scholarly journals Molecular Genetic Variability of Spigelia marilandica and S. gentianoides

2015 ◽  
Vol 140 (2) ◽  
pp. 120-128
Author(s):  
Amanda J. Hershberger ◽  
Tracie M. Jenkins ◽  
Carol Robacker
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Gene Diversity ◽  
Molecular Genetic ◽  
Genetic Distances ◽  
Population Variation ◽  
Group Method ◽  
Polymorphism Analysis ◽  
Two Samples

Despite the ecologic and ornamental potential of southeastern U.S. native Spigelia, little is known about the intraspecific or the interpopulation genetic variation. The southeastern U.S. native Spigelia habitat is becoming more and more fragmented as a result of human activity, making it imperative to gain an understanding of natural genetic variation among and within species and populations for the purpose of obtaining variability for plant breeding and preserve the genetic variability in Spigelia. Therefore, the objective of this study was to use amplified fragment length polymorphism analysis to determine interspecific and intraspecific genetic variation and to evaluate gene flow. Thirteen populations of two species of native Spigelia, S. marilandica (SM), S. gentianoides var. gentianoides (SGG), and S. gentianoides var. alabamensis (SGA), were analyzed using four primer pairs that amplified a total of 269 bands. Based on analysis of molecular variance and estimates of Nei’s coefficients of gene diversity (percentage of polymorphic loci, average genetic diversity within populations, average genetic diversity within species, and proportion of species genetic diversity attributed to among population variation), the majority of variation found in Spigelia occurs within populations. Both among-species and among-population variation was low, likely the effect of common ancestry as well as relatively frequent introgression among individuals (and populations) of Spigelia. When all individuals were evaluated using Nei’s unbiased genetic distances and viewed as a unweighted pair group method with arithmetic mean phenogram, three main groups were shown, one with two samples of SGG from one population, one with 13 individuals from both SGG populations used in this study, and one with all of the SM, SGA, and remaining SGG individuals. Further evaluation using STRUCTURE software showed introgression between populations and species, although all allele clusters have not entirely introgressed into all populations. The significance of these results is discussed in relation to breeding in Spigelia.

scholarly journals Genetic Diversity of Seven Deciduous Azalea Species (Rhododendron spp. section Pentanthera) Native to the Eastern United States

2008 ◽  
Vol 133 (3) ◽  
pp. 374-382 ◽  
Author(s):  
Matthew Chappell ◽  
Carol Robacker ◽  
Tracie M. Jenkins
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Diversity ◽  
Interspecific Variation ◽  
Genetic Distances ◽  
Anthropogenic Activity ◽  
Group Method ◽  
Aflp Analysis ◽  
Eastern United States

Despite the ecologic and economic importance of native deciduous azaleas (Rhododendron L. section Pentanthera G. Don), our understanding of interspecific variation of North American deciduous azalea species comes principally from morphologic studies. Furthermore, little is known concerning intraspecific or interpopulation genetic variation. With ever-increasing loss and fragmentation of native azalea habitat in the eastern United States due to anthropogenic activity, it is imperative that an understanding of natural genetic variation among and within species and populations is acquired. The present study addresses questions of genetic diversity through the use of amplified fragment length polymorphism (AFLP) analysis. Twenty-five populations of seven species of native azalea were analyzed using three primer pairs that amplified a total of 417 bands. Based on analysis of molecular variance (AMOVA) and estimates of Nei's coefficients of gene diversity (H S, H T, and G ST), the majority of variation found in deciduous azalea occurs within populations. Variation both among species and among population was low, likely the effect of common ancestry as well as frequent introgression among members (and populations) of section Pentanthera. The latter was evident in four populations of R. prunifolium (Small) Millais and R. canescens (Michaux) Sweet that were highly related to R. austrinum (Small) Rehder and R. viscosum (L.) Torrey, respectively. Despite these outliers, most populations were grouped into species based on Nei's unbiased genetic distances viewed as an unweighted pair group method with arithmetic mean (UPGMA) phenogram. The significance of these results is discussed in relation to breeding in section Pentanthera.

