Genetic diversity in African yam bean accessions based on AFLP markers: towards a platform for germplasm improvement and utilization

2014 ◽  
Vol 13 (2) ◽  
pp. 111-118 ◽  
Author(s):  
B. D. Adewale ◽  
I. Vroh-Bi ◽  
D. J. Dumet ◽  
S. Nnadi ◽  
O. B. Kehinde ◽  
...  
Keyword(s):  
Fragment Length Polymorphism ◽  
Aflp Markers ◽  
Fixation Index ◽  
Crop Species ◽  
Phenotypic Profile ◽  
African Yam Bean ◽  
Expected Heterozygosity ◽  
Underutilized Crop ◽  
Breeding Programmes ◽  
The Mean

Accurate knowledge of intra-specific diversity of underutilized crop species is a prerequisite for their genetic improvement and utilization. The diversity of 77 accessions of African yam bean (AYB, Sphenostylis stenocarpa) was assessed by amplified fragment length polymorphism (AFLP) markers. A total of EcoRI/MseI primer pairs were selected and 227 AFLP bands were generated, of which 59(26%) were found to be polymorphic in the 77 accessions of AYB. The most efficient primer combination for polymorphic detection was E-ACT/M-CAG with a polymorphic efficiency of 85.5%, while the least efficient was E-AGC/M-CAG with a polymorphic efficiency of 80.6%. The Jaccard genetic distance among the accessions of AYB ranged between 0.048 and 0.842 with a mean of 0.444. TSs98 and TSs104B were found to be the most similar accessions with a genetic similarity of 0.952. The neighbour-joining dendrogram grouped the 77 accessions of AYB into four distinct clusters comprising 8, 20, 21 and 28 accessions. The major clustering of the accessions was not related to their geographical origin. Cluster I was found to be the most diverse. The mean fixation index (0.203) and the mean expected heterozygosity (0.284) revealed a broad genetic base of the AYB accessions. The same germplasm set was previously evaluated for several agro-morphological traits. As the collection of additional AYB germplasm continues, the phenotypic profile, the clustering of the accessions and the AFLP primer combinations from this study can be used to augment breeding programmes.

scholarly journals Molecular characterization of two natural hybrids from the Iberian Peninsula: Ranunculus × luizetii and R. × peredae (Ranunculaceae)

Biologia ◽  
2012 ◽  
Vol 67 (5) ◽  
Author(s):  
Eduardo Cires ◽  
Candela Cuesta ◽  
José Prieto
Keyword(s):  
Pollen Fertility ◽  
Fragment Length Polymorphism ◽  
Pollen Viability ◽  
Mean Value ◽  
Aflp Markers ◽  
Rdna Sequences ◽  
The Mean ◽  
Rdna Polymorphisms ◽  
Fertility Estimation

AbstractTwo nothospecies, Ranunculus × luizetii and R. × peredae (Ranunculaceae), were analyzed and discussed. For this purpose, Amplified Fragment Length Polymorphism (AFLP) markers, nuclear rDNA sequences (ITS1, 5.8S and ITS2) and pollen viability were conducted. The profiles of these hybrid samples were compared to their putative progenitors. Several additive polymorphic sites detected in the ITS sequences of the hybrid samples (R. × luizetii and R. × peredae) also confirmed their derived origins from ribotypes of their parental taxa (R. parnassiifolius subsp. parnassiifolius × R. pyrenaeus; R. amplexicaulis × R. cabrerensis subsp. cabrerensis, respectively). Despite the lack of exclusive AFLP markers reported in both hybrids, presumably due to effects of introgression, the concerted evolution of many rDNA polymorphisms towards either of the parental ribotypes indicated their ancient origin. Pollen fertility estimation in R. × luizetii presented a mean value of 60.58%, which showed that hybrid samples are well established and fertile. However, a larger difference was observed in R. × peredae, where the mean value of pollen fertility was very low (18.91%).

scholarly journals Genetic variability of Nigerian sheep breeds at the insulin-like growth factor-1 (IGF-1) gene locus

