scholarly journals Genetic resources of barley and oat characterised by microsatellites

2008 ◽  
Vol 43 (No. 3) ◽  
pp. 97-104 ◽  
Author(s):  
L. Leišová ◽  
L. Kučera ◽  
L. Dotlačil
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Negative Impact ◽  
Diversity Index ◽  
Spring Barley ◽  
Germplasm Conservation ◽  
Principal Component ◽  
Microsatellite Data ◽  
Crop Species ◽  
Place Of Origin

Barley (<i>Hordeum vulgare</i> L.) and oat (<i>Avena sativa</i> L.) are important crop species. 1865 accessions of winter barley, 2707 accessions of spring barley and 1998 accessions of oat are maintained in RICP Gene bank. The expert core collection is used to be established as a tool for germplasm study, conservation of genetic variability and for the identification of useful genes. The main aim of this study was to evaluate genetic diversity of barley and oat genotypes within the expert core collections. Genetic variation of 176 barley accessions was analyzed using 26 microsatellite loci, covering all 6 chromosomes. 330 oat accessions were analyzed using 26 microsatellite loci that are mapped only into linkage groups. For 26 barley microsatellite loci, 328 alleles were detected. The average number of alleles per locus was 12.6. In oat, for 26 oat microsatellite loci, 353 alleles were detected. The average number of alleles per locus was 13.6. The average DI (diversity index) was 0.11 in barley and 0.09 in oat. Dendrogram and PCA (Principal Component Analysis) based on microsatellite data showed a different influence of the place of origin, age of variety and pedigree on grouping into clusters. PCA showed that the breeding process had a negative impact on the level of genetic diversity and therefore there is a necessity of barley and oat germplasm conservation.

scholarly journals Genetic Diversity in Commercial Rapeseed (Brassica napus L.) Varieties from Turkey as Revealed by RAPD

2013 ◽  
Vol 5 (1) ◽  
pp. 114-119 ◽  
Author(s):  
Özlem ÖZBEK ◽  
Betül Uçar GIDIK
Keyword(s):  
Genetic Diversity ◽  
Brassica Napus ◽  
Dna Analysis ◽  
Diversity Index ◽  
Principal Component ◽  
Brassica Napus L ◽  
Binary Matrix ◽  
Crop Species ◽  
Commercial Crop ◽  
The Mean

In cultivated commercial crop species, genetic diversity tends to decrease because of the extensive breeding processes. Therefore, germplasm of commercial crop species, such as Brassica napus L. should be evaluated and the genotypes, which have higher genetic diversity index, should be addressed as potential parental cross materials in breeding programs. In this study, the genetic diversity was analysed by using randomly amplified polymorphic DNA analysis (RAPD) technique in nine Turkish commercial rapeseed varieties. The RAPD primers (10-mer oligonucleotides) produced 51 scorable loci, 31 loci of which were polymorphic (60.78%) and 20 loci (39.22%) were monomorphic The RAPD bands were scored as binary matrix data and were analysed using POPGENE version 1.32. At locus level, the values of genetic diversity within population (Hs) and total (HT) were 0.15 and 0.19 respectively. The genetic differentiation (GST) and the gene flow (Nm) values between the populations were 0.20 and 2.05 respectively. The mean number of alleles (na), the mean number of effective alleles (nae), and the mean value of genetic diversity (He) were 2.00, 1.26, and 0.19 respectively. According to Pearson’s correlation, multiple regression and principal component analyses, eco-geographical conditions in combination had significant effect on genetic indices of commercial B. napus L. varieties were discussed.

scholarly journals Assessment of Genetic Diversity and Population Genetic Structure of Santalum album L. in India by Genic and Genomic SSR markers

2021 ◽  
Author(s):  
Tanzeem Fatima ◽  
Ashutosh Srivastava ◽  
Vageeshbabu S Hanur ◽  
M. Srinivasa Rao
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Germplasm Conservation ◽  
Principal Component ◽  
Santalum Album ◽  
High Genetic Diversity ◽  
Information Index ◽  
Genomic Ssr ◽  
Santalum Album L

