Functional traits and performance of woody species on oil-affected soils of the Ecuadorian Amazon / Rasgos funcionales y comportamiento de especies leñosas en suelos afectados por petróleo de la Amazonía ecuatoriana

Abstract Introduction: Plant functional traits are widely used to predict community productivity. However, they are rarely used to predict the performance (in terms of growth diameter, growth height, survival, and integral response index) of woody species planted in degraded soils. Objective: To evaluate the relationship between the functional traits and the performance of 25 woody species planted in disturbed soils affected by oil extraction activities in Ecuadorian Amazon. Methods: Eighteen permanent sampling plots were established and five 6-month-old seedlings of each 25 species were randomly planted in each plot (125 individuals per plot), at a distance of 4×4 m. Eight quantitative functional traits (leaf size, specific leaf area, leaf nitrogen concentration, leaf phosphorus concentration, leaf minimum unit, leaf dry matter content, stem specific density and leaf tensile strength) were determined for each species. Results: The woody species with high performance shows greater leaf size, specific leaf area and Stem Specific Density than those showing low performance. Leaf nitrogen concentration and stem specific density had a direct relationship with the integral response index. The leaf size, leaf phosphorus concentration, leaf dry matter content and leaf tensile strength showed a negative relationship with the integral response index. Conclusions: Our study demonstrated that the performance of woody species o disturbed soils can be predicted satisfyingly by leaf and stem functional traits, presumably because these traits capture most of environmental and neighborhood conditions.

Resumen Introducción: Los rasgos funcionales de las plantas han sido ampliamente utilizados para predecir la productividad (en términos de crecimiento en diámetro, crecimiento en altura, sobrevivencia e índice de respuesta integral) de las comunidades vegetales. Sin embargo, rara vez han sido utilizados para predecir el desempeño de las especies leñosas plantadas en suelos degradados. Objetivo: Evaluar la relación entre el desempeño y los rasgos funcionales de 25 especies leñosas plantadas en suelos afectados por actividades de extracción de petróleo en la Amazonía ecuatoriana. Métodos: Se establecieron 18 parcelas permanentes de muestreo y en cada parcela se sembraron aleatoriamente cinco plántulas de 6 meses de las 25 especies (125 individuos por parcela), a una distancia de 4×4 m. Se determinaron ocho rasgos funcionales (área foliar, área foliar específica, concentración de nitrógeno foliar, concentración de fósforo foliar, unidad mínima foliar, contenido foliar de materia seca, densidad específica del fuste y fuerza tensil foliar) de cada especie. Resultados: Las especies leñosas con alto desempeño presentaron mayor área foliar, área foliar específica y densidad específica del fuste que las especies de bajo desempeño. La concentración de nitrógeno foliar y la densidad específica del fuste mostraron una relación directa. El área foliar, la concentración de fósforo foliar, el contenido de materia seca foliar y la fuerza tensil foliar presentaron una relación inversa con el Índice de Respuesta Integral. Conclusión: Se demostró que el desempeño de las especies leñosas plantadas en suelos alterados puede predecirse satisfactoriamente por rasgos funcionales de hoja y de tallo, debido posiblemente a que los rasgos influyen en el crecimiento y supervivencia de las especies, y reflejan la mayoría de las condiciones ambientales.

Pleiotropic effects of the sdw1 locus in barley populations representing different rounds of recombination

Background In the present study populations, representing different rounds of recombination were used for the analysis of phenotypic effects associated with the sdw1/denso locus. Other studies have mostly focused only on one type of population. Many different QTLs mapped at the same position as the sdw1/denso locus may indicate a pleiotropy of this gene or a tight linkage between genes conditioning quantitative traits. To date, results of studies have not unequivocally proven either of these two phenomena. Results Both breeding and molecular mapping experiments were undertaken to examine 200 single seed descent (SSD) and 60 doubled haploid (DH) lines obtained from the Maresi (with a semi-dwarfing gene) and Pomo cross combination. They were evaluated for the type of juvenile growth habit and certain agronomic traits were measured after harvesting. The estimates of mean values, standard errors and significance of effects were analyzed. In terms of the analyzed characteristics, the greatest variability was obtained for genotypes with the prostrate growth habit. Microsatellite markers (SSR) were also used to identify co-segregation with the sdw1/denso locus and Bmag0013, Bmag0877, Bmag0306b markers were linked the closest. A partial linkage map of chromosome 3H with the sdw1/denso semi-dwarfing gene was constructed and QTLs were identified. Conclusions Our experiments confirmed the impact of the semi-dwarfing gene on plant height, heading and flowering date both in SSD and DH populations, which may indicate pleiotropy. Moreover, a partial linkage between sdw1/denso locus and grain weight per spike and 1000-grain weight was found in the SSD population.

