Phenotypic Distance Research Articles

Longitudinal analyses of development of the immune system during the first five years of life in relation to lifestyle.

Changes in immune cell composition during the immunological window within the first years after birth are not fully understood, especially the effect that different lifestyles might have on immune cell functionality. Peripheral blood mononuclear cells from mothers and their children at birth and at two anvd five years were analyzed by mass cytometry. Immune cell composition and functionality was analyzed according to family lifestyle (anthroposophic and non-anthroposophic). We found no significant differences in the proportions of major immune lineages between anthroposophic and non-anthroposophic children at each time point, but there were clear changes over time in the proportions of mononuclear leukocytes, especially in B-cells and T lymphocytes. Phenotypic distances between cord blood and maternal blood were high at birth but decreased sharply the first two years, indicating strong phenotypic convergence with maternal cells. We found that children exhibited similar stimulation responses at birth, but subsequently segregated into two discrete functional trajectories. Trajectory 1 was associated with a decrease in tumor necrosis factor alpha (TNFa) production by CD4+ T- and NK-cells, while Trajectory 2 depicted an increase in the production of IL-2 and interferon gamma (INFg) by T-cells. In both trajectories, there was an increase in IL-17A production by T-cells resulting in prominent differences at five years of age. This exploratory study suggests that leukocyte frequencies and cell phenotypes change with age in the same way across all children, while functional development follows one of two discrete trajectories that largely segregate by family lifestyle, supporting the hypothesis that early environmental exposures imprint immune cell function which may contribute to IgE sensitization. Our results also support that the first two years are critical for the environmental exposures to imprint the immune cells. Further studies with larger sample sizes are required to validate our findings.

Population genetics and independently replicated evolution of predator-associated burst speed ecophenotypy in mosquitofish.

Many species show replicated ecophenotypy due to recurring patterns of natural selection. Based on the presence or absence of pursuit predators, at least 17 species of fish repeatedly differentiated in body shape in a manner that increases burst swimming speed and the likelihood of predator escape. The predator-associated burst speed (PABS) ecophenotype is characterized by a small head and trunk and enlarged caudal region. Mechanisms promoting replicated phenotype-environment association include selection (without evolution), a single instance of adaptive evolution followed by biased habitat occupation, repeated instances of local adaptation, or adaptive phenotypic plasticity. Common garden rearing of mosquitofish, Gambusia affinis, demonstrated a likely heritable basis for PABS phenotypy, but it is unknown whether populations are otherwise genetically distinct or whether replicated ecophenotypy represents a single or replicated instances of adaptation. To genetically characterize the populations and test hypotheses of single or multiple adaptations, we characterized variation in 12 polymorphic DNA microsatellites in the previously studied G. affinis populations. Populations were genetically distinct by multilocus analysis, exhibited high allelic diversity, and were heterozygote deficient, which effects were attributed to G. affinis's shoaling nature and habitat patchiness. Genetic and phenotypic distances among populations were correlated for non-PABS but not PABS morphology. Multilocus analysis demonstrated ecophenotype polyphyly and scattered multivariate genetic structure which support only the replicated-adaptation model. As all of the diverse tests performed demonstrated lack of congruence between patterns of molecular genetic and PABS differentiation, it is likely that divergent natural selection drove multiple instances of adaptive evolution.

Immune-Mediated Reprogramming of Intestinal Stem Cells Drives STAT1-Dependent Myc Expression and Epithelial Regeneration in GI-Gvhd

