scholarly journals Multivariate trait analysis reveals diatom plasticity constrained to a reduced set of biological axes

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Phoebe A. Argyle ◽  
Nathan G. Walworth ◽  
Jana Hinners ◽  
Sinéad Collins ◽  
Naomi M. Levine ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Dimensional Space ◽  
Principal Component ◽  
Marine Diatom ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Theoretical Frameworks ◽  
Phytoplankton Ecology ◽  
Biogeochemical Models ◽  
Trade Offs

AbstractTrait-based approaches to phytoplankton ecology have gained traction in recent decades as phenotypic traits are incorporated into ecological and biogeochemical models. Here, we use high-throughput phenotyping to explore both intra- and interspecific constraints on trait combinations that are expressed in the cosmopolitan marine diatom genus Thalassiosira. We demonstrate that within Thalassiosira, phenotypic diversity cannot be predicted from genotypic diversity, and moreover, plasticity can create highly divergent phenotypes that are incongruent with taxonomic grouping. Significantly, multivariate phenotypes can be represented in reduced dimensional space using principal component analysis with 77.7% of the variance captured by two orthogonal axes, here termed a ‘trait-scape’. Furthermore, this trait-scape can be recovered with a reduced set of traits. Plastic responses to the new environments expanded phenotypic trait values and the trait-scape, however, the overall pattern of response to the new environments was similar between strains and many trait correlations remained constant. These findings demonstrate that trait-scapes can be used to reveal common constraints on multi-trait plasticity in phytoplankton with divergent underlying phenotypes. Understanding how to integrate trait correlational constraints and trade-offs into theoretical frameworks like biogeochemical models will be critical to predict how microbial responses to environmental change will impact elemental cycling now and into the future.

scholarly journals Variation of Phenotypic Traits in Twelve Bambara Groundnut (Vigna subterranea (L.) Verdc.) Genotypes and Two F2 Bi-Parental Segregating Populations

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1451
Author(s):  
Xiuqing Gao ◽  
Aliyu Siise Abdullah Bamba ◽  
Aloyce Callist Kundy ◽  
Kumbirai Ivyne Mateva ◽  
Hui Hui Chai ◽  
...  
Keyword(s):  
Southern Africa ◽  
Negative Relationship ◽  
Principal Component ◽  
Bambara Groundnut ◽  
Structured Populations ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Potential Contribution ◽  
Vigna Subterranea ◽  
East West

Underutilised species such as bambara groundnut (Vigna subterranea (L.) Verdc.) have the potential to contribute significantly to meeting food and nutritional needs worldwide. We evaluated phenotypic traits in twelve bambara groundnut genotypes from East, West and Southern Africa and Southeast Asia and two F2 bi-parental segregating populations derived from IITA-686 ×Tiga Nicuru and S19-3 ×DodR to determine phenotypic trait variation and their potential contribution to the development of improved crop varieties. All phenotypic traits in twelve genotypes were significantly influenced (p < 0.01) by genotypes. Principal component analysis (PCA) showed that PC1 accounted for 97.33% variation and was associated with four genotypes collected from East and Southern Africa. PC2 accounted for 2.48% of the variation and was associated with five genotypes collected from East, West and Southern Africa. Transgressive segregation for a number of traits was observed in the two F2 bi-parental populations, as some individual lines in the segregating populations showed trait values greater or less than their parents. The variability between twelve genotypes and the two F2 bi-parental segregating populations and the negative relationship between plant architectural traits and yield related traits provide resources for development of structured populations and breeding lines for bambara groundnut breeding programme.

scholarly journals Sclerotinia sclerotiorum Populations Infecting Canola from China and the United States Are Genetically and Phenotypically Distinct

2013 ◽  
Vol 103 (7) ◽  
pp. 750-761 ◽  
Author(s):  
Renuka N. Attanayake ◽  
Patrick A. Carter ◽  
Daohong Jiang ◽  
Luis del Río-Mendoza ◽  
Weidong Chen
Keyword(s):  
United States ◽  
Sclerotinia Sclerotiorum ◽  
Chinese Population ◽  
Phenotypic Diversity ◽  
The United States ◽  
Cross Resistance ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Type Locus ◽  
Two Populations

