scholarly journals Phenotyping the Genetic Diversity of Wild Agave Species that Coexist in the Same Spatial Region

2016 ◽  
Vol 44 (2) ◽  
pp. 640-648
Author(s):  
Elí Secundino PORRAS-RAMÍREZ ◽  
Yazmín SOSA-MARCOS ◽  
Felipe PALMA-CRUZ ◽  
Aroldo CISNEROS
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Morphological Characteristics ◽  
Principal Component ◽  
Culture Conditions ◽  
Field Trips ◽  
Main Cluster ◽  
Close Relationship ◽  
Agave Potatorum ◽  
Great Genetic Diversity

Phenotypic characteristics are important to identify species and provide valuable information for the uses in plant breeding. The aim of this study was to characterize through morphological traits the genetic diversity of the Agave genus under wild and semi-wild culture conditions in Maguey Largo region in Oaxaca, Mexico. Through field trips, eleven morphological characteristics of the Agave species were recorded. Principal component analysis (PCA), phylogenetic trees, and correlation analyses, were performed. Seven wild species were identified: Agave potatorum Zucc., A. seemanniana, A. nussaviorum subsp. nussaviorum, A. angustifolia Haw., A. marmorata Roezl., A. karwinskii Zucc. and A. americana var. Americana. Also, a semi-wild unclassified specie Agave sp. was found. The values of the first four principal components in the PCA explain more than 89% of the total morphological variance. The dendrogram of the agglomerative hierarchical clustering (AHC) shown a high similarity between the species and divide them in two main cluster with one unassociated specie (A. karwinskii Miahuatlán shape). Following the different analyses done, we observed a very close relationship between A. potatorum and A. nussaviorum, and dissociated from A. seemanniana, which are belonging to the “Tobala” complex and never described before. The results obtained in this work suggest a great genetic diversity expressed in a wide morphological variety of agaves in Oaxaca; which can be used in futures molecular studies.

scholarly journals Genetic admixture in pig population observed by microsatellite markers

2011 ◽  
Vol 54 (1) ◽  
pp. 51-60
Author(s):  
R. Židek ◽  
D. Jakabová ◽  
J. Trandžík ◽  
J. Buleca ◽  
D. Takáčová ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Phylogenetic Trees ◽  
Bayesian Method ◽  
Slovak Republic ◽  
Principal Component ◽  
Genetic Admixture ◽  
Scatter Diagram ◽  
Pig Breeds ◽  
High Degree

Abstract. The aim of presented study was estimation of genetic relationship within and between 3 mentioned pig breeds bred in the Slovak Republic. Genetic variability at 10 microsatellite loci (SW24, SO107, SO068, SW936, sw353, so386, so355, sw72, tnfb, and SO070) was analysed in 412 pigs of Landrace, Yorkshire and Slovak White Improved breeds. Variation amount of each population was measured with average number of alleles per locus, heterozygosities, polymorphism information content (PIC) value were calculated. Phylogenetic trees were constructed by UPGMA. The average number of alleles per locus was 11.5, ranging from 7 (SW72) to 16 (SO068). The Slovak White Improved, Landrace and Yorkshire pig breeds showed out high degree of genetic diversity with mean expected heterozygosities of 0.720, 0.697 and 0.705 respectively. Genetic distance ranged from 0.060 between Yorkshire and Slovak White Improved to 0.203 between Landrace and Slovak White Improved breeds. The scatter diagram from principal component displayed genetic differentiation among all three breeds. A Bayesian method was applied for individual assigning testing. On the base of our results the group of Slovak White Improved population was strongly mixed with Yorkshire breed and the group of all Landrace individuals was presented as enclosed population.

scholarly journals Evaluation of Genetic Diversity of Iranian Pomegranate Cultivars Using Fruit Morphological Characteristics and AFLP Markers

2012 ◽  
Vol 40 (1) ◽  
pp. 261 ◽  
Author(s):  
Zahra NEMATI ◽  
Ali TEHRANIFAR ◽  
Mohammad FARSI ◽  
Amin MIRSHAMSI KAKHKI ◽  
Hossein NEMATI ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Morphological Characteristics ◽  
Principal Component ◽  
Aflp Markers ◽  
Fruit Characteristics ◽  
Aflp Data ◽  
Breeding Programs ◽  
Low Genetic Diversity ◽  
Geographic Origins ◽  
The Relationship

The present research evaluated the diversity of a number of Iranian pomegranate cultivars using fruit morphological characteristics and AFLP markers. Thirty-one pomegranate cultivars were collected from Yazd Pomegranate Collection in Iran to study their diversity. Seven AFLP primer combinations were used to amplify a total of 112 polymorphic fragments (47.26%). By use of AFLPs, a low genetic diversity level was detected among cultivars. The relationship between fruit characteristics was analyzed using the principal component analysis (PCA). The cluster analysis based on both fruit characteristics and AFLP data indicated that cultivars were not grouped according to their geographic origins. Moreover, the correlation between the diversity matrix based on fruit characteristics and Dice’s genetic similarity coefficient was insignificant (r=0.06). The results obtained from this study can improve the conservation and management of pomegranate germplasm resources and could be helpful in optimizing breeding programs.

