Intermediate Phenotypic Traits Research Articles

Multi-character approach reveals a new mangrove population of the Yellow Warbler complex, Setophaga petechia, on Cozumel Island, Mexico.

The Setophaga petechia complex includes 43 subspecies distributed within the new world, of which some are migratory and others are resident, with only two resident subspecies in the Mexican Caribbean: Setophaga petechia bryanti a mangrove subspecies belonging to the erithachorides group resident on the mainland of the Yucatan Peninsula and Setophaga petechia rufivertex endemic to Cozumel Island and belonging to the petechia group. Recently, a new population of individuals presenting intermediate phenotypic traits and living in mangrove ecosystems was discovered and reported for Cozumel Island. In this study, we used a multi-character approach including genetic (five ISSR genetic markers), morphometric (eight traits), phenotypic (four characteristics of males), and acoustic dataset (11 parameters) to understand the process of differentiation and the status of these new island individuals in relation to the two well-established subspecies using a total of 60 individuals (20 for each group). Through multivariate analyses based on different dataset used in our study, we show how the new population is related to the endemic island subspecies, S. p. rufivertex and to the mainland subspecies, S. p. bryanti while demonstrating finite differences. We conclude that the new population of S. petechia on Cozumel Island is a well-established population with high level of differentiation.

Phenotype differentiation of Capsicum annuum var. glabriusculum of three regions in Mexico and its relation to climate

Background: Populations of Capsicum annuum var. glabriusculum are found in a wide portion of the Mexican territory, and it is ancestor of many cultivated forms relevant for the Mexican diet.
 Questions: What are the proportions of phenotypic and genetic variation distributed among its sampled regions, populations and within populations. How does the climate correlates to the population’s phenotypic variation.
 Species: Capsicum annuum var. glabriusculum.
 Study sites and years: 24 populations form three regions were sampled: Northwest, states of Sonora and Sinaloa; South: Oaxaca and Southeast Tabasco and Yucatán, in Mexico. The experiment was performed between years 2016 to 2018.
 Methods: Fruits from single plants were collected in wild populations. Plants were grown in a greenhouse. Nested ANOVAS were performed to estimate phenotypic and genetic variance components for different spatial scales. Climate correlation was estimated through univariate and multivariate methods.
 Results: 49.8 % of phenotypic variation was detected within families, 11.1 % among families (within populations), 21.3 % among populations and 17.6 % among regions. The genetic basis of phenotypic variation was 50.1% on average, for this genetic variation 34.2 % was found among regions, 39.4% among populations and 26.3 % within populations. Climate factors generated different patterns of correlations for vegetative, foliar and reproductive traits.
 Conclusions: Northwest plants were shorth, with small leaves and large fruits, Southeast plants were tall, with large leaves and small fruits, South plants developed intermediate phenotypic traits. Climate explained a large proportion of phenotypic differentiation.

Descriptive versus causal morphology: gynandromorphism and intersexuality

In animal species with separate sexes, abnormal individuals with a mix of phenotypically male and phenotypically female body parts are generally indicated as gynandromorphs, whereas individuals with intermediate sexual phenotypic traits are generally indicated as intersexes. However, this distinction, clear as it may seem, is neither universally agreed upon, nor free of critical issues. In consideration of the role of sex anomalies in understanding normal development, we reassess these phenomena of abnormal sexual development, taking into consideration the more recent advances in the study of sex determination and sexual differentiation. We argue that a distinction between gynandromorphism and intersexuality, although useful for descriptive purposes, is not always possible or sensible. We discuss the conceptual and terminological intricacies of the literature on this subject and provide reasons for largely, although not strictly, preferring a terminology based on descriptive rather than causal morphology, that is, on the observed phenotypic patterns rather on the causal process behind them.

Maternal control of early life history traits affects overwinter survival and seedling phenotypes in sunflower (Helianthus annuus L.).

