que permitan el desarrollo de estrategias de manejo para la conservación de esta especie. Por lo anterior, en el año 2013 se recolectó tejido de aleta caudal de 1044 individuos en siete centros piscícolas, que fueron procesados en laboratorio y a través del uso de siete loci de microsatélites se evaluaron métricas genéticas tales como: heterocigosidad observada y esperada, número de alelos, índices de fijación, estadísticos F, agrupamiento bayesiano y AMOVA. Se encontró baja heterocigosidad observada, correlacionada con procesos de endogamia, que contrastan con los altos valores obtenidos en el índice de heterocigosidad esperada y la cantidad de alelos detectados en los sistemas de reproductores de P. magdalenae. Se detectó una moderada diferenciación genética entre centros piscícolas y se observó la existencia de tres grupos genéticos a través del agrupamiento bayesiano. Pese a la baja diversidad reportada con respecto a otras especies del mismo género, las poblaciones mantenidas en cautiverio de Bocachico tienen potencial para restaurar la diversidad de las poblaciones silvestres. Por lo que se sugiere que cada estación piscícola debe establecer lotes de reproductores por separado, en función de su información genética para que exista una congruencia entre los individuos liberados y aquellos que habitan en el medio natural.

Prochilodus magdalenae is an endemic fish species of Colombia known as an important resource of commercial interest for many communities related to fishing activities as a livelihood activity. However, population deterioration has been observed in natural environments due to factors such as overfishing, fragmentation of ecosystems, among others. This makes it necessary to characterize the genetic diversity of P. magdalenae in the productive systems of some fish farms, which are used to restocking in other basins of Colombia and, thus, to propose technical and scientific criteria that allow the development of management strategies for the conservation of this species. Therefore, in 2013, caudal fin tissue was collected from 1044 individuals in seven fish farms, which were processed in the laboratory. Through the use of seven microsatellites, genetic metrics such as: observed and expected heterozygosity, number of alleles, fixation indexes, F statistics, Bayesian grouping and AMOVA were evaluated. We observed low heterozygosity, correlated with inbreeding processes, which contrast with the high values obtained in the expected heterozygosity index and the number of alleles detected in P. magdalenae productive systems. A moderate genetic differentiation between fish centers was detected and the existence of three genetic groups was observed through the Bayesian analysis. Despite the low diversity reported regarding the others species of the same genus, populations held in Bocachico captivity have the potential to restore the diversity of wild populations. Therefore, it is suggested that each fish station should establish batches of breeders separately, based on their genetic information so that there is congruence between the released individuals and those that inhabit the natural environment.

ISSR Analysis of Genetic Relationship and Population Structure of Turpinia arguta Fresh Leaves in Jiangxi Province / 中国实验方剂学杂志

Objective:To explore genetic relationship and population structure of Turpinia arguta in six locations of Jiangxi province by inter-simple sequence repeat （ISSR） molecular marker technique， and to provide theoretical basis for the protection and utilization of this medicinal material resource. Method:A total of 22 samples from six locations in four counties in Jiangxi province were collected， and genomic DNA was extracted by kit method. Polymerase chain reaction （PCR） amplification was performed using sixty-four universal ISSR molecular marker primers， and the products were detected with polyacrylamide gel electrophoresis （PAGE）. NTsys 2.10e software was selected to calculate the genetic similarity coefficient by unweighted pair group method with arithmetic mean （UPGMA） and cluster analysis. Population genetic structure was analyzed by Structure 2.1 software. Result:A total of forty-eight ISSR primers were amplified to obtain the product， the percent of polymorphic bands ranged from 45.45% to 100%. UPGMA cluster analysis showed that these plant individuals could not be clustered according to their respective executive locations. Analysis of population genetic structure showed that 22 samples of T. arguta could be divided into three populations. Conclusion:There is gene exchange among the populations of T. arguta in Jiangxi province， and it can affect the genetic structure of germplasm resources from different geographical sources.