Sandalwood (Santalum album L.) is highly valued aromatic tropical tree. It is known for its high quality heartwood and oil. In this study 39 genic and genomic SSR markers were used to analyze the genetic diversity and population structure of 177 S. album accessions from 14 populations of three states in India. High genetic diversity was observed in terms of number of alleles 127 expected heterozygosity (He) ranged from 0.63-0.87 and the average PIC was 0.85. The selected population had relatively high genetic diversity with Shannons information index (I) >1.0. 0.02 mean coefficient of genetic differentiation (FST) and 10.55 gene flow were observed. AMOVA revealed that 92% of the variation observed within individuals. Based on cluster and Structure result individuals were not clustered as per their geographical origin. Furthermore the clusters were clearly distinguished by principal component analysis analysis and the result revealed that PC1 reflected the moderate contribution in genetic variation (6%) followed by PC2 (5.5%). From this study, high genetic diversity and genetic differentiation was found in S. album populations. The genetic diversity information of S. album populations can be used for selection of superior genotypes and germplasm conservation to promote the tree improvement of S. album populations.

scholarly journals Evaluation of the Genetic Variation of Cowpea Landraces (Vigna unguiculata) from Western Cameroon Using Qualitative Traits

2017 ◽  
Vol 9 (4) ◽  
pp. 508-514 ◽  
Author(s):  
Toscani NGOMPE-DEFFO ◽  
Eric Bertrand KOUAM ◽  
Honoré BEYEGUE-DJONKO ◽  
Mariette ANOUMAA
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Growth Habit ◽  
Diversity Index ◽  
Diversity Indices ◽  
Crop Species ◽  
Qualitative Trait ◽  
Qualitative Traits ◽  
Leaf Hairiness

Characterization of the genetic diversity and analysis of the genetic relationship between accessions of a crop species is a key step in breeding superior cultivars. The main objective of the hereby study was to determine the genetic variation between 30 cowpea accessions collected throughout the eight divisions of the Western Region of Cameroon using qualitative traits. Phenotypic variation of these accessions was evaluated using diversity indices and cluster analyses. A total of twenty qualitative traits were used for the study. Fifteen of them (75%) were polymorphic, displaying each at least two phenotypic classes. The monomorphic characters were growth pattern, leaf color, leaf hairiness, plant hairiness and pod hairiness, each with only one phenotypic class. Results showed a relatively significant level of genetic diversity among the studied cowpea accessions. Overall, the average of the observed and effective number of phenotypic classes per qualitative trait were Na = 2.350 and Ne = 1.828 respectively. The Nei’s genetic diversity and the Shannon weaver diversity index were He = 0.369, ranging from zero (monomorphic trait) to 0.655 (growth habit) and H’ = 0.609, ranging from zero (monomorphic trait) to 0.996 (seed crowding), respectively. The dendrogram constructed from the twenty qualitative traits revealed 05 accessions clusters with the number of accessions in each cluster varying from one to eleven. Information obtained from this study is likely be useful for future cowpea breeding program.

scholarly journals Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10485
Author(s):  
Zhixin Wang ◽  
Yalin Sun ◽  
Xinfang Huang ◽  
Feng Li ◽  
Yuping Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Conservation ◽  
Principal Component ◽  
Snp Markers ◽  
Colocasia Esculenta ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Entire Collection ◽  
Tuber Crop

Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.

scholarly journals Genetic structure of East Antarctic populations of the mossCeratodon purpureus

2008 ◽  
Vol 21 (1) ◽  
pp. 51-58 ◽  
Author(s):  
Laurence J. Clarke ◽  
David J. Ayre ◽  
Sharon A. Robinson
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Environmental Change ◽  
Asexual Reproduction ◽  
Microsatellite Loci ◽  
Microsatellite Data ◽  
Genetic Studies ◽  
Total Genetic Diversity ◽  
Windmill Islands ◽  
Antarctic Mosses

AbstractThe capacity of the polar flora to adapt is of increasing concern given current and predicted environmental change in these regions. Previous genetic studies of Antarctic mosses have been of limited value due to a lack of variation in the markers or non-specificity of the methods used. We examined the power of five microsatellite loci developed for the cosmopolitan mossCeratodon purpureusto detect genetically distinct clones and infer the distribution of clones within and among populations from the Windmill Islands, East Antarctica. Our microsatellite data suggest that the extraordinarily high levels of variation reported in RAPD studies were artificially elevated by the presence of contaminants. We found surprisingly little contribution of asexual reproduction to the genetic structure of the Windmill Islands populations, but more loci are required to determine the distribution of individual clones within and among populations. It is apparent that Antarctic populations ofC. purpureuspossess less genetic diversity than temperate populations, and thus have less capacity for adaptive change in response to environmental variation, but more markers are needed to resolve the total genetic diversity in AntarcticC. purpureusand other mosses.