Crypt apoptosis and regeneration are characteristic findings in GI-GVHD. Intestinal stem cells (ISCs) are critical for maintaining the intestinal epithelium, but their frequencies are reduced in experimental GVHD, and the mechanisms driving crypt regeneration in this context are poorly understood.To better understand the impact of GVHD on individual epithelial components, we performed single cell RNA sequencing (scRNAseq) of purified small intestine crypts from B6 mice during homeostasis and five days after B6 into B6 syngeneic (syn) or B10.Br into B6 allogeneic (allo) BMT. Sequenced cells were first partitioned into distinct clusters using PhenoGraph, and the cluster identities were annotated based on their gene expression profiles. Unsupervised clustering indicated multiple subpopulations within the various recognized crypt components (Fig 1A). While secretory lineages clustered similarly across experimental conditions, there was highly distinct clustering among ISC populations and striking dissimilarity between allo and syn ISCs. Quantification by computing the subpopulation's phenotypic distance, a composite score integrating both the number and amplitude of differentially expressed genes, indicated that ISCs demonstrated the greatest transcriptional change in response to GVHD among all crypt lineages (Fig 1B). Gene Set Enrichment Analysis (GSEA) highlighted activation of the interferon-γ (IFNγ) pathway in allo ISCs, and differential gene expression indicated that STAT1 was their most highly upregulated transcription factor. We then performed MHC-mismatched allo-BMT into STAT1-floxed x villin-Cre recipients. Consistent with a role in IFNγ-related toxicity, STAT1-deficient recipients initially demonstrated reduced GVHD pathology, as well as a reduction in proliferating Ki67 + cells (Fig 2A). However, the pathology reduction in STAT1-deficient recipients was transient, while reduction in crypt proliferation persisted. STAT1-deficient recipients ultimately demonstrated increased mortality after allo-BMT, indicating a complex response to epithelial STAT1 signaling in GVHD.While IFNγ can induce epithelial apoptosis and kill organoid cultures, organoid exposure to IFNγ augmented size even at IFNγ concentrations that did not impair viability in a STAT1-dependent manner, and co-culture with allo T cells augmented organoid size (Fig 2B, C). Moreover, cell cycle analysis showed augmentation of cell cycle in ISCs after IFNγ treatment in association with upregulation of cyclin D1 (Fig 2D), and human organoids also showed increased size in response to IFNγ treatment, further suggesting that this growth promotion was not simply a secondary response to tissue injury.In addition to the IFNγ signaling, GSEA of allo ISCs indicated activation of the Myc pathway. scRNAseq data showed specific upregulation of Myc in allo ISCs (Fig 3A). Myc expression within individual ISCs indicated that greater STAT1 expression and IFNγ signaling directly correlated with Myc expression in the same ISCs, providing a potential direct link between T-cell-derived IFNγ and ISC-dependent regeneration (Fig 3B). Additionally, intestinal organoid qPCR showed that Myc expression was upregulated after IFNγ treatment, and scRNAseq of IFNγ-treated organoids indicated this Myc upregulation was restricted to the ISC/progenitor compartment. Although Myc is downstream of Wnt signaling, which is critical for ISC maintenance, expression of the representative Wnt target gene Axin2 was downregulated after IFNγ treatment, and Irf1, a representative IFNγ/STAT1 target gene, was upregulated, suggesting that IFNγ/STAT1 signaling could replace Wnt/β-catenin as a driver of ISC Myc expression. We next examined Myc function and found that treatment with the Myc inhibitor 10058-F4 suppressed IFNγ-dependent organoid growth (Fig 3C). Finally, immunofluorescent staining showed Myc protein expression in intestinal crypts after allo-BMT in a STAT1-dependent manner (Fig 3D), and Myc inhibitor treatment in vivo suppressed crypt epithelial proliferation in mice with GVHD.In summary, we found that epithelial STAT1 contributes to crypt regeneration in GVHD by transmitting T-cell-derived JAK/STAT cytokine signaling to activate Myc expression in ISCs. Clinical use of JAK inhibitors in GVHD may inhibit this regenerative response, necessitating concurrent interventions aimed at restoring it. [Display omitted] DisclosuresHanash: Evive Biotech: Ended employment in the past 24 months.

Follow-Up Care Barriers for Patients with Orofacial Clefts.

The aim of this study was to evaluate whether a patient with a cleft's age, associated syndrome, cleft phenotype or travel distance affects their follow-up rate. This study is a retrospective review of patients with CL/P treated by a craniofacial clinic. The setting was a craniofacial clinic at a tertiary care university hospital. Candidates were patients seen by the craniofacial clinic between January 2007 and December 2019. An initial pool of 589 patients was then reduced to 440 due to exclusion criteria. None. The outcome measure was actual patient attendance to the craniofacial team compared to the team goal expectation of annual return visits. The mean age of participants at the end of the study was 9.0 ± 5.4 years with a mean follow-up period (total possible follow-up period length based on patient age at presentation and study window) of 5.5 ± 3.6 years. There was no association between cleft phenotype, type of syndrome, or distance to the clinic with attendance. Children with syndromes had an 11% decrease in the odds of attending follow-up visits with each 1-year increase in age compared to a 4% decrease in children without syndromes. The only significant factors determining patient attendance were the presence of a syndrome and increasing age.

