Phenotypic variation of floral organs in flowering crabapples and its taxonomic significance

Abstract Background In angiosperms, phenotypic variation of floral organs is often considered as the traditional basis for the evolutionary relationship of different taxonomic groups above the species level. However, little is known about that at or below the species level. Here, we experimentally tested the phenotypic variation of Malus floral organs using combined methods of intraspecific uniformity test, interspecific distinctness analysis, principal component analysis, Pearson correlation analysis, and Q-type cluster analysis. The ancestor-inclined distribution characteristic analysis of Malus species and cultivars floral attributes was also carried out, so as to explore its taxonomic significance. Results 15/44 phenotypic traits (e.g., flower shape, flower type, flower diameter, ...) were highly consistent, distinguishable, and independent and could be used as the basis for Malus germplasm taxonomy. The studied 142 taxa were divided into two groups (A, B) and five sub-groups (A1, A2, B1, B2, B3), with significantly variable floral phenotypic attributes between groups and within sub-groups. Malus natural species were relatively clustered in the same section (series) while homologous cultivars showed evidence of ancestor-inclined distribution characteristics. However, no significant correlation between the evolutionary order of sections (Sect. Docyniopsis → Sect. Chloromeles → Sect. Sorbomalus → Sect. Eumalus) and group/sub-groups (B3 → B2 → B1 → A). Conclusions Phenotypic variation of floral organs could better explore the genetic relationship between Malus taxa. The findings improved our cognition of floral phenotypic variation taxonomic significance under the species level.

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Phenotypic characterization and principal component analyses of indigenous chicken breeds in Indonesia

Veterinary World ◽

10.14202/vetworld.2021.1665-1676 ◽

2021 ◽

pp. 1665-1676

Author(s):

Dyah Maharani ◽

Fatmawati Mustofa ◽

Aprilianna Putri Z. N. L. Sari ◽

Akhmad Fathoni ◽

Heru Sasongko ◽

...

Keyword(s):

Phenotypic Variation ◽

Quantitative Traits ◽

Principal Component ◽

Phenotypic Characterization ◽

Phenotypic Traits ◽

Indigenous Chicken ◽

Mean Values ◽

Indigenous Chickens ◽

Chicken Breeds ◽

Improvement Programs

Background and Aim: Understanding the phenotypic characteristics of indigenous livestock breeds is essential for their utilization and conservation. This study aimed to characterize indigenous chicken breeds in Indonesia based on phenotypic traits. Materials and Methods: Data on eight qualitative and 12 quantitative traits were recorded for 250 chickens from six breeds: Black Kedu, Gaga, Merawang, Nunukan, Pelung, and Sentul. Data were analyzed using descriptive statistics and one-way analysis of variance to test the effect of breed on observed traits. Moreover, principal component analysis (PCA) was conducted separately for each chicken breed. Data on quantitative traits were subjected to Kaiser-Meyer-Olkin, which was computed to test the sampling adequacy and the pattern of correlation among the traits, and Bathlett's tests were used to assess the validity of the factor analysis of each of the datasets and determine whether the partial correlations among traits were small. Results: We found considerable phenotypic variation in both qualitative and quantitative traits among indigenous chicken breeds. Multicolored plumage (96.40%), wild plumage (39.20%), gold feather flick (51.20%), yellow shank (36.80%), single comb (80.80%), red comb (94.80%), red earlobe (77.60%), and orange eyes (61.60%) were the most common features in the indigenous chickens. In addition, breed had a significant effect on all the quantitative traits that were analyzed (p<0.05). There were higher mean values for all quantitative traits for Pelung chickens than other chickens. In addition, the overall mean values for all quantitative traits in Merawang chicken were intermediate between Pelung chickens and Black Kedu, Gaga, and Nunukan chickens. The PCA showed two principal factors extracted that accounted for 77.80% and 78.38% of the total variance in the original variables for males and females, respectively. Conclusion: In general, body weight and body measurements, except wattle length, were loaded in PC1 as the primary factors responsible for the variation. The phenotypic variation observed in indigenous chickens in Indonesia could provide valuable basic information for the design of selection and genetic improvement programs.

