scholarly journals Pedigree Data Analysis of a Wheat Population

Proceedings ◽  
2020 ◽  
Vol 36 (1) ◽  
pp. 148
Author(s):  
Sepideh Rouholamin ◽  
Vivi Arief ◽  
Ian Delacy ◽  
Kaye Basford
Keyword(s):  
Genetic Diversity ◽  
Graphical Representation ◽  
Principal Component ◽  
Wheat Cultivars ◽  
Pedigree Data ◽  
Coefficient Of Parentage ◽  
Breeding Technique ◽  
Wheat Population ◽  
Crop Development ◽  
Inbred Populations

Genetic diversity is an essential part of successful crop development and can be evaluated by different methods, e.g. the Coefficient of Parentage (COP). This coefficient is established on pedigree data. This method can determine the variation among genotypes without the influence of environment effects as would be the case for field data. This study measured genetic diversity among 317 wheat cultivars from a population generated by the speed breeding technique. Using pedigree data, we determined the associations between parents and individuals, and then used the pattern analysis techniques of principal component analysis and clustering. The results enabled an appropriate graphical representation of wheat cultivars. This information is useful for selecting future parents in breeding programs. This demonstrates that using COP is a viable way to evaluate diversity among genotypes, especially in inbred populations.

scholarly journals Genetic diversity of Polish cultivars of common wheat (Triticum aestivum L.) based on molecular and protein markers

2020 ◽  
Vol 48 (2) ◽  
pp. 535-548
Author(s):  
Ewa FILIP ◽  
Aleksandra STROŃSKA ◽  
Magdalena SZENEJKO ◽  
Waldemar PLUTA
Keyword(s):  
Genetic Diversity ◽  
Common Wheat ◽  
Similarity Index ◽  
Principal Component ◽  
Shannon Index ◽  
Qualitative Assessment ◽  
Wheat Cultivars ◽  
Protein Markers ◽  
Binary Matrix ◽  
Sds Page

Knowledge of the composition subunits of proteins glutenins makes it much easier to determine the quality and suitability of the final product obtained from gluten. It is important to remember that not only molecular processes model gluten protein polymorphism. In this study, the genetic diversity of Polish common wheat cultivars was examined at the level of DNA and glutenin’s proteins HMW-GS. The SDS-PAGE and RAPD bands were evaluated in binary matrix, which was the basis for further analysis of results, using appropriate measures of variability: Q-Cochran  test (Cochran, 1950), p < 0.05; I-Shannon index; Si-Similarity index; PIC-Polymorphism Information Content; (PCA-Principal component analysis). Both types of markers proved to be useful in the overall assessment of genetic variability between tested of common wheat cultivars. The general genetic diversity indicates that good candidates with unique composition of HMW-GS subunits were selected among the examined cultivars and three OPA-02, OPA-03, OPB-08 primers with the highest power differentiating for the studied genotypes were selected. Results of the research revealed the potentials of RAPD and SDS-PAGE technique in determining genetical diversity and make a suitable qualitative assessment of common wheat cultivars.

scholarly journals Assessment of genetic diversity on a sample of cocoa accessions resistant to witches' broom disease based on RAPD and pedigree data

Bragantia ◽  
2005 ◽  
Vol 64 (3) ◽  
pp. 361-368 ◽  
Author(s):  
Ronaldo Carvalho dos Santos ◽  
José Luís Pires ◽  
Uilson Vanderley Lopes ◽  
Karina Peres G. Gramacho ◽  
Acassi Batista Flores ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relatedness ◽  
Genetic Distances ◽  
Pedigree Information ◽  
Germplasm Management ◽  
Pedigree Data ◽  
Coefficient Of Parentage ◽  
Low Genetic Diversity ◽  
Broom Disease ◽  
Different Sources