Spatial population structure: patterns of adaptation in populations of the water hyacinth grasshopper Cornops aquaticum (Bruner 1906)

AbstractThe water hyacinth grasshopper Cornops aquaticum (Bruner 1906) constitutes an appropriate model to assess phenotypic and karyotypic variability in the context of differentiation and adaptation of insect populations because it occurs over a wide latitudinal range. This study represents a general analysis of phenotype, karyotype and molecular variation in native populations of C. aquaticum in South America. This is also relevant because this insect is considered a promising biological control agent of water hyacinth, a native South American aquatic plant but a pest in South Africa. Along Paraná and Uruguay River Basins, body size correlated negatively with latitude, and positively so with temperature and rainfall in both sexes. To test whether the chromosomal and phenotypic patterns were adaptive, we compared them with neutral microsatellite loci variation in populations from the medium and lower course of the Paraná River. Firstly, the lack of pairwise association between karyotype and phenotype distance matrixes with that of neutral loci suggested non-neutrality. Secondly, phenotypic differentiation for all morphometric traits (PST) was significantly larger than molecular differentiation (FST), indicating a prevailing divergence selection effect on the observed phenotypic patterns. Finally, the phenotypic and genotypic spatial structures – inferred from Bayesian approaches – were discordant: neutral genetic structure clustered together most populations except for the two southernmost, downstream ones, whereas phenotypic spatial structure groups together all the deltaic populations and singles out the two northernmost ones. The results suggest directional selection leading to higher centric fusion frequencies in the downstream populations and favouring morphometric optimal differences in relation to the environment.

Is neutral genetic diversity related to quantitative variation in semen traits in bulls?

Conservation decisions based on neutral genetic diversity have been observed to promote retention of useful quantitative variation in biological populations. An experiment was undertaken to determine the association between microsatellite marker polymorphisms and phenotypic variation in semen production and cryosurvival traits in bulls. Thirty-five ejaculates were collected from ten bulls of two breeds and evaluated before and after cryopreservation for several semen traits. The bulls were also genotyped using a set of sixteen bovine-specific microsatellite marker loci. Fixation indices (FST ), heterozygosity and Nei's genetic distance measures were computed from allele frequency data for each of the bulls. Molecular and phenotypic data were used to compute tri-distance matrices for the ten bulls and correlated using Mantel's test in GenAIEx 6.5. The study revealed extensive heterogeneity in semen traits, heterozygosity and FST values among the bulls. Large pairwise phenotypic and genetic distances were also observed. Correlation between pairwise genetic distances and phenotypic distances was significant and highly positive for sperm viability (r=.61, p<.001) and moderately positive for sperm motility (r=.40-42, p<.05) variables. For sperm morphology, ejaculate volume and sperm concentration, correlation with genetic distances was positive, low and not significantly different from zero (p>.05). A tendency for a triangular-shaped relationship between genetic and phenotypic distances for post-thaw motility and viability traits was also observed. Accordingly, association with neutral genetic diversity was absent for semen production traits and moderate to highly positive for sperm cryosurvival traits. Given these findings, conservation decisions based on neutral genetic diversity may capture variation in some adaptive traits, but not others.

Assessment of Relationship for Both Seedling and Maturity Traits with SSR Markers under Drought Conditions in Bread Wheat (Triticum asetivum L.)

