scholarly journals Morphological and Genetic Diversity Studies of Chrysichthys nigrodigitatus from the Cross River, Nigeria, Using Microsatellite Markers

2020 ◽  
pp. 42-52
Author(s):  
Chioma Adelieje ◽  
Edak Aniedi Uyoh ◽  
Valentine Otang Ntui ◽  
Daniel Ama-Abasi
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Conservation Strategies ◽  
Head Width ◽  
Limited Information ◽  
Term Survival ◽  
Cross River ◽  
Fish Samples ◽  
Diversity Studies ◽  
Two Populations

Morphometric and genetic diversity studies were carried out on Chrysichthys nigrodigitatus sampled from middle and lower Cross River. The aim was to provide information on variations between these two populations and also augment the limited information currently available on genetic diversity in this species. A total of 79 fish samples were used for the morphometric analysis out of which 30 were used for the genetic study. Genomic DNA was extracted from caudal fin using a modified cetyltrimethylammonium bromide method and amplified using microsatellite markers.Twenty-three morphological features were studied from each fish sample out of which 19 showed significant differences (P<0.05) between the two populations. Principal Component Analysis identified head length, head width, caudal peduncle depth, standard length, preventral distance, snout length and anal fin length as key contributors to variation. Genetic analyses indicated low variability in the populations studied as evidenced by low Shannon`s information index (mean of 0.944 – 1.034), and positive coefficients of inbreeding (FIS) across both populations suggesting the presence of greater homozygosity in this species. Gene flow of 3.507 was observed between the lower and middle Cross River indicating the possibility of free mating between the two populations. The low levels of genetic diversity call for urgent management and conservation strategies to ensure long term survival of the species.

scholarly journals Phenotypic Characterisation for Growth and Nut Characteristics Revealed the Extent of Genetic Diversity in Wild Macadamia Germplasm

Agriculture ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 680
Author(s):  
Thuy T. P. Mai ◽  
Craig M. Hardner ◽  
Mobashwer M. Alam ◽  
Robert J. Henry ◽  
Bruce L. Topp
Keyword(s):  
Genetic Diversity ◽  
Growth Traits ◽  
Principal Component ◽  
Conservation Strategies ◽  
Wild Germplasm ◽  
Phenotypic Characterisation ◽  
Wide Range ◽  
Genetic And Environmental Factors ◽  
Positive Correlations ◽  
Wild Accessions

Macadamia is a recently domesticated Australian native nut crop, and a large proportion of its wild germplasm is unexploited. Aiming to explore the existing diversity, 247 wild accessions from four species and inter-specific hybrids were phenotyped. A wide range of variation was found in growth and nut traits. Broad-sense heritability of traits were moderate (0.43–0.64), which suggested that both genetic and environmental factors are equally important for the variability of the traits. Correlations among the growth traits were significantly positive (0.49–0.76). There were significant positive correlations among the nut traits except for kernel recovery. The association between kernel recovery and shell thickness was highly significant and negative. Principal component analysis of the traits separated representative species groups. Accessions from Macadamia integrifolia Maiden and Betche, M. tetraphylla L.A.S. Johnson, and admixtures were clustered into one group and those of M. ternifolia F. Muell were separated into another group. In both M. integrifolia and M. tetraphylla groups, variation within site was greater than across sites, which suggested that the conservation strategies should concentrate on increased sampling within sites to capture wide genetic diversity. This study provides a background on the utilisation of wild germplasm as a genetic resource to be used in breeding programs and the direction for gene pool conservation.

scholarly journals Testing the breeding strategy of Hungarian Bronze turkey strains for maintaining genetic diversity with microsatellites

2011 ◽  
Vol 54 (4) ◽  
pp. 419-429
Author(s):  
S. Kusza ◽  
S. Mihók ◽  
L. Czeglédi ◽  
A. Jávor ◽  
M. Árnyasi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Mating System ◽  
Breeding Strategy ◽  
Shannon Index ◽  
Inbreeding Coefficient ◽  
Control Population ◽  
Conservation Strategies ◽  
The Mean ◽  
Two Populations

Abstract. The aim of the study was to provide information on the genetic variability of the Hungarian Bronze turkey gene reserve population and its difference from the Broad-breasted turkey, and offer guidance and proposals for its future conservation strategies. Altogether, 239 Hungarian Bronze turkeys from 10 strains and 13 Broad-breasted turkeys as a control population were genotyped for 15 microsatellites. All loci were polymorphic with the average number of alleles per locus 3.20±1.146 in the Hungarian Bronze turkey. The mean expected (Hexp) and observed heterozygosity (Hobs) were not different (0.392 and 0.376, respectively) in the overall population, and similar values were obtained for hens and bucks and among hen strains. Inbreeding coefficient (FIS) and Shannon index (I) indicated that there was low inbreeding within hens and bucks. Our results confirm that the genetic diversity in the Hungarian Bronze turkey population has been preserved by the rotational mating system. Differences between the Hungarian Bronze turkey and the Broad-breasted turkey populations were determined. Nei’s unbiased values clearly indicated that the two populations are highly genetically differentiated.

