scholarly journals Principal Component and Cluster Analysis as a Tool in the Assessment of Tomato Hybrids and Cultivars

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
G. Evgenidis ◽  
E. Traka-Mavrona ◽  
M. Koutsika-Sotiriou
Keyword(s):  
Yield Components ◽  
Genetic Relationships ◽  
Crop Improvement ◽  
Principal Component ◽  
Breeding Value ◽  
Phenotypic Traits ◽  
Quality Stability ◽  
Germplasm Diversity ◽  
Data Yield ◽  
And Cluster Analysis

Determination of germplasm diversity and genetic relationships among breeding materials is an invaluable aid in crop improvement strategies. This study assessed the breeding value of tomato source material. Two commercial hybrids along with an experimental hybrid and four cultivars were assessed with cluster and principal component analyses based on morphophysiological data, yield and quality, stability of performance, heterosis, and combining abilities. The assessment of commercial hybrids revealed a related origin and subsequently does not support the identification of promising offspring in their crossing. The assessment of the cultivars discriminated them according to origin and evolutionary and selection effects. On the Principal Component 1, the largest group with positive loading included, yield components, heterosis, general and specific combining ability, whereas the largest negative loading was obtained by qualitative and descriptive traits. The Principal Component 2 revealed two smaller groups, a positive one with phenotypic traits and a negative one with tolerance to inbreeding. Stability of performance was loaded positively and/or negatively. In conclusion, combing ability, yield components, and heterosis provided a mechanism for ensuring continued improvement in plant selection programs.

GENETIC DIVERSITY OF EXTRA-EARLY YELLOW MAIZE HYBRIDS UNDER STRIGA ENVIRONMENTS

2021 ◽  
Vol 5 (1) ◽  
pp. 302-308
Author(s):  
Abdulwahab Saliu Shaibu
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Block Design ◽  
Crop Improvement ◽  
Principal Component ◽  
Environment Interaction ◽  
Maize Hybrids ◽  
Group I ◽  
Significant Difference ◽  
And Cluster Analysis

The success of any breeding program depends on the ability to determine germplasm diversity and genetic relationships among breeding materials. Genetic diversity is an invaluable aid in crop improvement. This study was carried out to determine the genetic diversity among 70 extra-early yellow maize hybrids under Striga environments. Cluster and principal component (PC) analyses were used to determine the genetic diversity of the hybrids. Data on morphological and agronomical data were collected. The experiment was set up in two locations (Abuja and Mokwa) in a randomized incomplete block design experiment with two replications. A significant difference was observed among the hybrids in all the traits studied and a significant genotype × environment interaction was observed for all traits except for plant height, anthesis silking interval and Striga count at 8 and 10 WAP. The principal component reveals that the first three components account for 86% variability. PC1 gave maximum variability (43%) and was loaded with PC1 and the first four PCs can be utilized in hybridization programs. The principal component biplot reveals the relationship among traits and the distance of each variable in determining variability among hybrids. The cluster diagram reveals five distinct groups. Group IV consisted of Striga tolerant hybrids and group I consisted of susceptible hybrids. Both principal component and cluster analysis revealed the genetic diversity among the hybrids and identified genotypes that were Striga tolerant and could be selected as choice of parental materials to develop Striga resistant materials

Genetic diversity among Italian melon inodorus (Cucumis melo L.) germplasm revealed by ISSR analysis and agronomic traits

2011 ◽  
Vol 9 (2) ◽  
pp. 214-217 ◽  
Author(s):  
S. Sestili ◽  
A. Giardini ◽  
N. Ficcadenti
Keyword(s):  
Agronomic Traits ◽  
Genetic Relationships ◽  
Molecular Data ◽  
Inter Simple Sequence Repeat ◽  
Phenotypic Traits ◽  
Phenotypic Data ◽  
Morphological And Molecular Data ◽  
And Cluster Analysis ◽  
Almost All ◽  
Issr Primers

The genetic relationships among 13 melon inodorus populations that were collected in southern Italy were assessed using 100 inter-simple-sequence repeat (ISSR) primers and 15 morphological traits. The dihaploid line Nad-1 and the cultivar Charentais-T, both of which belong to the botanical variety cantalupensis, were used as reference accessions in the molecular analysis. A total of 358 polymorphic bands were obtained from 39 of the 100 ISSR primers used, and 15 phenotypic traits were scored and used for genetic-similarity calculations and cluster analysis. The resulting dendrograms based on the ISSR and phenotypic data allowed almost all of the melon genotypes to be distinguished on the basis of the skin colour of the fruits. Mantel's test revealed a good correlation between the morphological and molecular data in their ability to detect genetic relationships among melon ecotypes (r = 0.50, P = 0.99). The data obtained confirm the effectiveness of this approach, and open new perspectives to reveal possible molecular associations with the phenotypic traits analysed.

