Principal component and morphological diversity analysis of Job&#8217;s-tears (Coix lacryma-jobi L.)

A morphological diversity analysis of Scoparia dulcis by macroscopy and microscopy has been conducted. The aim of this research is to determine the morphological and anatomical character of S. dulcis which grow in Opak watershed, Special Region of Yogyakarta. Samples were taken from Sleman (Cangkringan, Ngemplak Kalasan, and Prambanan) and Bantul (Imogiri and Pundong) region. Selection of sampling location is based on altitude difference. The samples are the third leaf order from the tip of the stem. They were measured in length and width. Microscopy analysis was performed by observing the number of glandular trichomes, palisade cells in the epidermis and stomata in the upper and lower epidermis. The data obtained were analyzed using principal component analysis (PCA). The results show that based on morphological and anatomical assessment, there were found 3 clusters of S. dulcis, i.e. Cangkringan-Ngemplak-Prambanan, Kalasan, and Imogiri-Pundong cluster.

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Evaluation of the morphological diversity of tea roses (Rosa x odorata) based on phenotypic traits

Plant Genetic Resources ◽

10.1017/s1479262120000179 ◽

2020 ◽

Vol 18 (3) ◽

pp. 149-158

Author(s):

Bixuan Cheng ◽

Chao Yu ◽

Heling Fu ◽

Lijun Zhou ◽

Le Luo ◽

...

Keyword(s):

Principal Component Analysis ◽

Correlation Analysis ◽

Morphological Traits ◽

Significant Positive Correlation ◽

Flower Colour ◽

Principal Component ◽

Morphological Diversity ◽

Component Analysis ◽

Germplasm Resources ◽

Trait Correlation

AbstractRosa x odorata (sect. Chinenses, Rosaceae) is an important species distributed only in Yunnan Province, China. There is an abundance of wild variation within the species. Using 22 germplasm resources collected from the wild, as well as R. chinensis var. spontanea, R. chinensis ‘Old Blush’ and R. lucidissima, this study involved morphological variation analysis, inter-trait correlation analysis, principal component analysis and clustering analysis based on 16 morphological traits. This study identified a high degree of morphological diversity in R. x odorata germplasm resources and the variation coefficients had a distribution range from 18.00 to 184.04%. The flower colour had the highest degree of variation, while leaflet length/width had the lowest degree of variation. Inter-trait correlation analysis revealed that there was an extremely significant positive correlation between leaflet length and leaflet width. There was also a significant positive correlation between the number of petals and duration of blooming, and the L* and a* values of flower colour were significantly negatively correlated. Principal component analysis screened five principal components with the highest cumulative contribution rate (81.679%) to population variance. Among the 16 morphological traits, style length, sepal width, flower diameter, flower colour, leaflet length and leaflet width were important indices that influenced the morphology of R. x odorata. This study offers guidance for the further development and utilization of R. x odorata germplasm resources.

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Comparison of Molecular and Morphological Diversity Analysis of Tetraploid Cotton (Gossypium hirsutum L.)

International Journal of Pure & Applied Bioscience ◽

10.18782/2320-7051.6718 ◽

2018 ◽

Vol 6 (5) ◽

pp. 367-376

Author(s):

Dharti Patel ◽

Keyword(s):

Gossypium Hirsutum ◽

Morphological Diversity ◽

Diversity Analysis ◽

Tetraploid Cotton ◽

Gossypium Hirsutum L

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Evaluation of morphological diversity of field pea [Pisum sativum subsp.arvense (L.)] germplasm under sub-tropical climate of Manipur

Legume Research - An International Journal ◽

10.18805/lr.v0iof.10756 ◽

2016 ◽

Author(s):

S. Bhuvaneswari ◽

Susheel Kumar Sharma ◽

P. Punitha ◽

K. S. Shashidhar ◽

K. L. Naveenkumar ◽

...

Keyword(s):

Seed Yield ◽

Quantitative Traits ◽

Principal Component ◽

Morphological Diversity ◽

Field Pea ◽

Plant Seed ◽

Diverse Field ◽

Early Maturing ◽

Linkage Method ◽

Practical Field

An investigation was carried out to evaluate 51 diverse field pea genotypes at Langol Research farm, ICAR, RC, NEH region, Manipur centre for nine yield related quantitative traits and four morphological qualitative traits for practical field pea improvement in Manipur. The combined analysis of variance of genotypes for all the nine traits was found to be significant. The amount of variability in one variable as a linear function of another variable was also measured through phenotypic and genotypic correlation among nine quantitative traits. The pod number per plant, seed number per pod and 100 seed weight showed significant positive correlation with seed yield per plant both at phenotypic and genotypic levels. Multivariate analysis using principal component analysis (PCA) indicated that three principal components (PCs) accounted for > 75% of the total variation. The genotypes were grouped into seven clusters using distance based Agglomerative “Average linkage” method. Three genotypes IPF-5-19, EC-8495, HUDP-15 belonging to cluster II and DDR-30, early maturing variety belonging to Cluster VI were found promising in terms of seed yield for the region.