TWENTY-ONE cultivars of bread wheat were evaluated for drought-stress tolerance atseedling and maturity stages under non-drought and drought-stress conditions. Significant differences among genotypes were obtained under non-drought and drought-stress conditions for all seedling and maturity characteristics. Highly positive and significant correlations were found for root length with respect to fresh weight of 0.74 and dry weight seedling of 0.80. However, negative and highly significant correlations were found for both drought susceptible index based on seedling traits (DSIST) and maturity traits (DSIST) with all seedling traits except root: shoot ratio, whereas no correlations were obtained for either DSIST or DSIMT with all maturity traits except 1000 kernel weight. Positive and highly significant correlation found between DSIST and DSIMT (0.85). SSR markers analysis showed that three bands produced by Xgwm596-7A (507bp), Xgwm497-1A (556bp) and Xgwm174-5D (409bp), they were presented in all tolerant genotypes based on DSIST. The three bands (507, 556 and 409bp) were correlated to DSIST, with R2 values of 81.05%, whereas the three bands were correlated to DSIMT with R2 values of 61.96%. Strong association was observed for genotypic distance with phenotypic distance based on seedling characteristics, that amounted to 0.66, whereas the correlation was less strong between genotypic distance and phenotypic distance based on maturity traits by 0.30. The seedling traits at 15% PEG were more association than maturity traits under drought-stress with SSR markers, this gives preference to using seedling traits as an indicator of drought-stress tolerance in breeding programs.

Morphological and ecogeographical diversity analysis of maize germplasm in the high altitude Andes region of Ecuador

AbstractThe Andean region of Ecuador is the place of origin of many maize landraces grouped into 24 races. Definition of priorities for maize diversity conservation in this region can be supported by the spatial identification of areas with a high eco-geographical and phenotypic diversity. Six hundred thirty-six maize samples were morphologically characterized using 14 descriptors and assigned to a distinctive race. Additionally, sampled farms were characterized by 12 environmental variables. From these data, maps of morphological and eco-geographical diversity were obtained by using techniques to determine eco-geographical and phenotypic distances and applying them to each geographical neighbourhood. The races Patillo Ecuatoriano, Racimo de Uva and Uchima exhibited high intra-racial morphological variation, particularly in the shape of the ear, kernel row layout, cob diameter and total kernel number. The highest number of different races was observed in Imbabura, Azuay and Chimborazo provinces. The highest levels of morphological diversity were found in three cells (10 × 10 km), located in Pichincha, Chimborazo and Loja provinces. Two ecological niches, located in Loja province, showed high levels of eco-geographical diversity. A comparison between diversity maps revealed shared hotspots of morphological and eco-geographical diversity in the central and southwest areas of Imbabura province. The Andean highlands of Ecuador are an optimal refuge for the conservation of maize diversity, and the criteria of eco-geographical and morphological diversity and race richness should be considered when defining priority in situ conservation areas.

Hybridization Outcomes Have Strong Genomic and Environmental Contingencies.

AbstractExtreme F2 phenotypes known as transgressive segregants can cause increased or decreased fitness in hybrids beyond the ranges seen in parental populations. Despite the usefulness of transgression for plant and animal breeding and its potential role in hybrid speciation, the genetic mechanisms and predictors of transgressive segregation remain largely untested. We generated seven hybrid crosses between five widely divergent Saccharomyces yeast species and measured the fitness of the parents and their viable F1 and F2 hybrids in seven stressful environments. We found that on average 16.6% of all replicate F2 hybrids had higher fitness than both parents. Against our predictions, transgression frequency was not a function of parental genetic and phenotypic distances across test environments. Within environments, some relationships were significant, but not in the predicted direction; for example, genetic distance was negatively related to transgression in ethanol and hydrogen peroxide. Significant effects of hybrid cross, test environment, and cross × environment interactions suggest that the amount of transgression produced in a hybrid cross is highly context specific and that outcomes of hybridization differ even among crosses made from the same two parents. If the goal is to reliably predict hybrid fitness and forecast the evolutionary potential of admixed populations, we need more efforts to identify patterns beyond the idiosyncrasies caused by specific genomic or environmental contexts.

Genomic and Phenotypic Diversity of Cultivated and Wild Tomatoes with Varying Levels of Heat Tolerance.