Genetic Variation in Invasive Populations of Yellow Toadflax (Linaria vulgaris) in the Western United States

Weed Science ◽  
2008 ◽  
Vol 56 (3) ◽  
pp. 394-399 ◽  
Author(s):  
Sarah M. Ward ◽  
Scott D. Reid ◽  
Judy Harrington ◽  
Jason Sutton ◽  
K George Beck
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Recombination ◽  
Diversity Index ◽  
Gene Diversity ◽  
Group Method ◽  
Restricted Gene Flow ◽  
Genetic Structuring ◽  
Invasive Weed ◽  
Yellow Toadflax

Intraspecific genetic variation may contribute significantly to invasiveness and control problems, but has been characterized to date in relatively few invasive weed species. We examined 56 intersimple sequence repeat (ISSR) loci in 220 individuals from 11 invading populations of yellow toadflax sampled across five western states. All populations showed high levels of genetic diversity. Estimated values for Shannon's diversity measure ranged from 0.217 to 0.388, and for expected heterozygosity from 0.178 to 0.260. Nei's total gene diversity index (HT), on the basis of all individuals across all populations, was 0.267. Partitioning of genetic variance using analysis of molecular variance revealed 1.7% of genetic variation among regional population groups, 29.1% among populations within groups, and 69.2% within populations, consistent with expectations for an outcrossing species but suggesting little geographic differentiation. Pairs of adjacent individuals identical at all ISSR loci that appeared to be ramets of a single clone were detected in only one population. This indicates that patch expansion in yellow toadflax is driven more by sexual reproduction via seed than by rhizomatous clonal spread, at least at the spatial scale of sampling for this study. Eight populations had significant values for Mantel's R at P = 0.05, suggesting some fine-scale positive genetic structuring, possibly from restricted gene flow. Population clustering on the basis of Nei's genetic distance between populations and unweighted pair group method with arithmetic mean did not reflect geographic location. It is likely that multiple introductions of this species have occurred across the Intermountain West, followed by extensive genetic recombination. High levels of genetic diversity within yellow toadflax populations pose management challenges, as already seen in reports of variable response to herbicide application and limited impacts of biocontrol agent releases.

scholarly journals Genetic Diversity and Variability in Endangered Pantesco and Two Other Sicilian Donkey Breeds Assessed by Microsatellite Markers

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Salvatore Bordonaro ◽  
Anna Maria Guastella ◽  
Andrea Criscione ◽  
Antonio Zuccaro ◽  
Donata Marletta
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Genetic Information ◽  
Gene Diversity ◽  
Genetic Distances ◽  
Conservation Strategies ◽  
Population Structure Analysis ◽  
The Mean ◽  
Differentiation Index

The genetic variability of Pantesco and other two Sicilian autochthonous donkey breeds (Ragusano and Grigio Siciliano) was assessed using a set of 14 microsatellites. The main goals were to describe the current differentiation among the breeds and to provide genetic information useful to safeguard the Pantesco breed as well as to manage Ragusano and Grigio Siciliano. In the whole sample, that included 108 donkeys representative of the three populations, a total of 85 alleles were detected. The mean number of alleles was lower in Pantesco (3.7), than in Grigio Siciliano and Ragusano (4.4 and 5.9, resp.). The three breeds showed a quite low level of gene diversity (He) ranging from 0.471 in Pantesco to 0.589 in Grigio. The overall genetic differentiation index (Fst) was quite high; more than 10% of the diversity was found among breeds. Reynolds’ () genetic distances, correspondence, and population structure analysis reproduced the same picture, revealing that, (a) Pantesco breed is the most differentiated in the context of the Sicilian indigenous breeds, (b) within Ragusano breed, two well-defined subgroups were observed. This information is worth of further investigation in order to provide suitable data for conservation strategies.

RAPD analysis on genetic diversity of typical tea populations in Hunan Province

2008 ◽  
Vol 5 (1) ◽  
pp. 67-72
Author(s):  
Shen Cheng-Wen ◽  
Huang Yi-Huan ◽  
Huang Jian-An ◽  
Luo Jun-Wu ◽  
Liu Chun-Lin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Genetic ◽  
Diversity Index ◽  
Gene Diversity ◽  
Population Variation ◽  
Hunan Province ◽  
Rapid Amplification ◽  
Population Genetic Variation ◽  
Shannon’S Diversity Index

