Genetic diversity among wild pomegranate (Punica granatum) in Azad Jammu and Kashmir region of Pakistan

BACKGROUND: Pomegranate (Punica granatum L.), one of the most important tropical fruits in Azad Jammu and Kashmir regions of Pakistan, is highly valued for its nutrition and medicinal purposes. Although pomegranate is native to this region, the genetic diversity among wild pomegranate accessions is currently unknown. Such information would be vital for germplasm conservation and breeding efforts. In the current study, genetic diversity among forty-eight wild pomegranate accessions collected from different agro-ecological zones of Azad Jammu and Kashmir was assessed using 41 simple sequence repeat (SSR) markers. RESULTS: The markers revealed 303 alleles averaging 7.39 alleles per marker. Polymorphic information content ranged from 0.12 (PGCT093B) to 0.88 (Pom006), with a mean of 0.54. The average genetic distance (GD) across all genotypes was 0.52, and was lowest between Chattar Class and Thorar genotypes (GD = 0.27), but highest between Khun Bandway and Akhor Ban (GD = 0.74). A neighbor-joining dendrogram separated the genotypes into three major clusters, with further sub-clustering within each cluster. CONCLUSIONS: Overall, the results presented here show significant genetic diversity among wild pomegranate accessions in Azad Jammu and Kashmir region of Pakistan. These accessions present a valuable genetic resource to breeding and cultivar improvement programs within the region.

Heterotic grouping of late-maturing maize inbred lines based on combining ability and molecular marker studies

Aim: To examine concurrence between yield based and SSR marker based heterotic grouping of late-maturing maize inbred lines. Methodology: A total of 45 F1 crosses derived from 10x10 diallel mating scheme were evaluated along with their parents and hybrid checks across two locations (New Delhi and Dharawada). To group the inbred lines at molecular level, 35 polymorphic SSR primers were used for PCR amplification of repeat sequences from the genomic DNA of each inbred isolated by CTAB method. Cluster analysis was carried out by using NTSYS-pc- 2.02. Results: Analysis of variance revealed significant (P<0.01) variation among the parents and their hybrids across two locations for all the traits. The yield SCA classified 10 late-maturing maize inbred lines into three heterotic groups. Similarly, molecular genetic diversity analysis also categorized the inbred lines into three major clusters. However, correlations between SCA effects and genetic distance were low (r=0.161) for grain yield. Interpretation: Heterosis prediction with the help of molecular markers alone was not found effective. Further, field-testing can be complimented with molecular markers for the elimination of inferior crosses.

Breastfeeding increases microbial community resilience / Aleitamento materno aumenta a resiliência da comunidade microbiana

Abstract Objective Since the present group had already described the composition of the intestinal microbiota of Brazilian infants under low social economic level, the aim of the present study was to analyze the microbial community structure changes in this group of infants during their early life due to external factors. Methods Fecal samples were collected from 11 infants monthly during the first year of life. The infants were followed regarding clinical and diet information and characterized according to breastfeeding practices. DNA was extracted from fecal samples of each child and subjected to Polymerase Chain Reaction - Denaturing Gradient Gel Electrophoresis. Results The results revealed a pattern of similarity between the time points for those who were on exclusive breastfeeding or predominant breastfeeding. Although there were changes in intensity and fluctuation of some bands, the Denaturing Gradient Gel Electrophoresis patterns in the one-year microbial analysis were stable for breastfeeding children. There was uninterrupted ecological succession despite the influence of external factors, such as complementary feeding and antibiotic administration, suggesting microbiota resilience. This was not observed for those children who had mixed feeding and introduction of solid food before the 5th month of life. Conclusion These results suggested an intestinal microbiota pattern resilient to external forces, due to the probiotic and prebiotic effects of exclusive breastfeeding, reinforcing the importance of exclusive breastfeeding until the 6th month of life.