When cultivated and wild plants hybridize, hybrids often show intermediate phenotypic traits relative to their parents, which makes them unfit in natural environments. However, maternal genetic effects may affect the outcome of hybridization by controlling expression of the earliest life history traits. Here, using wild, cultivated and reciprocal crop-wild sunflower (Helianthus annuus L.) hybrids, we evaluated the maternal effects on emergence timing and seedling establishment in the field and on seedling traits under controlled conditions. In the field, we evaluated reciprocal crop-wild hybrids between two wild populations with contrasting dormancy (the high dormant BAR and the low dormant DIA) and one cultivar (CROP) with low dormancy. Under controlled conditions, we evaluated reciprocal crop-wild hybrids between two wild populations (BAR and RCU) and one CROP under three contrasting temperature treatments. In the field, BAR overwintered as dormant seeds whereas DIA and CROP showed high autumn emergence (~50% of planted seeds), resulting in differential overwinter survival and seedling establishment in the spring. Reciprocal crop-wild hybrids resembled their female parents in emergence timing and success of seedling establishment. Under controlled conditions, we observed large maternal effects on most seedling traits across temperatures. Cotyledon size explained most of the variation in seedling traits, suggesting that the maternal effects on seed size have cascading effects on seedling traits. Maternal effects on early life history traits affect early plant survival and phenotypic variation of crop-wild hybrids, thus, they should be addressed in hybridization studies, especially those involving highly divergent parents, such as cultivated species and their wild ancestors.

The Transcriptomic Evidence on the Role of Abdominal Visceral vs. Subcutaneous Adipose Tissue in the Pathophysiology of Diabetes in Asian Indians Indicates the Involvement of Both.

The roles of abdominal visceral (VAT) and subcutaneous adipose tissue (SAT) in the molecular pathogenesis type-2 diabetics (T2D) among Asian Indians showing a “thin fat” phenotype largely remains obscure. In this study, we generated transcription profiles in biopsies of these adipose depots obtained during surgery in 19 diabetics (M: F ratio, 8:11) and 16 (M: F ratio 5:11) age- and BMI-matched non-diabetics. Gene set enrichment analysis (GSEA) was used for comparing transcription profile and showed that 19 gene sets, enriching inflammation and immune system-related pathways, were upregulated in diabetics with F.D.R. <25% and >25%, respectively, in VAT and SAT. Moreover, 13 out of the 19 significantly enriched pathways in VAT were among the top 20 pathways in SAT. On comparison of VAT vs. SAT among diabetics, none of the gene sets were found significant at F.D.R. <25%. The Weighted Gene Correlation Analysis (WGCNA) analysis of the correlation between measures of average gene expression and overall connectivity between VAT and SAT was significantly positive. Several modules of co-expressed genes in both the depots showed a bidirectional correlation with various diabetes-related intermediate phenotypic traits. They enriched several diabetes pathogenicity marker pathways, such as inflammation, adipogenesis, etc. It is concluded that, in Asian Indians, diabetes pathology inflicts similar molecular alternations in VAT and SAT, which are more intense in the former. Both adipose depots possibly play a role in the pathophysiology of T2D, and whether it is protective or pathogenic also depends on the nature of modules of co-expressed genes contained in them.

SUN-LB106 The Transcriptomic Evidences on Role of Abdominal Visceral vs. Subcutaneous Adipose Tissue in the Pathophysiology of Diabetes in Asian Indian Indicates the Involvement of Both