AbstractGenetic diversity and genetic variation of 240 adult plants of four tea populations in Hunan – Camellia sinensis var. sinensis, C. sinensis var. assamica cv. Duntsa, C. ptilophylla and C. sinensis var. assamica cv. Jianghua – were studied by rapid amplification of polymorphic DNA (RAPD) markers. The results showed 226 loci using 21 random primers (10 bp), of which 201 (88.9%) were polymorphic. The genetic diversity analysis indicated that Shannon's index was 0.43; 74.7% of which was within-population genetic diversity while 25.3% was among-population variation. The gene diversity indexes of total populations (HT), within populations (HS) and among populations (HST) were, respectively, 0.37, 0.28 and 0.09. The coefficient of gene differentiation (GST) among populations was 0.23, indicating a 76.7% variation within populations and 23.3% among populations. These results displayed a rich within-population genetic variation, as in Shannon's diversity index. Interpopulation gene flow (Nm) was 0.74, which indicates the limited genetic exchange between populations.

scholarly journals Genetic Variability Assay of Different Natural and Hatchery Populations of Rohu (Labeo rohita) in Bangladesh

2015 ◽  
Vol 9 (1) ◽  
pp. 30-36
Author(s):  
Shikder Saiful Islam ◽  
Md. Saifuddin Shah ◽  
Foyez Ibn Shams ◽  
Md. Rayhan Ali ◽  
Md. Lifat Rahi
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Labeo Rohita ◽  
Genetic Distances ◽  
Raw Material ◽  
Group Method ◽  
Pair Group ◽  
Fish Samples ◽  
Population Genetic Variation ◽  
High Level

The level of genetic variation determines the genetic status and provides the raw material for selective improvement of a stock. Randomly amplified polymorphic DNA (RAPD) technique was used to assess the genetic variability of 7 different natural (2) and hatchery (5) populations of Indian Major Carp, Labeo rohita (Rohu) in Bangladsh. In total, 140 fish samples were collected (20 from each of the populations). Genomic DNA was extracted from the muscle tissue, and 5 different oligonucleotide primers were used which revealed 80% polymorphic DNA bands. The polymorphic loci proportions were 0.71, 0.75, 0.75, 0.85, 0.84, 0.86 and 0.89 for Ma-Fatema hatchery, Chowdhuri hatchery, Niribili hatchery, Sonali hatchery, Kapotakha hatchery, the Halda river and the Baluhor Baor populations respectively. The pair-wise population differentiation (FST) values indicated a high level of genetic variation between different populations. The Unweighted Pair Group Method of Arithmetic Mean (UPGMA) dendogram based on Nei’s genetic distances also revealed high level of inter-population genetic variation among the populations. The populations were segregated into two groups: the Halda River and Baluhar Baor hatchery in one group and Kapotakha, Ma-Fatema, Chowdhuri, Niribili and Sonali hatcheries in another group. Overall, RAPD results clearly indicate the reduced genetic quality of the hatchery seeds.DOI: http://dx.doi.org/10.3126/ijls.v9i1.11923 International Journal of Life Sciences Vol.9(1) 2015 30-36

scholarly journals Genetic diversity analysis of tropical sugar beet (Beta vulgaris L.) varieties in Bangladesh using RAPD markers

Genetika ◽  
2016 ◽  
Vol 48 (1) ◽  
pp. 151-164
Author(s):  
Saidin Saclain ◽  
Abdul Latif ◽  
Babul Bala ◽  
Mithun Mallik ◽  
Shahidul Islam
Keyword(s):  
Genetic Variation ◽  
Sugar Beet ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Similarity Index ◽  
Genetic Distances ◽  
Group Method ◽  
Pair Group ◽  
Major Cluster

Knowledge on intra-specific genetic variation of an organism is important for its genetic improvement and conservation. In order to estimate genetic variation and relatedness in eleven tropical Sugar beet varieties we used randomly amplified polymorphic DNA (RAPD) markers. The RAPD analysis was performed using six decamer random primers, which amplified a total of 63 DNA fragments of which 43 (68.25%) were found polymorphic. The average polymorphic bands per primer was 7.17 and the overall gene diversity was 0.24. Among the 43 polymorphic loci studied, 2 were specific for 2K 310, 1 for Shubraha, 1 for Natura and 1 for HI-0473 varieties. Pair wise genetic distance and similarity indices were ranged from 0.12-0.51 and 66.73-92.91, respectively. Cauvery and 2K 310 were found to be the most distantly related with a higher genetic distance value (GD = 0.51) and lower similarity index (SI = 66.73), while Aranka and Serenada were the most closely related with their lower GD (0.12) and higher SI(92.91) values. In an unweighted pair group method of arithmetic mean dendrogram constructed on the basis of genetic distances, the eleven varieties grouped into two main clusters: 2K 310 alone was in one cluster whereas 10 other varieties grouped into a major cluster. This indicates that 2K 310 was distantly related with each of the other varieties. Distantly related varieties based on estimated genetic variation could be selected for future breeding program that could result in improvement of this crop.