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DIVA-GIS based insight into geographical distribution and diversity spectrum of Indian sunnhemp (Crotalaria juncea L.) accessions suitable for diversified applications

Legume Research - An International Journal ◽

10.18805/lr-4055 ◽

2019 ◽

Author(s):

R. T. Maruthi ◽

A. A. Kumar ◽

S. B. Choudhary ◽

H. K. Sharma ◽

Jiban Mitra

Keyword(s):

Geographical Distribution ◽

Seed Yield ◽

Diversity Index ◽

Principal Component ◽

Morphological Diversity ◽

Hierarchical Cluster ◽

Morphological Characters ◽

Mean Values ◽

North West ◽

Agglomerative Hierarchical Cluster Analysis

Commercial prospects of sunnhemp inspired present study to understand geographical distribution pattern(s) and to scale agro-morphological diversity spectrum of forty-four sunnhemp accessions naturalized across diverse habitats of India. Field experiment revealed broad spectrum diversity for all the 11 agro-morphological traits. Wider range of plant height (110.50 to 173.17 cm), number of pods per plant (35.33 to 143.00), seeds per pod (6.33-15.17g) and seed yield per plant (8.27-29.43g) highlighted the adequacy of present genetic resources to improve sunnhemp for diversified applications. Principal component analysis of the agro-morphological characters identified the first PC with 1109.6 eigen value explaining 61.70% of total variation followed by PC-II (22.9%) and PC-III (11.1%). In PC-I significant contribution was made by traits like NLP, NPP and PH. Agglomerative hierarchical cluster analysis grouped all accessions into four distinct seed producing clusters irrespective of their origin. Cluster wise mean values suggested that cluster-II is the best with outstanding trait values for majority of traits. DIVA-GIS based analysis identified accessions from Rajasthan, Western Gujarat and Jharkhand with high diversity index for number of leaves/plant. But, accessions from North West Jharkhand and Maharashtra with highest diversity index for seed yield/plant.

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Genetic Variability and Diversity Analysis in Pod and Seed Characters of Some Neglected and Underutilized Legumes (NULs)

Asian Journal of Biochemistry, Genetics and Molecular Biology ◽

10.9734/ajbgmb/2019/v2i330059 ◽

2019 ◽

pp. 1-8

Author(s):

J. O. Agbolade ◽

T. P. Olakunle ◽

K. M. Popoola ◽

J. A. Idowu ◽

A. I. Isiaka ◽

...

Keyword(s):

Genetic Variability ◽

Principal Component ◽

Morphological Characters ◽

Morphological Data ◽

Diversity Analysis ◽

International Institute ◽

Mean Values ◽

The Mean ◽

Pod Length ◽

100 Seed Weight

In response to the paucity of information challenge on the neglected and underutilized legumes, this paper explored pods and seeds morphological data of the twenty-four accessions of these crops with a view to establishing the occurrence of genetic variability and diversity analysis among the studied taxa. Twenty-four accessions of neglected and underutilized legumes (NULs) obtained from International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria were assessed for genetic variability and diversity analysis through Pod and seed morphological characters. Each accession was planted into plot of 5 ridges of 5 meter long, spaced 1 meter apart and replicated three times at the teaching and research farm of the Federal University Oye Ekiti, Ekiti State, Nigeria. Descriptive statistics was employed to evaluate differences in the mean values of the accessions while discriminatory traits among accessions were identified by Principal Component Analysis (PCA). Similarities among the studied plants were assessed by cluster analysis. The first two principal component axes explained 72% of the total variation. Pod length, pod width and 100-seed weight were traits that contributed most of the variations in the legume accessions. There was a display of intra-species similarities and inter-specific genetic diversity among the studied accessions.

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A morphometric study on Senecio erucifolius (Asteraceae) from Poland and its taxonomic implications

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.3505 ◽

2016 ◽

Vol 85 (2) ◽

Author(s):

Marek Podsiedlik ◽

Renata Nowińska ◽

Leszek Bednorz

Keyword(s):

Discriminant Analysis ◽

Lateral Lobe ◽

Principal Component ◽

Morphological Diversity ◽

Leaf Length ◽

Morphometric Study ◽

Stepwise Discriminant Analysis ◽

Morphological Heterogeneity ◽

Middle Leaf ◽

Tubular Flower

Twenty-three populations of Senecio erucifolius were sampled to study morphological diversity of the species in Poland. A total of 690 shoots, leaves, capitula, flowers, and fruits were characterized in respect to 27 quantitative traits and were subjected to morphometric analyses. Principal component analysis made it possible to distinguish two groups of individuals, corresponding to two infraspecific taxa – S. erucifolius subsp. tenuifolius (19 populations) and S. erucifolius subsp. erucifolius (four populations). The characters of the greatest importance in differentiating these two subspecies included the length of the upper lobe of the middle leaf, the width of the upper lobe, the width of the longest lateral lobe, the width of the upper lobe at the base, and the length of the tubular flower. Six of the 27 morphological features significantly differentiated populations within subspecies erucifolius according to a stepwise discriminant analysis. The length of the middle leaf, length of the tubular flower and width of the upper lobe at the base contributed most to the discrimination between the investigated populations. The discriminant analysis also showed considerable morphological heterogeneity of the 19 populations classified as subspecies tenuifolius. Seventeen characters significantly differentiated the populations, with the length of the achene and the ratio between the length and the width of the achene as the most important ones.