Geographical distribution and phenotypic diversity of wild/weedy sorghum [Sorghum bicolor (L.) Moench] in Ethiopia: implications for germplasm conservation and crop–wild gene flow

2012 ◽  
Vol 11 (1) ◽  
pp. 68-76 ◽  
Author(s):  
Asfaw Adugna ◽  
Endashaw Bekele
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Sorghum Bicolor ◽  
Phenotypic Diversity ◽  
Diversity Index ◽  
Germplasm Conservation ◽  
Morphological Data ◽  
Transgenic Crop ◽  
Average Value ◽  
Geographical Regions

Extensive studies of genetic diversity and population structure important for conservation of wild sorghum are yet lacking in Ethiopia, the centre of origin for cultivated sorghum. To assess both genetic diversity and the probability of gene flow between wild and cultivated types, collections of wild Sorghum bicolor were made from regions in Ethiopia where wild and cultivated sorghum coexist. Morphological data were recorded in situ for both quantitative and qualitative characters from 30 populations in five diverse geographical regions and eight agroecologies. High phenotypic diversity was observed among the wild and weedy sorghum populations. The overall standardized Shannon–Weaver diversity index (H′), computed from the frequencies of all qualitative traits, ranged from 0.47 to 0.98 with an average value of 0.76. Moreover, warm semi-arid lowland (SA2) agroecologies, which contain Tigray populations, supported the highest diversity for these traits. Subspecies verticilliflorum and drummondii (the two major subspecies of wild S. bicolor) were observed in diverse habitats throughout northern and central Ethiopia. In some areas, weedy types showed domestication traits including the absence of awns and reduced seed shattering. The existence of morphologically intermediate forms indicates that gene flow between cultivated and wild forms has likely occurred. Deployment of transgenic crop sorghum, therefore, would pose a distinct risk for transgene movement into wild Ethiopian populations.

scholarly journals Genetic Diversity of Seashore Paspalum Revealed with Simple Sequence Repeat Markers

2020 ◽  
Vol 145 (4) ◽  
pp. 228-235
Author(s):  
Qing Shen ◽  
Hua Bian ◽  
Hai-yan Wei ◽  
Li Liao ◽  
Zhi-yong Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Principal Component ◽  
Sequence Repeat ◽  
Similarity Coefficients ◽  
Seashore Paspalum ◽  
Simple Sequence

Seashore paspalum (Paspalum vaginatum) is an important warm-season turfgrass distributed in tropical and coastal areas. It has excellent resistance to abiotic stresses, such as salinity, drought, and low temperature. However, the research on genetic diversity of local P. vaginatum collections from China is limited. In this study, the genetic diversity among 58 P. vaginatum accessions from four different provinces in China and four cultivars were assessed using simple sequence repeat (SSR) markers. The results indicated that a total of 45 alleles were detected by 19 polymorphic markers, with a range of 2 to 4 and an average of 2.4 alleles per marker. The genetic similarity coefficients between each pair of the 58 P. vaginatum accessions and four cultivars ranged from 0.51 to 1.00, with an average of 0.77. The range of variation of Shannon diversity index of each SSR marker was 0.047 to 1.075, with an average of 0.486. The polymorphic information content of each SSR marker varies from 0.016 to 0.577, with an average of 0.249. The results of cluster analysis and principal component analysis (PCA) showed that 58 P. vaginatum accessions and four cultivars were divided into four groups. These results provide the theoretical basis for the genetic diversity assessments and molecular marker–assisted breeding of P. vaginatum species.

scholarly journals Analysis of the Genetic Structure and Diversity of Upland Cotton Groups in Different Planting Areas Based on SNP Markers

2021 ◽  
Author(s):  
Zeliang Zhang ◽  
Junduo Wang ◽  
Zhaolong Gong ◽  
Yajun Liang ◽  
Xiantao Ai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Gossypium Hirsutum ◽  
Diversity Index ◽  
Principal Component ◽  
Snp Markers ◽  
High Genetic Diversity ◽  
Origin And Evolution ◽  
Population Structure Analysis ◽  
Genetic Structure And Diversity