scholarly journals Genetic Diversity and Population Structure of Dendrobium Nobile in Southwest of China Based On Genotyping-by-Sequencing

2021 ◽  
Author(s):  
Tao He ◽  
Changrong Ye ◽  
Qin Zeng ◽  
Xiaoli Fan ◽  
Tianfang Huang
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Population Variation ◽  
Quality Data ◽  
Group Method ◽  
Dendrobium Nobile ◽  
Group Iii ◽  
Group I ◽  
Quality Value

Abstract Dendrobium nobile Lindl. is one of the most important Orchid plants worldwide. The genotype-by-sequencing (GBS) method has now been widely used to access genetic diversity because of its high-throughput and cost-effective in molecular markers. The goal of this study was to employ the GBS technique for diversity evaluation of D. nobile and determine genetic differences between populations. A total of 129 accessions of D. nobile collected originally between 2019 and 2020 from 10 imitation-wild cultivated populations growing in Sichuan, Guizhou and Yunnan of southwestern China were sequenced, a total of 135G clean reads and a total of 836,786 SNPs of high quality data was yielded and were used for final analysis of genetic diversity and population structure. The quality value 20(Q20) ≥ 92.61%, the quality value 30(Q30) ≥ 82.38%. The GC contents distributed between 37.58% and 38.82%. It was also found that more transitions than transversions, and the ratio of transition/transversion varied from 1.804 to 1.911. By the methods of STRUCTURE, the most appropriate number was found to be k=3, all accessions of D. nobile were classified into three groups, excepts for 14 accessions belonging to admixed group. Phylogenetic tree and principal component analysis (PCA) were consistent with the result. The first two principal components explained a total of 23.25% of the variation by PCA. The genetic diversity of ML population showed the lower genetic diversity as indicated by the effective number of alleles (Ne) = 1.287, polymorphism information content (PIC) = 0.141, and Shannon's information index (I) = 0.205, while WT population showed slightly higher genetic diversity by the Ne =1.512, PIC =0.256, and I =0.360. ML population and other nine populations (FB, FM, FX, LJ, SJ, SP, WL, WT and XM) were the most divergent between them respectively owing to all pairwise Fst values above 0.25, while FM population and FX population were considered identical because the pairwise Fst value was 0.0 between the two populations. Correlation analysis showed that highly significant correlation was observed between genetic distance and actual geographical distance (r = 0.854, P < 0.0001), indicating that the genetic differentiation of the 10 D.nobile populations conformed to the geographical isolation model. Analysis of molecular variance (AMOVA) revealed that the genetic variation was greater within populations (87.8%) than among populations (12.2%). This confirmed that intra-population variation was the main source of genetic variation in 10 D. nobile populations. The results also showed that Nm = 1.799 > 1, indicating that there was gene exchange between different populations. Analysis of unweighted pair-group method with arithmetic mean (UPGMA) suggested that the 10 populations were classified into three groups (Group I, Group II and Group III), Group III could be further divided into two subgroups (Group IIIa and Group IIIb). The results will not only provide valuable information for the level of genetic diversity of D.nobile growing in southwestern of China but also help for formulation of strategies for resource protection and utilization. Moreover, GBS appears as an efficient tool to detect intra-population variation.

scholarly journals Genetic Diversity and Relationships of Terebinth (Pistacia terebinthus L.) Genotypes Growing Wild in Turkey

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 671
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
Sezai Ercisli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
In Silico ◽  
Germplasm Collection ◽  
Genetic Distances ◽  
Group Method ◽  
Arithmetic Average ◽  
Principal Coordinates ◽  
Two Samples ◽  
Pistacia Terebinthus