Resumo Objetivo Como nosso grupo já havia descrito a composição da microbiota intestinal de neonatos brasileiros em baixo nível socioeconômico, o objetivo deste estudo foi analisar alterações estruturais da comunidade microbiana desse grupo de neonatos no início de sua vida devido a fatores externos. Métodos Amostras fecais foram coletadas mensalmente de 11 neonatos durante o primeiro ano de vida. Os neonatos foram acompanhados com relação a informações clínicas e nutricionais e caracterizados de acordo com práticas de amamentação. O DNA foi extraído das amostras fecais de cada criança e submetido a análise através da técnica de Reação em Cadeia da Polimerase - Eletroforese em Gel de Gradiente Desnaturante. Resultados Os resultados revelaram um padrão de similaridade entre seus próprios pontos temporais em indivíduos em aleitamento materno exclusivo ou predominante. Apesar de variações na intensidade e flutuação de algumas bandas, o padrão Eletroforese em Gel de Gradiente Desnaturante na análise microbiana de um ano foi estável em crianças em aleitamento materno. Houve sucessão ecológica ininterrupta apesar da influência de fatores externos, como alimentação complementar e administração de antibióticos, sugeriu resiliência da microbiota. Isso não foi observado nas crianças com alimentação heterogênea e introdução de alimentos sólidos antes do quinto mês de vida. Conclusão Nossos resultados sugerem um padrão de microbiota intestinal resiliente a forças externas, devido a efeitos probióticos e prebióticos do aleitamento materno exclusivo, reforçam a importância do aleitamento materno exclusivo até o sexto mês de vida.

Multivariate analysis of milk yield, lactation length, and calving interval in female buffaloes / Análisis multivariado de la producción de leche, duración de la lactancia y el intervalo entre partos en búfalas / Análise multivariada da produção de leite, duração da lactação e intervalo de parto em búfalas

Abstract Background: The global market has an increasing demand for buffalo by-products due to their unique nutritional characteristics. Many buffalo herds lack suitable breeding control programs, hindering the implementation of selection programs. Objective: To evaluate milk production per lactation (MP), lactation length (LL), and calving interval (CI) of a herd of crossbred Murrah buffaloes to support buffalo clustering according to their potential. Methods: Data from 543 lactations between 2002 and 2014 from 105 crossbred Murrah female buffaloes were used. Data were subjected to principal component analysis (PCA) and cluster analysis. Results: The first components (PCs) were responsible for 92.32% of the total variation, of which 61.45 and 30.87% were explained by the first (PC1) and second (PC2) components, respectively. The cluster analysis allowed three female buffalo groups according to their potentials. Conclusion: Buffalo farmers can make decisions on nutritional, reproductive management and cow culling based on grouping.

Resumen Antecedentes: La demanda de productos de leche de búfala en el mercado mundial viene creciendo en virtud de sus características nutricionales únicas. La mayoría de los hatos bufalinos no tienen adecuados controles, lo que dificulta la implementación de programas de selección. Objetivo: Analizar la producción de leche por lactancia (MP), duración de la lactancia (LL) y el intervalo entre partos (CI) para apoyar la clasificación de búfalos según su potencial. Métodos: Se recogieron 543 registros de lactancia de 105 búfalas Murrah mestizas entre los años 2002 y 2014. Los datos fueron sometidos a análisis de componentes principales (PCA) y análisis de conglomerados. Resultados: Los primeros componentes (PCs) fueron responsables del 92.32% de la variación total, de los cuales 61.45 y 30.87% fueron explicados por el primer (PC1) y segundo (PC2) componentes, respectivamente. El análisis de conglomerados permitió la formación de tres grupos de búfalas, según su potencial. Conclusión: Los productores pueden tomar decisiones específicas con respecto a la gestión nutricional, reproductiva, y el descarte de hembras bufalinas basados en estas agrupaciones.

Resumo Antecedentes: A demanda por produtos de origem do leite de búfalas no mercado mundial tem crescido em virtude de suas características nutricionais singulares. Grande parte dos rebanhos de búfalos não possuem controle zootécnicos adequados, dificultando a implementação de programas de seleção. Objetivo: Analisar conjuntamente as características produção de leite por lactação (MP), duração da lactação (LL) e intervalo de partos (CI) para subsidiar a classificação das búfalas de acordo com seu potencial. Métodos: Para esse estudo, 543 dados de lactação de 105 búfalas mestiças Murrah foram coletadas entre 2002 e 2014. Os dados foram analisados por análises de componentes principais (PCA) e análises de cluster. Resultados: Os primeiros componentes (PCs) foram responsáveis por 92.32% da variação total, dos quais 61.45 e 30.87% foram explicados pelo primeiro (PC1) e segundo (PC2) componentes, respectivamente. A análise de cluster permitiu a formação de três grupos de búfalas de acordo com o potencial das características estudadas. Conclusão: Baseado nesses agrupamentos, os produtores podem tomar decisões específicas quanto aos manejos nutricional e reprodutivo, e sobre o descarte de búfalas, de acordo com os agrupamentos.

