Mayor plasticidad fenotípica que diferenciación adaptativa entre procedencias de pino piñonero

The Mediterranean stone pine, Pinus pinea L., seems to be well adapted to the different climate zones of its distribution range that spans four thousand kilometres along the Northern shore of the Mediterranean Sea. But recent molecular studies revealed it to be extremely genetically depauperate for a widespread tree. In this context, a provenances trial should elucidate whether any differentiation in adaptative traits can be identified between 34 accessions covering its natural range. The presence of strong spatial autocorrelations throughout four test sites required iterative nearest-neighbours adjustments in their statistical analysis. No significant differences in survival or ontogeny were found between accessions, while height growth was slightly though significantly more vigorous in northern or inland provenances. But these differences were masked by a common, stable reaction norm in dependence on site and microsite. On the other hand, its strong developmental plasticity allows the stone pine to delay the heteroblastic phase change in order to survive in unfavourable conditions, a clear advantage in the limiting and unpredictable environments of Mediterranean ecosystems.El pino piñonero, Pinus pinea L., está aparentemente adaptado a diferentes zonas climáticas a lo largo de los cuatro mil kilómetros de su rango de distribución en el Mediterráneo. Sin embargo, estudios moleculares recientes le han descrito como genéticamente muy empobrecido para ser un árbol de amplia distribución. En este contexto, el presente ensayo de procedencias estudió la presencia de diferenciación en características adaptativas entre 34 procedencias representativas de su rango de distribución. Debido a la presencia de autocorrelaciones espaciales en los cuatro sitios de ensayo, el análisis estadístico usó ajustes iterativos basados en los vecinos más próximos de cada árbol. No se observaron diferencias significativas entre procedencias respecto a supervivencia y desarrollo ontogénico, pero el crecimiento en altura fue ligera, aunque significativamente mayor en procedencias del interior o mayor latitud. Sin embargo, estas diferencias fueron muy inferiores al efecto del sitio o micrositio, común para todas las procedencias. Por último, se observó que su alta plasticidad ontogénica le permite al pino piñonero retrasar en condiciones desfavorables el cambio de fase vegetativa a follaje y crecimiento adulto durante varios años para sobrevivir en forma juvenil, lo que es un recurso estratégico más para ambientes limitantes e impredecibles de los ecosistemas mediterráneos

Genetic Diversity in the SIR Model of Pathogen Evolution

We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR). We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts), where pathogens replicate and mutate. Hosts transmit pathogens to uninfected hosts. We show that the level of pathogen variation is well predicted by analytical expressions, such that pathogen neutral molecular variation is bounded by the level of infection and increases with the duration of infection. We then introduce selection in the model and study the invasion probability of a new pathogenic strain whose fitness (R0(1+s)) is higher than the fitness of the resident strain (R0). We show that this invasion probability is given by the relative increment in R0 of the new pathogen (s). By analyzing the patterns of genetic diversity in this framework, we identify the molecular signatures during the replacement and compare these with those observed in sequences of influenza A

Effect of lactation length adjustment procedures on genetic parameter estimates for buffalo milk yield

The objectives of this study were to estimate the genetic parameters for milk yield unadjusted and adjusted for days in milk and, subsequently, to assess the influence of adjusting for days in milk on sire rank. Complete lactations from 90 or 150 days of lactation to 270 or 350 days in milk were considered in these analyses. Milk yield was adjusted for days in milk by multiplicative correction factors, or by including lactation length as a covariable in the model. Milk yields adjusted by different procedures were considered as different traits. Heritability estimates varied from 0.17 to 0.28. Genetic correlation estimates between milk yields unadjusted and adjusted for days in milk were greater than 0.82. Adjusting for days in milk affected the parameter estimates. Multiplicative correction factors produced the highest heritability estimates. More reliable breeding value estimates can be expected by including short length lactation records in the analyses and adjusting the milk yields for days in milk, regardless of the method used for the adjustment. High selection intensity coupled to the inclusion of short length lactations and adjustment with multiplicative factors can change the sire rank.

High-throughput sequencing of black pepper root transcriptome

Background: Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host's root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. Results: The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant's root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. Conclusions: This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.Rede Paraense de Genomica e Proteomica (Governo do Estado do Para/SEDECT/FAPESPA)Rede Paraense de Genomica e Proteomica (Governo do Estado do Para/SEDECT/FAPESPA)PROPESP/UFPAPROPESP/UFPAFADESPFADESPFINEPFINEPCoordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)CAPES (Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior

High-throughput sequencing of black pepper root transcriptome

Abstract\ud \ud Background\ud Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host’s root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper.\ud \ud \ud Results\ud The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant’s root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology.\ud \ud \ud Conclusions\ud This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.FAPESPAUFPAFINEPCAPE

PCR Improves Diagnostic Yield from Lung Aspiration in Malawian Children with Radiologically Confirmed Pneumonia