Assessment of genetic variability in heat-tolerant tomato germplasm is a pre-requisite to improve yield and fruit quality under heat stress. We assessed the population structure and diversity in a panel of three Solanum pimpinellifolium (wild tomatoes) and 42 S. lycopersicum (cultivated tomatoes) lines and accessions with varying heat tolerance levels. The DArTseq marker was used for the sequencing and 5270 informative single nucleotide polymorphism (SNP) markers were retained for the genomic analysis. The germplasm was evaluated under two heat stress environments for five yield and flower related traits. The phenotypic evaluation revealed moderate broad-sense heritabilities for fruit weight per plant and high broad-sense heritabilities for fruit weight, number of inflorescences per plant, and number of flowers per inflorescence. The hierarchical clustering based on identity by state dissimilarity matrix and UPGMA grouped the germplasm into three clusters. The cluster analysis based on heat-tolerance traits separated the germplasm collection into five clusters. The correlation between the phenotypic and genomic-based distance matrices was low (r = 0.2, p < 0.05). The joint phenotypic and genomic-based clustering grouped the germplasm collection into five clusters well defined for their response to heat stress ranging from highly sensitive to highly tolerant groups. The heat-sensitive and heat-tolerant clusters of S. lycopersicum lines were differentiated by a specific pattern of minor allele frequency distribution on chromosome 11. The joint phenotypic and genomic analysis revealed important diversity within the germplasm collection. This study provides the basis for efficient selection of parental lines to breed heat-tolerant varieties.

Multidimensional Analysis of Diversity in DH Lines and Hybrids of Winter Oilseed Rape (Brassica napus L.)

Limited genetic variability is a major problem in rapeseed breeding, whose strict selection, limited geographical range and a short period of domestication has led to a reduction in genetic and phenotypic diversity. Assessing specific populations for the greatest genetic diversity for many traits simultaneously, requires the evaluation of multi-feature characteristics. The aim of this study was to estimate the variability of DH (doubled haploid) lines and two generations of winter oilseed rape hybrids. In addition, the relationship between the Mahalanobis distances of parental forms and the effect of heterosis in hybrids was investigated. The results of MANOVA showed that the genotypes and years as well as genotype × year interaction were significantly different (p &lt; 0.001) for all eight observed traits. The first (V1) and the second (V2) canonical variate explained 38.57% and 27.55% of the total variation in 2015, and 50.19% and 31.84% in 2016, respectively Canonical variate analysis showed that the traits, flowering time and number of branches per plant had a very large influence on the differentiation of genotypes. Graphs demonstrated that the tested DH lines and hybrids are characterized by a similar, wide range of variability. It was observed, that when using a diverse population of DH lines for crossbreeding with only one CMS/Rfo line, there was no significant reduction of variation in hybrid generations and between these generations. The phenotypic distance values determined by the results of Mahalanobis analysis were similar in both years, but slightly wider in 2016. The observed minimum and maximum ranged from 1.324 to 22.356 in 2015, and from 1.105 to 27.792 in 2016, respectively. No significant correlation was observed between the hybrid heterosis effect and the Mahalanobis distance of the parental lines.

Сравнительный анализ изменчивости формы семенных чешуй шишек Larix dahurica и L. cajanderi (Pinaceae)

Сравнительный анализ изменчивости формы семенных чешуй шишек Larix dahurica и L. cajanderi (Pinaceae)

Exploitation of Heterosis among Phenotypically Diverse Capsicum Parents for Important Fruit Traits

HIGHLIGHTS The effect of phenotypic distance between parental lines on the yield of C. annuum var. annuum × C. annuum var. grossum F1 hybrids was assessed. Simultaneously, the target of the research was transferring of the GMS ms10 gene from hot pepper to heat tolerant bell pepper inbreds. Over the BP, the hybrid MS-12 × PAU SM-31 was found to be superior in respect of total fruit yield plant-1 and pericarp thickness.