Introduction: Asian Indians show “thin fat phenotype” characterized by higher visceral adipose tissue(VAT) and lower subcutaneous adipose tissue(SAT) mass and their higher cardio-metabolic risk has been attributed to this fat distribution. However, the underlying molecular pathology and role of these adipose depots in the pathogenesis of T2D in them remains unknown.Hypothesis: The comparison of transcription profiles of abdominal VAT and SAT and their correlation with diabetes related intermediate phenotypic traits could shed some light on their role in the pathophysiology of diabetes.MethodologySubjects: 19 diabetics (M: F ratio, 8:11) and 16 age and BMI matched controls (M: F ratio 5:11) undergoing abdominal surgery (non-malignant and non-infective conditions).Clinical Parameters: Anthropometry, Serum glucose, insulin, HOMA-R, HbA1c, lipid profile, FFA, adipocytokines. Abdominal VAT, SAT and liver fat were estimated by MRI.Adipose tissue biopsy: SAT and VAT samples were taken during surgery. Genome-wide gene expression profiling of these biopsies was performed using Affymetrix GeneChipPrimeView® arrays. The data was submitted to NCBI-GEO (Accession # GSE78721). Selected genes were validated by qPCR. Gene set enrichment analysis (GSEA) for functional and Weighted Gene Correlation Analysis (WGCNA) for statistical comparison was done.Results:Diabetics had higher waist circumference (p=0.05), HOMA-R (p=0.0002), Visceral fat content (p=0.02) and adipocyte size (p=0.02)GSEA: diabetics vs. controls: In VAT 16 gene sets were upregulated (FDR < 25%) enriching various immune system and inflammation-related pathways. In SAT too, various inflammatory genes were upregulated however they were statistically non-significant (FDR > 25%). Moreover, 12 out of 16 significantly enriched pathways in VAT were among the top 20 pathways in SAT. GSEA in diabetics: VAT vs SAT: None of the gene sets were found significant at FDR < 25% which substantiated our hypothesis that overall pathophysioloigcal alteration in both depots are similar. WGCNA for statistical comparison of VAT and SAT depots The correlation between measures of average gene expression and overall connectivity between both depots was significantly positive. Several modules of co-expressed genes in both VAT and SAT showed positive as well as negative correlation with various intermediate phenotypic traits of diabetes. In both depots they enriched several pathways otherwise known to be associated with pathological adipose tissue like inflammation, adipogenesis etc.ConclusionsIn Asian Indians, diabetes pathology inflicts similar molecular alternations in VAT and SAT, which are more intense in the former. The role of both adipose depots in the pathophysiology of diabetes is along similar lines and they enrich several molecular pathways which are otherwise known to be implicated in pathological adipose tissue.

Functional Interactomes of Genes Showing Association with Type-2 Diabetes and Its Intermediate Phenotypic Traits Point towards Adipo-Centric Mechanisms in Its Pathophysiology.

The pathogenic mechanisms causing type 2 diabetes (T2D) are still poorly understood; a greater awareness of its causation can lead to the development of newer and better antidiabetic drugs. In this study, we used a network-based approach to assess the cellular processes associated with protein–protein interaction subnetworks of glycemic traits—HOMA-β and HOMA-IR. Their subnetworks were further analyzed in terms of their overlap with the differentially expressed genes (DEGs) in pancreatic, muscle, and adipose tissue in diabetics. We found several DEGs in these tissues showing an overlap with the HOMA-β subnetwork, suggesting a role of these tissues in β-cell failure. Many genes in the HOMA-IR subnetwork too showed an overlap with the HOMA-β subnetwork. For understanding the functional theme of these subnetworks, a pathway-to-pathway complementary network analysis was done, which identified various adipose biology-related pathways, containing genes involved in both insulin secretion and action. In conclusion, network analysis of genes showing an association between T2D and its intermediate phenotypic traits suggests their potential role in beta cell failure. These genes enriched the adipo-centric pathways and were expressed in both pancreatic and adipose tissue and, therefore, might be one of the potential targets for future antidiabetic treatment.

The common pathophysiologic threads between Asian Indian diabetic’s ‘Thin Fat Phenotype’ and partial lipodystrophy: the peripheral adipose tissue transcriptomic evidences

ABSTRACT T2D is a complex disease with poorly understood mechanisms. In Asian Indians, it is associated with “thin fat” phenotype which resembles with partial lipodystrophy. We hypothesized that disturbed expression of lipodystrophy genes might play a role in T2D pathogenesis. Therefore, we attempted to establish a link between these two diseases by studying the overlap between the network of lipodystrophy genes and the differentially expressed genes (DEGs) in the peripheral subcutaneous adipose tissue of Asian Indians diabetics. We found that 16, out of 138 lipodystrophy genes were differentially regulated in diabetics and around 18% overlap between their network and the DEGs; the expression level of lipodystrophy genes showed an association with disease-related intermediate phenotypic traits among diabetics but not in the control group. We also attempted to individualize the diabetic patients based on ±2 fold altered expression of lipodystrophy genes as compared to their average expression in the control group. In conclusion, significant overlap exists between some of the lipodystrophy genes and their network with DEGs in the peripheral adipose tissue in diabetics. They possibly play a role in the pathogenesis of diabetes and individualization of diabetics is possible based on their altered expression in their peripheral adipose tissue.