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Bioprospecting of Sechium spp. varieties for the selection of characters with pharmacological activity

Scientific Reports ◽

10.1038/s41598-021-85676-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

María Isabel Iñiguez-Luna ◽

Jorge Cadena-Iñiguez ◽

Ramón Marcos Soto-Hernández ◽

Francisco Javier Morales-Flores ◽

Moisés Cortes-Cruz ◽

...

Keyword(s):

Cell Lines ◽

Proliferative Activity ◽

Meta Analysis ◽

Pearson Correlation ◽

Statistical Significance ◽

Economic Value ◽

Principal Component ◽

Malignant Cell ◽

Length Polymorphisms ◽

Relevant Variables

AbstractBioprospecting identifies new sources of compounds with actual or potential economic value that come from biodiversity. An analysis was performed regarding bioprospecting purposes in ten genotypes of Sechium spp., through a meta-analysis of 20 information sources considering different variables: five morphological, 19 biochemical, anti-proliferative activity of extracts on five malignant cell lines, and 188 polymorphic bands of amplified fragment length polymorphisms, were used in order to identify the most relevant variables for the design of genetic interbreeding. Significant relationships between morphological and biochemical characters and anti-proliferative activity in cell lines were obtained, with five principal components for principal component analysis (SAS/ETS); variables were identified with a statistical significance (< 0.7 and Pearson values ≥ 0.7), with 80.81% of the accumulation of genetic variation and 110 genetic bands. Thirty-nine (39) variables were recovered using NTSYSpc software where 30 showed a Pearson correlation (> 0.5) and nine variables (< 0.05), Finally, using a cladistics analysis approach highlighted 65 genetic bands, in addition to color of the fruit, presence of thorns, bitter flavor, piriform and oblong shape, and also content of chlorophylls a and b, presence of cucurbitacins, and the IC50 effect of chayote extracts on the four cell lines.

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

Scientific Reports ◽

10.1038/s41598-021-83921-7 ◽

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.

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Towards Understanding Variability in Droughts in Response to Extreme Climate Conditions over the Different Agro-Ecological Zones of Pakistan

Sustainability ◽

10.3390/su13126910 ◽

2021 ◽

Vol 13 (12) ◽

pp. 6910

Author(s):

Adil Dilawar ◽

Baozhang Chen ◽

Arfan Arshad ◽

Lifeng Guo ◽

Muhammad Irfan Ehsan ◽

...

Keyword(s):

Pearson Correlation ◽

Principal Component ◽

Mitigation Strategies ◽

Precipitation Extremes ◽

Climate Mitigation ◽

Mean Annual Temperature ◽

Climate Extreme ◽

Ecological Zones ◽

The Mean ◽

Agro Ecological Zones

Here, we provided a comprehensive analysis of long-term drought and climate extreme patterns in the agro ecological zones (AEZs) of Pakistan during 1980–2019. Drought trends were investigated using the standardized precipitation evapotranspiration index (SPEI) at various timescales (SPEI-1, SPEI-3, SPEI-6, and SPEI-12). The results showed that droughts (seasonal and annual) were more persistent and severe in the southern, southwestern, southeastern, and central parts of the region. Drought exacerbated with slopes of −0.02, −0.07, −0.08, −0.01, and −0.02 per year. Drought prevailed in all AEZs in the spring season. The majority of AEZs in Pakistan’s southern, middle, and southwestern regions had experienced substantial warming. The mean annual temperature minimum (Tmin) increased faster than the mean annual temperature maximum (Tmax) in all zones. Precipitation decreased in the southern, northern, central, and southwestern parts of the region. Principal component analysis (PCA) revealed a robust increase in temperature extremes with a variance of 76% and a decrease in precipitation extremes with a variance of 91% in the region. Temperature and precipitation extremes indices had a strong Pearson correlation with drought events. Higher temperatures resulted in extreme drought (dry conditions), while higher precipitation levels resulted in wetting conditions (no drought) in different AEZs. In most AEZs, drought occurrences were more responsive to precipitation. The current findings are helpful for climate mitigation strategies and specific zonal efforts are needed to alleviate the environmental and societal impacts of drought.

