scholarly journals Selection of the Most Discriminating Morphological Qualitative Variables for Characterization of Fig Germplasm

2010 ◽  
Vol 135 (3) ◽  
pp. 240-249 ◽  
Author(s):  
Esther Giraldo ◽  
Margarita López-Corrales ◽  
José Ignacio Hormaza
Keyword(s):  
Principal Components ◽  
Principal Component ◽  
Group Method ◽  
Germplasm Collections ◽  
Pair Group ◽  
Morphological Studies ◽  
Production Type ◽  
Qualitative Variables ◽  
Total Variability

Most descriptor lists for the characterization of genetic resources in plants include a large number of traits whose evaluation is a lengthy and expensive process making the characterization of large germplasm collections difficult. Consequently, to facilitate the study and the conservation of germplasm, it is important to select carefully the most informative variables for each species. In this work, we applied sequential statistical procedures to select the most discriminant variables in fig (Ficus carica L.) from the initial 134 qualitative variables studied. A total of 34 variables was finally selected and broken down in 97 characters that were grouped by principal component analysis in 11 principal components that explain 93.34% of the total variability. The unweighted pair group method with arithmetic mean dendrogram derived from a similarity matrix generated using the Pearson's correlation coefficient among the 11 principal components selected classifies the cultivars in four main groups mainly based in the production type. These results show that redundant information can be obtained in morphological studies with a large number of variables resulting from correlation between variables. Consequently, a carefully selected and reduced number of highly discriminating variables can allow efficient fig germplasm characterization and discrimination resulting in significant savings of time and resources.

scholarly journals Characterization of Eastern Filbert Blight-resistant Hazelnut Germplasm Using Microsatellite Markers

2014 ◽  
Vol 139 (4) ◽  
pp. 399-432 ◽  
Author(s):  
Megan F. Muehlbauer ◽  
Josh A. Honig ◽  
John M. Capik ◽  
Jennifer N. Vaiciunas ◽  
Thomas J. Molnar
Keyword(s):  
Microsatellite Markers ◽  
Group Method ◽  
Germplasm Collections ◽  
Pair Group ◽  
Body Of Knowledge ◽  
Geographic Origins ◽  
Anisogramma Anomala ◽  
Eastern Filbert Blight ◽  
Genetic Pools

The development of new cultivars resistant to the disease eastern filbert blight (EFB), caused by Anisogramma anomala, is of primary importance to hazelnut (Corylus sp.) breeders in North America. Recently, a large number of EFB-resistant cultivars, grower selections, and seedlings from foreign germplasm collections were identified. However, for a significant number of these, little is known of their origin, relationships, or genetic background. In this study, 17 microsatellite markers were used to investigate the genetic diversity and population structure of 323 unique accessions, including EFB-resistant and tolerant germplasm of uncertain origins, in comparison with a panel of known reference accessions representing a wide diversity of Corylus cultivars, breeding selections, and interspecific hybrids. The resulting allelic data were used to construct an unweighted pair group method using arithmetic averages (UPGMA) dendrogram and STRUCTURE diagram to elucidate relationships among the accessions. Results showed 11 consensus groups with EFB-resistant or tolerant accessions in all, providing strong evidence that EFB resistance is relatively widespread across the genus Corylus. Furthermore, open-pollinated seedlings tended to group together with reference accessions of similar geographic origins, providing insight into their genetic backgrounds. The results of this study add to the growing body of knowledge of hazelnut genetic resources and highlight recently introduced EFB-resistant seedling germplasm as new, unrelated genetic pools of resistance.

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 Characterization of 14 Microsatellite Markers for Genetic Analysis and Cultivar Identification of Walnut

2005 ◽  
Vol 130 (3) ◽  
pp. 348-354 ◽  
Author(s):  
Gerald S. Dangl ◽  
Keith Woeste ◽  
Mallikarjuna K. Aradhya ◽  
Anne Koehmstedt ◽  
Chuck Simon ◽  
...  
Keyword(s):  
Cultivar Identification ◽  
Paternity Analysis ◽  
Group Method ◽  
Breeding Programs ◽  
Persian Walnut ◽  
Germplasm Collections ◽  
Pair Group ◽  
Shared Alleles ◽  
Simple Sequence