Genetic and phenotypic diversity and population differentiation of Sclerotinia sclerotiorum isolates infecting canola from China and the United States were investigated. Genetic diversity was assessed with eight microsatellite markers and mycelial compatibility groups (MCGs). Phenotypic diversity was assessed with sensitivity to three fungicides, production of oxalate and sclerotia, growth rate, and virulence on two canola cultivars. No shared MCGs or multilocus haplotypes were detected between the two populations, and populations differed significantly (P < 0.001). Recombination was detected in both populations but was greater in the Chinese population. A polymerase chain reaction detection assay showed that ~60% of the isolates were inversion-plus at the mating type locus. The two populations differed significantly (P < 0.05) for all of the phenotypic traits except for sensitivity to fungicide fluazinam and virulence. Isolates in the Chinese population were unique in several aspects. Despite the phenotypic differentiation, heritabilities of the phenotypic traits were similar for both populations. Significant correlations were found among five phenotypic traits. Cross resistance to benomyl and iprodione was detected. Virulence was not significantly correlated with any other phenotypic trait and had the least heritability. However, both populations were equally virulent on either a susceptible or a moderately resistant canola cultivars.

scholarly journals Evaluation on the phenotypic diversity of Calamansi (Citrus microcarpa) germplasm in Hainan island

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Yong-Hui Xin ◽  
Yuan-Xin Wu ◽  
Bin Qiao ◽  
Long Su ◽  
Shang-Qian Xie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Phenotypic Diversity ◽  
Principal Component ◽  
Hainan Island ◽  
Component Analysis ◽  
Cell Number ◽  
Tree Canopy ◽  
Soluble Solids ◽  
Phenotypic Traits

AbstractCalamansi or Philippine lime (Citrofortunella macrocarpa) is an important crop for local economic in Hainan Island. There is no study about Calamansi germplasm evaluation and cultivar development. In this study, Calamansi data were collected from 151 of Calamansi seedling trees, and 37 phenotypic traits were analyzed to investigate their genetic diversities. The cluster analysis and principal component analysis were conducted aiming to provide a theoretical basis for the Calamansi genetic improvement. The results of the diversity analysis revealed: (1) the diversity indexes for qualitative traits were ranged from 0.46–1.39, and the traits with the highest genetic diversity level were fruit shaped and pulp colored (H′ > 1.20); and the diversity indexes for quantitative traits ranged from 0.67–2.10, with the exception of a lower in fruit juice rate (1.08) and lower in number of petals (0.67). (2) The clustering analysis of phenotypic traits have arranged the samples into 4 categories: the first group characterized by fewer flesh Segment number per fruit (SNF) and more Oil cell number (OCN); the second group had 7 samples, all characterized with larger Crown breadth (CB), higher Yield per tree (YPT), the lager leaf, the higher Ascorbic acid (AA), and less Seed number per fruit (SNPF); the third group had 25 samples characterized by smaller Tree foot diameter (TFD),smaller Fruit shape index (FSI) and higher Total soluble solids (TSS) contain; the fourth group had 87 samples, they were characterized by shorter Petiole length (PEL), larger fruit, higher Juice ratio (JR), multiple Stamen number (SN) and longer Pistil length (PIL). (3) The principal component analysis showed the values of the first 9 major components characteristic vectors were all greater than 3, the cumulative contribution rate reach 72.20%, including the traits of single fruit weight, fruit diameter, tree height, tree canopy width etc. Finally, based on the comprehensive main component value of all samples, the Calamansi individuals with higher testing scores were selected for further observation. This study concludes that Calamansi seedling populations in the Hainan Island holds great genetic diversity in varies traits, and can be useful for the Calamansi variety improvements.

scholarly journals Phenotypic and alpha-acid content diversity of wild hop populations in Croatia

2010 ◽  
Vol 56 (No. 1) ◽  
pp. 37-42 ◽  
Author(s):  
S. Srečec ◽  
V. Zechner-Krpan ◽  
V. Petravić-Tominac ◽  
A. Čerenak ◽  
Z. Liber ◽  
...  
Keyword(s):  
Acid Content ◽  
Phenotypic Diversity ◽  
Population Diversity ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Pairwise Comparisons ◽  
Information Index ◽  
Content Diversity ◽  
Passport Data ◽  
Leaflet Number

An ecogeographical survey of wild hop populations was conducted in the northwest of Croatia in two consecutive years. A total of 121 plants was documented on eight locations. Along with the passport data, the data on three phenotypic traits (no. of leaflets, cone shape, aroma) were gathered during collection, while the content of &alpha;<i>-acids in hop cones was determined by lead conductance</i>. Shannon’s information index was calculated for each phenotypic trait and was used as a measure of intra- and inter-population diversity. For all analyzed traits, most of the total phenotypic diversity was attributable to differences among plants within populations. The differences in proportions of individuals having a particular trait state between all pairs of populations in the case of leaflet number and cone shapes were non-significant. Four out of 28 pairwise comparisons for aroma were proven significant, indicating the existence of differences in proportions of individuals across populations recorded to have ‘typical hoppy’, ‘fine hop’ or ‘rough’ aroma. No significant differences were observed for &alpha;-acids content among populations. Plants exhibiting elongated cone shape had significantly higher &alpha;-acids content than those having oval or round cone shapes. Similarly, plants categorized as ‘rough’ aroma hop cones had the highest content of &alpha;-acids compared with those categorized as ‘typical hoppy’ or ‘fine hop aroma’ hop cones.