El género Attalea (Arecaceae) de Bolivia: Afinidades con sistemas ecológicos regionales

La documentación de las especies neotropicales de la familia Arecaceae, basada en los recientes aportes a su taxonomía y su relación con los paisajes naturales, actualiza los patrones espaciales a los cuales se adaptan en su rango de distribución. En este caso se relevan 121 registros de especímenes de las 11 especies del género Attalea de Bolivia y su relación con 30 sistemas ecológicos que aproximan su ámbito de distribución a nivel regional. Para ello se sistematizó, se verificó y corrigieron las coordenadas geográficas vs. localidades de todos los especímenes coleccionados del género Attalea con el fin de cotejarlos con los sistemas ecológicos, utilizando las herramientas del ArgGis. Seguidamente elaboramos un dendrograma (especies vs. sistemas ecológicos) utilizando el método de distancia mínima en el programa R. El análisis de la relación de las especies con los sistemas ecológicos resalta una especie que no compone al sudoeste amazónico: A. eichleri y que procede de sistemas ecológicos del Cerrado. Entre las especies de Attalea amazónicas, A. blepharopus (endémica de Bolivia) se aísla de las demás y el resto subagrupa a especies según su presencia afín en bosques y sabanas, además del subandino y aluvial, como es para A. princeps, que se encuentra en 17 sistemas (57%). Ocho especies de Attalea son comunes con Perú y 10 con Brasil. Es importante relacionar la agrupación jerárquica de las especies de Attalea con los sistemas ecológicos en función a dinámicas paisajísticas para documentar sus patrones de espacio y también para su conservación.

The documentation of the Neotropical species of the Arecaceae family, based on the recent contributions to its taxonomy and its relationship with natural landscapes, updates the spatial patterns to which they adapt in their range of distribution. In this case 121 records of specimens of the 11 species of the genus Attalea of Bolivia and their relationship with 30 ecological systems that approximate their scope of distribution at regional level are released. To this end, the geographical coordinates were systematized, verified and corrected. Localities of all the specimens collected from the genus Attalea in order to compare them with ecological systems, using the ArgGis tools. We then elaborate a dendrogram (species vs. ecological systems) using the minimum distance method in the R program. The analysis of the relation of the species with the ecological systems highlights a species that does not compose to the southwest amazon: A. eichleri and that is native to ecological systems of the Cerrado. Among the SW Amazonian Attalea species, A. blepharopus (endemic to Bolivia) is isolated from the others and the rest subgroup species according to their presence in forests and savannas, in addition to the subandean and alluvial, as it is for A. princeps, which is found in 17 systems (57%). Eight species of Attalea are common with Peru and 10 with Brazil. It is important to relate the hierarchical grouping of the Attalea species with ecological systems in function of landscape dynamics to document their space patterns and also for their conservation.

Diversity Analysis of Some Traditional Rice Genotypes in Sri Lanka.

Aims: To study the diversity of traditional rice genotypes in Sri Lanka using cluster analysis and principle component analysis. Study Design: The experiment was carried out using one hundred rice genotypes with six modern rice cultivars and ninety four traditional rice cultivars. Rice genotypes were planted according to a randomized complete block design with four replications and 20 plants per plot with 15 cm X 20 cm spacing. Place and Duration of Study: A field experiment was carried out during 2011/2012 Maha season and 2012 Yala season at Faculty of Agriculture, University of Ruhuna, Sri Lanka. Methodology: Plant height (cm), number of tillers/plant and number of productive tillers/plant were measured before harvesting. Panicle length (cm), panicle weight (g), number of spikelets/panicle, number of fertile spikelets/panicle, 100 grain weight (g) and yield/plant (g) were measured after harvesting and drying of grains for 14% moisture content. Principal component analysis (PCA) and cluster analysis were performed using SPSS statistical software. Results: Among nine studied variables three principal components exhibited more than one Eigen value and showed about 89.6 % variability. The principal components (PC) 1, 2 and 3 had 51.07%, 22.08% and 16.46% variability among the genotypes for the evaluated traits respectively. The first PC was more related to panicle weight, number of spikelets/panicle, number of fertile spikelets/panicle, spikelet fertility percentage and yield (g/plant). Number of tillers/plant, number of productive tillers/plant and yield (g/plant) were more related traits in the second principal component. The highest contribution in third principal component was from the panicle weight, 100 grain weight and yield (g/plant). Based on the nine yield and yield attributing characters, the genotypes were grouped in to seven clusters in cluster analysis. The genotypes under cluster V recorded the highest divergence among them as it exhibited the highest intra-cluster distance. The lowest intracluster distance was recorded in the cluster VI. The modern rice cultivar BG 379/2 was fallen in to the cluster VI with 3 traditional rice cultivars namely Karayal I, Bathkiri el and Hondarawala. Conclusion: One hundred rice genotypes were grouped in to divergent groups by principle component analysis and cluster analysis. This clustering pattern can be used for the selection of parental materials with diverse characters.