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Contributions of source population and incubation temperature to phenotypic variation of hatchling Chinese skinks

Current Zoology ◽

10.1093/cz/zoaa063 ◽

2020 ◽

Author(s):

Hong-Liang Lu ◽

Yan-Fu Qu ◽

Hong Li ◽

Xiang Ji

Keyword(s):

Body Mass ◽

Phenotypic Variation ◽

Incubation Temperature ◽

Tail Length ◽

Population Variation ◽

Phenotypic Traits ◽

Source Population ◽

Relative Importance ◽

The Difference ◽

Hatchling Size

Abstract Phenotypic plasticity and local adaptation are viewed as the main factors that result in between-population variation in phenotypic traits, but contributions of these factors to phenotypic variation vary between traits and between species and have only been explored in a few species of reptiles. Here, we incubated eggs of the Chinese skink (Plestiodon chinensis) from 7 geographically separated populations in Southeast China at 3 constant temperatures (24, 28, and 32 °C) to evaluate the combined effects of clutch origin, source population, and incubation temperature on hatchling traits. The relative importance of these factors varied between traits. Nearly all examined hatchling traits, including body mass, snout–vent length (SVL), tail length, head size, limb length, tympanum diameter, and locomotor speed, varied among populations and were affected by incubation temperature. Measures for hatchling size (body mass and SVL) varied considerably among clutches. Source population explained much of the variation in hatchling body mass, whereas incubation temperature explained much of the variation in other examined traits. Our results indicate that between-population variation in hatchling traits of P. chinensis likely reflects the difference in natural incubation conditions and genetic divergence.

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Discovery of Spatial Peptide Signatures for Neuroblastoma Risk Assessment by MALDI Mass Spectrometry Imaging

Cancers ◽

10.3390/cancers13133184 ◽

2021 ◽

Vol 13 (13) ◽

pp. 3184

Author(s):

Zhiyang Wu ◽

Patrick Hundsdoerfer ◽

Johannes H. Schulte ◽

Kathy Astrahantseff ◽

Senguel Boral ◽

...

Keyword(s):

Mass Spectrometry ◽

Risk Assessment ◽

Mass Spectrometry Imaging ◽

Principal Component ◽

Therapy Resistance ◽

Risk Classification ◽

Intratumor Heterogeneity ◽

Ionization Mass ◽

Characteristic Analysis ◽

Analytical Strategy

Risk classification plays a crucial role in clinical management and therapy decisions in children with neuroblastoma. Risk assessment is currently based on patient criteria and molecular factors in single tumor biopsies at diagnosis. Growing evidence of extensive neuroblastoma intratumor heterogeneity drives the need for novel diagnostics to assess molecular profiles more comprehensively in spatial resolution to better predict risk for tumor progression and therapy resistance. We present a pilot study investigating the feasibility and potential of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to identify spatial peptide heterogeneity in neuroblastoma tissues of divergent current risk classification: high versus low/intermediate risk. Univariate (receiver operating characteristic analysis) and multivariate (segmentation, principal component analysis) statistical strategies identified spatially discriminative risk-associated MALDI-based peptide signatures. The AHNAK nucleoprotein and collapsin response mediator protein 1 (CRMP1) were identified as proteins associated with these peptide signatures, and their differential expression in the neuroblastomas of divergent risk was immunohistochemically validated. This proof-of-concept study demonstrates that MALDI-MSI combined with univariate and multivariate analysis strategies can identify spatially discriminative risk-associated peptide signatures in neuroblastoma tissues. These results suggest a promising new analytical strategy improving risk classification and providing new biological insights into neuroblastoma intratumor heterogeneity.