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Diversity analysis of mungbean [Vigna radiata (L.) Wilczek] genotypes for bruchid resistance

Indian Journal of Agricultural Research ◽

10.18805/ijare.a-5155 ◽

2019 ◽

Author(s):

Sanhita Ghosh ◽

Anindita Roy ◽

Sabyasachi Kundagrami

Keyword(s):

Vigna Radiata ◽

Crop Improvement ◽

Principal Component ◽

Storage Condition ◽

Physiological Traits ◽

Callosobruchus Chinensis ◽

Diversity Analysis ◽

Nutritional Requirement ◽

Total Production ◽

Improvement Program

Mungbean [Vigna radiata (L.) Wilczek] is one of the most important pulse crops in the tropical and sub-tropical areas. Although the total production of mungbean is not enough to supplement the nutritional requirement, an additional issue further augments the concern of its use: the post-harvest damage in the storage condition. Bruchids (Callosobruchus chinensis) are major polyphagous storage pest that causes substantial losses, both quantitatively and qualitatively. The objective of the current study was to classify the fifty-two mungbean genotypes into groups based on their bruchid resistant and susceptibility by using multivariate statistical analysis. Since the present study emphasizes the progressive breeding program, the multivariate analysis is expected to effectively demonstrate the diversity of bruchid attack and therefore identify and ensures the correct representation of the resistant genotypes. The Principal Component Analysis (PCA) displays the correlation of bruchid morpho-physiological traits and the diversity analysis groups the considered genotypes into four clusters (I-IV). The cluster III contains seven genotypes which are observed most effective against bruchid attack. The PC1 shows 70.83% of variability where PC2 shows 29.17% of variability. PCA picturize the most positive correlation between the number of egg laid (NOEL-0.922) and percentage of seed damage (POSD-0.975) among all the morpho-physiological traits. The cluster III thus helps selecting resistant parents for hybridization in future crop improvement program.

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Polymorphism analysis in some Algerian Opuntia species using morphological and phenological UPOV descriptors

Botanical Sciences ◽

10.17129/botsci.887 ◽

2017 ◽

Vol 95 (3) ◽

pp. 391 ◽

Cited By ~ 1

Author(s):

Boubakr Hadjkouider ◽

Ammar Boutekrabt ◽

Bahia Lallouche ◽

Salim Lamine ◽

Néjia Zoghlami

Keyword(s):

Cluster Analysis ◽

Hierarchical Cluster Analysis ◽

Phenotypic Diversity ◽

Principal Component ◽

Morphological Diversity ◽

Hierarchical Cluster ◽

Relative Magnitude ◽

Polymorphism Analysis ◽

Opuntia Ficus Indica ◽

New Varieties

Background: In the present study, we have investigated the morphological variation in a set of five Opuntia species from the Algerian steppes using 49 UPOV descriptors.Questions: which of the 49 descriptors that can be used as powerful estimators of the phenotypic diversity within Opuntia species? How is the morphological diversity patterned in Algerian Opuntia?Species study/ Mathematical model: Opuntia ficus-indica, Opuntia amycleae, Opuntia streptacantha, Opuntia engelmannii, Opuntia robusta. Principal Components Analysis (PCA) and Hierarchical Cluster Analysis were used.Study site: Four counties were studied located in the Algerian steppes. The present research was carried out during 2014.Methods: 49 descriptors adopted by the International Union for the Protection of New Varieties of Plants (UPOV) were employed in the present research, where cladode, flower and fruit traits were used to determine the overall degree of polymorphism among 5 Opuntia species.Results: Principal Component Analysis and Hierarchical Cluster Analysis indicated a consistent differentiation between all studied species. The relative magnitude of the first two PCA eigenvectors showed that 8 descriptors out of 49 were identified as the most important descriptors for the classification of the species. The dendrogram performed on the calculated Euclidean distances between all species pairs allowed the identification of 3 groups, unlike the PCA that identified 4 groups. The species Opuntia ficus-indica and Opuntia amycleae were identified as very close morphologically.Conclusions: The present outcome represents a paramount step towards the fast selection of interesting species and for their best management and conservation.

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Development and Application of Novel Indel Markers in Flax (Linum Usitatissimum L.) Through Whole-genome Re-sequencing

10.21203/rs.3.rs-700179/v2 ◽

2021 ◽

Author(s):

Hui Jiang ◽

Gen Pan ◽

Touming Liu ◽

Li Chang ◽

Siqi Huang ◽

...

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Snp Markers ◽

Diversity Analysis ◽

Whole Genome ◽

Chromosome 2 ◽

Sequencing Data ◽

Single Nucleotide ◽

Genetic Diversity Analysis ◽

Indel Markers

Abstract Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87-3 and 84-3) with the flax reference genome. The length of InDels ranged from 1–277 bp, with 1–15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among flax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using 32 pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 or InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the markers into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.

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