One hundred and forty-seven primer pairs originally designed to amplify microsatellites, also known as simple sequence repeats (SSR), in black walnut (Juglans nigra L.) were screened for utility in persian walnut (J. regia L.). Based on scorability and number of informative polymorphisms, the best 14 loci were selected to analyze a diverse group of 47 persian walnut accessions and one J. hindsii (Jepson) Jepson ex R.E. Sm × J. regia hybrid (Paradox) rootstock. Among the 48 accessions, there were 44 unique multi-locus profiles; the accessions with identical profiles appeared to be synonyms. The pairwise genetic distance based on proportion of shared alleles was calculated for all accessions and a UPGMA (unweighted pair group method with arithmetic mean) dendrogram constructed. The results agree well with what is known about the pedigree and/or origins of the genotypes. The SSR markers distinguished pairs of closely related cultivars and should be able to uniquely characterize all walnut cultivars with the exception of budsports. They provide a more powerful and reliable system for the molecular characterization of walnut germplasm than those previously tested. These markers have numerous applications for the walnut industry, including cultivar identification, verification of pedigrees for cultivar and rootstock breeding programs, paternity analysis, and understanding the genetic diversity of germplasm collections.

scholarly journals Feed efficiency of lactating Holstein cows is less reproducible when changing dietary starch and fibre concentrations than within diet over subsequent lactation stages

2021 ◽  
Author(s):  
Amélie Fischer ◽  
Philippe Gasnier ◽  
Philippe Faverdin
Keyword(s):  
Principal Components ◽  
Feed Efficiency ◽  
Nir Spectroscopy ◽  
Principal Component ◽  
Holstein Cows ◽  
Diet Change ◽  
Total Variability ◽  
The One ◽  
The Individual ◽  
Starch Diet

ABSTRACTBackgroundImproving feed efficiency has become a common target for dairy farmers to meet the requirement of producing more milk with fewer resources. To improve feed efficiency, a prerequisite is to ensure that the cows identified as most or least efficient will remain as such, independently of diet composition. Therefore, the current research analysed the ability of lactating dairy cows to maintain their feed efficiency while changing the energy density of the diet by changing its concentration in starch and fibre. A total of 60 lactating Holstein cows, including 33 primiparous cows, were first fed a high starch diet (diet E+P+), then switched over to a low starch diet (diet E−P−). Near infra-red (NIR) spectroscopy was performed on each individual feed ingredient, diet and individual refusals to check for sorting behaviour. A principal component analysis (PCA) was performed to analyse if the variability in NIR spectra of the refusals was explained by the differences in feed efficiency.ResultsThe error of reproducibility of feed efficiency across diets was 2.95 MJ/d. This error was significantly larger than the errors of repeatability estimated within diet over two subsequent lactation stages, which were 2.01 MJ/d within diet E−P− and 2.40 MJ/d within diet E+P+. The coefficient of correlation of concordance (CCC) was 0.64 between feed efficiency estimated within diet E+P+ and feed efficiency estimated within diet E−P−. This CCC was smaller than the one observed for feed efficiency estimated within diet between two subsequent lactation stages (CCC = 0.72 within diet E+P+ and 0.85 within diet E−P−). The first two principal components of the PCA explained 90% of the total variability of the NIR spectra of the individual refusals. Feed efficiency was poorly correlated to those principal components, which suggests that feed sorting behaviour did not explain differences in feed efficiency.ConclusionsFeed efficiency was significantly less reproducible across diets than repeatable within the same diet over subsequent lactation stages, but cow’s ranking for feed efficiency was not significantly affected by diet change. The differences in sorting behaviour between cows were not associated to feed efficiency differences in this trial neither with the E+P+ diet nor with the E−P− diet. Those results have to be confirmed with cows fed with more extreme diets (for example roughage only) to ensure that the least and most efficient cows will not change.

Characterization of Pyrenophora tritici-repentis in Tunisia and Comparison with a Global Pathogen Population

Plant Disease ◽  
2021 ◽  
Author(s):  
Marwa Laribi ◽  
Alireza Akhavan ◽  
Sarrah M'Barek ◽  
Amor Yahyaoui ◽  
Stephen Ernest Strelkov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Geographic Origin ◽  
Tan Spot ◽  
Pcr Analysis ◽  
Group Method ◽  
Region Of Origin ◽  
Pyrenophora Tritici Repentis ◽  
Pair Group ◽  
Necrotrophic Effector

Pyrenophora tritici-repentis (Ptr) causes tan spot, an important foliar disease of wheat. A collection of Ptr isolates from Tunisia, located in one of the main secondary centers of diversification of durum wheat, was tested for phenotypic race classification based on virulence on a host differential set, and for the presence of the necrotrophic effector (NE) genes ToxA, ToxB , and toxb by PCR analysis. While races 2, 4, 5, 6, 7, and 8 were identified according to their virulence phenotypes, PCR testing indicated the presence of ‘atypical’ isolates that induced necrosis on the wheat differential ‘Glenlea’, but lacked the expected ToxA gene, suggesting the involvement of other NEs in the Ptr/wheat interaction. Genetic diversity and the Ptr population structure were explored further by examining 59 Tunisian isolates and 35 isolates from Algeria, Azerbaijan, Canada, Iran, and Syria using 24 simple sequence repeat markers. Average genetic diversity, overall gene flow and percentage polymorphic loci were estimated as 0.58, 2.09 and 87%, respectively. Analysis of molecular variance showed that 81% of the genetic variance occurred within populations and 19% between populations. Cluster analysis by the unweighted pair group method indicated that ToxB- isolates grouped together and were distantly related to ToxB+ isolates. Based on Nei’s analysis, the global collection clustered into two distinct groups according to their region of origin. The results suggest that both geographic origin and the host-specificity imposed by different NEs can lead to differentiation among Ptr populations.