Genetic diversity in cocoa (Theobroma cacao L.) has been assessed based on morphological and molecular markers for germplasm management and breeding purposes. Pedigree data is available in cocoa but it has not been used for assessing genetic relatedness. The geneitic diversity of 30 clonal cocoa accessions resistant to witche´ broom disease, from the CEPEC series, were studied on the basis of RAPD data and pedigree information. Twenty of these accessions descend from the TSA-644 clone, originated from a cross between the Upper Amazon germplasm called Scavina-6, the main source of resistance to witches' broom disease, and IMC-67. The ten remaining clones come from different sources including Amazon and Trinitario germplasm. RAPD data was collected using 16 primers and pedigree information was obtained from the International Cocoa Germplasm Database. Genetic similarities, genetic distances and coefficient of parentage were calculated using available software. Relatively low genetic diversity was observed in this germplasm set, probably because of great genetic relatedness amongst accessions studied and the poor representation of the germplasm. The TSA-644 descendants were more diverse than the other accessions used in the study. This might be due to the origin of the TSA clone, which was derived from highly divergent genotypes. Association between genetic similarities based on RAPD data and coefficient of parentage, based on pedigree data, was very low, probably due to the homogeneity of the breeding stocks and poor pedigree information. These findings are useful to cocoa breeders in planning crosses for the development of hybrid and clonal cultivars.

scholarly journals Evaluation of genetic diversity of subdivided genealogical groups in Lithuanian Trakehner horse population using immunogenetic tools

2021 ◽  
Author(s):  
Alma Račkauskaitė ◽  
Rūta Šveistienė ◽  
Violeta Razmaitė ◽  
Virginija Jatkauskienė
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Allelic Frequency ◽  
Blood Groups ◽  
Protein Polymorphism ◽  
Blood Protein ◽  
Pedigree Data ◽  
Horse Population ◽  
Genetic Clustering ◽  
Selection Of

The objective of this study was to evaluate the inter-breed genetic diversity of Lithuanian Trakehner horses. The current population in Lithuania numbers 1 039 Trakehner horses. The study included the immunogenetic data analysis of 316 blood samples. Pedigree was traced back to 7–11 generations. The horses were assigned to genealogical clusters originating from East Prussian Trakehnen Stud, Thoroughbred and Arab sires. The first two clusters were subdivided into nine-horse groups according to the most important ancestors. The evaluation of genetic diversity was based on six blood groups and five protein polymorphism systems. The differences between genealogical groups were confirmed by principal component analysis and applied cluster analysis. According to the allelic frequency, the Trakehner population changed very slightly through a 30-year period, and only one rare (0.013) allele Tf<sup>RR</sup> (frequent in other Trakehner populations), has been newly found. The analysis of genetic polymorphism systems based on a very low rate of alleles Q<sup>abc</sup> (0.093) and D<sup>dkl</sup> (0.046), which are typical of other populations, indicated the exclusivity of the Trakehner population in Lithuania. The average expected heterozygosity by blood protein polymorphism and blood groups were 0.409 and 0.441, respectively. The genetic clustering diverged by observed heterozygosity of blood groups and by pedigree data in Pilger through Egoist, Bay Ronald through Dark Ronald and Dampfross through Hyperion subgroups. The determined distinctiveness of subdivided Trakehner horse groups suggests reconsidering the breeding strategies and conservation programme of Trakehner horses. Breeding and selection of subdivided sire lines could be among the appropriate solutions for the maintenance and extension of the genealogical structure.    

scholarly journals Genetic diversity of maize inbred lines as inferred from SSR markers

Genetika ◽  
2015 ◽  
Vol 47 (2) ◽  
pp. 489-498
Author(s):  
Ana Nikolic ◽  
Dragana Ignjatovic-Micic ◽  
Dragan Kovacevic ◽  
Zoran Camdzija ◽  
Milomir Filipovic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Principal Component ◽  
Inbred Lines ◽  
Yield Potential ◽  
Pedigree Data ◽  
Maize Breeding ◽  
Breeding Programs ◽  
Maize Inbred Lines ◽  
The World

Creating new maize hybrids with greater yield potential is a permanent goal of breeding programs all over the world. Long-time existing and new problems related to different biotic and abiotic stresses and the growing needs of the world market require constant work on finding new ways for advancing maize production. Molecular marker technology is one of the fastest developing fields and its implementation has already given results in solving different problems related to maize breeding improvement. The aim of the study presented herein was characterization and genetic similarity assessment of twenty-nine maize inbred lines from Maize Research Institute collection using Simple Sequence Repeats (SSR) markers. The analysis was done using 20 pairs of SSR primers with clearly visible and reproducible results. A total of 119 alleles were detected with a mean of 5.8 per locus. PIC (Polymorphism Information Content) values were in the range from 0.45 to 0.92 (average 0.74). Genetic similarities calculated using Jaccard?s coefficient ranged from 0.27 to 0.99. Cluster and Principal Component Analysis (PCA) analysis were done using matrices of similarity in the NTSYSpc software, version 2.1. Results of both classifications were moderately in agreement with the pedigree data of analysed genotypes. The information about genetic diversity of maize inbred lines revealed by SSR markers could be useful in planning strategies for future maize breeding programs.

