Novel strategies for genomic prediction of untested single-cross maize hybrids using unbalanced historical data.

KEY MESSAGE: Weighted outperformed unweighted genomic prediction using an unbalanced dataset representative of a commercial breeding program. Moreover, the use of the two cycles preceding predictions as training set achieved optimal prediction ability. Predicting the performance of untested single-cross hybrids through genomic prediction (GP) is highly desirable to increase genetic gain. Here, we evaluate the predictive ability (PA) of novel genomic strategies to predict single-cross maize hybrids using an unbalanced historical dataset of a tropical breeding program. Field data comprised 949 single-cross hybrids evaluated from 2006 to 2013, representing eight breeding cycles. Hybrid genotypes were inferred based on their parents' genotypes (inbred lines) using single-nucleotide polymorphism markers obtained via genotyping-by-sequencing. GP analyses were fitted using genomic best linear unbiased prediction via a stage-wise approach, considering two distinct cross-validation schemes. Results highlight the importance of taking into account the uncertainty regarding the adjusted means at each step of a stage-wise analysis, due to the highly unbalanced data structure and the expected heterogeneity of variances across years and locations of a commercial breeding program. Further, an increase in the size of the training set was not always advantageous even in the same breeding program. The use of the two cycles preceding predictions achieved optimal PA of untested single-cross hybrids in a forward prediction scenario, which could be used to replace the first step of field screening. Finally, in addition to the practical and theoretical results applied to maize hybrid breeding programs, the stage-wise analysis performed in this study may be applied to any crop historical unbalanced data.

Genital morphology and copulatory behavior in triatomine bugs (Reduviidae: Triatominae).

Triatomines (Heteroptera: Reduviidae) include around 139 species, widely known as vectors of Chagas disease. Our aim is to review the existing knowledge of the genital morphology and sexual behavior and provide some functional analysis of these traits in triatomines. A complex set of traits comprise genitalia and these are highly variable among species. The components of the phallus and seminal products (secreted by action of testes and two accessory glands) interact to allow successful sperm transfer to the female spermathecae (usually a pair of blind tubes that emerge from the common oviduct). Seminal products may inhibit female physiology and extend mating duration. Mating behavior in triatomines is best characterized as scramble competition. We suggest that males may evaluate female condition prior to copulation, given that female fitness is largely affected by food (blood) source. Although rearing several triatomine species may be difficult and discourage from undertaking studies on this group, any further investigation on sexual behavior and mating interactions may provide data for applicative studies including Chagas disease vectors control.

Aplicación de la Sonificación de Señales Cerebrales en Clasificación Automática / Applying Brain Signals Sonification for Automatic Classification

En años recientes la sonificación de electroencefalogramas (EEG) ha sido utilizada como una alternativa para analizar señales cerebrales al convertir el EEG en audio. En este trabajo se aplica la sonificación a señales de EEG durante el habla imaginada o habla no pronunciada, con el objetivo de mejorar la clasificación automática de 5 palabras del idioma español. Para comprobarlo, se procesó la señal cerebral de 27 sujetos sanos. Estas señales fueron sonificadas para después extraer características con dos métodos diferentes: la transformada Wavelet discreta (DWT); y los coeficientes cepstrales en la escala de Mel (MFCC). Éste último comúnmente utilizado en tareas de reconocimiento de voz. Para clasificar las señales se aplicaron tres algoritmos distintos de clasificación Naive Bayes (NB), Máquina de vectores de soporte (SVM) y Random Forest (RF). Se obtuvieron resultados usando los 4 canales más cercanos a las áreas de lenguaje de Broca y Wernicke, así como también los 14 canales del dispositivo EEG utilizado. Los porcentajes de exactitud promedio para los 27 sujetos en los dos conjuntos de 4 y 14 canales usando sonificación de EEG fueron de 55.83% y 64.14% respectivamente, con lo que se logró mejorar ligeramente los porcentajes de clasificación de las palabras imaginadas respecto a no utilizar sonificación.

