Genetic variation within and between strains of outbred Swiss mice

1993 ◽  
Vol 27 (2) ◽  
pp. 116-123 ◽  
Author(s):  
Shuliang Cui ◽  
Clive Chesson ◽  
Rory Hope
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Genetic Distances ◽  
Branching Pattern ◽  
Allozyme Electrophoresis ◽  
Polymorphic Variation ◽  
Swiss Mice ◽  
Allelic Substitution ◽  
Different Strains ◽  
Nei's Genetic Distance

The aim of this survey was to measure levels of genetic variation within and between 5 different strains of outbred Swiss mice. Ten to 15 animals from each strain (NIH, Q(S), ARC, IMVS and STUD) were typed, using allozyme electrophoresis, at 10 gene loci: Mod-1, Idh-1, Gpi-1, Es-1, Es-3, Hbb, Pep-3, Gr-1, Got-2 and Pgm-1. Polymorphic variation in at least one of the 5 strains was detected at all 10 loci. The proportion of polymorphic loci ranged from 0·3 (NIH) to 0·8 (IMVS) with a mean of 0·52. Average expected heterozygosities ranged from 0·08 (NIH) to 0·37 (IMVS) with a mean of 0·21. The inbred strain SWR was, as expected, homozygous at all 10 loci. The amount of allelic substitution between pairs of strains was quantified using Nei's genetic distance, and a dendrogram based on these genetic distances showed a close overall similarity in its branching pattern to the known genealogy of the strains. This survey showed that a considerable degree of genetic variation persists in the 5 strains examined, a level of variation similar to that previously detected by Rice and O'Brien (1980) in 3 other outbred Swiss strains.

scholarly journals Genetic Variation Among Colletotrichum graminicola Isolates from Four Hosts Using Isozyme Analysis

Plant Disease ◽  
2004 ◽  
Vol 88 (4) ◽  
pp. 402-406 ◽  
Author(s):  
B. J. Horvath ◽  
J. M. Vargas
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Geographic Origin ◽  
Creeping Bentgrass ◽  
Genetic Distances ◽  
Colletotrichum Graminicola ◽  
Annual Bluegrass ◽  
Close Relationship ◽  
Host Origin ◽  
Serious Disease

Anthracnose basal rot (ABR) is a serious disease of turfgrasses that is caused by the pathogen Colletotrichum graminicola. The relationships of isolates causing ABR on turfgrasses to those causing disease on important crop hosts (maize, sorghum) remain unresolved. Genetic variation among isolates from annual bluegrass, creeping bentgrass, maize, and sorghum was evaluated based on host origin and geographic origin. Isozymes were used to estimate the genetic variation of the isolates. Five enzyme systems comprising 16 alleles from 5 loci were used. Allele frequencies, genetic distance, and linkage disequilibrium values were calculated for isolates based on both host and geographic origin. Isolates from creeping bentgrass and annual bluegrass were the most closely related based on Nei's genetic distance, while isolates from maize and sorghum were the most distantly related, consistent with their known species-level relationship. Isolates from annual bluegrass and creeping bentgrass had different genetic distances to isolates from both maize and sorghum. Annual bluegrass isolates from different geographic regions had the smallest genetic distance values observed in this study, indicating a very close relationship regardless of geographic origin. Based on these data, it appears that host origin, not geographic origin, plays a more important role in the genetic diversity of these fungi.

scholarly journals Genetic studies revealed differences between European and North American populations of Calypogeia azurea

2016 ◽  
Vol 42 (1) ◽  
pp. 19-26 ◽  
Author(s):  
Katarzyna Buczkowska ◽  
Alina Bączkiewicz ◽  
Patrycja Gonera
Keyword(s):  
Genetic Variation ◽  
North America ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Oil Bodies ◽  
Genetic Studies ◽  
Isozyme Loci ◽  
The Mean ◽  
Different Parts ◽  
Nei's Genetic Distance