Genetic Structure Analysis of Y Chromosome STR and SNP in Population of Changshu / 法医学杂志

Objective To provide a theoretical basis for building a Y chromosome database in specific regions by analyzing the pedigree specific core haplogroup and region specific genetic structure in Changshu. Methods One thousand seven hundred and two samples from unrelated Han male individuals in Changshu were collected. Then 27 Y-STR were genotyped through YfilerTM Plus PCR Amplification Kit, Y-SNP haplogroup of each sample was speculated using Y-Predictor software and some samples were verified by amplification refractory mutation system-polymerase chain reaction （ARMS-PCR）. Results A total of 1 556 haplotypes were found on the 27 Y-STR genetic markers of the 1 702 samples. The haplotype diversity （HD） value was 0.999 827. DYS385 （0.933） had the highest gene diversity （GD） value while DYS438 （0.409） had the lowest. By the Y-Predictor software, all samples were confirmed to be from 162 sub-haplogroups of C, D, N, O, Q and R. Samples were randomly selected to verify the prediction results by the software and the prediction accuracy of Y-Predictor software was as high as 95.74%. Conclusion This study found that 27 Y-STR genetic markers have relatively high polymorphisms in the Changshu population, and have good forensic individual identification and paternity testing ability.

Effective gene flow patterns across a fragmented landscape in southern Costa Rica for Symphonia globulifera (Clusiaceae); a species with mobile seed and pollen dispersers

In tropical trees, forest fragmentation has been shown to affect mating and gene flow patterns. Mobile dispersal vectors should be less sensitive to fragmented landscapes and may ameliorate the genetic effects of forest fragmentation on plant populations. To test this hypothesis, we analyzed gene flow patterns in Symphonia globulifera, a tropical tree species with highly mobile pollinators and seed dispersers in the Osa Peninsula in southern Costa Rica. We used microsatellites to study genetic diversity and realized gene flow patterns between a continuous forest and a forest fragment. We found high levels of genetic diversity in adults and seedlings at both sites. Parentage analyses suggest near-neighbor matings and frequent long-distance gene flow events. Half the progeny beneath an adult was not sired by that tree and the majority of established seedlings were the result of long-distance gene dispersal. Gene flow from the forest into the fragment was more common than from the fragment into the continuous forests. Despite long distance gene flow events, seedling spatial genetic structure was stronger and extended further in the forest fragment likely due to limited seed dispersal. We conclude that fragmentation affects gene flow in this tropical tree and may compromise its genetic diversity in forest fragments even for a species with mobile pollen and seed vectors.

En árboles tropicales se ha demostrado que la fragmentación del bosque afecta los patrones de apareamiento y reduce el flujo génico. Las especies forestales cuyos dispersores y polinizadores son capaces de moverse largas distancias sobre ambientes alterados, serán menos sensibles a los efectos de la fragmentación y podrán intercambiar genes regularmente entre fragmentos. Para probar esta hipótesis, en la Península de Osa en el sur de Costa Rica, estudiamos los patrones de flujo génico de Symphonia globulifera, una especie de árbol tropical con polinizadores y dispersores de semillas altamente móviles. Utilizamos microsatélites para estudiar la diversidad genética y los patrones de flujo génico entre un bosque continuo y un fragmento de bosque. Encontramos altos niveles de diversidad genética tanto en adultos como en plántulas. Los análisis de parentesco indican apareamiento entre vecinos cercanos, sin embargo el flujo génico a larga distancia es frecuente. La mitad de la progenie debajo de un adulto no es engendrada por ese árbol y la mayoría de las plántulas establecidas son el resultado del flujo génico a larga distancia. El flujo de genes desde el bosque continuo hacia el fragmento era más frecuente que el movimiento inverso. A pesar del flujo génico a larga distancia, hay diferencias en frecuencias alélicas entre plántulas y la estructura espacial era más fuerte y se extendía a mayor distancia en el fragmento, probablemente por una dispersión limitada de semillas. Concluimos que la fragmentación afecta los patrones de flujo génico en esta especie de árbol tropical y puede afectar su diversidad genética en paisajes fragmentados, inclusive para una especies con polinizadores y dispersores con alta movilidad.

Population structure and genetic diversity in yellow catfish (Pelteobagrus fulvidraco) assessed with microsatellites

Yellow catfish (Pelteobagrus fulvidraco) is an important aquaculture species which is widely distributed, especially in the Yangtze River of China. To facilitate its conservation and stock improvement, 273 yellow catfish samples from the Yangtze River (seven populations) and Baiyangdian (BYD) Lake were genotyped using eight microsatellites in combination with capillary electrophoresis. A total of 250 alleles were detected at eight loci in eight populations showing high allelic (Na= 31.25 ± 7.38) and genetic diversity (He = 0.888–0.944). Both FST and clustering analyses revealed the presence of subtle population differences between the species of Yangtze River and the BYD lake. Mantel tests suggest that genetic distance is significantly correlated with geographical distance (R = 0.9294 and P < 0.05). The results of genetic diversity and population structure will help in conservation and improvement of yellow catfish.