Morphological and molecular genetic diversity analysis of pearl millet (Pennisetum glaucum) maintainers and restorers

The success of any pearl millet hybrid programme depends upon the assessment of the structure of parental diversity. In this investigation, polymorphism data generated using 42 simple sequence repeat (SSR) markers and 12 agromorphological traits were used for genetic diversity assessment among 32 genotypes (29 restorers and 3 maintainers) of pearl millet [Pennisetum glaucum (L.) R. Br.].In contrast to morphological data, SSR based clustering pattern and Principal Coordinate Analysis revealed that the genotypes were found to be consistent with their pedigree and origin. Polymorphism information content (PIC) values based on microsatellites ranged from 0.117 to 0.841 per locus with an average PIC of 0.348. Allelic richness varied from two to five per locus. The highest similarity index (0.74) was observed between restorers WGI 58 and WGI 148, whereas the lowest similarity index (0.27) was observed between seed parent 841 B and PPMI 269. AMOVA analysis observed more genetic variance among the individuals than within individuals.The study led to the identification of maintainer 841 B as a genetically diverse parent from other maintainers as well as among most of the restorers and hence may be used in future hybrid development programmes. Further, the correlation between phenotypic and genetic distance matrices was observed to be very low. Appropriate heterotic combinations were identified based on morphological and molecular diversity.

Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces

Germplasm should be conserved in such a way that the genetic integrity of a given accession is maintained. In most genebanks, landraces constitute a major portion of collections, wherein the extent of genetic diversity within and among landraces of crops vary depending on the extent of outcrossing and selection intensity infused by farmers. In this study, we assessed the level of diversity within and among 108 diverse landraces and wild accessions using both phenotypic and genotypic characterization. This included 36 accessions in each of sorghum, pearl millet, and pigeonpea, conserved at ICRISAT genebank. We genotyped about 15 to 25 individuals within each accession, totaling 1,980 individuals using the DArTSeq approach. This resulted in 45,249, 19,052, and 8,211 high-quality single nucleotide polymorphisms (SNPs) in pearl millet, sorghum, and pigeonpea, respectively. Sorghum had the lowest average phenotypic (0.090) and genotypic (0.135) within accession distances, while pearl millet had the highest average phenotypic (0.227) and genotypic (0.245) distances. Pigeonpea had an average of 0.203 phenotypic and 0.168 genotypic within accession distances. Analysis of molecular variance also confirms the lowest variability within accessions of sorghum (26.3%) and the highest of 80.2% in pearl millet, while an intermediate in pigeonpea (57.0%). The effective sample size required to capture maximum variability and to retain rare alleles while regeneration ranged from 47 to 101 for sorghum, 155 to 203 for pearl millet, and 77 to 89 for pigeonpea accessions. This study will support genebank curators, in understanding the dynamics of population within and among accessions, in devising appropriate germplasm conservation strategies, and aid in their utilization for crop improvement.

Convergence in sympatry: Evolution of blue-banded wing pattern in Morpho butterflies.

Species interactions such as mimicry can promote trait convergence but disentangling this effect from those of shared ecology, evolutionary history, and niche conservatism is often challenging. Here by focusing on wing colour pattern variation within and between three butterfly species living in sympatry in a large proportion of their range, we tested the effect of species interactions on trait diversification. These butterflies display a conspicuous iridescent blue coloration on the dorsal side of their wings and a cryptic brownish colour on the ventral side. Combined with an erratic and fast flight, these colour patterns increase the difficulty of capture by predators and contribute to the high escape abilities of these butterflies. We hypothesize that, beyond their direct contribution to predator escape, these wing patterns can be used as signals of escape abilities by predators, resulting in positive frequency-dependent selection favouring convergence in wing pattern in sympatry. To test this hypothesis, we quantified dorsal wing pattern variations of 723 butterflies from the three species sampled throughout their distribution, including sympatric and allopatric situations and compared the phenotypic distances between species, sex and localities. We detected a significant effect of localities on colour pattern, and higher inter-specific resemblance in sympatry as compared to allopatry, consistent with the hypothesis of local convergence of wing patterns. Our results provide support to the existence of escape mimicry in the wild and stress the importance of estimating trait variation within species to understand trait variation between species, and to a larger extent, trait diversification at the macro-evolutionary scale.