scholarly journals Population genetics and forensic utility of 23 autosomal PowerPlex Fusion 6C STR loci in the Kuwaiti population

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mahdi Haidar ◽  
Fatimah A. Abbas ◽  
Hussain Alsaleh ◽  
Penelope R. Haddrill
Keyword(s):  
Phylogenetic Trees ◽  
Principal Component ◽  
Match Probability ◽  
Close Relationship ◽  
Hardy Weinberg Equilibrium ◽  
Powerplex Fusion ◽  
Kuwaiti Population ◽  
Short Tandem Repeat Markers ◽  
First Time ◽  
Middle Easterners

AbstractThis study evaluates the forensic utility of 23 autosomal short tandem repeat markers in 400 samples from the Kuwaiti population, of which four markers (D10S1248, D22S1045, D2S441 and SE33) are reported for the first time for Kuwait. All the markers were shown to exhibit no deviation from Hardy–Weinberg equilibrium, nor any linkage disequilibrium between and within loci, indicating that these loci are inherited independently, and their allele frequencies can be used to estimate match probabilities in the Kuwaiti population. The low combined match probability of 7.37 × 10–30 and the high paternity indices generated by these loci demonstrate the usefulness of the PowerPlex Fusion 6C kit for human identification in this population, as well as to strengthen the power of paternity testing. Off-ladder alleles were seen at several loci, and these were identified by examining their underlying nucleotide sequences. Principal component analysis (PCA) and STRUCTURE showed no genetic structure within the Kuwaiti population. However, PCA revealed a correlation between geographic and genetic distance. Finally, phylogenetic trees demonstrated a close relationship between Kuwaitis and Middle Easterners at a global level, and a recent common ancestry for Kuwait with its northern neighbours of Iraq and Iran, at a regional level.

scholarly journals Gene flow and genetic structure between populations of Hesperis L. (Brassicaceae) species using molecular markers

Genetika ◽  
2021 ◽  
Vol 53 (2) ◽  
pp. 769-782
Author(s):  
Kuanhong Meng ◽  
Jia Yao ◽  
Cong He ◽  
Heravi Morabbi
Keyword(s):  
Genetic Diversity ◽  
Genetic Difference ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Shannon Index ◽  
The Other ◽  
Brassicaceae Species ◽  
Close Relationship ◽  
Geographical Populations ◽  
Dna Primers

Genetic variability and populations, structure were studied in seven geographical populations of Hesperis L. Genetic diversity parameters were determined in these populations. 5 of 10 random amplified polymorphic DNA primers produced 62 reproducible bands with average of 7.1 bands per primer and 55% of polymorphism. Hesperis hyrcana showed the highest number of effective allele (Ne), Shannon index (I) and genetic diversity (H). The highest values of genetic diversity were obtained in Hesperis hyrcana. NJ trees grouped the populations in two different clusters/groups, indicating their genetic difference which is discussed in details. The results of this study showed that the level of genetic variation in Hesperis is relatively high. NJ-based dendrogram showed a close relationship between members of Hesperis straussii and Hesperis hyrcana while the Hesperis luristanica protected population differ the most from the other populations. Principal component analysis, however, showed some minor differences with NJ-based dendrograms.

scholarly journals GENETIC DIVERSITY IN VEGETABLE PEA (Pisum sativum L.)

2013 ◽  
Vol 26 (1) ◽  
pp. 35-40
Author(s):  
M. Rahman ◽  
M. Hasan ◽  
R. N. Chowdhury ◽  
N. A. Ivy ◽  
M. M. Hossain
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Pisum Sativum ◽  
Genetic Divergence ◽  
Principal Component ◽  
Reducing Sugar ◽  
Pisum Sativum L ◽  
Close Relationship ◽  
Cluster Distance ◽  
Minimum Number

An investigation was carried out to identify the extent of genetic divergence of seventeen vegetable pea genotypes at the Bangabandhu Sheikh Mujibur Rahman Agricultural University, Bangladesh. Genetic divergence was estimated using D2 and principal component analysis. The genotypes under study fell into 4 clusters. The distribution pattern indicated that the maximum numbers of genotypes (6) were included in cluster II and cluster III and the minimum number in cluster IV (1). The inter-cluster distance was higher than the intra-cluster distance which indicated wider genetic diversity among the accessions of different groups. The highest inter-cluster distance was observed between II and IV. The lowest inter-cluster distance was observed between clusters II and III suggesting a close relationship among the genotypes of these two clusters. The highest intra-cluster distance was observed for the cluster II. The positive values of vector I and vector II for plant height, 50% flowering and non-reducing sugar indicated that these characters had the highest contribution towards the divergence among the pea genotypes. The genotypes of vegetable pea from cluster II and cluster IV maybe selected as parents in future hybridization program.DOI: http://dx.doi.org/10.3329/bjpbg.v26i1.19982

Review of genetic diversity studies in almond (Prunus dulcis)