scholarly journals A High-Throughput Assay for Quantifying Phenotypic Traits of Microalgae

2021 ◽  
Vol 12 ◽  
Author(s):  
Phoebe A. Argyle ◽  
Jana Hinners ◽  
Nathan G. Walworth ◽  
Sinead Collins ◽  
Naomi M. Levine ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Experimental Studies ◽  
Principal Component ◽  
Two Dimensions ◽  
Marine Diatom ◽  
Phenotypic Traits ◽  
Low Volume ◽  
Commercial Applications ◽  
High Throughput Assay

High-throughput methods for phenotyping microalgae are in demand across a variety of research and commercial purposes. Many microalgae can be readily cultivated in multi-well plates for experimental studies which can reduce overall costs, while measuring traits from low volume samples can reduce handling. Here we develop a high-throughput quantitative phenotypic assay (QPA) that can be used to phenotype microalgae grown in multi-well plates. The QPA integrates 10 low-volume, relatively high-throughput trait measurements (growth rate, cell size, granularity, chlorophyll a, neutral lipid content, silicification, reactive oxygen species accumulation, and photophysiology parameters: ETRmax, Ik, and alpha) into one workflow. We demonstrate the utility of the QPA on Thalassiosira spp., a cosmopolitan marine diatom, phenotyping six strains in a standard nutrient rich environment (f/2 media) using the full 10-trait assay. The multivariate phenotypes of strains can be simplified into two dimensions using principal component analysis, generating a trait-scape. We determine that traits show a consistent pattern when grown in small volume compared to more typical large volumes. The QPA can thus be used for quantifying traits across different growth environments without requiring exhaustive large-scale culturing experiments, which facilitates experiments on trait plasticity. We confirm that this assay can be used to phenotype newly isolated diatom strains within 4 weeks of isolation. The QPA described here is highly amenable to customisation for other traits or unicellular taxa and provides a framework for designing high-throughput experiments. This method will have applications in experimental evolution, modelling, and for commercial applications where screening of phytoplankton traits is of high importance.

scholarly journals Comparison of Molecular Marker and Morphological Data to Determine Minimum Distance among Tomato Cultivars

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 772B-772
Author(s):  
Julie Villand ◽  
James Nienhuis ◽  
Paul Skroch ◽  
Jan Tivang
Keyword(s):  
Molecular Marker ◽  
Minimum Distance ◽  
Patent Protection ◽  
Distance Measure ◽  
Principal Component ◽  
Morphological Data ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Sampling Variance ◽  
Tomato Cultivars

Precise cultivar descriptions are necessary to support Plant Variety Protection and utility applications for patent protection. However, accurate discrimination among cultivars is contingent upon the dependability of the method used to delineate lines. The efficiency and reliability of Amplified Fragment Length Polymorphisms (AFLPs), Random Amplified Polymorphic DNAs (RAPDs), microsatellite polymorphisms, and phenotypic traits were studied in order to determine a method's ability to accurately predict pedigree relationships among a set of 20 California processing tomato cultivars. All molecular marker and phenotypic trait data sets were independently produced using identical cultivar seed sources. Data was reduced to a genetic distance measure and presented as a multidimensional scaling (MDS) plot. Principal component analysis using the scored quantitative phenotypic traits was computed and is compared to molecular marker data results. Experimental error, sampling variance, and independence of scored bands for each molecular marker technique are presented. These estimates should assist breeders to determine a sufficient level of characterization, determine a minimum distance considered to be unique, and defend pedigree relationships.