Germplasm diversity and differentiation ofHelianthus tuberosusL. revealed by AFLP marker and phenotypic traits

2013 ◽  
Vol 152 (5) ◽  
pp. 779-789 ◽  
Author(s):  
Y. X. KOU ◽  
J. ZENG ◽  
J. Q. LIU ◽  
C. M. ZHAO
Keyword(s):  
East Asia ◽  
Genetic Relationships ◽  
Phenotypic Variability ◽  
Sugar Content ◽  
Regional Differentiation ◽  
Phenotypic Traits ◽  
Germplasm Management ◽  
Strong Base ◽  
Group I ◽  
Germplasm Diversity

SUMMARYHelianthus tuberosusL. is regarded as one of the most important bioenergy crops because of its tolerance to arid conditions and its high biomass production. Future breeding programmes will rely on the available germplasm, thus necessitating a critical assessment of genetic diversity and differentiation in the species. The germplasm diversity and regional differentiation ofH. tuberosusL. was assessed for 60 accessions collected from East Asia and Europe by means of amplified fragment length polymorphisms (AFLPs), phenotypic traits and chemical analysis. The analysis did not reveal separate clusters for accessions from East Asia and Europe, with 5% for genetic and 0·27% for phenotypic variability, although some regional accessions were closely related to each other with respect to morphological, chemical and genetic variation. Both phenotypic and genetic relationships showed a moderate correlation with colour of tubers, which can be used as an important criterion for germplasm management of the crop. Three major genetic groups were identified from the accessions. Within the groups derived from the genetic data, both morphological and chemical traits were very variable. The most important features of Groups I, II and III were: Group I, strong sexual reproduction, higher above-ground biomass and nutrient content; Group II, longer vegetative growth; Group III, higher tuber yield and total sugar content. High diversity was found in both European and East Asian accessions as well as within each genetic group, suggesting that there is a strong base for future breeding from these plants.

scholarly journals Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6861 ◽  
Author(s):  
Weian Du ◽  
Chunlei Feng ◽  
Ting Yao ◽  
Cheng Xiao ◽  
Hongyan Huang ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Regional Distribution ◽  
Principal Component ◽  
Personal Identification ◽  
Bonferroni Correction ◽  
Forensic Application ◽  
Discrimination Power ◽  
Forensic Efficiency ◽  
Hardy Weinberg Equilibrium ◽  
And Cluster Analysis

Aim In this study, we used a series of diallelic genetic marker insertion/deletion polymorphism (indel) to investigate three populations of Yao, Kelao, and Zhuang groups in the Guangxi region of China and to evaluate their efficiency in forensic application. Result No deviations for all 30 loci were observed from the Hardy–Weinberg equilibrium after Bonferroni correction (p > 0.05/30 = 0.0017). The allele frequencies of the short allele (DIP-) for the above three populations were in the range of 0.0520–0.9480, 0.0950–0.8780, and 0.0850–0.915, respectively. The observed heterozygosity of the 30 loci for the three populations was in the ranges 0.0802–0.5802, 0.1908–0.6053, and 0.1400–0.5600, respectively. The cumulative power of exclusion and combined discrimination power for Yao, Kelao, and Zhuang groups were (0.9843 and 0.9999999999433), (0.9972 and 0.9999999999184), and (0.9845 and 0.9999999999608), respectively. The DA distance, principal component analysis, and cluster analysis indicated a clear regional distribution. In addition, Zhuang groups had close genetic relationships with the Yao and Kelao populations in the Guangxi region. Conclusion This study indicated that the 30 loci were qualified for personal identification; moreover, they could be used as complementary genetic markers for paternity testing in forensic cases for the studied populations.

scholarly journals Variation of phenotypic and physiological traits of Robinia pseudoacacia L. from 20 provenances