Genetic diversity studies of alfalfa germplasm (Medicago sativa L. subsp. sativa) of United States origin using microsatellite analysis

2017 ◽  
Author(s):  
Shuying Yin ◽  
Yanrong Wang ◽  
Zhibiao Nan
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Polymorphic Information Content ◽  
The United States ◽  
Microsatellite Analysis ◽  
Information Index ◽  
Diversity Studies ◽  
Two Populations

This study aimed to understand the genetic diversity and population structure of alfalfa germplasm from the United States. In this study, the population structure and genetic diversity of six alfalfa cultivars of United States origin were investigated by microsatellite analysis with 40 individuals per cultivar. A total of 312 discernible alleles were amplified from the whole genome with an average of 31.2 alleles per locus. The average values of polymorphic information content and Shannon’s information index were 0.928 and 0.133, respectively, showing high levels of genetic diversity. Two populations were identified by STRUCTURE software with principal coordinate analysis and neighbour-joining clustering. Analysis of molecular variance analysis (AMOVA) revealed that the majority of genetic variation was within cultivars (96.42%) rather than between cultivars (3.58%). In conclusion, analyses of genetic diversity and population structure may be useful for the genetic analysis and utilization of genetic variation in alfalfa breeding.

Genetic variation in two Chamaecrista species (Leguminosae), one endangered and narrowly distributed and another widespread in the Serra do Espinhaço, Brazil

2007 ◽  
Vol 85 (7) ◽  
pp. 629-636 ◽  
Author(s):  
Reinaldo Moreira da Silva ◽  
G. Wilson Fernandes ◽  
Maria Bernadete Lovato
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Habitat Destruction ◽  
Conservation Strategies ◽  
Lower Percentage ◽  
Endemic Plant ◽  
Endemic Plant Species ◽  
Two Populations ◽  
Shannon’S Diversity Index

The Serra do Espinhaço in Brazil is under continuous and increasing levels of human disturbance. It has a large number of endemic plant species such as Chamaecrista semaphora (Irwin and Barneby), an endangered species with extremely narrow range. We studied the genetic diversity of C. semaphora and compared it with Chamaecrista mucronata (Spreng.) Irwin and Barneby, a widespread congeneric species distributed over the entire Serra do Espinhaço, in an attempt to provide information for conservation strategies. Two populations of C. mucronata and the only two known populations of C. semaphora from Serra do Cipó were screened for variability using random amplified polymorphic DNA (RAPD) markers. Populations of C. semaphora exhibited a lower percentage of polymorphic markers (16.9%) and Shannon’s Diversity Index (H′pop = 0.124) than C. mucronata populations (43.3% and H′pop = 0.299). Most of the genetic variability of both species studied was distributed within populations; C. semaphora populations (ΦST = 0.198) were less divergent than C. mucronata populations (ΦST = 0.378). The risk of extinction for C. semaphora is large owing to its low level of genetic diversity compared with its widespread congener and because of increasing habitat destruction. Both populations of C. semaphora urgently need protection to maximize the genetic diversity of this species and diminish further substantial loss within the populations.

Quantification of morphological variations among populations of Channa gachua (Hamilton, 1822) from different geographical locations in India

2020 ◽  
Vol 67 (2) ◽  
Author(s):  
Ravi Kumar ◽  
A. K. Jaiswar ◽  
Rama Sharma ◽  
Laxmi Prasad
Keyword(s):  
Eastern Himalaya ◽  
Head Width ◽  
Classification Rate ◽  
Gangetic Plains ◽  
Linear Discriminant ◽  
Morphological Variations ◽  
Significant Difference ◽  
Fish Samples ◽  
Two Populations ◽  
Geographical Locations