In recent years sonification of electroencephalograms (EEG) has been used as an alternative to analyze brain signals after converting EEG to audio. In this paper we applied the sonification to EEG signals during the imagined speech or unspoken speech, with the aim of improving the automatic classification of 5 words of Spanish. To check this, the brain signals of 27 healthy subjects were processed. These sonificated signals were processed to extract features with two different methods: discrete wavelet transform (DWT); and the Mel-frequencies cepstral coefficients (MFCC). The latter commonly used in speech recognition tasks. To classify the signals three different classification algorithms Naive Bayes (NB), Support Vector Machine (SVM) and Random Forest (RF) were applied. Results were obtained using the 4 channels closest to the language areas of Broca and Wernicke, as well as the 14 channels of the EEG device used. The percentages of average accuracy for the 27 subjects in the two sets of 4 and 14 channels using EEG sonification were 55.83% and 64.14% respectively, which are improvements in the classification rates of the imagined words compared with a scheme without sonification.

Validation of Prediction Equations of Energy Values of a Single Ingredient or Their Combinations in Male Broilers.

A set of prediction equations to estimate the nitrogen-corrected apparent metabolizable energy (AMEn) of individual ingredients and diets used in the poultry feed industry was evaluated. The AMEn values of three energy ingredients (maize, sorghum and defatted maize germ meal), four protein ingredients (soybean meal, maize gluten meal 60% crude protein, integral micronized soy and roasted whole soybean) and four diets (three containing four feedstuffs, complex diets, and one containing only corn-soybean meal, basal diet) were determined using a metabolism assay with male broilers from 1 to 7, 8 to 21, 22 to 35, and 36 to 42 days old. These values were compared to the AMEn values presented in the tables of energy composition or estimated by equation predictions based on chemical composition data of feedstuffs. In general, the equation predictions more precisely estimated the AMEn of feedstuffs when compared to the tables of energy composition. The equation AMEn (dry matter [DM] basis) = 4,164.187+51.006 ether extract (% in DM basis)-197.663 ash-35.689 crude fiber (% in DM basis)-20.593 neutral detergent fiber (% in DM basis) (R(2) = 0.75) was the most applicable for the prediction of the energy values of feedstuffs and diets used in the poultry feed industry.

Numerical and experimental study of stochastic resistive switching.

In this paper we study the role of noise in the context of resistive switching phenomena by means of experiments and numerical simulations. Experiments are conducted on a manganite sample. We show that the addition of external Gaussian noise to a small amplitude driving signal yields a contrast ratio between low- and high-resistance states, comparable to that obtained by the application of a large amplitude noiseless signal. Furthermore, excellent agreement between numerical simulation and measurement allows us to study resistive switching under varying input conditions and, thus, properly characterize the beneficial role of noise. We believe these results might be of relevance in the area of memory devices where the large scale of electronic integration renders the presence of noise unavoidable.

Análisis de señales electroencefalográficas para la clasificación de habla imaginada / Electroencephalographic Signals Analysis for Imagined Speech Classification

El presente trabajo tiene como objetivo interpretar las señales de EEG registradas durante la pronunciación imaginada de palabras de un vocabulario reducido, sin emitir sonidos ni articular movimientos (habla imaginada o no pronunciada) con la intención de controlar un dispositivo. Específicamente, el vocabulario permitiría controlar el cursor de la computadora, y consta de las palabras del lenguaje español: "arriba", "abajo", "izquierda", "derecha", y "seleccionar". Para ello, se registraron las señales de EEG de 27 individuos utilizando un protocolo básico para saber a priori en qué segmentos de la señal la persona imagina la pronunciación de la palabra indicada. Posteriormente, se utiliza la transformada wavelet discreta (DWT) para extraer características de los segmentos que son usados para calcular la energía relativa wavelet (RWE) en cada una de los niveles en los que la señal es descompuesta, y se selecciona un subconjunto de valores RWE provenientes de los rangos de frecuencia menores a 32 Hz. Enseguida, éstas se concatenan en dos configuraciones distintas: 14 canales (completa) y 4 canales (los más cercanos a las áreas de Broca y Wernicke). Para ambas configuraciones se entrenan tres clasificadores: Naive Bayes (NB), Random Forest (RF) y Máquina de vectores de soporte (SVM). Los mejores porcentajes de exactitud se obtuvieron con RF cuyos promedios fueron 60.11% y 47.93% usando las configuraciones de 14 canales y 4 canales, respectivamente. A pesar de que los resultados aún son preliminares, éstos están arriba del 20%, es decir, arriba del azar para cinco clases. Con lo que se puede conjeturar que las señales de EEG podrían contener información que hace posible la clasificación de las pronunciaciones imaginadas de las palabras del vocabulario reducido.

