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

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

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Genetic Variability of Rotylenchulus reniformis

Plant Disease ◽

10.1094/pdis-02-11-0132 ◽

2012 ◽

Vol 96 (1) ◽

pp. 30-36 ◽

Cited By ~ 13

Author(s):

Megan Leach ◽

Paula Agudelo ◽

Amy Lawton-Rauh

Keyword(s):

United States ◽

Genetic Variation ◽

Southeastern United States ◽

Genetic Connectivity ◽

Group Method ◽

Reniform Nematode ◽

Rotylenchulus Reniformis ◽

Pair Group ◽

High Level ◽

The Impact

Rotylenchulus reniformis, reniform nematode, is a polyphagous pest commonly found parasitizing cotton in the southeastern United States. We developed and optimized 10 polymorphic microsatellite loci found in reniform nematode and tested them on 160 individual reniform nematodes to determine informative genetic variation of isolates from the southeastern United States, Colombia, Japan, and from the species Rotylenchulus parvus. No significant gametic disequilibrium was detected between any pair of loci, and most loci were not in expected Hardy-Weinberg proportions. A positive FIS coefficient was observed at all 10 loci, suggesting a high level of inbreeding at these loci. Most isolate locations exhibited significant genotypic differentiation and moderate to very high genetic differentiation based on FST analysis. The most consistently differentiated isolates were found reproducing parthenogenetically in Japan. These isolates were also found to represent the most basal locality in this study based on unweighted pair group method with arithmetic mean (UPGMA) clustering analysis and were distinct from other localities based on STRUCTURE V 2.3 analysis. These results support previous reports suggesting that the parthenogenetically reproducing isolates from Japan are another species. Taken together, our results can serve as the foundation for more extensive characterization of population structure and genetic variation among isolates of R. reniformis variants to help discern the impact of alternative processes on genetic connectivity and differentiation in the genetically undercharacterized reniform nematode.

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Genetic Diversity and Population Structure of Alnus cremastogyne as Revealed by Microsatellite Markers

Forests ◽

10.3390/f10030278 ◽

2019 ◽

Vol 10 (3) ◽

pp. 278 ◽

Cited By ~ 2

Author(s):

Hong-Ying Guo ◽

Ze-Liang Wang ◽

Zhen Huang ◽

Zhi Chen ◽

Han-Bo Yang ◽

...

Keyword(s):

Genetic Diversity ◽

Geographical Distribution ◽

Mantel Test ◽

Group Method ◽

Arithmetic Means ◽

Mountain Area ◽

Pair Group ◽

Hill Area ◽

Population Genetic Variation ◽

High Level

Alnus cremastogyne Burk. is a nonleguminous, nitrogen-fixing tree species. It is also the most important endemic species of Alnus Mill. in China, possessing important ecological functions. This study investigated population genetic variation in A. cremastogyne using 175 trees sampled from 14 populations native to Sichuan Province with 25 simple sequence repeat (SSR) markers. Our analysis showed that A. cremastogyne has an average of 5.83 alleles, 3.37 effective alleles, an expected heterozygosity of 0.63, and an observed heterozygosity of 0.739, indicating a relatively high level of genetic diversity. The A. cremastogyne populations in Liangshan Prefecture (Meigu, Mianning) showed the highest level of genetic diversity, whereas the Yanting population had the lowest. Our analysis also showed that the average genetic differentiation of 14 A. cremastogyne populations was 0.021. Analysis of molecular variance (AMOVA) revealed that 97% of the variation existed within populations; only 3% was among populations. Unweighted pair-group method with arithmetic means (UPGMA) clustering and genetic structure analysis showed that the 14 A. cremastogyne populations could be clearly divided into three clusters: Liangshan Prefecture population, Ganzi Prefecture population, the other population in the mountain area around the Sichuan Basin and central Sichuan hill area, indicating some geographical distribution. Further analysis using the Mantel test showed that this geographical distribution was significantly correlated with elevation.

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

Genetika ◽

10.2298/gensr1601151s ◽

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.