Genetic diversity and population structure of two endemic Cupressus (Cupressaceae) species on the Qinghai-Tibetan plateau

Cupressus gigantea and C. torulosa are ecologically and economically important endemic species of the conifer family Cupressaceae on the Qinghai-Tibetan plateau. C. gigantea was previously classified as a subspecies of C. torulosa because of their similar morphological characteristics and close distribution. In this study, 401 individuals were sampled from 16 populations of the two Cupressus species. The specimens were genotyped using 10 polymorphic microsatellite loci through fluorescence polymerase chain reaction (PCR). The genetic diversity of C. gigantea and C. torulosa populations was generally low, with the highest genetic diversity detected in the population LLS of C. gigantea. Distance-based phylogenetic and principal co-ordinates analyses indicated a clear genetic structures for the 16 populations of the two Cupressus species. Moreover, Mantel test results showed indistinctive correlations between population-pairwise Fst values and geographic distances, as well as between genetic distances and geographic distances in C. gigantea and C. torulosa, respectively. AMOVA suggested that genetic variation mostly resided within populations. Sixteen naturalpopulations were evidently clustered into two major groups in the constructed neighbour-joining tree. The results demonstrated that C. gigantea and C. torulosa are different Cupressus species. The genetic information provided important theoretical references for conservation and management of the two endangered Cupressus species.

Genetic diversity analysis of germplasm resouces of Paris genus in Shaanxi Province by SCoT molecular makers / 中草药

Objective: To study the genetic diversity and genetic structure of Paris genus in Shaanxi Province. Methods: Start Codon Targeted Polymorphism (SCoT) molecular markers were performed on 48 samples from six taxas of Paris genus in Shaanxi. Genetic distance was calculated by POPGENE 3.2 software, and cluster analysis was generated by NTSYS 2.10 software based on unweighted mean distance method (UPGMA) method. Results: A total of 152 bands were produced by 12 primers, among which 135 bands were polymorphic bands, and the percentage of polymorphic bands was 88.82%. The average value of Nei’s genetic diversity index (H) was 0.267 4, Shannon’s information index (I) was 0.404 1, genetic differentiation coefficient (Gst) was 0.517 9, and the gene flow (Nm) was 0.465 4. Six taxas were ranked by genetic diversity: Paris polyphylla > Paris polyphylla var. latifolia > Paris fargesii var. petiolata > Paris polyphylla var. stenophylla > Paris polyphylla var. yunnanensis > Paris verticillata. Cluster analysis distinguished others from Paris verticillata; When the genetic distance was certain, six taxas of the genus were completely separated. Conclusion: SCoT molecular markers can obtain polymorphic and clear band amplification map, which indicates that the technology can be used for molecular identification and genetic relationship of major taxas in Paris genus in Shaanxi Province, providing a scientific basis for screening alternative resource types close to the Pharmacopoeia collection and guiding the rational use of local species.

Study on genetic structure differences and adjustment strategies in different areas of China / 中华流行病学杂志

Objective To describe the genetic structure of populations in different areas of China,and explore the effects of different strategies to control the confounding factors of the genetic structure in cohort studies.Methods By using the genome-wide association study (GWAS) on data of 4 500 samples from 10 areas of the China Kadoorie Biobank (CKB),we performed principal components analysis to extract the fast and second principal components of the samples for the component two-dimensional diagram generation,and then compared them with the source of sample area to analyze the characteristics of genetic structure of the samples from different areas of China.Based on the CKB cohort data,a simulation data set with cluster sample characteristics such as genetic structure differences and extensive kinship was generated;and the effects of different analysis strategies including traditional analysis scheme and mixed linear model on the inflation factor (λ) were evaluated.Results There were significant genetic structure differences in different areas of China.Distribution of the principal components of the population genetic structure was basically consistent with the geographical distribution of the project area.The first principal component corresponds to the latitude of different areas,and the second principal component corresponds to the longitude of different areas.The generated simulation data showed high false positive rate (λ =1.16),even if the principal components of the genetic structure was adjusted or the area specific subgroup analysis was performed,λ could not be effectively controlled (λ ＞ 1.05);while,by using a mixed linear model adjusting for the kinship matrix,λ was effectively controlled regardless of whether the genetic structure principal component was further adjusted (λ =0.99).Conclusions There were large differences in genetic structure among populations in different areas of China.In molecular epidemiology studies,bias caused by population genetic structure needs to be carefully treated.For large cohort data with complex genetic structure and extensive kinship,it is necessary to use a mixed linear model for association analysis.