Distinct Genetic Backgrounds in Quantitative Traits Preceding Type 2 Diabetes: One Reason for Missing Heritability.

Genome-wide association studies (GWAS) have identified variants associated with type 2 diabetes (T2D), but less than five percent of the genetic variance associated with T2D is accounted for in GWAS studies performed using T2D as endpoint. These findings suggest relevance of assessing preceding quantitative traits (QTs) or sub-phenotypes and their respective markers for contributing to the appearance of glycemic thresholds defining T2D. The QTs first appear in gestation and childhood when birth weight and childhood weight gain have an influence on T2D. Changes in fetal growth are associated with metabolic programming for T2D in adulthood. Subsequently gains in body fat leading to obesity, ectopic lipid deposition in liver and muscle, dyslipidemia and hypertension express in the β-cells, hypothalamus, adipocytes, myocytes, liver and kidney, and are associated with worsening insulin resistance and β-cell failure preceding overt T2D. Obesity, an increasingly common trait is associated with gene variants that regulate energy balance but have no association with T2D with few exceptions. For instance, FTO gene variants are associated with early onset of obesity and have also been associated with T2D and hypertension suggesting pleiotropism. Non-alcoholic fatty liver disease (NAFLD) has an independent genetic background and is considered as a new addition to the metabolic syndrome. Association of NAFLD with dyslipidemia, cardiovascular disease and hepatic insulin resistance contributes to progression to T2D. The classic dyslipidemia encountered in insulin resistant states consisting of increased triglyceride, low high-density lipoprotein cholesterol (HDL-C) and molding of triglyceridecontaining lipoproteins to form atherogenic LDL particles and dysfunctional HDL particles, has strong environmental and genetic association. In addition evidence is accumulating to show that the abnormal lipoproteins have a direct effect on β-cells leading to failure and possible acceleration of diabetes onset. Consequently known variants affecting either the dyslipidemia or β-cell function have a compound effect on T2D. Like other preceding traits the genetic background for commonly encountered hypertension is independent of diabetes although it remains a predictive trait. However, increasing evidence supports a role for the renin-angiotensin system in causing oxidative stress and insulin resistance. Finally when glucose intolerance has progressed to overt T2D, reversibility is usually no longer possible; therefore recognition of preceding prediabetic glycemic thresholds and both their genetic and environmental associations may facilitate and serve as signals for prevention. Thus a better understanding of the sequential expression of the respective QTs and genetic variation affecting their metabolic effects leading to T2D could initiate more effective prevention strategies.

Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants.

The enormous population growth, climate change and global warming are now considered major threats to agriculture and world’s food security. To improve the productivity and sustainability of agriculture, the development of highyielding and durable abiotic and biotic stress-tolerant cultivars and/climate resilient crops is essential. Henceforth, understanding the molecular mechanism and dissection of complex quantitative yield and stress tolerance traits is the prime objective in current agricultural biotechnology research. In recent years, tremendous progress has been made in plant genomics and molecular breeding research pertaining to conventional and next-generation whole genome, transcriptome and epigenome sequencing efforts, generation of huge genomic, transcriptomic and epigenomic resources and development of modern genomics-assisted breeding approaches in diverse crop genotypes with contrasting yield and abiotic stress tolerance traits. Unfortunately, the detailed molecular mechanism and gene regulatory networks controlling such complex quantitative traits is not yet well understood in crop plants. Therefore, we propose an integrated strategies involving available enormous and diverse traditional and modern –omics (structural, functional, comparative and epigenomics) approaches/resources and genomics-assisted breeding methods which agricultural biotechnologist can adopt/utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in crop plants. This would provide clues and much needed inputs for rapid selection of novel functionally relevant molecular tags regulating such complex traits to expedite traditional and modern marker-assisted genetic enhancement studies in target crop species for developing high-yielding stress-tolerant varieties.