scholarly journals Genetic diversity within local and introduced cultivars of wheat (Triticum aestivum L.) grown under Mediterranean environment as revealed by AFLP markers

2019 ◽  
Vol 63 (1) ◽  
pp. 25-30
Author(s):  
Mohammed Imad Eddin Arabi ◽  
Amina Shoaib ◽  
Eyad Al-Shehadah ◽  
Mohammed Jawhar
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Principal Component ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Aflp Markers ◽  
Group Method ◽  
Wheat Cultivars ◽  
Arithmetic Means

Information on genetic diversity among cultivars is critical in wheat improvement. In this work, heterogeneity within local and introduced cultivars of bread wheat grown in Syria was investigated using amplified fragment length polymorphism (AFLP) markers. The eight primer pairs were used to detect 177 polymorphic bands among the 21 cultivars resulting in an average of 22.13 (57.3%) polymorphic loci per primer pair. Major allelic frequency ranged from 0.50 to 0.75 with a mean 0.64, and estimated gene diversity was 0.45. Values of average polymorphic information content (PIC) for these markers were estimated to be 0.34. This low value might be attributed to the rigorous selection pressure aimed at cultivar purity and associated breeding practices. Dissimilarity values ranged from 0.32 to 0.66 with an average of 0.54, indicating that such techniques sample distinct genome regions. Three major subgroups of wheat cultivars were identified using the unweighted pair-group method with arithmetic means analysis (UPGMA), with all local cultivars falling into one cluster, which was confirmed by a principal component analysis (PCA). The narrow genetic diversity observed among Syrian wheat cultivars suggests the need of broadening the genetic base of wheat breeding materials, including local landraces.

Genetic Base of Wheat Cultivars Recommended in Nepal

1970 ◽  
Vol 6 ◽  
pp. 1-9 ◽  
Author(s):  
Umesh R Rosyara ◽  
Bal K Joshi
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Genetic Background ◽  
Triticum Aestivum L ◽  
Pedigree Information ◽  
Wheat Cultivars ◽  
Coefficient Of Parentage ◽  
Total Contribution ◽  
Research Journal ◽  
Genetic Base

Plant breeding success is dependent, in part, upon the genetic diversity found within geneticresources. The genetic base of wheat (Triticum aestivum L.) cultivars recommended in Nepal is notwell characterized. Therefore this study was carried out to quantify the genetic base of Nepalesewheat cultivars by coefficient of parentage (COP). Analysis of pedigree information was based onInternational Wheat Information System of the International Center for Maize and WheatImprovement (CIMMYT), which consists of WCOP for calculation of COP and WPDEND forgenerating Mendelgram with contribution of ancestors to the cultivar if fully expanded. Onehundred eighteen ancestors from 23 countries were identified in the pedigree of 24 recommendedNepalese cultivars. Of these, 32 ancestors contributed at least 1% each to the genetic base ofNepalese cultivars, with a total contribution of 79%. Ancestors originating from USA contributed19.8% of the genes, India 11.2%, Japan 9.5%, Argentina 7.5%, Kenya 7.5% Australia 6.2%, Brazil5.6%, Canada 5.5%, Italy 4.1% and remaining from other countries. At 30% similarity, 18 clusterswere formed with largest cluster of five members. None of Nepalese landraces were traced in thepedigree of these cultivars. Relatively large amount of diversity in Nepalese cultivars exits based ontheir genetic background although small number of cultivars is recommended for cultivation.Key words: Coefficient of parentage; diversity; Triticum aestivum; wheat breedingDOI: 10.3126/narj.v6i0.3338Nepal Agriculture Research Journal Vol.6 2005 pp.1-9

scholarly journals SNP-based genetic diversity assessment among hungarian bread wheat (Triticum aestivum L.) genotypes