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Genetic variation and relationship among and within Withania species as revealed by AFLP markers

Genome ◽

10.1139/g00-073 ◽

2000 ◽

Vol 43 (6) ◽

pp. 975-980 ◽

Cited By ~ 7

Author(s):

M S Negi ◽

A Singh ◽

M Lakshmikumaran

Keyword(s):

Genetic Variation ◽

Medicinal Plant ◽

Genetic Relationships ◽

Similarity Coefficient ◽

Aflp Markers ◽

Group Method ◽

Intermediate Type ◽

Aflp Data ◽

Pair Group ◽

High Level

Withania somnifera is an important medicinal plant, and its anticancerous properties have been attributed to various classes of withanolide compounds. The objective of the present study was to investigate the inter- and intraspecific genetic variation present in 35 individuals of W. somnifera and 5 individuals of W. coagulans using AFLP (amplified fragment length polymorphism) marker technique. The information about genetic variation determined from AFLP data for 40 individuals was employed to estimate similarity matrix value based on Jaccard's coefficient. The similarity values were further used to construct a phenetic dendrogram revealing the genetic relationships. The dendrogram generated by UPGMA (unweighted pair group method of arithmetic averages) distinguished W. somnifera from W. coagulans and formed two major clusters. These two main clusters shared a similarity coefficient of 0.3, correlating with the high level of polymorphism detected. The dendrogram further separated W. somnifera into three subclasses corresponding to Kashmiri and Nagori groups and an intermediate type. The AFLP profile of Kashmiri individuals was distinct from that of the Nagori group of plants. The intermediate genotype was distinct as it shared bands with both the Kashmiri and Nagori individuals, even though it was identified as a Kashmiri morphotype. Furthermore, the intermediate type shared a similarity coefficient of 0.8 with the Kashmiri individuals. The present work revealed low levels of variation within a population though high levels of polymorphism were detected between Nagori and Kashmiri populations. The ability of AFLP markers for efficient and rapid detection of genetic variations at the species as well as intraspecific level qualifies it as an efficient tool for estimating genetic similarity in plant species and effective management of genetic resources.Key words: Withania, AFLP, genetic variation, phenetic relationships, medicinal plant.

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High level of genetic diversity among spelt germplasm revealed by microsatellite markers

Genome ◽

10.1139/g04-065 ◽

2004 ◽

Vol 47 (6) ◽

pp. 1043-1052 ◽

Cited By ~ 14

Author(s):

P Bertin ◽

D Grégoire ◽

S Massart ◽

D de Froidmont

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum L ◽

Genetic Distances ◽

Group Method ◽

Germplasm Collections ◽

Pair Group ◽

Genetic Diversity And Structure ◽

The Mean ◽

High Level ◽

Shared Alleles

The genetic diversity of spelt (Triticum aestivum (L.) Thell. subsp. spelta (L.) Thell.) cultivated presently is very narrow. Although the germplasm collections of spelt are extensive, the related genetic knowledge is often lacking and makes their use for genetic improvement difficult. The genetic diversity and structure of the spelt gene pool held in gene banks was determined using 19 simple sequence repeat (SSR) markers applied to 170 spelt accessions collected from 27 countries and 4 continents. The genetic distances (1 – proportion of shared alleles) were calculated and an unweighted pair-group method with arithmetic averaging (UPGMA)-based dendrogram was generated. The genetic diversity was high: 259 alleles were found and the mean interaccession genetic distance was 0.782 ± 0.141. The dendrogram demonstrated the much higher genetic diversity of spelt held in germplasm collections than in the currently used genotypes. Accessions with the same geographical origin often tended to cluster together. Those from the Middle East were isolated first. All but one of the Spanish accessions were found in a unique subcluster. Most accessions from eastern Europe clustered together, while those from northwestern Europe were divided into two subclusters. The accessions from Africa and North America were not separated from the European ones. This analysis demonstrates the extent of genetic diversity of spelts held in germplasm collections and should help to widen the genetic basis of cultivated spelt in future breeding programs.Key words: spelt, SSR, microsatellites, genetic diversity, germplasm.

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Molecular Characterization of Persian Walnut Populations in Iran with Microsatellite Markers

HortScience ◽

10.21273/hortsci.45.9.1403 ◽

2010 ◽

Vol 45 (9) ◽

pp. 1403-1406 ◽

Cited By ~ 18

Author(s):

Rohollah Karimi ◽

Ahmad Ershadi ◽

Kourosh Vahdati ◽

Keith Woeste

Keyword(s):

Juglans Regia ◽

Natural Populations ◽

Genetic Distances ◽

Group Method ◽

Restricted Gene Flow ◽

Pair Group ◽

Hardy Weinberg Equilibrium ◽

High Level ◽

Genetic Structure And Diversity

The genetic structure and diversity of natural populations of Juglans regia L. in Iran were characterized using 11 microsatellite loci. A total of 105 individuals from seven populations were sampled. A high level of genetic diversity was observed within populations with the number of alleles per locus (A) ranging from three to 11 (average = 5.73), the proportion of polymorphic loci was 100%, and the expected heterozygosity ranged from 0.598 to 0.848 (average = 0.707). The proportion of genetic differentiation present among populations accounted for 12% of the total variation. Such considerable interpopulation differentiation detected in J. regia L. could have resulted from several factors, including restricted gene flow between populations. Significant departures from Hardy-Weinberg equilibrium were observed for WGA276, WGA32, and WGA321 loci. The deviations were primarily the result of the surplus of heterozygotes. The unweighted pair group method with arithmetic mean cluster analyses based on Nei's unbiased genetic distances separated the seven populations into two main groups.