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Codon usage bias and environmental adaptation in microbial organisms

Molecular Genetics and Genomics ◽

10.1007/s00438-021-01771-4 ◽

2021 ◽

Author(s):

Davide Arella ◽

Maddalena Dilucca ◽

Andrea Giansanti

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Pathogenic Bacteria ◽

Large Scale ◽

Synonymous Codon ◽

Principal Component ◽

Gene Copy ◽

Phenotypic Traits ◽

Translational Efficiency ◽

Microbial Organisms

AbstractIn each genome, synonymous codons are used with different frequencies; this general phenomenon is known as codon usage bias. It has been previously recognised that codon usage bias could affect the cellular fitness and might be associated with the ecology of microbial organisms. In this exploratory study, we investigated the relationship between codon usage bias, lifestyles (thermophiles vs. mesophiles; pathogenic vs. non-pathogenic; halophilic vs. non-halophilic; aerobic vs. anaerobic and facultative) and habitats (aquatic, terrestrial, host-associated, specialised, multiple) of 615 microbial organisms (544 bacteria and 71 archaea). Principal component analysis revealed that species with given phenotypic traits and living in similar environmental conditions have similar codon preferences, as represented by the relative synonymous codon usage (RSCU) index, and similar spectra of tRNA availability, as gauged by the tRNA gene copy number (tGCN). Moreover, by measuring the average tRNA adaptation index (tAI) for each genome, an index that can be associated with translational efficiency, we observed that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, are characterised by a reduced translational efficiency, consistently with their need to adapt to different environments. Our results show that synonymous codon choices might be under strong translational selection, which modulates the choice of the codons to differently match tRNA availability, depending on the organism’s lifestyle needs. To our knowledge, this is the first large-scale study that examines the role of codon bias and translational efficiency in the adaptation of microbial organisms to the environment in which they live.

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Key soil parameters affecting the survival of Panax notoginseng under continuous cropping

Scientific Reports ◽

10.1038/s41598-021-85171-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Wumei Xu ◽

Fengyun Wu ◽

Haoji Wang ◽

Linyan Zhao ◽

Xue Liu ◽

...

Keyword(s):

Soil Ph ◽

Pearson Correlation ◽

Principal Component ◽

Panax Notoginseng ◽

Soil Parameters ◽

Continuous Cropping ◽

Poor Growth ◽

Available N ◽

The Poor ◽

Replant Problem

AbstractNegative plant-soil feedbacks lead to the poor growth of Panax notoginseng (Sanqi), a well-known herb in Asia and has been used worldwide, under continuous cropping. However, the key soil parameters causing the replant problem are still unclear. Here we conducted a field experiment after 5-year continuous cropping. Sanqi seedlings were cultivated in 7 plots (1.5 m × 2 m), which were randomly assigned along a survival gradient. In total, 13 important soil parameters were measured to understand their relationship with Sanqi’s survival. Pearson correlation analysis showed that 6 soil parameters, including phosphatase, urease, cellulase, bacteria/fungi ratio, available N, and pH, were all correlated with Sanqi’s survival rate (P < 0.05). Principal component analysis (PCA) indicated that they explained 61% of the variances based on the first component, with soil pH being closely correlated with other parameters affecting Sanqi’s survival. The optimum pH for Sanqi growth is about 6.5, but the mean soil pH in the study area is 5.27 (4.86–5.68), therefore it is possible to ameliorate the poor growth of Sanqi by increasing soil pH. This study may also help to reduce the replant problem of other crops under continuous cropping since it is widespread in agricultural production.

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PSXIII-26 Supplementation with a polyphenolic pine bark extract reduces ammonia nitrogen production in a RUSITEC system as determined by principal component analysis

Journal of Animal Science ◽

10.1093/jas/skab235.779 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 435-436

Author(s):

Nelson Vera ◽

Constanza Gutierrez ◽

Pamela Williams ◽

Cecilia Fuentealba ◽

Rodrigo Allende ◽

...