Accurate data on childhood pneumonia aetiology are essential especially from regions where mortality is high, in order to inform case-management guidelines and the potential of prevention strategies such as bacterial conjugate vaccines. Yield from blood culture is low, but lung aspirate culture provides a higher diagnostic yield. We aimed to determine if diagnostic yield could be increased further by polymerase chain reaction (PCR) detection of bacteria (Streptococcus pneumoniae and Haemophilus influenzae b) and viruses in lung aspirate fluid.A total of 95 children with radiological focal, lobar or segmental consolidation had lung aspirate performed and sent for bacterial culture and for PCR for detection of bacteria, viruses and Pneumocystis jirovecii. In children with a pneumococcal aetiology, pneumococcal bacterial loads were calculated in blood and lung aspirate fluid.Blood culture identified a bacterial pathogen in only 8 patients (8%). With the addition of PCR on lung aspirate samples, causative pathogens (bacterial, viral, pneumocystis) were identified singly or as co-infections in 59 children (62%). The commonest bacterial organism was S.pneumoniae (41%), followed by H. influenzae b (6%), and the commonest virus identified was adenovirus (16%), followed by human bocavirus (HBoV) (4%), either as single or co-infection.In a select group of African children, lung aspirate PCR significantly improves diagnostic yield. Our study confirms a major role of S.pneumoniae and viruses in the aetiology of childhood pneumonia in Africa

Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure

Abstract\ud \ud Background\ud Saturated fatty acids can be detrimental to human health and have received considerable attention in recent years. Several studies using taurine breeds showed the existence of genetic variability and thus the possibility of genetic improvement of the fatty acid profile in beef. This study identified the regions of the genome associated with saturated, mono- and polyunsaturated fatty acids, and n-6 to n-3 ratios in the Longissimus thoracis of Nellore finished in feedlot, using the single-step method.\ud \ud \ud Results\ud The results showed that 115 windows explain more than 1 % of the additive genetic variance for the 22 studied fatty acids. Thirty-one genomic regions that explain more than 1 % of the additive genetic variance were observed for total saturated fatty acids, C12:0, C14:0, C16:0 and C18:0. Nineteen genomic regions, distributed in sixteen different chromosomes accounted for more than 1 % of the additive genetic variance for the monounsaturated fatty acids, such as the sum of monounsaturated fatty acids, C14:1 cis-9, C18:1 trans-11, C18:1 cis-9, and C18:1 trans-9. Forty genomic regions explained more than 1 % of the additive variance for the polyunsaturated fatty acids group, which are related to the total polyunsaturated fatty acids, C20:4 n-6, C18:2 cis-9 cis12 n-6, C18:3 n-3, C18:3 n-6, C22:6 n-3 and C20:3 n-6 cis-8 cis-11 cis-14. Twenty-one genomic regions accounted for more than 1 % of the genetic variance for the group of omega-3, omega-6 and the n-6:n-3 ratio.\ud \ud \ud Conclusions\ud The identification of such regions and the respective candidate genes, such as ELOVL5, ESSRG, PCYT1A and genes of the ABC group (ABC5, ABC6 and ABC10), should contribute to form a genetic basis of the fatty acid profile of Nellore (Bos indicus) beef, contributing to better selection of the traits associated with improving human health.MVA Lemos, (FAPESP, Fundação de Amparo à Pesquisa do Estado de São\ud Paulo). HLJ Chiaia, MP Berton, FLB Feitosa received scholarships from the\ud Coordination Office for Advancement of University-level Personnel (CAPES;\ud Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) in conjunction\ud with the Postgraduate Program on Genetics and Animal Breeding, Faculdade\ud de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (FCAV,\ud UNESP). F Baldi (FAPESP, Fundação de Amparo à Pesquisa do Estado de São\ud Paulo grant #2011/21241-0). Lucia G. Albuquerque (FAPESP, Fundação de\ud Amparo à Pesquisa do Estado de São Paulo grant #2009/16118-5)

Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome

A major question in evolutionary biology is how natural selection has shaped patterns of genetic variation across the human genome. Previous work has documented a reduction in genetic diversity in regions of the genome with low recombination rates. However, it is unclear whether other summaries of genetic variation, like allele frequencies, are also correlated with recombination rate and whether these correlations can be explained solely by negative selection against deleterious mutations or whether positive selection acting on favorable alleles is also required. Here we attempt to address these questions by analyzing three different genome-wide resequencing datasets from European individuals. We document several significant correlations between different genomic features. In particular, we find that average minor allele frequency and diversity are reduced in regions of low recombination and that human diversity, human-chimp divergence, and average minor allele frequency are reduced near genes. Population genetic simulations show that either positive natural selection acting on favorable mutations or negative natural selection acting against deleterious mutations can explain these correlations. However, models with strong positive selection on nonsynonymous mutations and little negative selection predict a stronger negative correlation between neutral diversity and nonsynonymous divergence than observed in the actual data, supporting the importance of negative, rather than positive, selection throughout the genome. Further, we show that the widespread presence of weakly deleterious alleles, rather than a small number of strongly positively selected mutations, is responsible for the correlation between neutral genetic diversity and recombination rate. This work suggests that natural selection has affected multiple aspects of linked neutral variation throughout the human genome and that positive selection is not required to explain these observations