Molecular Markers, Yield Performance and Berry Sensory Attributes in 10 Grape Cultivars Cultivated in Assiut Governorate

Yield performance and berry sensory attributes in 10 grape cultivars were studied under Assiut conditions. In addition, the genetic variability and relationships among these cultivars were determined based on RAPD and SRAP molecular markers. Genetic variations were observed between the tested cultivars in all studied traits of yield and yield components as well as in berry sensory attributes. 100 sites of grape genome were amplified by RAPD and SRAP primers and used to study the interrelationships between 10 grape cultivars. The highest interrelationships were found between “Black Muscat and Provano”, “Palomino and Bez El-Naka”, and between “Palomino and Ruby Seedless”. The lowest relatedness was found between Beauty Seedless and the other nine grape cultivars. The phenotypic data and molecular markers were effective in estimating the genetic variability between grape cultivars. The study indicated the presence of abundant genetic variability among some of the important commercial grape cultivars. Significant positive correlation was found between the phenotypic and genotypic distance indicated that the studied RAPD and SRAP markers were able to bind to effective regions in the genome.

Temporal encoding of bacterial identity and traits in growth dynamics

In biology, it is often critical to determine the identity of an organism and phenotypic traits of interest. Whole-genome sequencing can be useful for this but has limited power for trait prediction. However, we can take advantage of the inherent information content of phenotypes to bypass these limitations. We demonstrate, in clinical and environmental bacterial isolates, that growth dynamics in standardized conditions can differentiate between genotypes, even among strains from the same species. We find that for pairs of isolates, there is little correlation between genetic distance, according to phylogenetic analysis, and phenotypic distance, as determined by growth dynamics. This absence of correlation underscores the challenge in using genomics to infer phenotypes and vice versa. Bypassing this complexity, we show that growth dynamics alone can robustly predict antibiotic responses. These findings are a foundation for a method to identify traits not easily traced to a genetic mechanism.

Genetic diversity analysis of common bean (Phaseolus vulgaris L.) genotypes for resistance to Mexican bean weevil (Zabrotes subfasciatus), using single nucleotide polymorphism and phenotypic markers

ABSTRACT The objective of this study was to examine the genetic diversity present among 297 common bean genotypes using 2554 SNPs and 12 insects and seed-related traits. The phenotyping was done under laboratory condition while the genotyping was conducted by using the Illumina SNP BeadChip. High phenotypic diversity among traits were recorded, ranging from 0.87 to 0.96, with a mean of 0.92. Principal component and discriminant analyses identified four PCs and three discriminant functions, which explained 82% and 100% of the total phenotypic variations among genotypes, respectively. Polymorphic Information Content ranged from 0.21 to 0.38, with a mean of 0.34. The mean gene diversity among genotypes ranged from 0.24 to 0.50, with a mean of 0.44. Genetic distance ranged from 0.19 to 0.82, with a mean of 0.62, while the phenotypic distance ranged from 0.00 to 1.00, with a mean of 0.64 were observed aamong genotypes. The analysis of molecular variance revealed highly significant differences (p<0.001) among and within individuals and among populations. Both the SNP and the phenotypic markers grouped the 297 genotypes into two major distinct clusters and three sub-clusters. This information is useful for identification and development of common bean germplasm with economically valuable traits and the conservation and utilization of genotypes.

Estimating phenotypic heritability of sexual and unisexually reproducing rock lizards (genus Darevskia)

The difference between phenotypic and genotypic differentiation of conspecific populations is commonly used for detecting natural selection. However, phenotypic variation integrates both genetic and non-genetic components, and this may lead researchers to false conclusions. To avoid bias, the analysis of the heritability of individual phenotypic characters is important, but the means are labor–intensive and require controlled crosses. In this paper, we tried to get around these difficulties by working with a natural system comprised of the coexisting sexually reproducing lizard Darevskia portschinskii, and its daughter parthenogenetic form, Darevskia dahli. The excess of individual and between-population variation in the sexual form relative to the parthenogen was used as a measure of heritability of each of 21 scalation traits and principal components extracted from their analysis. We compared these data with microsatellite genotypes based on the analysis of five variable loci. We showed that D. portschinskii had higher individual and between-population phenotypic diversity than D. dahli. Phenotypic differences between populations of D. portschinskii (but not D. dahli) correlate with both the geographic distances and pairwise fixation indices based on the analysis of the genetic markers. This correlation substantially increased when, instead of the original phenotypic distances, the corrected Qst values are used to assess the heritability of the characters. A similar analysis pattern is recommended for various natural systems with coexisting sexually and asexually reproducing organisms.