Keyword(s):

Principal Component Analysis ◽

Repeated Measures ◽

Pearson Correlation ◽

Principal Component ◽

Component Analysis ◽

Ammonia Nitrogen ◽

Pine Bark ◽

Bark Extract ◽

Ruminal Fermentation ◽

Fermentation Parameters

Abstract The aim of the study was to correlate the effects of supplementation with a polyphenolic pine bark extract (PBE) in diets with different forage to concentrate (F:C) ratio on methane (CH4), ammonia nitrogen (NH3–N) production and ruminal fermentation parameters using the Rumen Simulation Technique (RUSITEC). The experimental diets were F:C 70:30 (HF) or F:C 30:70 (HC) with or without 2% PBE on a DM basis. The four diets were isoproteic (15% CP), with similar OM (HF 94% and HC 96%), but different NDF (HF 40% and HC 25%). The treatments, in duplicate, were assigned in an 8 fermenter RUSITEC apparatus. Incubations were run twice, with 5 days of sampling after 10 days adaptation. The experimental design was a 2x2 factorial arrangement in a randomized complete block with repeated measures. Pearson correlation and principal component analysis (PCA) were conducted to elucidate relationships among PBE total polyphenols (TP) and the variables evaluated. The TP was highly correlated with NH3–N (r = –0.98; P < 0.001) and butyrate (r = –0.85; P < 0.001), and had a high correlation with propionate (r = 0.75; P < 0.001) and acetate (r = 0.68; P = 0.001). Correlation with total VFA was moderate (r = –0.59; P = 0.006), and CH4 yield and IVDMD there were not correlated (r ≤ –0.07; P ≥ 0.188). The PCA (KMO = 0.655; BTS < 0.001) shows that 75.2% of the total variation is explained by the first two principal components (PC1 = 46.5% and PC2 = 28.7%). In the score plot, PC1 discriminated between diets with and without PBE, while the PC2 separated based on NDF. The loading plot showed that TP and propionate were clustered, and had inverse directions to NH3–N. In conclusion, the PBE supplementation reduces NH3–N production in a RUSITEC system without decreasing CH4 yield or negatively affecting ruminal fermentation parameters.

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Rhamnella intermedia (Rhamnaceae), a new evergreen species from southwest Guangxi

PhytoKeys ◽

10.3897/phytokeys.159.53177 ◽

2020 ◽

Vol 159 ◽

pp. 115-126

Author(s):

Zhiqiang Lu ◽

Yongshuai Sun

Keyword(s):

New Species ◽

Related Species ◽

Principal Component ◽

Phenotypic Traits ◽

Evergreen Species ◽

Closely Related Species ◽

Field Investigations ◽

Sequence Variations ◽

Dried Fruit ◽

Nuclear Its

Rhamnella intermedia, a new evergreen species from southwest Guangxi, is described and illustrated in this study. This species is similar to R. brachycarpa by the size and ratio of length to width of dried fruit and seeds, by which it differs from R. rubrinervis and R. tonkinensis. However, it differs from R. brachycarpa by rarely mucronate seed apices, larger ratio of length to width of leaves, leaf apices acuminate to long acuminate, shorter leaf petioles, and longer fruiting pedicels. Principal component analysis based on phenotypic traits further recognised three separated groups. Rhamnella rubrinervis and R. tonkinensis were clustered into one group; the other two groups represented R. brachycarpa and two Guangxi populations, respectively. Furthermore, phylogenetic analysis of nuclear ITS sequence variations highly supported that the two Guangxi populations represented an independent evolutionary lineage and were closest to R. rubrinervis. Four fixed nucleotide sites were found and were different from R. rubrinervis. However, besides the differentiated traits in seeds and fruit, densely pilose young branches also separated them from R. rubrinervis. In addition, during our field investigations, none of the three closely related species were found at locations where this new species was distributed. Therefore, this new species, based on the two Guangxi populations, is named R. intermedia. The key to four closely related species is also presented.

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