2020 ◽  
Vol 45 (1) ◽  
pp. 51-60
Author(s):  
A. Mohammed ◽  
A. O. Raji ◽  
J. U. Igwebuike
Keyword(s):  
Genetic Variability ◽  
Random Mating ◽  
General Pattern ◽  
Fixation Index ◽  
Mean Values ◽  
Sheep Breeds ◽  
Expected Heterozygosity ◽  
The Mean ◽  
High Level ◽  
The University

The genetic variability of some Nigerian breeds of sheep at the IGF 1 locus was investigate blood samples from 150 sheep (50 each of Yankasa, Balami and Uda sheep) were collected from the Maiduguri abbatoir and analysed at the Biotechnology centre of the University of Maiduguri. A relatively high level of genetic variability was detected in Nigerian sheep; the mean observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.433 and 0.476, respectively. Comparison of expected heterozygosity of alleles between the populations showed that yankasa was the most heterozygous of the sheep populations though the unbiased expected heterozygosity (0.503) for the Yankasa was the same as that of the Balami. All populations were 100% polymorphic at the IGF 1 locus with fixation index ranging from -0.169 to 0.378 and a mean of 0.093, which suggests a general pattern of random mating. Similarly, low mean values for Fis (0.093), F (0.089), Fis (0.089), Fit (0.130) and Fst (0.045) supports the assertion that inbreeding was limited due to outcrossing with relatively high level of gene-flow (Nm = 5.292). The analysis of molecular variance (AMOVA) revealed that only 1% of the total variations observed in the sampled populations is accounted for by the population differences while individual differences accounted for 85%. The UPGMA phylogenetic tree revealed that the Uda and Yankasa populations are closer to each than each is to Balami. Thus, it can be concluded that sufficient genetic variation exist in the studied Nigerian sheep breeds and these populations are unlikely to decline due to inbreeding.  

scholarly journals Genetic diversity revealed by AFLP markers in Albanian goat breeds

2012 ◽  
Vol 64 (2) ◽  
pp. 799-807 ◽  
Author(s):  
Anila Hoda ◽  
Lumturi Sena ◽  
Gentian Hykaj
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Fragment Length Polymorphism ◽  
Similarity Index ◽  
Shannon Index ◽  
Upgma Tree ◽  
Expected Heterozygosity ◽  
The Mean ◽  
High Level ◽  
Aflp Technique

The amplified fragment length polymorphism (AFLP) technique with three EcoRI/TaqI primer combinations was used in 185 unrelated individuals, representative of 6 local goat breeds of Albania, and 107 markers were generated. The mean Nei?s expected heterozygosity value for the whole population was 0.199 and the mean Shannon index was 0.249, indicating a high level of within-breed diversity. Wright?s FST index, Nei?s unbiased genetic distance and Reynolds? genetic distance were calculated. Pairwise Fst values among the populations ranged from 0.019 to 0.047. A highly significant average FST of 0.031 was estimated, showing a low level of breed subdivision. Most of the variation is accounted for by differences among individuals. Cluster analysis based on Reynolds? genetic distance between breeds and PCA were performed. An individual UPGMA tree based on Jaccard?s similarity index showed clusters with individuals from all goat breeds. Analysis of population structure points to a high level of admixture among breeds.

scholarly journals Treatment of segmental tibial defects by bone transport with circular external fixation and a locking plate

2020 ◽  
Vol 48 (4) ◽  
pp. 030006052092040
Author(s):  
Yao Lu ◽  
Teng Ma ◽  
Cheng Ren ◽  
Zhong Li ◽  
Liang Sun ◽  
...  
Keyword(s):  
External Fixation ◽  
Locking Plate ◽  
Short Form ◽  
Clinical Results ◽  
Bone Transport ◽  
Fixation Index ◽  
Fixation Time ◽  
Sf 36 ◽  
Health Related ◽  
The Mean