Assessment of genetic diversity in Brassica juncea Brassicaceae genotypes using phenotypic differences and SSR markers / Evaluación de la diversidad genética en genotipos de Brassica juncea Brassicaceae utilizando diferencias fenotípicas y marcadores SSR

Brassica mustard species represent one of the most important oilseed crops in India, nevertheless, their genetic diversity is barely known. A better understanding on this topic is essential for the proper utilization of genotypes in breeding programmes. We evaluated the genetic diversity among 44 Indian mustard Brassica juncea genotypes including varieties/purelines from different agro-climatic zones of India and few exotic genotypes Australia, Poland and China. For this, we used A and B genome specific SSR markers and phenotypic data on 12 yield and yield contributing traits. Out of the 143 primers tested, 134 reported polymorphism and a total of 355 alleles were amplified. Dendrograms based on Jaccards similarity coefficients and Manhattan dissimilarity coefficients were generated based on an average linkage algorithm UPGMA using marker data and phenotypic data. Genotypes were grouped into four clusters based on genetic distances. Both the clustering patterns based on Jaccards similarity and Manhattan dissimilarity coefficients, independently, discriminated the genotypes effectively as per their pedigree and origin. PCoA revealed that, the grouping of genotypes based on SSR marker data is more convincing than phenotypic data, however, the correlation between phenotypic and genetic distance matrices was observed to be very low r=0.11. Hence, for diversity studies reliability on molecular markers is worth proving and SSR markers are the stronger tools than quantitative traits in discriminating B. juncea genotypes.

Las especies de mostaza del género Brassica representan uno de los cultivos de semillas oleaginosas más importantes en India, sin embargo, su diversidad genética es poco conocida. Para la utilización de genotipos en programas de cultivos resulta esencial un mayor conocimiento sobre este tema. Debido a ello, se evaluó la diversidad genética entre 44 genotipos de mostaza de la India Brassica juncea incluyendo variedades y líneas puras de diferentes zonas agro-climáticas de la India y algunos genotipos exóticos Australia, Polonia y China. Para ello, se utilizaron marcadores SSR específicos del genoma A y B y datos fenotípicos del rendimiento de 12 cosechas y sus características. De los 143 primers evaluados, 134 reportaron polimorfismo y un total de 355 alelos fueron amplificados. Se generaron dendrogramas a partir de los coeficientes de similitud de Jaccard y de disimilitud Manhattan, basados en un algoritmo de vinculación promedio UPGMA. Se utilizaron datos de marcadores genéticos y datos fenotípicos. Los genotipos se agruparon en cuatro grupos basados en las distancias genéticas. Ambos patrones de agrupamiento, tanto los basados en los coeficientes de similitud de Jaccard como los basados en los de disimilitud Manhattan, separaron independientemente los genotipos por su genealogía y origen, de una manera efectiva. El PCoA reveló que la agrupación de genotipos basada en datos de marcadores SSR, es más convincente que los datos fenotípicos, sin embargo, se observó que la correlación entre las matrices de distancia fenotípica y genética resultó muy baja r=0.11. Por lo tanto, para estudios de diversidad basados en marcadores moleculares es necesario realizar más pruebas. Los marcadores SSR constituyen herramientas más eficientes para discriminar entre genotipos de B. juncea, que las características cuantitativas.

Gene Set Analyses of Genome-Wide Association Studies on 49 Quantitative Traits Measured in a Single Genetic Epidemiology Dataset

Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP) genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO) terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (pcorr < 0.05). Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.

Morphoagronomic genetic diversity in american wild rice species

To characterize the genetic variability among species and populations of South American wild rice, eleven populations of Oryza glumaepatula, seven of O. grandiglumis, four of O. latifolia and one of O. alta, from Brazil and Argentina, were evaluated. A greenhouse experiment was conducted in completely randomized blocks with 23 treatments. Twenty morphoagronomic traits were assessed. Univariate analyses were performed with 16 quantitative traits with the partitioning of populations within species. Significant differences (p<0.001) between species were observed for all the traits as well as among populations within the species. The most variable was O. glumaepatula followed by O. latifolia. Multivariate discriminant canonical and cluster analyses confirmed the separation of the highly diverse O. glumaepatula populations from the tetraploid species, and the high genetic variation among O. latifolia populations. Morphological differences among the three tetraploid species seemed to be enough to ascribe them at least the condition of species in statu nascendi.