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0262278
Author(s):  
Qi Guo ◽  
Yuhan Sun ◽  
Jiangtao Zhang ◽  
Yun Li
Keyword(s):  
Robinia Pseudoacacia ◽  
Base Material ◽  
Principal Component ◽  
Leaf Length ◽  
Phenotypic Traits ◽  
Physiological Indicators ◽  
Coefficients Of Variation ◽  
Leaflet Number ◽  
And Cluster Analysis ◽  
Robinia Pseudoacacia L

To select elite Robinia pseudoacacia L. germplasm resources for production, 13 phenotypes and three physiological indicators of 214 seedlings from 20 provenances were systematically evaluated and analyzed. The leaf phenotypic and physiological coefficients of variation among the genotypes ranged from 3.741% to 19.599% and from 8.260% to 42.363%, respectively. The Kentucky provenance had the largest coefficient of variation (18.541%). The average differentiation coefficients between and within provenances were 34.161% and 38.756%, respectively. These close percentages showed that R. pseudoacacia presented high genetic variation among and within provenances, which can be useful for assisted migration and breeding programs. Furthermore, based on the results of correlations, principal component analysis and cluster analysis, breeding improvements targeting R. pseudoacacia’s ornamental value, food value, and stress resistance of were performed. Forty and 30 excellent individuals, accounting for 18.692% and 14.019%, respectively, of the total resources. They were ultimately screened, after comprehensively taking into considering leaf phenotypic traits including compound leaf length, leaflet number and leaflet area and physiological characteristics including proline and soluble protein contents. These selected individuals could provide a base material for improved variety conservation and selection.

scholarly journals Diversity in Phenotypic Traits and Mineral Elements of Okra (Abelmoschus esculentus L. Moench) Genotypes

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Ronke Justina Komolafe ◽  
Omolayo Johnson Ariyo ◽  
Christopher Olusanya Alake
Keyword(s):  
Principal Component Analysis ◽  
Cluster Analysis ◽  
Crop Improvement ◽  
Research Work ◽  
Germplasm Collection ◽  
Principal Component ◽  
Component Analysis ◽  
Mineral Elements ◽  
Phenotypic Traits ◽  
Nutrient Enhancement

African indigenous vegetables need to be improved for yield and nutrient enhancement. This can initially be done through germplasm characterization to know the pattern of genetic diversity for germplasm collection, conservation, and plant breeding programme. This research work was carried out to elucidate the diversity present in forty genotypes of okra in Nigeria as regards their qualitative and quantitative traits together with their mineral elements using cluster analysis and principal component analysis so as to help breeders in crop improvement programmes to select appropriate parents to produce new and better varieties. The experiment was carried out at the Teaching and Research Farm of the Department of Crop, Soil and Pest Management, Federal University of Technology, Akure, during the rainy season in 2019. Principal component analysis and cluster analysis were employed to study the diversity present in the okra genotypes. There was great diversity among the forty genotypes of okra studied with respect to qualitative traits. There were highly significant differences P < 0.01 for all the quantitative characters, which indicated the presence of a great amount of diversity in all the characters studied. Single-linkage cluster analysis shows that, at 100% level of similarity, all the genotypes were distinct from one another. Results of the principal component analysis showed that 76.30% of the total variability among the okra genotypes evaluated in this study was accounted for the first five principal components. This study suggests that there is great diversity among the genotypes studied, which could be used by breeders for okra improvement.

scholarly journals Morphologic and Agronomic Diversity of Brassica napus Crops

2008 ◽  
Vol 133 (1) ◽  
pp. 48-54 ◽  
Author(s):  
Pilar Soengas ◽  
Maria Elena Cartea ◽  
Pablo Velasco ◽  
Guillermo Padilla ◽  
Amando Ordás
Keyword(s):  
Cluster Analysis ◽  
Brassica Napus ◽  
Agronomic Traits ◽  
Genetic Relationships ◽  
Winter Season ◽  
Principal Component ◽  
Group Method ◽  
Pair Group ◽  
Total Variability ◽  
And Cluster Analysis