Morphological variations among distinctly distributed populations of Channa gachua (Hamilton, 1822) from three different geographical locations in India, viz., Gangetic Plains (GP), Western Hills and Plateau (WHP) and Eastern Himalaya (EH), were studied based on 200 specimens collected from these regions. The average total length of C. gachua was recorded as 128.5±4.0 mm, 126.3±5.5 mm and 123.1±6.9 mm from GP, WHP and EH, respectively. The analysis revealed variations in sixteen morphometric variables out of twenty measured variables among the GP and other two populations (p<0.05), except eye diameter, head width, anal fin base length and caudal fin length. However, WHP and EH populations did not show any significant difference among the measured characters. Principal component analysis (PCA) indicated that first three PCs explained 90.12% of the total variance. Linear discriminant analysis (LDA) revealed that 108 out of 200 fish samples (54.0%) were correctly classified to the actual sampling locations whereas remaining samples (46.0%) showed overlapping spatial distribution. The corrected classification rate of each population ranged from 24 to 67%. It is concluded that despite morphometric variability in head and jaws, features among GP and other two populations studied, the three must still be considered to be of the same species. The study indicates the existence of two distinct stocks of C. gachua; - one in the Gangetic Plains and another in Western Hills and Plateau and Eastern Himalayan regions.

scholarly journals Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli (Brassica oleracea L. var. italica) in China

2021 ◽  
Vol 12 ◽  
Author(s):  
Yusen Shen ◽  
Jiansheng Wang ◽  
Ranjan K. Shaw ◽  
Huifang Yu ◽  
Xiaoguang Sheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Brassica Oleracea ◽  
Structure Analysis ◽  
Genetic Relatedness ◽  
Gene Diversity ◽  
Principal Component ◽  
Resolving Power ◽  
Limited Information ◽  
Large Collection

Broccoli (Brassica oleracea var. italica) is one of the most important and nutritious vegetables widely cultivated in China. In the recent four decades, several improved varieties were bred and developed by Chinese breeders. However, the efforts for improvement of broccoli are hindered by limited information of genetic diversity and genetic relatedness contained within the available germplasms. This study evaluated the genetic diversity, genetic relationship, population structure, and fingerprinting of 372 accessions of broccoli representing most of the variability of broccoli in China. Millions of SNPs were identified by whole-genome sequencing of 23 representative broccoli genotypes. Through several stringent selection criteria, a total of 1,167 SNPs were selected to characterize genetic diversity and population structure. Of these markers, 1,067 SNPs were genotyped by target sequencing (GBTS), and 100 SNPs were genotyped by kompetitive allele specific PCR (KASP) assay. The average polymorphism information content (PIC) and expected heterozygosity (gene diversity) values were 0.33 and 0.42, respectively. Diversity analysis revealed the prevalence of low to moderate genetic diversity in the broccoli accessions indicating a narrow genetic base. Phylogenetic and principal component analyses revealed that the 372 accessions could be clustered into two main groups but with weak groupings. STRUCTURE analysis also suggested the presence of two subpopulations with weak genetic structure. Analysis of molecular variance (AMOVA) identified 13% variance among populations and 87% within populations revealing very low population differentiation, which could be attributed to massive gene flow and the reproductive biology of the crop. Based on high resolving power, a set of 28 KASP markers was chosen for DNA fingerprinting of the broccoli accessions for seed authentication and varietal identification. To the best of our knowledge, this is the first comprehensive study to measure diversity and population structure of a large collection of broccoli in China and also the first application of GBTS and KASP techniques in genetic characterization of broccoli. This work broadens the understanding of diversity, phylogeny, and population structure of a large collection of broccoli, which may enhance future breeding efforts to achieve higher productivity.

scholarly journals Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers

2022 ◽  
Vol 25 (8) ◽  
pp. 831-838
Author(s):  
R. B. Aitnazarov ◽  
T. M. Mishakova ◽  
N. S. Yudin
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Population Distribution ◽  
Cattle Breed ◽  
Principal Component ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
Novosibirsk Region ◽  
Breed Improvement ◽  
Two Populations