2011 ◽  
Vol 59 (4) ◽  
pp. 379-395 ◽  
Author(s):  
B. Szikriszt ◽  
A. Hegedűs ◽  
J. Halász
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Agronomic Traits ◽  
Morphological Characteristics ◽  
Prunus Dulcis ◽  
Detection Methods ◽  
Breeding Programmes ◽  
Great Genetic Diversity ◽  
Recent Occurrence ◽  
Diversity Studies

Almond [Prunus dulcis (Mill.) D.A. Webb.] is cultivated for its nuts and is one of the oldest domesticated plants. Due to the genetically controlled self-incompatibility system that operates in this species, almond is characterized by great genetic diversity, the estimation of which has benefited from a range of marker techniques, including morphological characteristics, isoenzyme detection and molecular markers. Among the DNA-based molecular markers, simple sequence repeats (SSR) have been used most widely, although analyses have ranged from restriction fragment length polymorphism to the most recent single nucleotide polymorphism detection methods. Molecular markers have also been used to trace specific agronomic traits, e.g. self-(in)compatibility or kernel bitterness. Genetic diversity studies in almond have not revealed a direct relationship between the level of diversity and the origin of the germplasm. This might be explained by the relatively recent occurrence of self-compatibility in almond, which has not yet caused a serious loss of genetic diversity. The markers reviewed will be useful in monitoring and maintaining genetic diversity in almond breeding programmes, while others may permit marker-assisted selection for favourable agronomic traits. The cultivation, breeding and conservation of wild-growing almonds may equally benefit from the genetic diversity studies (especially those applying molecular markers).

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 > 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 Local and Exotic Avena sativa L. (Oat) Germplasm Using Multivariate Analysis

Agronomy ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1713
Author(s):  
Mohammad Ihsan ◽  
Nausheen Nazir ◽  
Abdul Ghafoor ◽  
Atif Khalil ◽  
Muhammad Zahoor ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Avena Sativa ◽  
Morphological Characteristics ◽  
Principal Component ◽  
Human Consumption ◽  
Local Conditions ◽  
Yield Production ◽  
Sds Page ◽  
Poaceae Family ◽  
Elite Germplasm

Avena sativa L., also known as Oat belongs to the Poaceae family, is one of the most significant crops that is grown for its seeds, fodder as well as for human consumption as oatmeal. In the current study, 236 genotypes of A. sativa were analysed for genetic diversity through agro-morphological and SDS-PAGE analysis. Cluster analysis based on agro-morphological characteristics grouped all the genotypes into nine clusters, whereas genotype numbers 537 and 728 were highly different from others. The seed yield production of cluster 9 genotypes was the highest per plant (38.2 ± 0.20 g), while cluster 2 genotypes produced maximum biomass per plant (122.5 ± 9.55 g) as compared to other clusters. In a principal component analysis where four variables were studied, and the observed total variations were 57.60%. Among the genotypes, a maximum grain yield of 38.2 g (each) was recorded for genotypes 22,350 and 728, followed by genotypes 737 and 22,390 (with 36.4 g and 35.6 g of seed productions, respectively). The SDS-PAGE analysis resulted in 13 bands and all the genotypes were grouped into seventeen clusters. At the extreme periphery of the dendrogram, genotype 537 and 22,332 were considered to be the most diverse genotypes. Our findings have implications for both understanding the diversity and relationships among these diverse genotypes of A. sativa and will provide a basis for obtaining the elite germplasm optimally adapted to local conditions. The selected genotypes based on agronomic performance may be potential breeding material to raise successful future cultivars.

scholarly journals ISSR Analysis of Genetic Diversity and Structure of Plum Varieties Cultivated in Southern China

Biology ◽  
2018 ◽  
Vol 8 (1) ◽  
pp. 2 ◽  
Author(s):  
Weifeng Wu ◽  
Faxing Chen ◽  
Kaiwun Yeh ◽  
Jianjun Chen
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationship ◽  
Phylogenetic Trees ◽  
Southern China ◽  
Morphological Characteristics ◽  
Relationship Analysis ◽  
Genetic Diversity And Structure ◽  
Plum Varieties ◽  
Index Value

Plums (Prunus spp.) are important deciduous fruit crops in the world. China is a major producer of P. salicina Lindl., but the genetic relationship of Chinese plums in key production regions remain unclear. In this study, 14 University of British Columbia (UBC) inter simple sequence repeats (ISSR) primers were used to analyze 33 plum varieties cultivated in Fujian Province to determine their genetic diversity and population structure. A total of 146 bands were generated, of which 130 were polymorphic. Mean percentage of polymorphic bands was 89.04%, Shannon’s information index value was 0.38, and the Nei’s genetic index value was 0.24. Using unrooted trees (Neighbor-Joining method), 33 varieties were classified into four groups. Split graph separated them into two major groups, each with two subgroups. The two phylogenetic trees indicate that environmental or natural selection pressure is an important factor influencing their genetic relationship. Analysis of population structure revealed that they have frequent genetic exchanges among closed subpopulations; thus, genetic variation mainly occurs within the population. Additionally, based on the phylogenetic analysis and unique morphological characteristics of fruits, we propose that the Chinese landrace Nai could contribute significantly to development of the famous variety Wickson.

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