Molecular Diversity Analysis of Lentil (Lens culinaris Medik.) through RAPD Markers

2012 ◽  
Vol 22 (1) ◽  
pp. 51-58 ◽  
Author(s):  
M.E. Hoque ◽  
M.M. Hasan
Keyword(s):  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Group Method ◽  
Diversity Analysis ◽  
Pair Group ◽  
Molecular Genetic Diversity

Random Amplified Polymorphic DNA (RAPD) markers were used to study the molecular genetic diversity analysis among six BARI released lentil varieties viz. BARI masur-1, BARI masur-2, BARI masur-3, BARI masur-4, BARI masur-5 and BARI masur-6. PCR amplified products were visualized on 1.0% agarose gel and the band for each primer were scored. Ten RAPD markers were used in this study. Out of them 7 primers showed amplification of 53 DNA fragments with 60.37% of them being polymorphic. The highest number of polymorphic loci was noticed in the variety BARI masur-3. The same variety also showed maximum Nei’s gene diversity value (0.0552). The highest Nei’s genetic distance (0.5002) was observed in BARI masur-1 vs. BARI masur-5 whereas, the lowest genetic distance (0.0692) was found in BARI masur-1 vs. BARI masur-2. The unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei’s genetic distance grouped the six cultivars into two main clusters. BARI masur-1, BARI masur-2 and BARI masur-3 were in cluster I and BARI masur-4, BARI masur-5 and BARI masur-6 were in cluster II. The cultivar BARI masur-4 was closest to the cultivar BARI masur-6 with the lowest genetic distance (0.0972) and the highest genetic distance (0.5002) was found between BARI masur-1 and BARI masur-5. The RAPD markers were found to be useful in molecular characterization of lentil varieties which could be utilized by the breeders for the improvement of lentil cultivars. DOI: http://dx.doi.org/10.3329/ptcb.v22i1.11260 Plant Tissue Cult. & Biotech. 22(1): 51-58, 2012 (June)

scholarly journals Molecular Characterization of 12 Mango Germplasm Using RAPD markers

2010 ◽  
Vol 20 (1) ◽  
pp. 91-99
Author(s):  
R. C. Jena ◽  
K. C. Samal ◽  
P. K. Chand ◽  
B. K. Das
Keyword(s):  
Molecular Characterization ◽  
Rapd Markers ◽  
Mangifera Indica ◽  
Pcr Amplification ◽  
Similarity Coefficient ◽  
Group Method ◽  
Base Pairs ◽  
Relationship Analysis ◽  
Pair Group

Randomly amplified polymorphic DNA (RAPD) markers were used for the genetic variation and relationship analysis among 12 Mango (Mangifera indica L.) germplasm. Five oligonucleotide primers were employed to amplify DNA from 12 cultivars. PCR amplification with five primers generated 45 reproducible, clear and distinct bands, out of which 41 bands are considered polymorphic and the remaining four fragments (8.88%)  monomorphic. The size of amplified product ranged from 200 (RPI-5) to 3000 base pairs (RPI-1) with an average of nine bands per primer. The average polymorphism in all the 12 cultivars using the five primers was found to be 91.91%. Among all the primers RPI-2 and RPI-4 have shown 100% polymorphism while RPI-5 was found to be least polymorphism (81.81%). One specific band, namely was found with RPI-5, in a particular variety, Chiratpuri. The UPGMA (Unweighted Pair Group Method of Arithmetic Mean) dendrogram based on Jaccard’s similarity coefficient segregated the 12 mango germplasm into two clusters. Langra, Chiratpuri, Pravasankar, Alphanso, Sindhu and Kesar formed one cluster and rest six mango germplasm grouped together into another cluster. Sindhu and Alphanso cultivar pair was very close to each other with highest similarity coefficient (0.78), which was comparatively higher than all other cultivar pairs. On the other hand, Pravasankar and Neelam cultivar pair was more distinct to each other with the lowest intervarietal similarity coefficient 0.38. This study showed clearly that cultivars from Orissa unveiled maximum diversity and indicated the potential of RAPD markers for the identification of management of mango germplasm for breeding purposes.  Key words: Molecular characterization, Mango germplasm, Dversity  D.O.I. 10.3329/ptcb.v20i1.5972 Plant Tissue Cult. & Biotech. 20(1): 91-99, 2010 (June)