Abstract Calypogeia azurea, a widespread, subboreal-montane liverwort species, is one of a few representatives of the Calypogeia genus that are characterized by the occurrence of blue oil bodies. The aim of the study was to investigate the genetic variation and population structure of C. azurea originating from different parts of its distribution range (Europe and North America). Plants of C. azurea were compared with C. peruviana, another Calypogeia species with blue oil bodies. In general, 339 gametophytes from 15 populations of C. azurea were examined. Total gene diversity (HT) estimated on the basis of nine isozyme loci of C. azurea at the species level was 0.201. The mean Nei’s genetic distance between European populations was equal to 0.083, whereas the mean genetic distance between populations originating from Europe and North America was 0.413. The analysis of molecular variance (AMOVA) showed that 69% of C. azurea genetic variation was distributed among regions (Europe and North America), 15% - among populations within regions, and 16% - within populations. Our study revealed that C. azurea showed genetic diversity within its geographic distribution. All examined samples classified as C. azurea differed in respect of isozyme patterns from C. peruviana.

Lack of isozyme similarity between Vigna unguiculata and other species of subgenus Vigna (Leguminosae)

1993 ◽  
Vol 71 (4) ◽  
pp. 586-591 ◽  
Author(s):  
R. E. Vaillancourt ◽  
N. F. Weeden
Keyword(s):  
Genetic Distance ◽  
Vigna Unguiculata ◽  
Genetic Distances ◽  
Close Relative ◽  
Tropical Africa ◽  
The Third ◽  
Upgma Cluster Analysis ◽  
Isozyme Loci ◽  
The Relationship ◽  
Nei's Genetic Distance

The cowpea (Vigna unguiculata (L.) Walp.) is an important crop of tropical Africa, Asia, and South America. However, the relationship between the cowpea and other species of subg. Vigna is relatively unknown. The objective of this study was to assess the genetic distance among species of subg. Vigna using isozymes. Twenty-four populations of the cowpea species and 39 populations from 10 other species (at least one species per section of subgenus Vigna) were sampled. Nei's genetic distance was calculated from allelic frequencies at 26 isozyme loci. UPGMA cluster analysis was performed. The range of genetic distance among species of subg. Vigna (0.41 – 2.69) was greater than previously reported in most plant genera. Three clusters of species were apparent. The first cluster included three species of sect. Vigna (V. luteola, V. oblongifolia, and V. subterranea (the Bambara groundnut)). The second cluster grouped together sections Liebrechtsia and Macrodontae. The third cluster included V. unguiculata, V. reticulata, and V. vexillata. The distances between species of this cluster were large and of similar size in all combinations (range from 0.92 to 0.95). None of the species included in this survey can be called a close relative of V. unguiculata. Key words: Vigna, cowpea, isozymes, genetic distances.

RAPD analysis off genetic variation in the Australian fan flower, Scaevola

Genome ◽  
1997 ◽  
Vol 40 (5) ◽  
pp. 600-606 ◽  
Author(s):  
Ines Swoboda ◽  
Prem L. Bhalla
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Genetic Distance ◽  
Rapd Analysis ◽  
Genetic Distances ◽  
Randomly Amplified Polymorphic Dna ◽  
Similarity Coefficients ◽  
Arbitrary Primers ◽  
Australian Species ◽  
Commercial Cultivars

The use of randomly amplified polymorphic DNA (RAPD) to study genetic variability in Scaevola (family Goodeniaceae), a native Australian species used in ornamental horticulture, is demonstrated. Plants of the genus Scaevola are commonly known as "fan flowers," due to the fan-like shape of the flowers. Nineteen accessions of Scaevola (12 cultivated and 7 wild) were studied using 20 random decamer arbitrary primers. Eight primers gave a distinct reproducible amplification profile of 90 scorable polymorphic fragments, enabling the differentiation of the Scaevola accessions. RAPD amplification of genomic DNA revealed a high genetic variability among the different species of Scaevola studied. Molecular markers were used to calculate the similarity coefficients, which were then used for determining genetic distances between each of the accessions. Based on genetic distances, a dendrogram was constructed. Though the dendrogram is in general agreement with the taxonomy, it also highlights discrepancies in the classification. The RAPD data showed that Scaevola aemula (series Pogogynae) is closer to Scaevola glandulifera of series Globuliferae than to the rest of members of series Pogogynae. In addition, the RAPD banding pattern of white flower S. aemula, one of the commercial cultivars, was identical to that of Scaevola albida, indicating their genetic similarity. Our study showed that there is a large genetic distance between commercial cultivars of Scaevola (Purple Fanfare, Pink Perfection, and Mauve Cluster), indicating considerable genetic variation among them. The use of RAPDs in intra- and inter-specific breeding of Scaevola is also explored.Key words: Scaevola, Australian native, RAPD, genetic distance, genetic variability.