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Molecular Genetic Variability of Spigelia marilandica and S. gentianoides

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.140.2.120 ◽

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.

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Genetic variability of Corynespora cassiicola isolates from Amazonas, Brazil

Arquivos do Instituto Biológico ◽

10.1590/1808-1657000992017 ◽

2018 ◽

Vol 85 (0) ◽

Author(s):

Jânia Lília da Silva Bentes ◽

Francy Mary Galúcio Sousa ◽

Maria Teresa Gomes Lopes ◽

Mágno Sávio Ferreira Valente ◽

Fabíola Viana Almeida ◽

...

Keyword(s):

Genetic Variation ◽

Molecular Markers ◽

Genetic Variability ◽

The Other ◽

Group Method ◽

Corynespora Cassiicola ◽

Emerging Pathogen ◽

Pair Group ◽

Genetic Groups ◽

Unweighted Pair Group Method

ABSTRACT: Corynespora cassiicola is a cosmopolitan ascomycete widely known as phytopathogen in several crops, and more recently as an emerging pathogen in humans. In this study the genetic variability of 60 isolates of Corynespora cassiicola from different hosts and cities of Amazonas was evaluated, using AFLP molecular markers. Seven genetic groups were identified according to a dendrogram obtained by the Unweighted Pair Group Method using Arithmetical Averages, indicating significant variability among the isolates. Three isolates of different hosts (28, obtained from papaya; 55, obtained from cucumber; and 58, from tomato) remained as single individuals in distinct groups, suggesting marked genetic variation in comparison to the other isolates and possible specificity by the host.

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Genetic Variability of Passion Fruit Multispecific Hybrids and Their Respective Wild Parents Determined by Microsatellite Markers

Journal of Agricultural Science ◽

10.5539/jas.v11n10p302 ◽

2019 ◽

Vol 11 (10) ◽

pp. 302

Author(s):

Mara Cecília de Mattos Grisi ◽

Fábio Gelape Faleiro ◽

Nilton Tadeu Vilela Junqueira ◽

Jamile da Silva Oliveira

Keyword(s):

Genetic Variability ◽

Microsatellite Markers ◽

Genetic Distances ◽

Passion Fruit ◽

Group Method ◽

Breeding Programs ◽

Promising Alternative ◽

Pair Group ◽

Principal Coordinates ◽

Wild Accessions

The Passiflora genus comprises more than 500 species that are used for food, industrial, ornamental, and pharmaceutical purposes. The sour passion fruit (P. edulis Sims) has low genetic variability for disease resistance, and the use of wild species in the cross-breeding basis is a promising alternative for introgression of resistance genes. The objective of this study was to characterize multispecific hybrids and wild materials with potential to be used as parents in passion fruit genetic breeding programs, using microsatellite markers. Genomic DNA from 33 accessions was extracted and analyzed using 23 microsatellite markers, which were used to estimate the genetic dissimilarities among accessions. The genetic dissimilarity matrices were used to perform clustering analysis by dendrogram using the Unweighted Pair-Group Method as grouping criterion and by graphic dispersion based on multidimensional scale, using the principal coordinates method. Genetic distances between accessions ranged from 0.067 to 1.00. The markers indicated genetic variability among the studied accessions and also the efficiency of the recurrent genome recovery within the backcross program. The genetic structure among the accessions shows the clustering tendency between the wild accessions of P. hatschbachii and P. quadrifaria and the accessions obtained by crossing these species. The same occurred for P. incarnata and P. edulis accessions. The knowledge generated by the molecular characterization provides information on the diversity of accessions and contributes to the work of breeders in the selection of parents.

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Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

Sustainability ◽

10.3390/su13126830 ◽

2021 ◽

Vol 13 (12) ◽

pp. 6830

Author(s):

Murat Guney ◽

Salih Kafkas ◽

Hakan Keles ◽

Mozhgan Zarifikhosroshahi ◽

Muhammet Ali Gundesli ◽

...

Keyword(s):

Genetic Diversity ◽

Plant Genetic Resources ◽

Juglans Regia ◽

Genetic Distances ◽

Mean Value ◽

Central Anatolia ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

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