Genetic diversity, kinship and population genetic structure analyses of Gossypium hirsutum germplasm can provide a better understanding of the origin and evolution of G. hirsutum biodiversity. In this study, 1313331 SNP molecular markers were used to construct a phylogenetic tree of each sample using MEGAX, to perform population structure analysis by ADMIXTURE software and principal component analysis (PCA) by EIGENSOFT software, and to estimate relatedness using SPAGeDi. ADMIXTURE software divided the experimental cotton population into 16 subgroups, and the Gossypium hirsutum samples could be roughly clustered according to source place, but there were some overlapping characteristics among samples. The experimental cotton population was divided into six groups according to source to calculate the genetic diversity index (H), and the obtained value (0.306) was close to that for germplasm collected by others in China. Cluster 4 had a relatively high genetic diversity level (0.390). The degrees of genetic differentiation within the experimental cotton population groups were low (the population differentiation indexes ranged from 0.02368 to 0.10664). The genetic distance among cotton accessions varied from 0.000332651 to 0.562664014, with an average of 0.25240429. The results of this study may provide a basis for mining elite alleles and using them for subsequent association analysis.

scholarly journals ISSR markers and morphometry determine genetic diversity and population structure in Hedera helix L.

2021 ◽  
Author(s):  
Abdul Shakoor ◽  
Gul Zaib ◽  
Fang Zhao ◽  
Wuyang Li ◽  
Xincan Lan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Similarity ◽  
Diversity Index ◽  
Morphological Characteristics ◽  
Principal Component ◽  
Mantel Test ◽  
Hedera Helix ◽  
Plant Populations ◽  
High Genetic Diversity

Hedera helix L. is an invasive, but medicinally important plant. In Iran, there is no available study on the H. helix population to reveal the genetic diversity and population structure. Fifty-six individual plants belonging to nine geographical populations were collected in four provinces of Iran. High genetic diversity, polymorphisms, and a Shannon diversity index of 0.269 were detected in Mazandaran, Kandovan (Population 3). Analysis of the molecular variance indicated 40% of total genetic variation of the whole population was present in the subpopulation. A high genetic similarity (0.922) between plant Populations 5 (Kermanshah; Islamabad) and 6 (Kermanshah; Paveh) was noted. On the other hand, a low genetic similarity was observed between plant Populations 1 (Tehran; Darband) and 8 (Ardabil; Hur). The Mantel test revealed a correlation between the genetic and geographical distances. Furthermore, it demonstrated the isolation mechanism responsible for the population structure in the H. helix plant populations. The principal component analysis explained the majority of the variation in the morphological characteristics. Three components explained 87% of the variation, and the first component explained 60% of the variation. For instance, the leaf morphology showed a correlation of &gt; 0.7 between leaf morphological and floral characters. The plant leaves and quantitative flower characteristics separated the plant populations according to the differences in length. The current results have implications for plant conservation and management.

scholarly journals Genetic diversity in Bambara groundnut {Vigna subterranea (L.) Verdc.}

2021 ◽  
Vol 54 (1) ◽  
pp. 89-96
Author(s):  
Nwakuche Chinenye Onwubiko
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Block Design ◽  
Crop Improvement ◽  
Morphological Variability ◽  
Germplasm Conservation ◽  
Principal Component ◽  
Bambara Groundnut ◽  
Grain Legume ◽  
International Institute

Abstract Bambara groundnut is a grain legume with enormous morphological variability. In order to genetically establish the variation that exists in this crop, an assessment of genetic diversity was therefore carried out with 20 accessions of Bambara groundnut collected from International Institute of Tropical Agriculture (IITA) Ibadan. The design of the experiment was randomised complete block design with three replications. Results from analysis of variance (ANOVA), and principal component analysis (PCA) showed outstanding genetic diversity among the collections. The first four principal components accounted for 91.89% of the total variability. Cluster analysis and the dendrogram discretely grouped the accessions into four genetically distinct groups. One accession TVSU 353 singly formed a group in cluster analysis and dendrogram, which implies that TVSU 353 was genetically distinct from the rest of the accessions. Morphological characters assessed provided a useful measure of genetic differences among Bambara groundnut accessions, which can facilitate identification and selection of potential breeding lines for crop improvement as well as germplasm conservation.

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