A Brassica napus L. crop called nabicol traditionally has been grown by farmers in northwestern Spain for many years and is an important horticultural product during the winter season. The relationship of nabicol to other B. napus crops has been studied based on simple sequence repeat (SSR) data. However, molecular and morphologic classifications often disagree. The objectives of this research were to study the morphologic and agronomic relationships of nabicol landraces to other B. napus crops and to compare those relationships with the ones already known, based on SSR data. Thirty-five B. napus populations from different geographic origins and uses were evaluated. Data were recorded on 17 morphologic and agronomic traits. Principal component analysis and cluster analysis were performed to classify the populations. Eight principal components (94% of the total variability) were standardized to produce the Mahalanobis' generalized distances, and a cluster analysis was conducted using the unweighted pair group method with arithmetic averages. There are no major differences between B. napus var. pabularia (DC.) Rchb. (nabicol, couve-nabiça, forage rape) and B. napus var. oleifera DC. (oilseed rape), and they probably share a common origin. Rape kale (B. napus var. pabularia) and rutabaga [B. napus var. napobrassica (L.) Rchb.] cultivars are separated from the rest and probably they have an independent origin or domestication. Molecular and morphologic classifications are complementary, and both are necessary to classify germplasm correctly and to clarify genetic relationships among B. napus crops.

scholarly journals Karyotypic Characteristics and Genetic Relationships of Apricot Accessions from Different Ecological Groups

2021 ◽  
Vol 146 (1) ◽  
pp. 68-76
Author(s):  
Wenwen Li ◽  
Liqiang Liu ◽  
Weiquan Zhou ◽  
Yanan Wang ◽  
Xiang Ding ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Principal Component ◽  
Small Chromosome ◽  
Prunus Armeniaca ◽  
Ecological Group ◽  
Ecological Groups ◽  
Central Asian ◽  
Satellite Chromosomes ◽  
And Cluster Analysis ◽  
Karyotype Symmetry

The present study aims to reveal the karyotypic characteristics and genetic relationships of apricot (Prunus armeniaca L.) accessions from different ecological groups. Fourteen, 9, and 30 accessions from the Central Asian ecological group, North China ecological group, and Dzhungar-Ili ecological group, respectively, were analyzed according to the conventional pressing plate method. The results showed that all the apricot accessions from the different ecological groups were diploid (2n = 2x = 16). The total haploid length of the chromosome set of the selected accessions ranged from 8.11 to 12.75 μm, which was a small chromosome, and no satellite chromosomes were detected. All accessions had different numbers of median-centromere chromosomes or sub-median-centromere chromosomes. The karyotypes of the selected accessions were classified as 1A or 2A. Principal component analysis revealed that the long-arm/short-arm ratio (0.968) and the karyotype symmetry index (−0.979) were the most valuable parameters, and cluster analysis revealed that the accessions from the Central Asian ecological group and Dzhungar-Ili ecological group clustered together. In terms of karyotypic characteristics, the accessions from the Dzhungar-Ili ecological group and Central Asian ecological group were closely related.

The Utilization of Ftir (Fourier Transform Infra-Red) Method Combined with Chemometrics For Authentication of Indonesian Coffee Powder

2017 ◽  
Vol 9 (3) ◽  
Author(s):  
Firmansyah A. ◽  
Winingsih W. ◽  
Soebara Y S
Keyword(s):  
Fourier Transform ◽  
Natural Product ◽  
High Performance ◽  
Principal Component ◽  
Raw Material ◽  
Attenuated Total Reflectance ◽  
Coffee Bean ◽  
Product Analysis ◽  
Total Reflectance ◽  
And Cluster Analysis

Analysis of natural product remain challenging issues for analytical chemist, since natural products are complicated system of mixture. The most popular methods of choice used for quality control of raw material and finished product are high performance liquid chromatography (HPLC), gas chromatography (GC) and mass spectrometry (MS). The utilization of FTIR-ATR (Fourier Transform Infrared-Attenuated Total Reflectance) method in natural product analysis is still limited. This study attempts to expand the use of FTIR spectroscopy in authenticating Indonesian coffee powder.The coffee samples studied were taken from nine regions in Indonesia, namely Aceh Gayo, Flores, Kintamani, Mandheling, Papua, Sidikalang, Toraja, Kerinci and Lampung.The samples in the form of coffee bean from various regions were powdered . The next step conducted was to determine the spectrum using the FTIR-ATR (Attenuated Total Reflectance) using ZnSe crystal of 8000 resolution. Spectrum samples, then, were analyzed using chemometrics. The utilized chemometric model was the principal component analysis (PCA) and cluster analysis (CA). Based on the chemometric analysis, there are similarities between Aceh Gayo coffee with Toraja coffee, Mandailing coffee, Kintamani coffee and Flores coffee. Sidikalang coffee has a similarity to Flores coffee; Papua coffee has a similarity to Sidikalang coffee; Lampung coffee has a similarity to Sidikalang coffee, while Kerinci coffee has a similarity to Papua coffee.

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