scholarly journals Biochemical phylogeny of the eight species in the Drosophila melanogaster subgroup, including D. sechellia and D. orena

1987 ◽  
Vol 50 (3) ◽  
pp. 181-185 ◽  
Author(s):  
Marie Louise Cariou
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Phylogenetic Relationships ◽  
Species Divergence ◽  
Allozyme Data ◽  
Drosophila Melanogaster Subgroup ◽  
The Times ◽  
Nei's Genetic Distance

SummaryThe phylogenetic relationships of the eight species of the Drosophila melanogaster subgroup are examined on the basis of genetic variation at 33 putative enzyme loci. Values of Nei's genetic distance (ds) range from 0·28 to 1·74. D. sechellia appears closer to D. simulans than to D. mauritiana, the two former being the most closely related. D. orena is quite distantly related to D. erecta (ds = 1). Genetic differentiation supports the existence of three main lineages within the melanogaster subgroup and the yakuba-teissieri pair appears to be closer to the melanogaster lineage than to the erecta-orena one. Inferences of the times of species divergence from allozyme data are made and their agreement to other estimates is discussed.

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 variation and phylogenetic analysis of Indonesian indigenous catfish (baung fish) based on mitochondrial 12S rRNA gene

2021 ◽  
Vol 14 (3) ◽  
pp. 751-757
Author(s):  
Rini Widayanti ◽  
Ken Ayik Kusumaastuti ◽  
Joana Martha Novi ◽  
Fadila Khairuna Adani ◽  
Catrine Relia Patrecia Gultom ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Phylogenetic Relationships ◽  
Population Based ◽  
Genetic Distances ◽  
12S Rrna ◽  
Rrna Gene ◽  
Mystus Vittatus ◽  
12S Rrna Gene ◽  
Mitochondrial 12S Rrna

Background and Aim: Baung fish is an essential commodity in Indonesia; however, few studies have explored the genetic diversity of Indonesian catfish. Thus, this study aimed to analyze the genetic variation and phylogenetic relationships among Indonesian catfish based on the mitochondrial 12S ribosomal RNA (rRNA) gene. Materials and Methods: In total, 28 catfish were collected from nine rivers in seven provinces and from the Indian Ocean. Catfish genomes were obtained from epaxial and hepaxial muscle samples. The mitochondrial 12S rRNA gene was amplified by polymerase chain reaction using a pair of primers (Baung12SF and Baung12SR). The 12S rRNA sequences were analyzed using MEGA X to determine genetic variation and phylogenetic relationships. Results: In total, 178 variation sites in the 12S rRNA gene were substituted among Indonesian catfish. The genetic distance between all Indonesian catfish samples was 0.1-16.0%. The closest genetic distance was between MP and PM catfish, whereas the farthest genetic distances were between BF and EM and PD and EM. For the entire population, based on mean diversity calculations, the number of base substitutions per site was 0.08. Conclusion: Indonesian catfish were divided into four clades based on the 12S rRNA gene. The catfish MP, KR, PM, MS, BB, and KS were grouped with Hemibagrus nemurus, the catfish EM was grouped with Mystus vittatus, the catfish BSBJ was grouped with Pangasius pangasius, and the catfish PD and BF were grouped with Netuma thalassina.