The use of RAPD markers to distinguish among juniper and cedar cultivars

2000 ◽  
Vol 78 (5) ◽  
pp. 655-659 ◽  
Author(s):  
Tom Hsiang ◽  
Junbin Huang
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Unknown Origin ◽  
Genetic Distances ◽  
Group Method ◽  
Pair Group ◽  
Juniperus Chinensis ◽  
Juniperus Scopulorum ◽  
Close Relatives

Two species of Chamaecyparis and six cultivars each of Juniperus chinensis L. and Juniperus scopulorum Sarg. (Cupressaceae) were subjected to random amplified polymorphic DNA (RAPD) analysis using seven primers. Unweighted pair group method with averages (UPGMA) and principal component analyses of genetic distances between cultivars showed that 42 polymorphic RAPD bands could distinguish among all cultivars and properly group them by species and genera. Where the origin of a specific juniper cultivar is uncertain, analysis of genetic distance can pinpoint close relatives. For example, we were unable to trace the origin of J. chinensis 'Alps', and we initially thought it was a mislabeled J. chinensis 'Blue Alps'. However, we found 'Alps' to be closer to J. chinensis 'Fairview' and 'Mountbatten' than to 'Blue Alps'. Similarly, 'Wichita Blue' has an unknown origin, but it had the highest genetic similarity with 'Medora'.Key words: juniper, cedar, RAPD, cultivars, phylogenetics.

scholarly journals Allozyme analysis of geographical and seasonal variation of Illex coindetii (Cephalopoda: Ommastrephidae) from central Mediterranean and Iberian Atlantic

2005 ◽  
Vol 85 (1) ◽  
pp. 177-184 ◽  
Author(s):  
P. Martínez ◽  
P. Belcari ◽  
A. Sanjuan ◽  
A. Guerra
Keyword(s):  
Minimum Spanning Tree ◽  
Geographical Area ◽  
Genetic Distances ◽  
Group Method ◽  
Central Mediterranean ◽  
Homogeneous Population ◽  
Pair Group ◽  
Morphological Studies ◽  
Temporal Variance ◽  
Population Pattern

Previous morphological studies of Illex coindetii from the Mediterranean have shown both juvenile and mature individuals all year round suggesting an homogeneous population pattern, however, seasonal spawning variation seems to exist varying with geographical area. Present work analysed 240 individuals from the northern Tyrrhenian and Atlantic Iberian waters at the four year-round seasons using 33 presumptive enzyme-coding loci to compare geographical and temporal variances. Genetic variability was low (Ho=0·02–0·04). Moderate variation at some loci was found due to both temporal and geographical factors (12% of total genetic variance) and to temporal variance (FST=0·004–0·015). Unweighted pair-group method using arithmetric averages (UPGMA) and Multidimensional scaling–minimum spanning tree (MDS–MST) analyses after Cavalli-Sforza & Edwards (1967) chord genetic distances showed the summer Italian and the spring Atlantic samples as the most divergent among the whole.

scholarly journals DAKSHIN BHARTIYA PADHAR PAR HONE WALI MONSOON WARSHA KA PRADHAN AVYAV VISHLESHAN

MAUSAM ◽  
2021 ◽  
Vol 48 (1) ◽  
pp. 77-82
Author(s):  
O.P. SINGH
Keyword(s):  
Principal Components ◽  
Andhra Pradesh ◽  
Monsoon Rainfall ◽  
Principal Component ◽  
Southwest Monsoon ◽  
Northeast Monsoon ◽  
Northeast Monsoon Rainfall ◽  
Total Variability ◽  
Southwest Monsoon Rainfall ◽  
The Impact

 The result of the Principal Component Analysis of southwest and northeast monsoon rainfall on the southern India plateau have been discussed. Monsoon rainfall data of five meteorological sub-divisions, i.e., Coastal Andhra Pradesh, Rayalseema, Tamilnadu, Interior parts of South Karnataka & Kerala, for a period of 33 years (1960-92), have been utilized. The results indicate that the rainfall of Coastal Andhra Pradesh and Rayalseema has maximum impact on first principal component of southwest monsoon rainfall of five meteorological sub-divisions. The study of only first principal component is sufficient in order to understand the 49% of total variability of southwest monsoon rainfall. Analysis of first three principal components is important to understand 85% of total variability of the rainfall of this season.   On the first principal component of northeast monsoon rainfall of aforesaid five meteorological sub-divisions the impact of the rainfall of Kerala and south interior Karnataka has been found maximum. In order to understand the 56% of total variability the analysis of first principal component is sufficient.   The special negative relation is found between northeast monsoon rainfall on the Coastal Andhra Pradesh and southwest monsoon rainfall of previous year on this very sub-division and Rayalseema. The principal components of southwest monsoon rainfall may prove useful for forecasting the northeast monsoon rainfall of southern Indian plateau.  

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