Transcriptome profiling reveals association of peripheral adipose tissue pathology with type-2 diabetes in Asian Indians

ABSTRACT Type 2 diabetes (T2D) is a complex disease with an elusive link between its molecular aetiology and clinical presentation. Although, the role of visceral adipose tissue in insulin-resistance and T2D is known, limited information is available on the role of peripheral-subcutaneous adipose tissue especially in Asian Indians. In this microarray-based study of diabetic and normal glucose tolerant Asian Indians, we generated the transcriptome of their thigh adipose tissue and analyzed differentially expressed genes (DEGs) using weighted gene co-expression network analysis; further we identified perturbed pathways implicated by these DEGs in relevant co-expression modules. We also attempted to link these pathways with known aspects of T2D pathophysiology in terms of their association with some of their intermediate traits, namely; adipocyte size, HOMA-B, HOMA-R, Hb1Ac, insulin, glucose-level, TNF-α, IL-6, VLDLs, LDLs, HDLs, and NEFAs. It was observed that several modules of co-expressed genes show an association with diabetes and some of its intermediate phenotypic traits mentioned above. Therefore, these findings suggest a role of peripheral subcutaneous adipose tissue in the pathophsiology of T2D in Asian Indians. Additionally, our study indicated that the peripheral subcutaneous adipose tissue in diabetics shows pathologic changes characterized by adipocyte hypertrophy and up-regulation of inflammation-related pathways.

Characterization of sympatric Platanthera bifolia and Platanthera chlorantha (Orchidaceae) populations with intermediate plants.

Platanthera bifolia and P. chlorantha are terrestrial and rewarding orchids with a wide Eurasian distribution. Although genetically closely related, they exhibit significant morphological, phenological and ecological differences that maintain reproductive isolation between the species. However, where both species co-occur, individuals with intermediate phenotypic traits, often considered as hybrids, are frequently observed. Here, we combined neutral genetic markers (AFLPs), morphometrics and floral scent analysis (GC-MS) to investigate two mixed Platanthera populations where morphologically intermediate plants were found. Self-pollination experiments revealed a low level of autogamy and artificial crossings combined with assessments of fruit set and seed viability, showed compatibility between the two species. The results of the genetic analyses showed that morphologically intermediate plants had similar genetic patterns as the P. bifolia group. These results are corroborated also by floral scent analyses, which confirmed a strong similarity in floral scent composition between intermediate morphotypes and P. bifolia. Therefore, this study provided a much more detailed picture of the genetic structure of a sympatric zone between two closely allied species and supports the hypothesis that intermediate morphotypes in sympatry could reflect an adaptive evolution in response to local pollinator-mediated selection.

Genetic inheritance of cytochrome P450-mediated metabolic resistance to chlorsulfuron in a multiple herbicide resistant Lolium rigidum population

Field evolved resistance to acetolactate synthase (ALS)-inhibiting herbicides in a multiple resistant Lolium rigidum population (VLR69) is known to be mainly due to enhanced rates of herbicide metabolism, likely involving cytochrome P450 monooxygenases. The present study investigates genetic inheritance of P450-mediated metabolic resistance to the ALS-inhibiting herbicide chlorsulfuron. To this end, a P450-mediated, metabolism-based resistant sub-set of VLR69 was carefully selected using plant vegetative cloning, appropriate herbicide screen test and the known P450 inhibitor malathion. Both intermediate and near-dominant nuclear-encoded phenotypic resistance traits were observed in 14 reciprocal F1 families. The segregation of phenotypic chlorsulfuron resistance in ψ-F2 families was analysed using genetic inheritance models involving one or two loci. The results from four ψ-F2 families revealed complex patterns of genetic inheritance of P450-mediated metabolic resistance in genetically diverse and cross-pollinated species L. rigidum: multiple loci are likely involved and interact with herbicide rates and environmental conditions in mediating the resistance phenotype.

Identification of Hybrids of Painted and Milky Storks Using FTA Card-Collected Blood, Molecular Markers, and Morphologies

Suspicious hybrids of painted storks and milky storks were found in a Malaysian zoo. Blood of these birds was sampled on FTA cards for DNA fingerprinting. Of 44 optimized primers, 6 produced diagnostic markers that could identify hybrids. The markers were based on simple, direct PCR-generated multilocus banding patterns that provided two sets of genetic data, one for each of the two stork species and another for the hybrids. It also revealed that large DNA fragments (3,000 bp) could be amplified from blood collected on FTA cards. When the results of each individual bird's DNA fingerprint were compared with plumage characters, the hybrids were found to express a range of intermediate phenotypic traits of the pure breeds with no dominant plumage characteristic from either parental species.