Objective To evaluate the effectiveness of bone transport involving circular external fixation and locking plate application for the treatment of segmental tibial defects. Methods A retrospective review of 12 patients with segmental tibial defects who underwent bone transport with circular external fixation and locking plate application. We evaluated external fixation time, external fixation index, time to achieve union, and complications. Clinical results were assessed using the Association for the Study and Application of the Methods of Ilizarov (ASAMI) score. Generic health-related outcome was assessed using the 36-Item Short-Form Health Survey questionnaire (SF-36). Results The mean follow-up was 25.8 months, and the mean defect size was 6.7 cm. All of the patients achieved union at the distraction callus and docking site. The average external fixation time was 299.5 days. The mean external fixation index was 16.5 days/cm, and the mean healing index was 44.9 days/cm. The functional outcomes were excellent in eight cases and good in four. The average SF-36 score was 92. Conclusion Bone transport with external fixation and locking plate application may be a promising method for the treatment of segmental tibial defects.

Development of microsatellite markers at the National Agrobiodiversity Center in Korea for the genetic assessment of underutilized crops

2014 ◽  
Vol 12 (S1) ◽  
pp. S125-S129
Author(s):  
Gi-An Lee ◽  
Sok-Young Lee ◽  
Ho-Sun Lee ◽  
Kyung-Ho Ma ◽  
Jae-Gyun Gwag ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Germplasm Management ◽  
Underutilized Crops ◽  
Crop Species ◽  
Closely Related Species ◽  
Polymorphic Loci ◽  
Allele Number ◽  
The Mean ◽  
Genetic Assessment

The RDA Genebank at the National Agrobiodiversity Center (NAAS, RDA, Republic of Korea) has conserved about 182,000 accessions in 1777 species and is working at preserving agricultural genetic resources for the conservation and sustainable utilization of genetic diversity. The detection of genetic variability in conserved resources is important for germplasm management, but the molecular evaluation tools providing genetic information are insufficient for underutilized crops, unlike those for major crops. In this regard, the Korean National Agrobiodiversity Center has been developing microsatellite markers for several underutilized crops. We designed 3640 primer pairs flanking simple sequence repeat (SSR) motifs for 6310 SSR clones in 21 crop species. Polymorphic loci were revealed in each species (7–36), and the mean ratio of polymorphic loci to all the loci tested was 12%. The average allele number was 5.1 (2.8–10.3) and the expected heterozygosity 0.51 (0.31–0.74). Some SSRs were transferable to closely related species, such as within the genera Fagopyrum and Allium. These SSR markers might be used for studying the genetic diversity of conserved underutilized crops.

scholarly journals Reduced Translocation Is Associated with Tolerance of Common Lambsquarters (Chenopodium album) to Glyphosate

Weed Science ◽  
2013 ◽  
Vol 61 (3) ◽  
pp. 353-360 ◽  
Author(s):  
Melinda K. Yerka ◽  
Andrew T. Wiersma ◽  
R. Bradley Lindenmayer ◽  
Philip Westra ◽  
William G. Johnson ◽  
...  
Keyword(s):  
Competitive Ability ◽  
Chenopodium Album ◽  
Protein Abundance ◽  
Crop Species ◽  
Common Lambsquarters ◽  
Treated Leaf ◽  
The Mean ◽  
Shoot Mass ◽  
Sites Of Action

Common lambsquarters tolerance to glyphosate is problematic because of the species' widespread distribution, competitive ability with many crop species, the widespread use of glyphosate in agriculture, and the weed's potential to develop decreased sensitivity to multiple herbicide sites of action. The mechanism that confers common lambsquarters tolerance to glyphosate is not known. Therefore, we conducted experiments to determine the mechanism of tolerance to glyphosate in an accession of common lambsquarters from Indiana relative to a sensitive accession from Wisconsin. The ED50(the effective dose that reduced shoot mass 50% relative to nontreated plants) value for the tolerant accession (1.6 kg ae ha−1± 0.4 standard error of the mean [SEM]) was eightfold greater than the ED50for the sensitive accession (0.2 kg ae ha−1± 0.2 SEM) 28 d after treatment. The glyphosate target-site (EPSPS) DNA sequence at proline 106, shikimate accumulation as an estimate of EPSPS sensitivity, and EPSPS protein abundance did not differ between accessions. Absorption of14C-glyphosate was slightly greater in the tolerant accession than it was in the sensitive accession at 48 and 72 h after treatment (HAT). However, the tolerant accession translocated a smaller percentage of absorbed14C-glyphosate to the tissue above the treated leaf, which included the shoot apical meristem, at 24, 48, and 72 HAT (P ≤ 0.05, 0.01, and 0.10, respectively). These results suggest an important role of reduced translocation in conferring tolerance of common lambsquarters to glyphosate.