This work aims to interpret the EEG signals associated with actions to imagine the pronunciation of words that belong to a reduced vocabulary without moving the articulatory muscles and without uttering any audible sound (imagined or unspoken speech). Specifically, the vocabulary reflects movements to control the cursor on the computer, and consists of the Spanish language words: "arriba", "abajo", "izquierda", "derecha", and "seleccionar". To do this, we have recorded EEG signals from 27 subjects using a basic protocol to know a priori in what segments of the signal a subject imagines the pronunciation of the indicated word. Subsequently, discrete wavelet transform (DWT) is used to extract features from the segments. These are used to compute relative wavelet energy (RWE) in each of the levels in that EEG signal is decomposed and, it is selected a RWE values subset with the frequencies smaller than 32 Hz. Then, these are concatenated in two different configurations: 14 channels (full) and 4 channels (the channels nearest to the brain areas of Wernicke and Broca). The following three classifiers were trained using both configurations: Naive Bayes (NB), Random Forest (RF) and support vector machines (SVM). The best accuracies were obtained by RF whose averages were 60.11% and 47.93% using both configurations, respectively. Even though, the results are still preliminary, these are above 20%, this means they are more accurate than chance for five classes. Based on them, we can conjecture that the EEG signals could contain information needed for the classification of the imagined pronunciations of the words belonging to a reduced vocabulary.

Immunoexpression of matrix metalloproteinases and their inhibitors in different areas of oral squamous cell carcinoma.

BACKGROUND: Several studies have shown the participation of MMPs in oral squamous cell carcinoma, the most frequent malignant neoplasm of the oral cavity. The expression of some MMPs correlates with a more aggressive biological behaviour. The objective of this study was to determine which MMPs and TIMPs were expressed in both neoplastic and peritumoural stromal cells in different histopathology areas. METHODS: Patients who underwent primary tumour neck dissection for oral squamous cell carcinoma were included. Immunoexpression of MMP-1, -2, -3, -7, -9, -11, -13, and TIMP-1 and -2 in different areas of pathologic specimens (in situ carcinoma, primary tumour, invasive front, distant invasion carcinoma, and lymph node metastasis) was evaluated. Enzyme expression on mucosa adjacent to tumour served as control. RESULTS: Thirty cases were included. Only 6 MMPs and 1 TIMP were expressed in the studied areas. Statistically significant differences in the number of cases with positive MMPs or TIMP expression, in both neoplastic and peritumoural cells, between control and the rest of the areas were observed. MMP-2 expression was constant in the areas with a more aggressive biological behaviour. CONCLUSIONS: MMP-2 expression may represent a dynamic interaction between host and tumour that favours the establishment of neoplastic cells at distant sites.

Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences.

Managed environments in the form of well watered and water stressed trials were performed to study the genetic basis of grain yield and stay green in sorghum with the objective of validating previously detected QTL. As variations in phenology and plant height may influence QTL detection for the target traits, QTL for flowering time and plant height were introduced as cofactors in QTL analyses for yield and stay green. All but one of the flowering time QTL were detected near yield and stay green QTL. Similar co-localization was observed for two plant height QTL. QTL analysis for yield, using flowering time/plant height cofactors, led to yield QTL on chromosomes 2, 3, 6, 8 and 10. For stay green, QTL on chromosomes 3, 4, 8 and 10 were not related to differences in flowering time/plant height. The physical positions for markers in QTL regions projected on the sorghum genome suggest that the previously detected plant height QTL, Sb-HT9-1, and Dw2, in addition to the maturity gene, Ma5, had a major confounding impact on the expression of yield and stay green QTL. Co-localization between an apparently novel stay green QTL and a yield QTL on chromosome 3 suggests there is potential for indirect selection based on stay green to improve drought tolerance in sorghum. Our QTL study was carried out with a moderately sized population and spanned a limited geographic range, but still the results strongly emphasize the necessity of corrections for phenology in QTL mapping for drought tolerance traits in sorghum.

A molecular linkage map for Drosophila mediopunctata confirms synteny with Drosophila melanogaster and suggests a region that controls the variation in the number of abdominal spots.

The classic approach to gene discovery relies on the construction of linkage maps. We report the first molecular-based linkage map for Drosophila mediopunctata, a neotropical species of the tripunctata group. Eight hundred F(2) individuals were genotyped at 49 microsatellite loci, resulting in a map that is ≈450 centimorgans long. Five linkage groups were detected, and the species' chromosomes were identified through cross-references to BLASTn searches and Müller elements. Strong synteny was observed when compared with the Drosophila melanogaster chromosome arms, but little conservation in the gene order was seen. The incorporation of morphological data corresponding to the number of central abdominal spots on the map was consistent with the expected location of a genomic region responsible for the phenotype on the second chromosome.

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.

[Level of satisfaction from patients who undergone an endoscopic procedure and related factors]. / Nivel de satisfacción de pacientes tras un procedimiento endoscópico y factores asociados.

BACKGROUND: Patient satisfaction is a cognitive and emotional evaluation of the patient on the performance of health staff and is based on relevant aspects of their experience in health care. AIM: To determine the satisfaction level of patients after an endoscopic procedure in the gastrointestinal endoscopy service Specialty Hospital National Medical Center La Raza and to evaluate associated factors. MATERIAL AND METHODS: A modified and validated questionnaire was applied to assess patient satisfaction after an endoscopic procedure (mGHAA-9) in patients who underwent a gastroscopy or colonoscopy. Factors that influenced patient satisfaction were assessed. RESULTS: Two-hundred questionnaires were applied (response rate: 89.5%), in 62 men (34.6%) and 117 women (65.4%). Mean patient age was 51.3 years. The average score for the overall group was 30.9 (maximum score of 35). In the overall assessment of satisfaction patients reported 60.9% excellent, very good 29.6%, good 8.9% and 0.6% regular. Factors that influenced patient satisfaction were: waiting time for appointment (OR 3.104), explaining and answering questions (OR 2.961) and waiting time for performing the procedure (OR 2.408) Some factors did not influence on patient satisfaction: Sex: Male 58.1%, female 62.4% (p = 0.63), age 52 vs. 50 years (p = 0.48) and sedation 64.7% vs. 60.5% (p = 0.8) CONCLUSIONS: The level of satisfaction of patients undergoing a gastroscopy or colonoscopy is good. The factors that influence the satisfaction of these patients are related to communication between doctor and patient, and waiting time for the study.

Precision of distances and ordering of microsatellite markers in consensus linkage maps of chromosomes 1, 3 and 4 from two reciprocal chicken populations using bootstrap sampling.

Some factors complicate comparisons between linkage maps from different studies. This problem can be resolved if measures of precision, such as confidence intervals and frequency distributions, are associated with markers. We examined the precision of distances and ordering of microsatellite markers in the consensus linkage maps of chromosomes 1, 3 and 4 from two F(2) reciprocal Brazilian chicken populations, using bootstrap sampling. Single and consensus maps were constructed. The consensus map was compared with the International Consensus Linkage Map and with the whole genome sequence. Some loci showed segregation distortion and missing data, but this did not affect the analyses negatively. Several inversions and position shifts were detected, based on 95% confidence intervals and frequency distributions of loci. Some discrepancies in distances between loci and in ordering were due to chance, whereas others could be attributed to other effects, including reciprocal crosses, sampling error of the founder animals from the two populations, F(2) population structure, number of and distance between microsatellite markers, number of informative meioses, loci segregation patterns, and sex. In the Brazilian consensus GGA1, locus LEI1038 was in a position closer to the true genome sequence than in the International Consensus Map, whereas for GGA3 and GGA4, no such differences were found. Extending these analyses to the remaining chromosomes should facilitate comparisons and the integration of several available genetic maps, allowing meta-analyses for map construction and quantitative trait loci (QTL) mapping. The precision of the estimates of QTL positions and their effects would be increased with such information.

Evaluation of algorithms used to order markers on genetic maps.

When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with 100 and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results.

Characterization of new polymorphic functional markers for sugarcane.

Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 EST-SSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These EST-SSR markers were used to screen 18 sugarcane (Saccharum spp.) varieties. A high proportion (65.5%) of the above EST-SSRs, which gave amplified fragments of foreseen size, detected polymorphism. The number of alleles ranged from 2 to 24 with an average of 7.55 alleles per locus, while polymorphism information content values ranged from 0.16 to 0.94, with an average of 0.73. The ability of each set of EST-SSR markers to discriminate between varieties was generally higher than the polymorphism information content analysis. When tested for functionality, 82.1% of these 224 EST-SSRs were found to be functional, showing homology to known genes. As the EST-SSRs are within the expressed portion of the genome, they are likely to be associated to a particular gene of interest, improving their utility for genetic mapping; identification of quantitative trait loci, and comparative genomics studies of sugarcane. The development of new EST-SSR markers will have important implications for the genetic analysis and exploitation of the genetic resources of sugarcane and related species and will provide a more direct estimate of functional diversity.

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. The software is freely available at http://www.ciagri.usp.br/ approximately aafgarci/OneMap/.

Antimicrobial properties of moderately halotolerant bacteria from cenotes of the Yucatan peninsula.

AIMS: Isolation and antimicrobial evaluation of aquatic bacterial strains from two cenotes. METHODS AND RESULTS: A total of 258 bacterial strains were isolated from the water and sediment of two cenotes in the Yucatan peninsula, all of which were screened against six pathogenic micro-organisms. Antimicrobial activity was detected in 46 of the isolated strains against at least one of the target strains tested. Antimicrobially active isolates were identified as: Aeromonas, Bacillus, Burkholderia, Photobacterium, Pseudomonas, Serratia, Shewanella, Stenotrophomonas genera, and 13 remained unidentified. All antimicrobially active strains were able to grow in salt medium at a concentration of 75 g l(-1), thus classifying as moderately halotolerant bacteria. Most of the antimicrobially active strains exhibited a broad action spectrum, where 61% was because of uncharacterized antimicrobial substances, 25% because of bacteriocins and 13% because of siderophores. Ten strains were able to biosynthesize biosurfactant metabolites. CONCLUSIONS: Native bacteria from the Yucatan peninsula showed an interesting antimicrobial activity, diverse mode of action and moderate halotolerance to salt. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report on bacterial isolates from cenotes of the Yucatan peninsula and their antimicrobial characterization, with great potential for future biotechnological applications.

Use of the etonogestrel-releasing implant is associated with hypoactivation of the coagulation cascade.

BACKGROUND: The role of progestogens in haemostasis is controversial. Our objective is to evaluate the haemostatic effects of an etonogestrel-releasing implant. METHODS: This open-label, self-controlled, longitudinal study involved 20 healthy women receiving subcutaneous etonogestrel-releasing implants. At baseline, 1, 3 and 6 months, we measured the following: activated partial thromboplastin time; prothrombin time; thrombin time; fibrinogen; coagulation factors II, V, VII, VIII, IX, X and XI; von Willebrand factor; activated protein C (APC); antithrombin; free protein S; plasminogen activator inhibitor type 1 (PAI-1); alpha2-antiplasmin; thrombin-antithrombin (TAT) complex; prothrombin fragment 1 + 2 (F1 + 2); D-dimers; APC resistance. Statistical analyses included the Friedman test and ANOVA. RESULTS: Levels of APC (P < 0.01), factor II (P = 0.02), factor VII (P = 0.006), factor X (P = 0.01) and F1 + 2 (P < 0.001) were reduced, whereas those of PAI-1 (P = 0.01) and factor XI (P = 0.006) were transitory increased. All of these values, however, remained within normal ranges. Surprisingly, TAT concentrations fell below the normal range (P < 0.001). CONCLUSIONS: Our findings suggest that the etonogestrel-releasing implant does not induce a prothrombotic pattern during the first six months of use, and that its use is associated with a reduction in thrombin generation.

Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases.

Sugarcane (Saccharum spp.) is a clonally propagated outcrossing polyploid crop of great importance in tropical agriculture. Up to now, all sugarcane genetic maps had been developed using either full-sib progenies derived from interspecific crosses or from selfing, both approaches not directly adopted in conventional breeding. We have developed a single integrated genetic map using a population derived from a cross between two pre-commercial cultivars ('SP80-180' x 'SP80-4966') using a novel approach based on the simultaneous maximum-likelihood estimation of linkage and linkage phases method specially designed for outcrossing species. From a total of 1,118 single-dose markers (RFLP, SSR and AFLP) identified, 39% derived from a testcross configuration between the parents segregating in a 1:1 fashion, while 61% segregated 3:1, representing heterozygous markers in both parents with the same genotypes. The markers segregating 3:1 were used to establish linkage between the testcross markers. The final map comprised of 357 linked markers, including 57 RFLPs, 64 SSRs and 236 AFLPs that were assigned to 131 co-segregation groups, considering a LOD score of 5, and a recombination fraction of 37.5 cM with map distances estimated by Kosambi function. The co-segregation groups represented a total map length of 2,602.4 cM, with a marker density of 7.3 cM. When the same data were analyzed using JoinMap software, only 217 linked markers were assigned to 98 co-segregation groups, spanning 1,340 cM, with a marker density of 6.2 cM. The maximum-likelihood approach reduced the number of unlinked markers to 761 (68.0%), compared to 901 (80.5%) using JoinMap. All the co-segregation groups obtained using JoinMap were present in the map constructed based on the maximum-likelihood method. Differences on the marker order within the co-segregation groups were observed between the two maps. Based on RFLP and SSR markers, 42 of the 131 co-segregation groups were assembled into 12 putative homology groups. Overall, the simultaneous maximum-likelihood estimation of linkage and linkage phases was more efficient than the method used by JoinMap to generate an integrated genetic map of sugarcane.

Tropical maize germplasm: what can we say about its genetic diversity in the light of molecular markers?

Knowledge about genetic variability of a crop allows for more efficient and effective use of resources in plant improvement programs. The genetic variation within temperate maize has been studied extensively, but the levels and patterns of diversity in tropical maize are still not well understood. Brazilian maize germplasm represents a very important pool of genetic diversity due to many past introductions of exotic material. To improve our knowledge of the genetic diversity in tropical maize inbred lines, we fingerprinted 85 lines with 569 AFLP bands and 50 microsatellite loci. These markers revealed substantial variability among lines, with high rates of polymorphism. Cluster analysis was used to identify groups of related lines. Well-defined groups were not observed, indicating that the tropical maize studied is not as well organized as temperate maize. Three types of genetic distance measurements were applied (Jaccard's coefficient, Modified Rogers' distance and molecular coefficient of coancestry), and the values obtained with all of them indicated that the genetic similarities were small among the lines. The different coefficients did not substantially affect the results of cluster analysis, but marker types had a large effect on genetic similarity estimates. Regardless of genetic similarity coefficient used, estimates based on AFLPs were poorly correlated with those based on SSRs. Analyses using AFLP and SSR data together do not seem to be the most efficient manner of assessing variability in highly diverse materials because the result was similar to using AFLPs alone. It was seen that molecular markers can help to organize the genetic variability and expose useful diversity for breeding purposes.

Analysis of genetic similarity detected by AFLP and coefficient of parentage among genotypes of sugar cane ( Saccharum spp.).

Despite the economical importance of sugar cane, until the present-date no studies have been carried out to determine the correlation of the molecular-based genetic similarity (GS) and the coefficient of parentage ( f)-estimates generated for cultivars. A comprehensive knowledge of the amount of genetic diversity in parental cultivars, could improve the effectiveness of breeding programmes. In this study, amplified fragment length polymorphism (AFLP) and pedigree data were used to investigate the genetic relationship in a group of 79 cultivars (interspecific hybrids), used as parents in one of the Brazilian breeding programmes, and four species of Saccharum ( Saccharum sinense, Saccharum barberi and two of Saccharum officinarum). The objectives of this study were to assess the level of genetic similarity among the sugar-cane cultivars and to investigate the correlation between the AFLP-based GS and f, based on pedigree information. Twenty one primer combinations were used to obtain the AFLP molecular markers, generating a total of 2,331 bands, of which 1,121 were polymorphic, with a polymorphism rate, on average, of 50% per primer combination. GSs were determined using Jaccard's similarity coefficient, and a final dendrogram was constructed using an unweighted pair-group method using arithmetic average (UPGMA). AFLP-based GS ranged from 0.28 to 0.89, with a mean of 0.47, whereas f ranged from 0 to 0.503, with a mean of 0.057. Cluster analysis using GS divided the genotypes into related subgroups suggesting that there is important genetic relationship among the cultivars. AFLP-based GS and f were significantly correlated ( r= 0.42, P< 0.001), thus the significance of this r value suggests that the AFLP data may help to more-accurately quantify the degree of relationship among sugar-cane cultivars.