Genetic diversity among native varieties and commercial cultivars of Solanum tuberosum ssp. tuberosum L. present in Chile

Background: The object of this work was to determine the genetic and allelic diversity of Solanum species present in Chile, assessing allelic distribution among native varieties and commercial cultivars of Solanum tuberosum ssp. tuberosum L., using microsatellite markers. Results: A high level of allelic richness was found in the potatoes studied. The seven microsatellite markers used presented a total of 64 allelic variants among native varieties and commercial cultivars of Solanum tuberosum ssp. tuberosum. The SSR loci generated an average of 9.16 alleles/locus. The group with the highest PIC was that of native varieties collected in the Chiloe archipelago. The high PIC values found indicate that the native varieties from Chiloe have a low level of interrelation, representing wide genetic diversity. Conclusions: The markers with the highest number of alleles in native varieties corresponded to loci STG 0016 and LEMALX. Commercial cultivars do not present the same genetic variability as native varieties, and the allelic richness of commercial cultivars is lower than that of native varieties of S. tuberosum ssp. tuberosum. Most of the native varieties were clustered in accordance with their geographical location, while commercial cultivars, were clustered in accordance with their breeding programs in Chile and Europe, with the exception of Shepody.

Comparative genetic diversity and genetic structure of three chinese silkworm species Bombyx mori L. (Lepidoptera: Bombycidae), Antheraea pernyi Guérin-Meneville and Samia cynthia ricini donovan (Lepidoptera: Saturniidae)

The genetic diversity and genetic structure of three Chinese silkworm species Bombyx mori L., Antheraea pernyi Guérin-Meneville and Samia cynthia ricini Donovan were comparatively assessed based on RAPD markers. At the species level, A. pernyi and B. mori showed high levels of genetic diversity, whereas S. cynthia ricini showed low level of genetic diversity. However, at the strain level, A. pernyi had relatively highest genetic diversity and B. mori had lowest genetic diversity. Analysis of molecular variance (AMOVA) suggested that 60 percent and 72 percent of genetic variation resided within strains in A. pernyi and S. cynthia ricini, respectively, whereas only 16 percent of genetic variation occurred within strains in B. mori. In UPGMA dendrogram, individuals of A. pernyi and B. mori formed the strain-specific genetic clades, whereas those of S. cynthia ricini were distributed in a mixed way. The implications of these results for the conservation and utilization in breeding programs of three silkworm species are discussed.

A comparative study on intertidal faunal biodiversity of selected beaches of Mumbai coast.

Comparative study has been done to examine the biodiversity and ecological status of the intertidal region of Tata Institute of Fundamental Research (TIFR), Bandstand and National Centre for Performing Arts (NCPA) rocky beaches in Mumbai, West coast of India. A total of 50 species of intertidal organisms were recorded from these shores. Shannon and Simpson’s diversity index, Margalef’s richness index and Pielou’s evenness index indicated different level of ecological state of the shore in different months. Dendrograms and 2-D non metric MDS ordination from Bray-Curtis similarity matrix of occurrence of intertidal organisms from these sites showed highest similarity and combination pattern of occurrence between Nerita oryzarum and Planaxis sulcatus in TIFR and Bandstand shore. Nerita oryzarum and Tactarius malaccanus at NCPA shore. Abundance/ biomass comparison (ABC) method of determining level of disturbance also pointed towards the polluted status of these shores. Study concludes that though these beaches are highly disturbed due to anthropogenic activities, they still support a rich intertidal biodiversity which need immediate attention for protection and conservation.

Molecular diversity in rice genotypes differing in physiological mechanisms of salt tolerance through SSR and ISSR markers.

Two different DNA-based techniques viz, simple sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers were used to estimate genetic diversity among 20 rice genotypes possessing different physiological mechanisms contributing to salt tolerance. A total of 11 clear and repeatable bands were amplified from ten selected SSR primers pairs and 43 fragments were detected from nine ISSR primers. The level of polymorphism was 1.1% with SSR compared to 90.7% with ISSRs. Mean genetic similarity of 0.88 based on SSRs and 0.85 using ISSRs was observed. A total of 43 (39 polymorphic) and 11 bands were detected using 9 ISSR primers and 10 well distributed mapped SSR markers, respectively. Estimates of genetic similarity of ISSRs based on the 39 polymorphic markers between 20 rice cultivars ranged from 0.55 for PR108/CSR19 to 0.94 for Pokkali/CSR20 with an average of 0.81. The estimates revealed by the 11 polymorphic SSR bands showed the average value (0.94) and also the range of genetic similarity (from 0.86 to 1.00 for CSR22/CSR18 and CSR24/CSR20, respectively) reflecting their hyper variability and their high resolution power. The findings are likely to expedite breeding new salt tolerant cultivars by involving parents from diverse molecular clusters.