Genetic diversity and relationships of 54 wild-grown terebinths (Pistacia terebinthus L.) were determined using 40 SSR (simple sequence repeat) markers (38 in silico polymorphic SSR markers and 2 SSR markers). In silico polymorphic SSR analysis, 430 alleles were identified. The number of alleles per locus ranged from 3 to 25 with a mean value of 11 alleles per locus. The values of polymorphism information content (PIC) ranged from 0.34 (CUPOhBa4344) to 0.91 (CUPSiBa4072) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), the Structure, and Principal Coordinates (PCoA) based clustering. The structure analysis and UPGMA clustering of the genotypes depicted two major clusters. PCoA results supported cluster analysis results. The dendrogram revealed two major clusters. Forty-two samples were obtained from the Kazankaya canyon and 12 samples from the Karanlıkdere region. The two regions are 130 km apart from each other but in a dendrogram, we did not find geographical isolation. The results proved the efficiency of SSRs for genetic diversity analysis in the terebinth. Based on the results, SSRs can be applied as a trustworthy tool for the evaluation of genetic diversity in terebinth genotypes. Molecular analysis on the terebinth genotypes in this study will promote the germplasm collection and the selection of the populations in future studies on terebinths for genetic mapping, genetic diversity, germplasm characterization, and rootstock breeding.

scholarly journals Genetic diversity and relatedness within and between species of the genus Oligoryzomys (Rodentia; Sigmodontinae)

2007 ◽  
Vol 67 (1) ◽  
pp. 153-160 ◽  
Author(s):  
A. Trott ◽  
SM. Callegari-Jacques ◽  
LFB. Oliveira ◽  
A. Langguth ◽  
MS. Mattevi
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Genetic Heterogeneity ◽  
Rain Forest ◽  
Rapd Analysis ◽  
Genetic Distances ◽  
Wide Area ◽  
Atlantic Rain Forest

A RAPD analysis on six species of the rodent genus Oligoryzomys trapped in a wide area (ranging from 01° N to 32° S) of Brazilian territory was performed in order to determine the levels of genetic variability within and between its populations and species. One-hundred and ninety-three animals were collected in 13 different sites (corresponding to 17 samples) located at Pampas, Atlantic Rain Forest, Cerrado, and Amazon domains. Oligoryzomys sp., O. nigripes (8 populations), O. flavescens (4 populations), O. moojeni, O. stramineus, and O. fornesi were the taxa analyzed. Of the 20 primers tested, 4 generated a total of 75 polymorphic products simultaneously amplified in 151 specimens. Various diversity estimators analyzed showed considerable differences between species and populations, indicating a great genetic variation occurring in the Oligoryzomys taxa investigated. A cluster analysis was made using Nei's standard genetic distances, however, it did not correlate the genetic heterogeneity of the species and populations with the geographical areas.

scholarly journals Estimation of Genetic Diversity among Canola Accessions using Simple Sequence Repeat Markers

2021 ◽  
Vol 8 (4) ◽  
pp. 86-94
Author(s):  
Jaleel Ahmad ◽  
Muhammad Baber ◽  
Wajid Nazeer ◽  
Sana Hamdullah ◽  
Aleena Ahmad Somroo
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Molecular Genetic ◽  
Genetic Distances ◽  
Genetic Studies ◽  
Molecular Genetic Basis ◽  
Ssr Primers ◽  
Minimum Genetic Distance ◽  
Simple Sequence

Genetic studies through molecular markers proved important to find out the genetic diversity of canola. In this study, 50 lines of canola were used to find the polymorphism using 15 SSR primers and investigated the genetic diversity, PIC values, frequency-based genetic distance, and allelic frequencies. Mean gene diversity, frequency-based genetic distance, and PIC values were 0.8777, 0.233 and 0.8666, respectively for the canola lines. A good range of genetic diversity was found among studied canola lines with value 85.91% polymorphism. Maximum and minimum genetic distances among 50 lines were 1 and 0.26, respectively. Accessions ACC-26068, ACC-24241, ACC-24244, ACC-24233, ACC-24423 and ACC-24224 have maximum genetic distance. Accessions ACC-24879 and ACC-24169 had minimum genetic distance i.e., 0.26. Dendrogram based on genetic distances showed four main clusters that were further dividing into several sub-clusters. The primers utilized in the present study, were valuable to identify different accessions of canola to find the variability present. This variability will be helpful to initiate the breeding program with their molecular genetic basis.

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