Type-2 diabetes related intermediate phenotypic traits in north Indian diabetics.

Asian Indians are known to be at a higher risk of developing T2DM, but the underlying genetic factor in this population is still not well understood. T2DM is a complex genetic trait and assessment of disease related intermediate phenotypic traits is an important initial step towards any systematic genomic study. Therefore, in the present study we have assessed diabetes related intermediate phenotypic traits of insulin secretion and insulin resistance in the patients belonging to this population. The study included 157 T2DM patients of either sex ranging in age from 45-80 years and 84 non-diabetic subjects with no family history of diabetes, ranging in age from 45 to 75 years served as controls. Intermediate phenotypic traits studied were BMI, W: H ratio, fasting free fatty acid level and Insulin resistance and secretion. Diabetics were found to have significantly higher W: H ratio (p<0.001), FFA (p<0.001) and HOMA-R (p<0.001) as compared to non-diabetics. However, there was no significant difference in their BMI and HOMA-β. There was a positive correlation between FFA level and HOMA-R among diabetics, but not among controls. These findings suggest that in abdominal obesity FFA mediated insulin resistance is an important causative factor underlying T2DM in this population. Moreover, comparable HOMA-β in diabetics reflects compensatory insulin hyper secretion in these subjects. There is a need to examine relative contribution and precise nature of genetic factor in their tendency for central obesity, free fatty acidemia and insulin resistance.

Abstract #789: Type 2 Diabetes-Related Intermediate Phenotypic Traits in North Indian Patients with Diabetes

Abstract #789: Type 2 Diabetes-Related Intermediate Phenotypic Traits in North Indian Patients with Diabetes

Hyperhomocysteinemia, MTHFR 677C→T Polymorphism, and Stroke

To the Editor: We welcome the report from Madonna and co-workers examining the role of prothrombotic and homocysteine (Hcy) pathway polymorphisms in risk of ischemic stroke in young adults.1 We wish to comment on several issues raised by their article relating to the design of studies of genetic risk factors for complex phenotypes such as ischemic stroke, which we believe to be important when interpreting their findings. As the report points out, genetic predisposition to a complex human phenotype such as stroke is unlikely to be mediated by a large influence of 1 or 2 genes. Many observers agree that it is likely to result from a combination of relatively small individual effects of several genes, each predisposing to stroke via their influence on intermediate phenotypic traits, such as hypertension or hyperlipidemia.2–4⇓⇓ This assumption has several implications for the design of epidemiological studies examining candidate genetic risk factors for stroke. First, given the small anticipated effect size associated with any single candidate polymorphism, the group sample sizes required to robustly demonstrate an association will be very large. This is important to avoid a potentially erroneous conclusion that no association exists (type 2 error). This point is particularly relevant in the case of the MTHFR 677C→T polymorphism. Most prospective and retrospective studies to date have indicated that mildly elevated …

Biología floral de poblaciones silvestres y cultivadas de Phaseolus coccineus L. II. Sistemas reproductivos

Se comparan diferentes características reproductivas entre poblaciones silvestres y un cultivar de Phaseolus coccineus que se distribuyen a lo largo de un gradiente altitudinal (2,200-3,000 m) y crecen en diferentes condiciones ambientales. Se sugiere que las poblaciones de elevada altitud están aisladas genéticamente del cultivar y de las poblaciones de baja elevación, debido a diferencias en sus sistemas reproductivos. En las poblaciones de elevada altitud se encontraron mecanismos de autoincompatibilidad, ausentes en el cultivar y poblaciones de baja elevación; existen también diferencias en los agentes polinizadores, en características florales cuantitativas y en la fenología. Las poblaciones de mayor altitud producen menos flores por inflorescencia pero proporcionalmente más frutos que el resto de las poblaciones. El cultivar estudiado presenta un menor número de semillas por vaina, siendo éstas ocho veces más pesadas que las de cualquier población silvestre. Se detectaron muchas semejanzas entre las poblaciones silvestres de baja elevación y el cultivar, salvo para las características directamente afectadas por la domesticación, tales como el número y peso de las semillas por fruto. La población silvestre adyacente al cultivar presenta en general valores fenotípicos intermedios, lo que sugiere contacto genético con el cultivar.