There are currently over a thousand indigenous cattle breeds well adapted to local habitat conditions thanks to their long history of evolution and breeding. Identification of the genetic variations controlling the adaptation of local cattle breeds for their further introduction into the genome of highly productive global breeds is a matter of great relevance. Studying individual populations of the same breed with the use of microsatellite markers makes it possible to assess their genetic diversity, relationships, and breed improvement potential. Although the Black Pied breed is the most common dairy cattle breed in Russia, there are only a few studies on genetic diversity in local Black Pied populations in some Russian regions. The goal of the present study was to analyze the genetic diversity in Black Pied cattle populations in the Novosibirsk Region and compare them with other Russian populations; to identify significantly divergent populations with a view to preserving them under the programs aimed at maintaining the genetic diversity of the domestic Black Pied breed. DNA samples from 4788 animals of the Black Pied breed from six breeding enterprises in the Novosibirsk Region have been studied using 11 microsatellite markers. No significant differences in genetic variability parameters were found between individual populations. Private alleles have been identified in five out of six populations. Five populations have shown inbreeding coefficient values (FIS) below zero, which indicates heterozygosity excess. The population distribution test, principal component analysis, FST and DEST values, cluster analysis, and phylogenetic analysis have revealed two populations genetically distinct from the others. Essentially, the genetic diversity parameters of the six studied Black Pied cattle populations from the Novosibirsk Region show no significant differences from other Russian populations of the breed. Excess heterozygosity is observed in most breeding enterprises, which is a sign of a low inbreeding rate. To maintain the genetic diversity of the Russian Black Pied cattle, we recommend focusing on the two populations with significant genetic distinctions from the others.

scholarly journals Morphological Characterization of Wild and Cultured Clarias gariepinus (Burchell 1822) using Principal Component and Cluster Analyses

2016 ◽  
Vol 8 (4) ◽  
pp. 428-436 ◽  
Author(s):  
Folasade A. OLA-OLADIMEJI ◽  
Michael O. AWODIRAN ◽  
Omotayo FAGBUARO ◽  
Adetola O. AKOMOLAFE
Keyword(s):  
Phenotypic Diversity ◽  
Clarias Gariepinus ◽  
Principal Component ◽  
Morphological Characterization ◽  
Meristic Characters ◽  
Cluster Analyses ◽  
Fish Samples ◽  
In The Wild ◽  
Student’S T ◽  
Two Populations

The study was designed to describe the phenotypic variations in morphometric and meristic characters of Clarias gariepinus between two populations in different towns in Ekiti State, Nigeria. Fish samples were collected from Ero dam (wild population at Ikun Ekiti) and Christeve Aquaculture (cultured population at Iyin Ekiti) using cast net and dragging net. The samples were brought to Zoology Laboratory in Ekiti State University and measurements for morphometrics (24) and meristics (11) of each of the investigated catfish specimen were taken using standard procedures. To test the significance of morphological differences between the wild and cultured populations, all the data on morphometrics and meristics were subjected to student's t-test at 5% level of significance. Principal Component Analyses and cluster analyses were then employed to analyse the data obtained from the morphological traits using Paleontological Statistics (PAST) software. Significant differences were observed in the means of the morphometric and meristic traits. The multivariate analysis also showed differences between the studied populations.  These differences revealed the occurrence of heterogeneity between the two populations. Higher variations and sex related variations were also observed in the wild than in cultured population. The result show the potential for commercial purposes of the population. However, genetic markers can be used in further studies to confirm the phenotypic diversity observed and assess the amount of variation in these populations. 

scholarly journals Comparison of projection of distance techniques for genetic diversity studies

2019 ◽  
Vol 42 ◽  
pp. e42483
Author(s):  
Isabela de Castro Sant'Anna ◽  
Gabi Nunes Silva ◽  
Vinicius Quintão Carneiro ◽  
Daiana Salles Pontes ◽  
Moyses Nascimento ◽  
...  
Keyword(s):  
Experimental Data ◽  
Genetic Diversity ◽  
Three Dimensional ◽  
Principal Component ◽  
Dispersion Analysis ◽  
Principal Coordinate Analysis ◽  
Projection Technique ◽  
Analysis Techniques ◽  
The Mean ◽  
Diversity Studies

The objective of this study was to compare different graphical dispersion analysis techniques in two- or three-dimensional planes. In this study, the data from different published works were used in order to determine the best methodology for analyzing the genetic diversity of different species. In this study, efficiency is measured by the amount of original distance absorbed by the projection of distances technique, which in the case of major components is equal to the amount of total variation originally available and retained by the principal components used for dispersion purposes. The projection of dissimilarity measurement technique, principal component analysis (PCA), and principal coordinate analysis (PCoA) were used. Considering the analysis by means of three orthogonal axes, the graphical dispersion efficiency was 82.22 for PCA, 87.22 for PCoA, and 85.25 for the projection of distances technique. For the 2D analysis, considering the two main axes, the mean dispersion efficiency was 69.90 for the PCA, 75.06 for the projection technique, and 78.16 for PCoA. Considering the studies carried out with experimental data of six different species, it is concluded that the principal coordinate analysis is superior.

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