OneMap: software for genetic mapping in outcrossing species

OneMap is an environment for constructing linkage maps of outcrossing plant species, using full-sib families derived from two outbred parents. The analyses are performed using a novel methodology based on the maximum likelihood approach for simultaneous estimation of linkage and linkage phases (WU et al. 2002), which has been successfully applied to sugarcane (GARCIA et al. 2006). It is implemented as a set of functions for the freely distributed software R, and handles pairwise marker analysis, marker ordering and map refinement.1443787

Molecular mapping in tropical maize (Zea mays L.) using microsatellite markers. 1. Map construction and localization of loci showing distorted segregation

Microsatellites have become the most important class of markers for mapping procedures. Primarily based on restriction fragment length polymorphism (RFLP) markers, several molecular genetic maps of maize have been developed, mainly using temperate inbred maize lines. To characterize the level of polymorphism of microsatellite loci and construct a genetic map in tropical maize, two elite inbred lines, L-08-05F and L-14-4B, were crossed to produce 400 F-2 individuals that were used as a mapping population. A survey of 859 primer pair sequences of microsatellites was used. The polymorphism screens of each microsatellite and genotype assignment were performed using high-resolution agarose gels. About 54 % of the primer sets gave clearly scorable amplification products, 13 % did not amplify and 33% could not be scored on agarose gels. A total of 213 polymorphic markers were identified and used to genotype the mapping population. Among the polymorphic markers, 40 showed loci deviating from expected Mendelian ratios and clusters of deviating markers were located in three chromosome regions. Non-Mendelian scoring was present in 19 markers. The final genetic map with 117 markers spanned 1634 cM in length with an average interval of 14 cM between adjacent markers.13929610

Functional markers for gene mapping and genetic diversity studies in sugarcane

<p>Abstract</p> <p>Background</p> <p>The database of sugarcane expressed sequence tags (EST) offers a great opportunity for developing molecular markers that are directly associated with important agronomic traits. The development of new EST-SSR markers represents an important tool for genetic analysis. In sugarcane breeding programs, functional markers can be used to accelerate the process and select important agronomic traits, especially in the mapping of quantitative traits loci (QTL) and plant resistant pathogens or qualitative resistance loci (QRL). The aim of this work was to develop new simple sequence repeat (SSR) markers in sugarcane using the sugarcane expressed sequence tag (SUCEST database).</p> <p>Findings</p> <p>A total of 365 EST-SSR molecular markers with trinucleotide motifs were developed and evaluated in a collection of 18 genotypes of sugarcane (15 varieties and 3 species). In total, 287 of the EST-SSRs markers amplified fragments of the expected size and were polymorphic in the analyzed sugarcane varieties. The number of alleles ranged from 2-18, with an average of 6 alleles per locus, while polymorphism information content values ranged from 0.21-0.92, with an average of 0.69. The discrimination power was high for the majority of the EST-SSRs, with an average value of 0.80. Among the markers characterized in this study some have particular interest, those that are related to bacterial defense responses, generation of precursor metabolites and energy and those involved in carbohydrate metabolic process.</p> <p>Conclusions</p> <p>These EST-SSR markers presented in this work can be efficiently used for genetic mapping studies of segregating sugarcane populations. The high Polymorphism Information Content (PIC) and Discriminant Power (DP) presented facilitate the QTL identification and marker-assisted selection due the association with functional regions of the genome became an important tool for the sugarcane breeding program.</p

Experience of nurses in the process of donation of organs and tissues for transplant

OBJETIVO: conhecer o significado da ação de enfermeiros no processo de doação para viabilizar órgãos e tecidos para transplante. MÉTODO: pesquisa qualitativa, com abordagem da Fenomenologia Social, foi realizada por meio de entrevistas individuais com dez enfermeiros de três Serviços de Procura de Órgãos e Tecidos da cidade de São Paulo. RESULTADOS: a vivência dos enfermeiros no processo de doação foi representada pelas categorias: obstáculos vivenciados no processo de doação e intervenções realizadas. O significado da ação para viabilizar órgãos e tecidos para transplante foi descrito pelas categorias: mudar paradigmas, humanizar o processo de doação, aumentar a doação e salvar vidas. CONSIDERAÇÕES FINAIS: o conhecimento da vivência dos enfermeiros nesse processo oferece subsídios aos profissionais de saúde, que atuam em diferentes realidades, sinalizando estratégias para otimizar a obtenção de órgãos e tecidos para transplante.OBJECTIVE: to investigate the meaning of the action of nurses in the donation process to maintain the viability of organs and tissues for transplantation. METHOD: this qualitative study with a social phenomenological approach was conducted through individual interviews with ten nurses of three Organ and Tissue Procurement Services of the city of São Paulo. RESULTS: the experience of the nurses in the donation process was represented by the categories: obstacles experienced in the donation process, and interventions performed. The meaning of the action to maintain the viability of organs and tissues for transplantation was described by the categories: to change paradigms, to humanize the donation process, to expand the donation, and to save lives. FINAL CONSIDERATIONS: knowledge of the experience of the nurses in this process is important for healthcare professionals who work in different realities, indicating strategies to optimize the procurement of organs and tissues for transplantation.OBJETIVO: conocer el significado de la acción de enfermeros en el proceso de donación órganos y tejidos para dar viabilidad al trasplante. MÉTODO: investigación cualitativa, con abordaje de la Fenomenología Social, fue realizada por medio de entrevistas individuales con diez enfermeros de tres Servicios de Búsqueda de Órganos y Tejidos de la ciudad de Sao Paulo. RESULTADOS: la vivencia de los enfermeros en el proceso de donación fue representada por las categorías: obstáculos experimentados en el proceso de donación e intervenciones realizadas. El significado de la acción para dar viabilidad al proceso trasplante de órganos y tejidos fue descrito por las categorías: cambiar paradigmas, humanizar el proceso de donación, aumentar la donación y salvar vidas. CONSIDERACIONES FINALES: el conocimiento de la vivencia de los enfermeros en ese proceso ofrece informaciones importantes a los profesionales de salud que actúan en diferentes realidades, señalando estrategias para optimizar la obtención de órganos y tejidos para trasplante

A mixed model QTL analysis for sugarcane multiple-harvest-location trial data

Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane

Genetic diversity in cultivated carioca common beans based on molecular marker analysis

A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm