Sorghum hybrids grown in hydroponics contrast for phosphorus use efficiency / Híbridos de sorgo crescidos em hidroponia contrastam para eficiência de uso de fósforo

Phosphorus (P) use efficiency is crucial for sorghum production. P acquisition efficiency is the most important component of P use efficiency. The early-stage evaluation of plant development is a useful tool for identifying P-efficient genotypes. This study aimed to identify sorghum hybrids that are efficient in P use efficiency and assess the genetic diversity among hybrids based on traits related to P acquisition efficiency. Thus, 38 sorghum hybrids and two inbred lines (checks) were evaluated under low and high P in a paper pouch system with nutrient solution. Biomass and root traits related to P efficiency were measured. There was no interaction between genotypes and P levels concerning all evaluated traits. The biomass and root traits, except root diameter, presented smaller means under low P than high P. Efficient and inefficient hybrids under each P level were identified. The genetic diversity assessment grouped these genotypes in different clusters. The hybrids AG1090, MSK326, AG1060, 1G100, AS 4639, DKB 540, and DKB 590 were superior under low-P and high-P. Hybrids SC121, 1236020 e 1167017 presented the lowest means than all other hybrids, under both conditions. The evaluated hybrids showed phenotypic diversity for traits related to P acquisition, such as root length and root surface area, which can be useful for establishing selection strategies for sorghum breeding programs and increasing P use efficiency.

A eficiência do uso do fósforo (P) é fundamental para a produção de sorgo. A avaliação no estágio inicial do desenvolvimento da planta é uma ferramenta útil para a identificação de genótipos eficientes de P. Este trabalho teve como objetivo identificar híbridos de sorgo que sejam eficientes ao uso de P e avaliar a diversidade genética entre os híbridos com base em características relacionadas à eficiência de aquisição de P. Assim, 38 híbridos de sorgo e duas linhagens (testemunhas) foram avaliados sob baixo e alto P em sistema de pastas de papel com solução nutritiva. Características de biomassa e de raiz relacionadas à eficiência de P foram mensuradas. Não houve interação entre genótipos e níveis de P em todas as características avaliadas. As características de biomassa e raiz, exceto o diâmetro da raiz, apresentaram médias menores sob baixo P em comparação com alto P. Híbridos eficientes e ineficientes sob cada nível de P foram identificados e agrupados quanto à diversidade genética. Os híbridos AG1090, MSK326, AG1060, 1G100, AS 4639, DKB 540 e DKB 590 foram superiores sob baixo-P e alto-P. Os híbridos SC121, 1236020 e 1167017 apresentaram as menores médias que todos os outros híbridos, em ambas condições. Os híbridos avaliados apresentaram diversidade fenotípica para características relacionadas à aquisição de P, como comprimento e área superficial da raiz, o que pode ser útil para estabelecer estratégias de seleção para programas de melhoramento de sorgo e aumentar a eficiência de uso do P.

Genetic parameters of agronomic traits and yield components of soybean genotypes in the Colombian Altillanura / Parámetros genéticos de rasgos agronómicos y componentes de rendimiento de genotipos de soja en la Altillanura colombiana

ABSTRACT Soybean cultivation expansion in Colombia has generated the need to seek varieties with high genetic merit. A soybean genetic breeding program seeks to generate varieties with competitive and sustainable yields, and high-quality grain adapted to the conditions of the low tropics. The aim was to determine the genetic parameters and expected gains in quantitative traits of interest in a soybean breeding process using biometric tools. Sixty lines and four commercial varieties were evaluated in an 8x8 alpha lattice design (genotypes x blocks) planted in oxisols from the Altillanura region of Colombia. The estimation of the parameters was performed by applying mixed models with a random-effects adjustment through the REML method. Wide genetic variability was observed for all the evaluated traits, except for plant height. High heritability values were registered for the characters at flowering and maturity. Heritability was high for yield components such as the number of pods and the weight of 100 grains. Overall, the environmental effect was low, with values close to or higher than 1, except for embryonic abortions, number of empty pods, and grain yield. The genetic gain as a mean percentage was high for plant height, moderate for grain yield, and low for the rest of the characters. Moderate heritability and grain yield gain indicate an additive action of the genes ideal for recurrent selection. The most discriminating characters in the evaluated conditions were the grain yield, weight of 100 grains, and number of pods.

RESUMEN La expansión del cultivo de soya en Colombia genera la necesidad de buscar variedades con alto mérito genético y su mejoramiento, la generación de variedades con rendimientos competitivos y con alta calidad de grano, adaptadas a las condiciones del trópico bajo. El objetivo fue determinar, mediante herramientas biométricas, los parámetros genéticos y las ganancias esperadas, en caracteres cuantitativos de interés, para el proceso de mejora de soya. Se evaluaron 60 líneas y 4 variedades comerciales, en un diseño alfa látice 8x8, en oxisoles de la Altillanura. La estimación de los parámetros, se realizó mediante la aplicación de modelos mixtos, con ajuste de efectos aleatorios, por el método REML. Se observó amplia variabilidad genética para todos los rasgos evaluados, exceptuando la altura de planta. Se registraron valores altos de heredabilidad, para los caracteres de floración y madurez. En los componentes de rendimiento, la heredabilidad fue alta para número de vainas y peso de 100 granos. El efecto ambiental fue bajo, con valores cercanos o superiores a 1, con excepción de abortos embrionarios, número de vainas vanas y rendimiento de grano. La ganancia genética, como porcentaje de la media fue alta, para altura de planta; moderada, para rendimiento de grano y baja, para el resto de los caracteres. La heredabilidad y la ganancia moderadas de rendimiento de grano indican una acción aditiva de los genes, ideal para la selección recurrente. Los caracteres más discriminantes en las condiciones evaluadas fueron rendimiento de grano, peso de 100 granos y número de vainas.

Serological and molecular characterization of hepatitis B virus infection in chronic kidney disease patients from Rio de Janeiro, Brazil

ABSTRACT Chronic kidney disease (CKD) patients undergoing hemodialysis (HD) are more vulnerable to blood-borne viral infections due to frequent invasive procedures. Hepatitis B virus (HBV) infection in this cohort of patients has been a matter of concern worldwide. The objective of this cross-sectional study was to evaluate the frequency of serological markers for hepatitis B, and the occurrence of overt and occult HBV infection (OBI) and its molecular characterization in serum samples from 644 CKD patients in HD units located in Rio de Janeiro, Brazil, from 2013 to 2017. HBV DNA was investigated in HBsAg reactive and "anti-HBc alone" samples to determine infecting genotypes and genetic relatedness between sequences. The prevalence of serological markers HBsAg+, anti-HBc alone, anti-HBc+/anti-HBs+, anti-HBs+, anti-HBc/anti-HBs/HBsAg were 5.9%, 2.8%, 30.7%, 26.6%, 34.0%, respectively. HBV DNA was detected in 39.5% (15/38) of the HBsAg+ and in 5/18 (27.8%) of the "anti-HBc alone" individuals, indicating a high prevalence of OBI within this group. We found a higher prevalence of HBV/A1 (65%), followed by HBV/D3 (20%), and HBV/A2 (15%). Bayesian MCC tree with a highly supported clade, genetic distance comparison, and identical nucleotide sequences suggested a nosocomial spread of HBV in some units. The high prevalence of HBV infection and low number of individuals immune to infection reinforces the need for vaccination in this group. The presence of closely related strains in the same HD unit reinforces the importance of continuous improvement of safety control measures and laboratory surveillance of serological markers to prevent the risk of infection and transmission of HBV.

Spondias mombin (Anarcadiaceae): molecular characterization and conservation / Spondias mombin (Anarcadiaceae): caracterización molecular y conservación

Abstract Introduction: The fruit of the yellow mombin (Spondias mombin L.) is notable due to its sensory and functional qualities. However, there is little knowledge regarding the genetic diversity of this species, and this would aid the implantation of the cultivation of the fruit as a crop, since current production is based on extractivism. Objective: Evaluate the diversity and genetic structure of natural populations of S. mombin in the state of Mato Grosso, Brazil, through microsatellite molecular markers in order to assist in the implementation of conservation strategies and the collection of genetic resources. Methods: A total of 139 S. mombin individuals were sampled in ten natural populations. PCR amplifications were performed with seven fluorescence-marked microsatellite primers. Genetic diversity was evaluated by the number of alleles, expected (He) and observed heterozygosity (Ho), polymorphic information content (PIC), fixation index (ƒ), rare and exclusive alleles. The genetic structure was evaluated using AMOVA, UPGMA dendrogram and Bayesian statistical analysis. Results: 46 alleles were amplified, which had an average of 6.6 alleles per locus. He was higher than Ho and f was positive, indicating the presence of inbreeding. The PIC ranged from 0.048 to 0.700, and only two loci were poorly informative. We found 27 rare alleles and 16 unique alleles. The largest component of variation was intrapopulational (90.64 %). The estimated gene flow was 1.99, which indicates that there is no genetic isolation between populations, and justifies the FST value (0.0963). The ten populations were grouped into two groups, and two populations constituted an isolated group. The Mantel test demonstrated that the genetic structure is not related to the geographic distance between populations. Conclusion: There is genetic diversity in the populations of S. mombin, which must be conserved in situ or ex situ, due to the diversity they present and because they are promising sources for collection of germplasm.

Resumen Introducción: El fruto amarillo del jobo o yuplón (Spondias mombin L.) destaca por sus cualidades sensoriales y funcionales. Sin embargo, existe poco conocimiento sobre la diversidad genética de esta especie, lo que ayudaría a la implantación del cultivo del fruto como cultivo, ya que la producción actual se basa en el extractivismo. Objetivo: Evaluar la diversidad y estructura genética de poblaciones naturales de S. mombin en el estado de Mato Grosso, Brasil, a través de marcadores moleculares microsatélites para ayudar en la implementación de estrategias de conservación y recolección de recursos genéticos. Métodos: Se muestrearon un total de 139 individuos de S. mombin en diez poblaciones naturales. Las amplificaciones por PCR se realizaron con siete cebadores de microsatélites marcados con fluorescencia. La diversidad genética se evaluó por el número de alelos, heterocigosidad esperada (He) y observada (Ho), contenido de información polimórfica (PIC), índice de fijación (ƒ), alelos raros y exclusivos. La estructura genética se evaluó mediante AMOVA, dendrograma UPGMA y análisis estadístico bayesiano. Resultados: Se amplificaron 46 alelos, los cuales tenían un promedio de 6.6 alelos por locus. Fue más alto que Ho y f positivo, lo que indica la presencia de endogamia. El PIC osciló entre 0.048 y 0.700, y solo dos loci fueron poco informativos. Encontramos 27 alelos raros y 16 alelos únicos. El mayor componente de variación fue intrapoblacional (90.64 %). El flujo de genes estimado fue de 1.99, lo que indica que no hay aislamiento genético entre poblaciones y justifica el valor de FST (0.0963). Las diez poblaciones se agruparon en dos grupos y dos poblaciones constituyeron un grupo aislado. La prueba de Mantel demostró que la estructura genética no está relacionada con la distancia geográfica entre poblaciones. Conclusión: Existe diversidad genética en las poblaciones de S. mombin, la cual debe ser conservada in situ o ex situ, por la diversidad que presentan y porque son fuentes promisorias para la recolección de germoplasma.

Variabilidad genética del ADN mitocondrial de Vultur gryphus (cóndor andino) en Cusco y Apurímac a partir de plumas de muda / Genetic variability of mitochondrial DNA of Vultur gryphus (Andean Condor) in Cusco and Apurimac from molting feathers

Resumen La variabilidad genética intrapoblacional de Vultur gryphus (cóndores andinos) de las regiones de Cusco y Apurímac fue evaluada mediante amplificación y secuenciación del ADN mitocondrial correspondientes a la región control y subunidad ribosomal 12S (D-Loop-ARNr12S), y a los genes Citocromo Oxidasa subunidad I (COI) y NADH deshidrogenasa subunidad II (ND2). El ADN se extrajo a partir de cálamos de plumas de muda de ejemplares en cautiverio y silvestres. Se analizaron los principales índices de diversidad genética como son: la diversidad haplotípica, la diversidad nucleotídica, el número promedio de diferencias nucleotídicas y el número de sitios polimórficos. La tasa de éxito de amplificación mediante PCR fue de 100% para las tres regiones de ADN analizadas. Se secuenció 600 pb de la región D-Loop-ARNr12S caracterizándose cuatro haplotipos, 704 pb del gen COI caracterizándose seis haplotipos y 1090 pb del gen ND2 caracterizándose cinco haplotipos. El gen COI presentó el mayor valor de diversidad haplotípica (Hd = 0.468), la región del gen D-Loop-ARNr12S presentó el mayor índice de diversidad nucleotídica (π = 0.00086), mientras que el gen COI presentó el mayor número promedio de diferencias nucleotídicas (K = 0.52615). Los resultados muestran bajos niveles de variabilidad genética en los genes mitocondriales de los cóndores andinos de la zona de estudio, que indicarían una población con estructura genética homogénea.

Abstract The intrapopulation genetic variability of Vultur gryphus (Andean condors) from Cusco and Apurimac regions was evaluated by amplification and sequencing of mitochondrial DNA corresponding to the control region and 12S ribosomal subunit (D-Loop-RNAr12S), Cytochrome Oxidase subunit I (COI) genes and NADH dehydrogenase subunit II (ND2) gene. DNA was extracted from the calamus of feathers recollected from captive and wild specimens. The main indices of genetic diversity such as the haplotype diversity, the nucleotide diversity, the average number of nucleotide differences and the number of polymorphic sites were analyzed. The PCR amplification success rate was 100% for the three mitochondrial amplified sequences. Four haplotypes were identified from the 600 bp sequenced of D-Loop-RNAr12S region; six haplotypes from the 704 bp sequenced of the COI gene; five haplotypes from the 1090 bp sequenced of the ND2 gene. The COI gene presented the highest haplotype diversity (Hd = 0.468), the D-Loop-RNAr12S region presented the highest index of nucleotide diversity (π = 0.00086), while the COI gene presented the highest average number of nucleotide differences (K = 0.52615). The results show low levels of genetic variability in the mitochondrial genes of the Andean Condor in the study area, indicating a population with a homogeneous genetic structure.

Polymorphism analysis on the 5′ flanking region of CD25 gene of Han males in naturally high radiation background area / 中国职业医学

OBJECTIVE: To explore the distribution characteristics of single nucleotide polymorphism(SNP) rs7072793 and rs3118470 in the 5′ flanking region of(cluster of differentiation 25, CD25) gene in Han males in the naturally high radiation background area(HBRA). METHODS: A random sampling method was used to select 48 and 51 healthy Han males from Tangkou town(HBRA group) in Yangjiang City and Hengpo town(control group) in Enping City, respectively, as the study subjects. The molecular mass array method was used to classify the genotype of the SNP sites rs7072793 and rs3118470 of CD25 gene in these subjects. The distribution difference of the alleles and genotypes was analyzed in individuals of these two groups. The allele frequency of HBRA population was compared with the distribution data of different populations in the Human Genome Project.RESULTS: The distribution of allele frequencies of rs7072793 and rs3118470 in both groups were consistent with the H-W equilibrium law of genetics(all P>0.05). In the HBRA group, variant allele C(58.3%) and genotype TC(50.0%) were dominant at rs7072793, wild-type allele T(55.2%) and genotype TC(56.2%) were dominant at rs3118470. There was no significant difference in the allele and genotype distributions between these two groups(all P>0.05). There was a difference of rs7072793 in the HBRA group compared to that of African and European populations, and rs3118470 in the HBRA group compared with the allele distribution frequencies in Africa, Europe and America populations(all P<0.05). CONCLUSION: In the male population of Han nationality in Yangjiang HBRA area, the alleles of rs7072793 and rs3118470 in the 5′ flanking region of CD25 gene were mainly C and T, respectively, and the genotypes were mainly TC. These two loci may have high genetic variability.

Testing accession genetic composition of a germ-plasm bank for mangabeira (Hancornia speciosa)

The objective of the current study was to measure the genetic variability of natural populations of Hancornia speciosa using RAPD type molecular markers to assay variation in existing sampled genotypes, using morphological variables, and so assess germplasm bank composition. Morphological and chemical characteristics H. speciosa fruits and seeds were evaluated using descriptive statistics and principal components analysis. Cluster analyzes was conducted using Jaccard's similarity index, via the UPGMA hierarchical agglomerative method. Phenotypic variability was found in the two studied populations. However, variability was higher in the São Judas population, where the variables: pulp yield and soluble solids content were higher than those in the Canaã population. High genetic variability was found in both study populations, and between- and within-population morphological and genetic variation was present in the studied populations. The nine primers generated 70 bands, of which 68 were polymorphic, with the primers A-08 and C-04 generating the highest number of polymorphic bands. The two populations differ principally in the pulp ratio and the proportion of total solids in the pulp (°Brix). RAPD markers used gave acceptable results and, to initiate the Federal University of Tocantins Active Mangaba Germplasm Bank, seven genotypes were sampled from the Canaã population and five from the São Judas Tadeu population.

Selection of somaclonal variants of maracuyá (passiflora Edulis var Flavicarpa. Deneger) tolerants to water deficit / Selección de variantes somaclonales de maracuyá (Passiflora edulis var flavicarpa. Deneger) tolerantes a déficit hídrico

ABSTRACT Climate change will have an impact on the Colombian agricultural sector, by 2050 increases in temperature and distribution of erratic rainfall are expected. Passion fruit cultivation does not tolerate water deficit, it reduces flower induction, generates fruit drop and defoliation. To tackle this problem, somaclonal variants (VS) of passion fruit were selected in-vitro, seeking tolerance to water deficit. Four phases were developed: I) callogenesis, II) direct and indirect organogenesis, II) Induction and evaluation of the water deficit with Polyethylene glycol 6000 (PEG 6000) and IV) in vitro selection of VS by morphometric measurements, chlorophyll and total sugars contents. Differences in callogenesis were found with different concentrations of 2,4-D, the concentration of 2 mg L-1 presented better results producing calluses in less time and in greater quantity (8 days, 90% of the leaf area). In indirect and direct organogenesis the medium MS + ANA + BAP (0.3: 0.6), showed significant statistical differences with respect to other means, for the variables root length (15.14 cm), stem (16.72 cm) and leaves ( 14.51 cm) and root thickness (0.76 cm) stem (1.25) and leaf width (6.75). The influence of PEG 6000 showed significant differences, the treatment with 30 g L-1 showed the smallest leaf width, the greatest width was found in 25 g L1. Statistical differences were found in chlorophyll levels and total sugar contents, the highest contents were recorded in the VS 25VS1, showing the possibility of obtaining seedlings tolerant to the water deficit of passion fruit by inducing somaclonal variation.

RESUMEN El cambio climático tendrá impactos en el sector agropecuario colombiano, para el 2050 se prevén aumentos de temperatura y distribución de lluvias erráticas. El cultivo de maracuyá no tolera el déficit hídrico, este disminuye la inducción floral, genera caída de frutos y defoliación. Para abordar esta problemática se seleccionaron in-vitro variantes somaclonales (VS) de maracuyá, buscando tolerancia al déficit hídrico. Se desarrollaron cuatro fases: I) callogénesis, II) organogénesis directa e indirecta, III) Inducción y evaluación del déficit hídrico con Polientilenglicol 6000 (PEG 6000) y IV) selección in vitro de VS por mediciones morfométricas, contenidos de clorofila y azúcares totales. Se hallaron diferencias en callogénesis con diferentes concentraciones de 2,4-D, la concentración de 2 mg-L-1 presentó mejores resultados produciendo callos en menor tiempo y en mayor cantidad (8 días, 90% del área foliar); en organogénesis indirecta y directa el medio MS + ANA + BAP (0.3:0.6), mostró diferencias estadísticas significativas respecto a otros medios, para las variables longitud de raíz (15.14 cm), tallo (16.72 cm) y hojas (14.51 cm) y grosor de raíz (0.76 cm) tallo (1.25) y ancho de hojas (6.75). La influencia de PEG 6000 mostró diferencias significativas, el tratamiento con 30 g-L-1 mostró menor ancho de hojas, el mayor ancho se encontró en 25 g-L-1. Se hallaron diferencias estadísticas en niveles de clorofila y contenidos de azúcares totales, los mayores contenidos se registraron en el VS 25VS1, mostrando la posibilidad de obtener plántulas tolerantes al déficit hídrico de maracuyá mediante la inducción de variación somaclonal.

Transferability of heterologous primers in Brycon falcatus

The genus Bryconcomprises fish species of significant socioeconomic and biological importance in Brazil. Despite that, the genetic knowledge about these species is scarce, especially regardingBrycon falcatus. Thus, the objective of this study was to evaluate the transferability of heterologous microsatellite primers inB. falcatus for the first time. Heterologous primers obtained from B. opalinus, B. hilarii, B. insignis, B. orbignyanus, B. amazonicus, Prochilodus argenteus, Prochilodus lineatus, Piaractus mesopotamicus, and Colossoma macropomum were evaluated. The primers that showed the best amplification patterns were applied to a sample of 22 individuals and the genetic parameters were calculated. Nine primers displayed satisfactory cross-amplification withB. falcatus: BoM5 (Brycon opalinus); Bh8, Bh13 and Bh16 (B. hilarii); Borg59 (B. orbignyanus); Bag22 (B. amazonicus); Par12 and Par80 (P. argenteus), and Cm1A8 (C. macropomum). The genetic parameters (number of alleles, effective alleles, allele richness, and expected and observed heterozygosity) and the polymorphic information content (PIC) confirmed the viability of these primers for population genetics analyses. Our study demonstrates the potential of transferability of microsatellite markers from related species and even different genera to B. falcatus, providing usefull tools for future population genetic studies in this species. (AU)

Assessment of genetic variability of chilli in Western Himalayan Region

Aim: The present study was conducted with the aim to collect and evaluate the available genetic diversity of chilli (Capsicum annuum L.) in order to identify promising accessions for cultivation as well as use in crop improvement. Methodology: A total 78 accessions of chilli were collected from Western himalayan region, i.e., Kashmir valley of India. Collected germplasm was evaluated at one location for fifteen quantitative traits of horticultural importance. Results: With ample diversity in these traits, a high coefficient of variation was found. Principal Component Analysis (PCA) revealed that first five principal components possessed eigen value > 1, cumulatively contributed > 65.2 percent of total variability. All the genotypes were grouped into five clusters showing non parallelism between geographic and genetic diversity. Interpretation: The genotypes grouped in different clusters may be utilized for hybridization programme to produce more heterotic recombinants.

Barnyardgrass control using tank-mixed herbicides with saflufenacil and its influence in photosynthesis and chlorophyll fluorescence / Controle de capim-arroz mediante associações de herbicidas com saflufenacil e influência na fotossíntese e fluorescência de clorofila

ABSTRACT: The objectives of this research were to evaluate the interaction between herbicides mixed with saflufenacil for the control of barnyardgrass and to determine the effect on photosynthetic and chlorophyll fluorescence parameters. The experiment was conducted in a greenhouse in a 2x8 factorial scheme, whose factor A tested resistant and susceptible biotypes; and factor B the herbicides: saflufenacil (70 g a.i. ha-1), clomazone (180 g a.i. ha-1), imazapyr + imazapic (73.5 + 24.5 g a.i. ha-1), and cyhalofop (360 g a.i. ha-1), the mixtures of these herbicides with saflufenacil, and control without treatment. Weed control was assessed 7, 14, 21 and 28 days after herbicide application (DAA), as well as shoot dry matter at 28 DAA, photosynthetic parameters using infrared gas analyzer (IRGA), and emission of chlorophyll a fluorescence after 24 and 28 hours of application of treatments, respectively, and interaction of herbicides. Combination of saflufenacil with the herbicides tested in general did not change the response of both barnyardgrass biotypes to the herbicides used. The resistant biotype showed a lower negative effect on chlorophyll fluorescence and photosynthesis parameters in the combination of herbicides with saflufenacil. The herbicide cyhalofop was effective for the control of ALS-susceptible and resistant barnyardgrass.

RESUMO: O objetivo deste trabalho foi avaliar a interação entre herbicidas associados ao saflufenacil para o controle de capim-arroz e a determinação do efeito dos herbicidas sobre os parâmetros fotossintéticos e de fluorescência de clorofila. O experimento foi conduzido em casa de vegetação em esquema fatorial 2x8, cujo fator A testou os biótipos resistente e suscetível; e o fator B os herbicidas: saflufenacil (70 g i.a. ha-1), clomazone (180 g i.a. ha-1), imazapyr+imazapic (73,5+24,5 g i.a. ha-1), cyhalofop (360 g i.a. ha-1), as associações desses com saflufenacil, e testemunha sem tratamento. Foi avaliado o controle aos 7, 14, 21 e 28 dias após a aplicação dos herbicidas (DAA), massa seca da parte aérea aos 28 DAA, avaliação de parâmetros fotossintéticos com analisador de gás infravermelho (IRGA) e emissão de fluorescência da clorofila a 24 e 48 horas após aplicação dos tratamentos, respectivamente, e interação dos herbicidas. A associação de saflufenacil com herbicidas testados na maior parte não modificou a resposta dos herbicidas para o controle de capim-arroz em ambos os biótipos. O biótipo resistente apresentou menor efeito negativo nos processos de fluorescência de clorofila e parâmetros de fotossíntese na associação de herbicidas com saflufenacil. O herbicida cyhalofop associado ao saflufenacil demonstra ser eficiente para o controle de capim-arroz suscetível e resistente a ALS.

Role of genetic variability in Mendelian and multifactorial diseases

The first draft of the human genome sequencing published in 2001 reported a large number of single nucleotide polymorphisms (SNPs). Given that these polymorphisms could practically represent all the variability involved in the susceptibility, protection, severity, among other aspects, of various common diseases, as well as in their response to medications, it was thought that they might be “the biomarkers of choice” in personalized genomic medicine. With the new information obtained from the sequencing of a larger number of genomes, we have understood that SNPs are only an important part of the genetic markers involved in these traits. In addition to SNPs, other variants have been identified, such as insertions/deletions (INDELs) and copy number variants (CNVs), which – in addition to classic variable number tandem repeats (VNTRs) and short tandem repeats (STRs) – originate or contribute to the development of diseases. The use of these markers has served to identify regions of the genome involved in Mendelian diseases (one gene-one disease) or genes directly associated with multifactorial diseases. This review has the purpose to describe the role of STRs, VNTRs, SNPs, CNVs and INDELs in linkage and association studies and their role in Mendelian and multifactorial diseases.

Análisis de la variabilidad genética de una muestra de la población de Bogotá: hacia la constitución de un mapa de haplotipos / Genetic variability analysis in a population from Bogotá: Towards a haplotype map

Resumen Introducción. Los proyectos del mapa de haplotipos (HapMap) y de los 1.000 genomas han sido fundamentales para la compresión del componente genético de las enfermedades comunes y los fenotipos normales. Sin embargo, la variabilidad genética colombiana incluida en estos proyectos no es representativa del país. Objetivo. Contribuir al conocimiento de la variabilidad genética de la población colombiana a partir del estudio genómico de una muestra de individuos de Bogotá. Materiales y métodos. Se genotipificaron 2'372.784 marcadores genéticos de 32 individuos nacidos en Bogotá y de padres originarios de la misma ciudad utilizando la plataforma Illumina™. Los niveles de variabilidad genética se determinaron y se compararon con los datos disponibles de otras poblaciones del proyecto de los 1.000 genomas. Resultados. Los individuos analizados presentaron una variabilidad genética semejante a la de poblaciones con las que comparten ancestros. No obstante, a pesar de la poca diferenciación genética detectada en la población de Bogotá y en la de Medellín, el análisis de los componentes principales sugiere una composición genética diferente en las dos poblaciones. Conclusiones. El análisis genómico de la muestra de Bogotá permitió detectar similitudes y diferencias con otras poblaciones americanas. El aumento de tamaño de la muestra bogotana y la inclusión de muestras de otras regiones del país permitirán una mejor compresión de la variabilidad genética en Colombia, lo cual es fundamental para los estudios de salud humana, y la prevención y el tratamiento de enfermedades comunes en el país.

Abstract Introduction: The HapMap and the 1000 Genomes projects have been important for understanding the genetic component of common diseases and normal phenotypes. However, the Colombian genetic variability included in these projects is not fully representative of our country. Objective: To contribute to the knowledge of the Colombian genetic variability through the genomic study of a sample of individuals from Bogotá. Materials and methods: A total of 2,372,784 genetic markers were genotyped in 32 individuals born in Bogotá whose parents are from the same region, using the Illumina™ platform. The genetic variability levels were determined and compared with the data available from other populations of the 1000 Genomes Project. Results: The genetic variability detected in the individuals from Bogotá was similar to those with shared ancestry. However, despite the low levels of genetic differentiation between Bogotá and Medellín, populations the principal component analysis suggested a different genetic composition in them. Conclusions: Our genomic analysis of a Bogotá sample allowed us to detect similarities and differences with other American populations. The increase of the Bogotá sample and the inclusion of samples from other regions of the country will improve our understanding of the genetic variability in Colombia, essential for studies of human health and the prevention and treatment of common diseases in our country.

Parameters and genetic trends for reproductive characteristics of a closed Angus herd / Parámetros y tendencias genéticas de características reprodutivas de um rebaño cerrado Angus / Parâmetros e tendências de carcaterísticas reprodutivas de um rebanho fechado Angus

Abstract Background: Closed breeding populations are useful to conduct basic and applied research. The Wye Angus herd is one of them. It was founded using only a few animals. The pedigree of the descendants of the original herd can be completely described by historical records resulting from strong selection. Wye Angus genetics has influenced that of Aberdeen Angus, Red Angus, and Brangus cattle worldwide. Objective: To evaluate parameters and genetic trends associated with the reproduction traits of the Wye Angus herd between the years 1937 and 2012. Methods: We used pedigree information of 11,692 individuals. The reproductive traits assessed were age at first calving (AFC), calving interval (CI), and scrotal circumference (SC). The covariance components were estimated by Bayesian inference. The genetic trends were obtained by linear regression of the genetic values over birth years of the animals. Results: The heritability estimates for AFC, and CI were negligible, although a small genetic gain was associated with CI. Because the AFC and CI values of the herd are small, past reproductive management has produced favourable results for the heifers. Conclusion: The Wye Angus herd has enough genetic variability for genetic gain through selection on SC.

Resumen Antecedentes: Las poblaciones reproductivas cerradas son útiles para realizar investigacion básica y aplicada. El hato Wye Angus es uno de ellos. Fue fundado utilizando sólo unos pocos animales. El pedigrí de los descendientes del hato original puede describirse completamente mediante registros históricos resultantes de una fuerte selección. La genética del Wye Angus ha influido en la del Aberdeen Angus, Red Angus y Brangus en todo el mundo. Objetivo: Evaluar los parámetros y las tendencias genéticas de características reproductivas del rebaño Wye Angus en el periodo entre 1937 y 2012. Métodos: Utilizamos información de pedigrí de 11.692 individuos. Las características evaluadas fueron circunferencia escrotal (SC), edad al primer parto (AFC) y el intervalo entre partos (CI). Los componentes de (co)variancia fueron obtenidos mediante metodología Bayesiana. Las tendencias genéticas fueron obtenidas por regresión lineal ponderada de los valores genéticos sobre el año de nacimiento del animal. Resultados: Las estimaciones de heredabilidad para AFC y CI fueron insignificantes, aunque se asoció un pequeño beneficio genético con CI. Sin embargo, la AFC y el CI del rebaño son bajos, indicando que el manejo reproductivo ha traído resultados favorables para las novillas. Conclusion: El rebaño Wye Angus posee suficiente variabilidad genética para la ganancia genética por medio de la selección para SC.

Resumo Antecedentes: O rebanho Wye Angus foi fundado a partir de poucos animais e destaca-se por ser um rebanho fechado, com informações completas de pedigree e forte seleção, oferecendo vantagens únicas em termos de realização de pesquisas em melhoramento genético animal. Além disso, a genética de Wye Angus tem influenciado os de Aberdeen Angus, Red Angus e Brangus em todo o mundo. Objetivo: Avaliar os parâmetros genéticos e tendências de características reprodutivas do rebanho Wye Angus no período entre 1937 e 2012. Métodos: Foram usadas informações do pedigree de 11.692 individuos. As características avaliadas foram: perímetro escrotal (SC), idade ao primeiro parto (AFC), e do intervalo entre partos (CI). Componentes de (co) variância foram obtidos por meio da metodologia Bayesiana. As tendências genéticas foram obtidas por regressão linear ponderada dos valores genéticos sobre o ano de nascimento do animal. Resultados: Hereditariedade para AFC e CI foram insignificantes, embora um pequeno ganho genético tenha sido associado a CI. No entanto, os valores para AFC e CI do rebanho são baixos, indicando que o manejo reprodutivo trouxe resultados favoráveis para as novilhas. Conclusão: O rebanho Wye Angus tem variabilidade genética suficiente para ganho genético através de seleção para SC.

Prueba de interacción en el análisis molecular de varianza / Test of interaction in the analysis of molecular variance

La diversidad genómica, expresada en las diferencias entre haplotipos moleculares de un conjunto de individuos, puede dividirse en componentes de variabilidad entre y dentro de algún factor de clasificación de los individuos. Para tal partición de varianzas, se usa análisis molecular de la varianza (AMOVA), el cual se construye a partir de las distancias multivariadas entre pares de haplotipos. El AMOVA clásico permite evaluar la significancia estadística de dos o más factores jerárquicos y consecuentemente no existe prueba de interacción entre factores. Sin embargo, existen situaciones donde los factores que clasifican a los individuos están cruzados y no anidados, es decir todos los niveles de un factor se encuentran representados en cada nivel del otro factor. Este trabajo propone una prueba estadística para evaluar la interacción entre factores cruzados en un AMOVA No-Jerárquico. La hipótesis nula de interacción establece que las diferencias moleculares entre individuos de distintos niveles de un factor son las mismas para todos los niveles del otro factor que los clasifica. La propuesta de análisis de interacción de factores a partir de distancias en un AMOVA No-Jerárquico comprende: cálculo de la matriz de distancia y partición de la misma en bloques, posterior cálculo de residuos y análisis de varianza no-paramétrico sobre los residuos. Su implementación es ilustrada en escenarios simulados y real. Los resultados sugieren que la prueba de interacción propuesta para el AMOVA No- Jerárquico presenta alta potencia.

The genomic diversity, expressed in the differences between molecular haplotypes of a group of individuals, can be divided into components of variability between and within some factor of classification of the individuals. For such variance partitioning, molecular analysis of variance (AMOVA) is used, which is constructed from the multivariate distances between pairs of haplotypes. The classical AMOVA allows the evaluation of the statistical significance of two or more hierarchical factors and consequently there is no interaction test between factors. However, there are situations where the factors that classify individuals are crossed rather than nested, that is, all the levels of a factor are represented in each level of the other one. This paper proposes a statistical test to evaluate the interaction between crossed factors in a Non-Hierarchical AMOVA. The null hypothesis of interaction establishes that the molecular differences between individuals of different levels of a factor are the same for all the levels of the other factor that classifies them. The proposed analysis of interaction in a Non- Hierarchical AMOVA includes: calculation of the distance matrix and partition of it into blocks, subsequent calculation of residuals and analysis of non-parametric variance on the residuals. Its implementation is illustrated in simulated and real scenarios. The results suggest that the proposed interaction test for the Non-Hierarchical AMOVA presents high power.

Population Structure and Genetic Diversity of Sweet Cassava Accessions from the Midwestern, Southeastern and Southern Regions of Brazil

Abstract The objective of this work was to screen sweet cassava accessions collected in smallholding areas in the Midwestern, Southeastern and Southern regions of Brazil, using 15 SSR molecular markers, to determine population structure and genetic diversity. Polymorphism was detected in every loci analyzed, with mean of 6.33 alleles per locus, and mean polymorphism information content (PIC) of 0.6057, pointing out that the primers were highly informative. The observed heterozygosity ranged from 0.0709 (SSRY 101) to 0.9398 (GA 12), with a mean of 0.6511, and mean genetic diversity of 0.6578, ranging from 0.3592 (GA 136) to 0.8116 (SSRY 21). The most dissimilar combinations observed were BGM526PR-BGM596MS, BGM526PR-BGM622MS and BGM526PR-BGM629MS. The traditional cassava cultivars assessed were divided into four distinct groups: two with cultivars from the South, one from the Southeast and one from the Midwestern region of Brazil. The variances among and within groups determined by the analysis of molecular variance were 44 and 56%, respectively. The PhiPT parameter (analogue to Fst) of 0.44 indicates high differentiation among groups. Broad genetic diversity was found among the traditional sweet cassava cultivars assessed, and the most divergent groups were formed by cultivars from the South and the Midwestern regions of Brazil.

Genetic diversity in Mexican wild populations of the Great Curassow (Crax rubra) / Diversidad genética en poblaciones silvestres mexicanas del hocofaisán (Crax rubra)

Abstract The Great Curassow (Crax rubra) is a Neotropical bird with a wide distribution; it is classified under different threat categories and is listed as a vulnerable species by the IUCN. The Official Mexican Standard, the NOM-059-SEMARNAT-2010, indicates that the Great Curassow is a threatened species, and the subspecies Crax rubra griscomi, which is restricted to the island of Cozumel, is classified as critically endangered. Habitat loss and fragmentation, hunting, overexploitation, and illegal trade are among the main factors that have placed the bird at an endangered status. The objective of the present study was to determine the genetic structure and variation of the species within the Mexican populations of Crax rubra by using three mitochondrial markers, and one nuclear marker (COI, ND2, Cyt b, and MUSK). We used 47 samples obtained by noninvasive collection (feathers) including the two different color phases of the female plumage: dark brown and barred (rare in Mexico). Gene flow between the remaining populations is recent and extensive, even between the continental and the island population (C. r. griscomi). The results indicate that the subspecies C. r. rubra and C. r. griscomi do not present a marked genetic differentiation because the second exhibits an exclusive haplotype and a shared haplotype. With this study, we provide the first genetic-geographic approximation of the curassow in Mexico, where a gradual geographic differentiation is observed between the western and eastern populations of the Isthmus of Tehuantepec, and we provide a baseline for future studies. Finally, the information obtained indicates that important genetic diversity persists in the Mexican populations of the Great Curassow and that sufficient conservation within the ecosystems of these subspecies can be obtained by protecting them from overexploitation and by conserving and restoring their habitat.

Resumen El hocofaisán (Crax rubra) es un ave de la región Neotropical con amplia distribución, que se encuentra en diferentes categorías de riesgo, por la IUCN está catalogada como una especie Vulnerable. A nivel nacional, dentro de la NOM-059-SEMARNAT-2010 está considerada como una especie amenazada, y la subespecie Crax rubra griscomi restringida a la isla de Cozumel, está categorizada como en peligro de extinción. Entre los factores principales por los que se encuentra en grave riesgo, destacan la pérdida y fragmentación del hábitat, la cacería, la sobreexplotación, la extracción y el comercio ilegal. El objetivo del presente estudio es conocer la estructura y variación genética de la especie dentro de las poblaciones silvestres mexicanas de Crax rubra, mediante el uso de tres marcadores mitocondriales y uno nuclear (COI, ND2, Cyt b y MUSK). A partir de 47 muestras obtenidas mediante colecta no invasiva (plumas) que incluyen las dos fases de plumaje de la hembra: café oscura y barrada (rara en México). Se observó que el flujo génico entre las poblaciones remanentes es reciente y extenso, incluso entre las poblaciones continentales y la isleña (C. r. griscomi). Los resultados indican que las subespecies C. r. rubra y C. r. griscomi no presentan una marcada diferenciación genética dado que la segunda presentó un haplotipo exclusivo y uno compartido. Con el presente estudio brindamos la primera aproximación genético-geográfica del hocofaisán en México y una línea de base para futuros estudios, en el que se observa una diferenciación geográfica gradual entre las poblaciones del oeste y del este del Istmo de Tehuantepec. Finalmente, la información obtenida indica que en las poblaciones mexicanas del hocofaisán persiste una diversidad genética importante y que su conservación en los ecosistemas puede ser suficiente mediante la protección a la sobreexplotación, la conservación y restauración de su hábitat.

Simulation of pattern of gene flow in Canjerana fragments in the Brazilian Atlantic Rainforest for evaluating genetic conservation strategies / Simulação do padrão de fluxo gênico em fragmentos de Canjerana no bioma Mata Atlântica para definição de estratégias de conservação genética

ABSTRACT: Gene flow is important for the conservation of genetic resources to allow connectivity of geographically isolated populations and which genetic variability is reduced. Gene movement is a function of flow rate and model. Understanding how gene flow occurs can contribute to the conservation and selection of priority populations that could benefit from an eventual intervention. Simulation softwares allow making inferences about past events based on current datasets or predict future phenomena under real genetic scenarios. Adverse phenomena can be predicted and actions can be taken to avoid them. The aim of this study was to identify a model and the gene flow rates that could explain genetic structure of eight forest fragments of Cabralea canjerana in development in the Brazilian Atlantic Rainforest. To do this, simulations were performed with the EASYPOP software using a microsatellite marker dataset obtained for the species by Melo and collaborators, in 2012, 2014 and 2016. We tested five models and nine migration rates and we selected the model that produced values closer to those previously obtained for them. Criteria used for selection were the observed and expected heterozygosity and the Wright's F Statistics obtained in the simulations. The gene flow model selected was the isolation by distance model that used a rate of 0.1. We observed high levels of genetic differentiation among the fragments as result of their reproductive isolation. To allow homogenization of the allelic frequencies through gene flow, the solution would be to create ecological corridors with the aim of connecting distant fragments.

RESUMO: O fluxo gênico, cuja efetividade é função do modelo e da taxa, assume especial importância na conservação de recursos genéticos por permitir a conectividade de populações isoladas geograficamente, sujeitas à redução da variabilidade genética. O entendimento de como o fluxo gênico ocorre pode contribuir no planejamento de ações para a conservação e na seleção de populações prioritárias para uma eventual intervenção. Programas de simulação permitem inferir sobre eventos passados, a partir de dados atuais ou prever fenômenos futuros sob cenários genéticos reais. Fenômenos adversos podem ser previstos e medidas podem ser tomadas para contorná-los. O objetivo deste estudo foi identificar o modelo e a taxa de fluxo gênico que melhor explicam a estrutura genética de oito fragmentos da espécie arbórea florestal Cabralea canjerana, em desenvolvimento na região brasileira do bioma Mata Atlântica. Foram realizadas simulações com o programa EASYPOP usando dados de marcadores microssatélites obtidos por Melo e colaboradores, em 2012, 2014 e 2016, sendo testados cinco modelos e nove taxas de migração, selecionando-se o modelo que apresentou os valores mais próximos daqueles que foram publicados. Os critérios usados para a seleção do modelo foram a heterozigosidade observada e esperada e as estatísticas F de Wright obtidas nas simulações. O modelo de fluxo gênico entre os fragmentos foi o de isolamento por distância a uma taxa de 0.1. Foram observados elevados índices de diferenciação genética entre os fragmentos em decorrência do seu isolamento reprodutivo. Desse modo, sugere-se a construção de corredores ecológicos com vistas a conectar fragmentos distantes e, desta forma, permitir a homogeneização das frequências alélicas por meio do fluxo gênico.

Protein, lipid and isoflavone contents of food-type soybean lines at two sowing dates / Teores de proteína, óleo e isoflavonas de linhagens de soja tipo alimento em duas épocas de semeadura

Few works have reported the relationship among genotype, temperature, rainfall and the chemical compounds of soybean. Therefore, the aim of this study was to investigate the interaction effect between soybean food-type inbred lines sowed in two different dates and the contents of protein, oil and isoflavones. Eight lines with null lipoxygenase seeds classified as food-type soybean were sowed in October 7 (early sowing) and October 29 (late sowing) at 2013/2014 crop year. The oil, protein and isoflavones contents were determined and the data were analyzed by variance analysis (ANOVA), principal component analysis (PCA) and UPGMA hierarchical. The genetic variability, sowing date and interactions between inbred lines and sowing date showed differences for all characteristics, except for oil content that did not showed a significant effect to the interaction. The greater participation of complex interaction was attributed to protein content with 87.82 %. According to PCA and UPGMA results, the food-type soybean lines were separated into three groups and were consistent in both sowing dates. The UEL 131 and UEL 153 lines showed the highest isoflavones content for the two sowing dates, indicating these genotypes as promising for breeding programs.

Poucos trabalhos relataram a relação entre genótipo, temperatura, precipitação e os compostos químicos de grãos de soja. Portanto, o objetivo deste estudo foi investigar o efeito da interação entre linhagens de soja tipo alimento semeadas em duas épocas nos teores de proteína, óleo e isoflavonas nos grãos. Oito linhagens de soja ausentes das enzimas lipoxigenases e classificadas como tipo alimento foram semeadas em 7 de outubro (semeadura precoce) e 29 de outubro (semeadura tardia) no ano agrícola 2013/2014. Os conteúdos de óleo, proteína e isoflavonas foram determinados e os dados foram submetidos a análise de variância (ANAVA), análise de componentes principais (PCA) e UPGMA hierárquica. A variabilidade genética, a época de semeadura e as interações entre linhagens e a época de semeadura mostraram diferenças para todas as características, com exceção do teor de óleo que não apresentou efeito significativo na interação. A maior participação da interação complexa foi atribuída ao teor de proteína com 87,82%. De acordo com os resultados da PCA e UPGMA, as linhagens de soja tipo alimento foram separadas em três grupos que se mantiveram com a mudança da época de semeadura. As linhagens UEL 131 e UEL 153 mostraram o maior teor de isoflavonas em ambas as épocas de semeadura, indicando que esses genótipos são promissores para programas de melhoramento.

Molecular characterization of yellow passion fruit genotypes with different yield and disease resistance levels / Caracterização molecular de genótipos de maracujazeiro azedo com diferentes níveis de produtividade e resistência a doenças

Brazil is the largest passion fruit producer in the world. However, the yield is still considered low, and the cultivation of unsuitable varieties is one of the factors directly influencing this trait. As a consequence, breeding studies have been developed with the purpose of obtaining genetic materials with high yield, high fruit quality, and disease resistance. The objective of this study was to characterize and quantify the genetic variability in 18 genotypes of yellow passion fruit (Passiflora edulis Sims) with different levels of yield and disease resistance, using RAPD markers. The RAPD markers were obtained from 10 decamer primers and converted into a matrix of binary data. Estimations of the genetic dissimilarities between different genotypes and cluster analysis were performed. A total of 58 markers were generated, 63.80% of which were polymorphic. The genetic distances among genotypes varied from 0.040 to 0.354 and genotypes were subdivided into at least 5 groups of similarity. The dispersion graphs showed a low clustering tendency for yield and resistance to different diseases (septoriosis, anthracnose, scab, bacterial spot, and passion fruit woodiness disease). These results demonstrate a high genetic variability among the evaluated genotypes, which is valuable information when selecting promising materials to be used per se or as parents in genetic breeding programs.

O Brasil é o maior produtor mundial de maracujá. Entretanto, a produtividade ainda é considerada baixa e o cultivo de variedades inadequadas é um dos fatores que influenciam diretamente esta característica. Como consequência, trabalhos de melhoramento genético tem sido desenvolvidos com a finalidade de obter materiais genéticos com alta produtividade, qualidade de frutos e resistência a doenças. Este trabalho objetivou caracterizar e quantificar a variabilidade genética em 18 genótipos de maracujazeiro azedo (Passiflora edulis Sims) com diferentes níveis de produtividade e resistência a doenças, utilizando marcadores moleculares RAPD. Os marcadores RAPD, obtidos por meio de 10 iniciadores decâmeros, foram convertidos em uma matriz de dados binários. Estimativas de dissimilaridades genéticas entre os diferentes genótipos e análises de agrupamento foram realizadas. Um total de 58 marcadores foram gerados, dos quais 63,80% foram polimórficos. As distâncias genéticas entre os genótipos variaram de 0,040 a 0,354 e os genótipos foram subdivididas em pelo menos 5 grupos de similaridade. Os gráficos de dispersão mostraram uma baixa tendência de agrupamento para produtividade e resistência à septoriose, antracnose, verrugose, bacteriose e virose do endurecimento dos frutos. Estes resultados demonstram uma alta variabilidade genética entre os genótipos estudados, que é uma informação valiosa para a seleção de materiais promissores para serem utilizados per se ou como parentais em programas de melhoramento genético.