Is NDM-1 actually being imported to UK from India.

A recent article in Lancet Infectious Diseases suggested that Enterobacteriacea containing New Delhi metallo-Blactamase (NDM-1) gene were being imported into UK from India. Since the study findings had widespread public health implications, it was necessary to scrutinise the adequacy of the evidence. The article was critically appraised on epidemiological, biological, and molecular evidence, the ethical principle of research, potential conflict of interest, and the justifiability of the recommendations. The study design was inappropriate to establish a causal chain between hospitalization in India and importation of NDM-1 in UK. Out of the total 29 NDM-1 positive UK patients, the NDM-1 gene was present in equal proportion among those who were hospitalized in India (44.3%) and those who were not (51.7%) statistically significant strain relatedness between Indian and UK isolates could not be proved through dendrogram. There was a potential conflict of interest that was not disclosed. We found that the study findings did not support the authors' conclusion that India was a source for NDM-1 positive UK patients. Misplaced conclusions had the potential to cause unfounded scare and panic.

Genomic Variation of The Rice Rim2/Hipa Superfamily and Dendrogram and Fingerprinting Analysis of Rice Germplasm Based on Rim2/Hipa Paralog Display / 生物化学与生物物理进展

The rice Rim2/Hipa is a stress-induced transposon superfamily recently identified in Oryza genomes. Genomic variation was found in the Rim2 core region among rice genetic resources/genomes, indicative of high genomic divergence accumulated during the Rim2 evolution. Based on the divergence and quiescent state of the Rim2 elements, a Rim2 paralog display-based fingerprinting approach was developed to effectively identify rice genetic resources and explore their genetic relationships within a set of rice germplasm including 45 accessions ofO. sativa and 8 accessions of its wild relatives O. rufipogon. A dendrogram showed not only clear genetic diversity of rice germplasm, but also considerable genetic differentiation among wild rice resources. The wild rice relatives were either clustered as an independent group, or among the japonica varieties. This Rim2-based fingerprinting approach could also serve as a sensitive tool to identify rice hybrids from their parents, and variety stability, demonstrating its great potential in evolution study ofrice genomes and in rice breeding and seed production.

Analysis of intraspecific variation of Chinese Carthamus tinctorius L. using AFLP markers / 药学学报

Aim To investigate the intraspecific variation of Carthamus tinctorius L. (safflower) and establish foundation for further breeding of safflower germplasm resource and screening the quality correlation genes. Methods Amplified fragment length polymorphism (AFLP) was carried out to analyze genetic variation of 28 safflower populations collected in China. Unweighed pair-group method of with arithmetical averages (UPGMA) cluster analysis was used to construct a dendrogram and to estimate the genetic distances among the populations. Results All populations could be uniquely distinguished using 12 selected primer combinations. Similarity coefficients ranged from 0. 48 to 0. 96 among the populations.Dendrogram revealed distinct segregation of all the cultivars into three main groups and one midst group.Conclusion Limited genetic diversity exists within the tested 28 collections at intra specific level and AFLP-based phylogeny was not absolutely consistent with that based on morphological characters may be due to the interaction effect between genotype and environment.

SPORE CELLULAR FATTY ACIDS ANALYSIS OF SOME AEROBIC ENDOSPORE-FORMING BACILLI / 微生物学通报

A gas chromatographic analysis method was employed to determine the cellular fatty acids (CFAs)profiles of the spores of some aerobic endospore forming bacilli.Purified spore cultures of 51 experimentas strains were processed to acquire whole cell fatty acids methyl esters for the subsequent gas chromatographic analysis,and the corresponding vegetative cells were set as control.The reproducibility study of spore fatty acids revealed that,the fatty acids components of spores were stable enough for research purpose,provided under standardized experimentas procedure.The dendrograms obtained by cluster analysis provided some meaningful taxonomic information of the experimental strains.The fatty acids analysis of spores seemed to be a promising supplementary tool for the chemotaxonomic research of aerobic endospore-forming bacilli.