Visando caracterizar a diversidade genética entre espécies e populações de arroz selvagem da América do Sul, foram avaliadas 11 populações de Oryza glumaepatula, sete de O. grandiglumis, quatro de O. latifolia e uma população de O. alta, originárias do Brasil e Argentina. Foi conduzido um experimento em casa-de-vegetação em blocos ao acaso com 23 tratamentos. Vinte caracteres agro-morfológicos foram avaliados. Análises univariadas foram realizadas para 16 caracteres quantitativos, desdobrando-se o efeito de populações dentro de espécies. Diferenças significativas (p<0,001) entre espécies foram observadas para todos os caracteres bem como entre populações dentro de espécies. A mais variável foi O. glumaepatula seguida de O. latifolia. Análises de agrupamento e discriminante canônica confirmaram a separação das populações de O. glumaepatula das espécies tetraplóides, e a grande variação genética entre populações de O. latifolia. Diferenças morfológicas entre as três espécies tetraplóides parecem suficientes para classificá-las como espécies pelo menos na condição statu nascendi.

Estimation of heritability attributable to single-locus effects with a regression of offspring on mid-parent (ROMP) method for cardiovascular risk factors / 한국역학회지

PURPOSE: The objective of this study was to estimate the heritability attributable to single-locus effects with a regression of offspring on mid-parent (ROMP) method for cardiovascular risk factors. METHODS: The regression of offspring on mid-parent is determined with and without the inclusion of a single-locus effect, and the difference between the slopes of these two regression is an estimate of the heritability attributable to the single-locus effect. The study population included 1,550 family members of 295 patients, derived from cardiovascular genome center. The risk factors considered were total serum cholesterol, triglyceride, LDL cholesterol, apoAI and apoB. Heritability was estimated from the slope of the linear regression of offspring on mid-parents. RESULTS: Estimated heritability was 35 to 46% for total cholesterol with 6.2% attributable to polymorphism S128R. For triglyceride, the estimated heritability was 47.6% with 2% attributable to polymorphism G-217A. The heritability was 36-46% for LDL-cholesterol. For LDL cholesterol, S128R specific effect was 8.7%. Estimated heritability was 62.2% for apoAI with 3.2% attributable to polymorphism G-217A and 58 to 75% for apoB with 5.4% attributable to polymorphism S128R. CONCLUSIONS: These traits were significantly associated with polymorphism S128R. These results highlight the importance of considering genetic factors in studies of cardiovascular risk factors. Unlike traditional population-based tests of association, ROMP appears to be robust with respect to population stratification.

Study on morphologic quantitative characteristics of Oncomelania hupensis Ⅲ. Morphologic variations and their spatial correlation among snail populations / 中国血吸虫病防治杂志

Objective To explore morphologic variations and their spatial correlation among Oncomelania hupensis populations from the mainland of China. Methods Twenty-seven snail populations from ten provinces were collected. The morphologic indices of shells and geographic distances between the snail spots were measured respectively, and the morphologic variations among snail populations and the correlations between morphologic variations and geographical distances were analyzed. Results The median of Euclidean distances was 3.24 (95% CI: 2.88-3.81) among 20 snail populations of O.h.hupensis including a snail population from Guangxi Province, and was 3.15 (95% CI: 2.86-3.76) excluding the Guangxi snail population; the median was 1.69 (95% CI: 1.33-2.27) among 6 populations of O.h.robertsoni. Whether including a snail population from Guangxi Province or not, the median among O.h.robertsoni was less than that among O.h.hupensis (P0.05). The correlation coefficient was 0.2655 for O.h.hupensis including a snail population from Guangxi Province, 0.2567 not including it; and was 0.3121 for ribbed-shell population. Conclusions Morphologic variation among O.h.hupensis is bigger than that among O.h.robertsoni, and morphologic variation among ribbed-shell populations is bigger than that among smooth-shell populations. There is significant spatial structure among ribbed-shell snail populations of Oncomelania hupensis distributed in the mainland of China.