Hormones and Behavior

2019 ◽  
pp. 11-26
Author(s):  
Maren N. Vitousek ◽  
Laura A. Schoenle
Keyword(s):  
Life History ◽  
Life Histories ◽  
Life History Traits ◽  
Developmental Plasticity ◽  
Endocrine System ◽  
Phenotypic Traits ◽  
Social Environments ◽  
Trade Offs ◽  
And Behavior

Hormones mediate the expression of life history traits—phenotypic traits that contribute to lifetime fitness (i.e., reproductive timing, growth rate, number and size of offspring). The endocrine system shapes phenotype by organizing tissues during developmental periods and by activating changes in behavior, physiology, and morphology in response to varying physical and social environments. Because hormones can simultaneously regulate many traits (hormonal pleiotropy), they are important mediators of life history trade-offs among growth, reproduction, and survival. This chapter reviews the role of hormones in shaping life histories with an emphasis on developmental plasticity and reversible flexibility in endocrine and life history traits. It also discusses the advantages of studying hormone–behavior interactions from an evolutionary perspective. Recent research in evolutionary endocrinology has provided insight into the heritability of endocrine traits, how selection on hormone systems may influence the evolution of life histories, and the role of hormonal pleiotropy in driving or constraining evolution.

scholarly journals Normal approximation for mixtures of normal distributions and the evolution of phenotypic traits

2021 ◽  
Vol 53 (1) ◽  
pp. 162-188
Author(s):  
Krzysztof Bartoszek ◽  
Torkel Erhardsson
Keyword(s):  
Normal Distribution ◽  
Phenotypic Trait ◽  
Phenotypic Traits ◽  
Normal Distributions ◽  
Average Value ◽  
Conditional Moments ◽  
Mixture Of Normal Distributions ◽  
Explicit Bounds ◽  
Mixtures Of Normal Distributions ◽  
Parameter Values

AbstractExplicit bounds are given for the Kolmogorov and Wasserstein distances between a mixture of normal distributions, by which we mean that the conditional distribution given some $\sigma$ -algebra is normal, and a normal distribution with properly chosen parameter values. The bounds depend only on the first two moments of the first two conditional moments given the $\sigma$ -algebra. The proof is based on Stein’s method. As an application, we consider the Yule–Ornstein–Uhlenbeck model, used in the field of phylogenetic comparative methods. We obtain bounds for both distances between the distribution of the average value of a phenotypic trait over n related species, and a normal distribution. The bounds imply and extend earlier limit theorems by Bartoszek and Sagitov.

scholarly journals Evaluation of indigenous aromatic rice cultivars from sub-Himalayan Terai region of India for nutritional attributes and blast resistance

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Debayan Mondal ◽  
Prudveesh Kantamraju ◽  
Susmita Jha ◽  
Gadge Sushant Sundarrao ◽  
Arpan Bhowmik ◽  
...  
Keyword(s):  
Nutritive Value ◽  
Amylose Content ◽  
Blast Resistance ◽  
Starch Content ◽  
Low Cost ◽  
Principal Component ◽  
Blast Disease ◽  
Basmati Rice ◽  
Phenotypic Traits ◽  
Rice Cultivars

AbstractIndigenous folk rice cultivars often possess remarkable but unrevealed potential in terms of nutritional attributes and biotic stress tolerance. The unique cooking qualities and blissful aroma of many of these landraces make it an attractive low-cost alternative to high priced Basmati rice. Sub-Himalayan Terai region is bestowed with great agrobiodiversity in traditional heirloom rice cultivars. In the present study, ninety-nine folk rice cultivars from these regions were collected, purified and characterized for morphological and yield traits. Based on traditional importance and presence of aroma, thirty-five genotypes were selected and analyzed for genetic diversity using micro-satellite marker system. The genotypes were found to be genetically distinct and of high nutritive value. The resistant starch content, amylose content, glycemic index and antioxidant potential of these genotypes represented wide variability and ‘Kataribhog’, ‘Sadanunia’, ‘Chakhao’ etc. were identified as promising genotypes in terms of different nutritional attributes. These cultivars were screened further for resistance against blast disease in field trials and cultivars like ‘Sadanunia’, ‘T4M-3-5’, ‘Chakhao Sampark’ were found to be highly resistant to the blast disease whereas ‘Kalonunia’, ‘Gobindabhog’, ‘Konkanijoha’ were found to be highly susceptible. Principal Component analysis divided the genotypes in distinct groups for nutritional potential and blast tolerance. The resistant and susceptible genotypes were screened for the presence of the blast resistant pi genes and association analysis was performed with disease tolerance. Finally, a logistic model based on phenotypic traits for prediction of the blast susceptibility of the genotypes is proposed with more than 80% accuracy.

scholarly journals Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Jaewon Lim ◽  
Hong-Tae Park ◽  
Seyoung Ko ◽  
Hyun-Eui Park ◽  
Gyumin Lee ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Phenotypic Diversity ◽  
Control Strategies ◽  
Genomic Diversity ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genomic Features ◽  
Phenotypic Differences ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Type Strains

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

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