scholarly journals Population structure and phylogenetic relationships in Brassica rapa L. subspecies by using isozyme markers

2020 ◽  
Author(s):  
R. H. Sammour ◽  
M. A. Karam ◽  
Y. S. Morsi ◽  
R. M. Ali
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Brassica Rapa ◽  
Phylogenetic Relationships ◽  
Fixation Index ◽  
Distribution Area ◽  
Enzyme Analysis ◽  
Breeding Programs ◽  
Expected Heterozygosity ◽  
Wide Range

Abstract The present study aimed to assess population structure and phylogenetic relationships of nine subspecies of Brassica rapa L. represented with thirty-five accessions cover a wide range of species distribution area using isozyme analysis in order to select more diverse accessions as supplementary resources that can be utilized for improvement of B. napus. Enzyme analysis resulted in detecting 14 putative polymorphic loci with 27 alleles. Mean allele frequency 0.04 (rare alleles) was observed in Cat4A and Cat4B in sub species Oleifera accession CR 2204/79 and in subspecies trilocularis accessions CR 2215/88 and CR 2244/88. The highest genetic diversity measures were observed in subspecies dichotoma, accession CR 1585/96 (the highest average of observed (H0) and expected heterozygosity (He), and number of alleles per locus (Ae)). These observations make this accession valuable genetic resource to be included in breeding programs for the improvement of oilseed B. napus. The average fixation index (F) is significantly higher than zero for the analysis accessions indicating a significant deficiency of heteozygosity. The divergence among subspecies indicated very great genetic differentiation (FST = 0.8972) which means that about 90% of genetic diversity is distributed among subspecies, while 10% of the diversity is distributed within subspecies. This coincides with low value of gene flow (Nm = 0.0287). B. rapa ssp. oleifera (turnip rape) and B. rapa ssp. trilocularis (sarson) were grouped under one cluster which coincides with the morphological classification.

scholarly journals Development of microsatellite markers for a giant water bug, Appasus japonicus, distributed in East Asia

2020 ◽  
Author(s):  
Tomoya Suzuki ◽  
Akira S. Hirao ◽  
Masaki Takenaka ◽  
Koki Yano ◽  
Koji Tojo
Keyword(s):  
Microsatellite Markers ◽  
East Asia ◽  
Local Level ◽  
Mainland China ◽  
Fixation Index ◽  
Japanese Archipelago ◽  
Red Data Book ◽  
Expected Heterozygosity ◽  
Data Book ◽  
Polymorphic Microsatellite

AbstractWe developed microsatellite markers for Appasus japonicus (Hemiptera: Belostomatidae). This belostomatid bug is distributed in East Asia (Japanese Archipelago, Korean Peninsula, and Mainland China), and often listed as endangered species in the ‘Red List’ or the ‘Red Data Book’ at the national and local level in Japan. Here we describe twenty novel polymorphic microsatellite loci developed for A. japonicus, and marker suitability was evaluated on 56 individuals from four A. japonicus populations (Nagano, Hiroshima, and Yamaguchi prefecture, Japan, and Chungcheongnam-do, Korea). The number of alleles per locus ranged 1–12 (mean = 2.5), and average observed and expected heterozygosity, and fixation index per locus were 0.270, 0.323, and 0.153, respectively. The 20 markers described here will be useful for investigating the genetic structure of A. japonicus populations, which can contribute in population genetics studies of this species.

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