2019 ◽  
Vol 48 (1) ◽  
pp. 1-7 ◽  
Author(s):  
P. Körmöczi ◽  
B. Tóth ◽  
A. Nagy-György ◽  
K. Kocsis ◽  
J. Óvári ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Triticum Aestivum L ◽  
Pedigree Data ◽  
Wheat Varieties ◽  
Allele Distribution ◽  
Dwarfing Gene ◽  
Wheat Population ◽  
Diversity Assessment ◽  
Starting Point

AbstractWorld’s food supply will be a great challenge due to the rapid growth of human population. Therefore, wheat breeders are facing a great task to improve further the crop quality and quantity. Genetic improvement could be the key in this progression, which is based on the exploitation of genetic resources. So it is important to hold exact information about the wheat population structure, especially the genetic diversity of elite crop germplasm. Here, we provide the characterisation of 85 Hungarian wheat varieties from 3 different Hungarian breeding programmes (Szeged, Martonvásár and Karcag) trough Competitive Allele-Specific PCR (KASP) technique. Population structure of these accessions were examined by STRUCTURE software and the ΔK values were calculating by the STRUCTURE HARVESTER. These investigations revealed 3 subgroups in our wheat population with 21, 19 and 45 genotypes in GrI, GrII and GrIII, respectively. We could conclude that the GrI and GrIII subgroups contained genotypes from all three origins while GrII contained genotypes only from Szeged. We also examined the allele distribution of the Xgwm261 locus since the 192 bp allele is reported to be linked to semi-dwarfing gene Rht8, which has important role in the breeding process. Altogether we could observe 5 size variant products, but the 174 bp (22.35%), 192 bp (55.29%), and 198 bp (12.94%) long fragments could be found the most frequently. The present study confirms that population structure and genotype relatedness, based on molecular data, are consistent with the geography origin and available pedigree data. Moreover, this study could be the starting point of a following association mapping work.

Genetic Analysis of Chinese Cucumber Collections in the U.S. National Germplasm Collection

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 534e-534 ◽  
Author(s):  
J. Staub ◽  
Felix Sequen ◽  
Tom Horejsi ◽  
Jin Feng Chen
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Allelic Variation ◽  
Germplasm Collection ◽  
Principal Component ◽  
Isozyme Loci ◽  
National Plant Germplasm System ◽  
The U.S

Genetic variation in cucumber accessions from China was assessed by examining variation at 21 polymorphic isozyme loci. Principal component analysis of allelic variation allowed for the depiction of two distinct groupings of Chinese accessions collected in 1994 and 1996 (67 accessions). Six isozyme loci (Gpi, Gr, Mdh-2, Mpi-2, Pep-gl, and Pep-la) were important in elucidating these major groups. These groupings were different from a single grouping of Chinese 146 accessions acquired before 1994. Allelic variation in Chinese accessions allowed for comparisons with other accessions in the U.S. National Plant Germplasm System (U.S. NPGS) collection grouped by continent and sub-continent. When Chinese accessions taken collectively were compared with an array of 853 C. sativus U.S. NPGS accessions examined previously, relationships differed between accessions grouped by country or subcontinent. Data indicate that acquisition of additional Chinese and Indian cucumber accessions would be strategically important for increasing genetic diversity in the U.S. NPGS cucumber collection.

Multivariate Analysis, Genetic Diversity and Phenotypic Correlation of Nineteen Exotic Groundnut Accessions

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
YPJ AMARASINGHE ◽  
G . WIJESINGHE ◽  
R W PUSHPAKUMARA
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Growth Parameters ◽  
Principal Component ◽  
Phenotypic Correlation ◽  
Clustering Method ◽  
Yield Parameters ◽  
Arachis Hypogaea L ◽  
Semi Arid ◽  
Number Of Branches

19 Groundnut ( Arachis hypogaea L. ) genotypes receiv ed from International Crops Research Institute for Semi Arid T ropics (ICRISA T) India w ere ev aluated in a non replicated trial and the characters w ere subjected to multiv ariate analysis to study the v ariability within the genotypes. The first 5 axes of the principal component analysis captured 78% of the total v ariability and identified yield parameters such as number of pods per plant, pod w eight per plant and growth parameters such as number of branches per plant, plant spread, and pod characteristics as the characters contributing most to total v ariation. Phenotypic correlation analysis rev ealed that the yield has positiv e correlation with the characters such as number of pods per plant and number of branches per plant. W ards clustering method has grouped the genotypes into 3 distinct clusters. The results can be applied in order to strengthen the breeding program

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