Allozyme variations in six natural populations of scots pine (Pinus sylvestris) in Turkey

Biologia ◽  
2007 ◽  
Vol 62 (6) ◽  
Author(s):  
Behiye Bilgen ◽  
Nuray Kaya
Keyword(s):  
Genetic Variation ◽  
Pinus Sylvestris ◽  
Genetic Distance ◽  
Scots Pine ◽  
Natural Populations ◽  
Mean Value ◽  
Population Variation ◽  
Starch Gel Electrophoresis ◽  
The Mean ◽  
Nei's Genetic Distance

AbstractGenetic variation in six natural populations of Scots pine (Pinus sylvestris L.) was determined with isoenzyme analyses. For this purpose, haploid female gametophytes of seeds and horizontal starch gel electrophoresis technique were used. A total of 17 loci and 58 alleles were observed in studying 10 enzyme systems. The average proportion of polymorphic loci for populations ranged from 58.8% to 70.6%. The average number of alleles per locus per population was 2.65. The mean estimated expected heterozygosity (He) of populations was 0.294. A rather high proportion of genetic diversity (96.4%) was due to within-population variation and the remaining (3.6%) was due to variation among populations. The level of gene flow (Nem) was found to be 6.69 per generation. Nei’s genetic distance coefficient ranged from 0.006 to 0.027 (mean 0.017) among all possible population pairs. The mean value of Nei’s genetic distance is similar to the values reported for other European Scots pine populations. The low mean value of Nei’s genetic distance among populations is enough to explain low interpopulation variation. According to genetic variation parameters, three out of six populations (Akdagmadeni-Yozgat, Refahiye-Erzincan and Vezirkopru-Samsun) appear to be preferable populations for genetic conservation and forest tree breeding programs.

scholarly journals ANALISIS KERAGAMAN GENETIK TIGA STRAIN NILA MERAH (Oreochromis sp) DENGAN ANOVA RAPD

2017 ◽  
Vol 1 (1) ◽  
pp. 21
Author(s):  
Iskandariah Iskandariah ◽  
Otong Zenal Arifin ◽  
Rudhy Gustiano
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Nile Tilapia ◽  
Genetic Variance ◽  
Laboratory Research ◽  
Red Tilapia ◽  
Freshwater Aquaculture ◽  
Genetic Strain ◽  
Different Strains ◽  
Random Amplified Polymorphism Dna

Analysis Genetic Variation of Three Strains of Red Tilapia by Anova of RAPD.          Study on the genetic variance of three strains of red tilapia (Oreochromis sp) had been conducted in the Biology Molecular Laboratory, Research Institute for Freshwater Aquaculture (RIFA) Bogor.  Three different strains, Red NIFI from Thailand,  Red Tilapia from Lido lake and Red Tilapia from Bogor’s farmer were analyzed in the study.  Observation used Random Amplified Polymorphism DNA (RAPD) with OPA-03, OPA-04, OPC 14 and OPC-15 primers.  The results showed that only OPA-03 primer was able to amplify numerous samples.  Further analysis showed that the percentage of polimorphic range was between 16.67 – 38.89%, heterozygosity value 0.0378 – 0.1536 and genetic distance among strain 0.3051 – 0.6037.Keywords : RAPD, genetic, strain, nile tilapia, oreochromis ABSTRAK           Penelitian mengenai variasi genetik tiga strain nila merah dari 3 lokasi yang berbeda telah dilakukan di Laboratorium Molekuler Biologi, Balai Riset Perikanan Budidaya Air Tawar (BRPBAT) Bogor.  Strain yang diamati meliputi jenis nila Red NIFI dari Thailand, nila merah dari Danau Lido dan nila merah dari Petani Bogor. Penelitian menggunakan metode analisis Random Amplified Polymorphism DNA (RAPD), dengan menggunakan primer OPA-03, OPA-04, OPC-14 dan OPC-15.  Hasil pengamatan menunjukkan hanya OPA-03 yang dapat menghasilkan amplifikasi dalam jumlah sampel yang memadai.  Hasil analisis menunjukkan bahwa persentase polimorfik berkisar antara 20.00-40.00%, dengan nilai heterozigositas 0.0604–0.1516 dan jarak genetik antar strain 0.1770-0.4865.  Kata kunci : RAPD, genetik, strain, ikan nila, oreochromis

Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

2015 ◽  
Vol 3 (1) ◽  
pp. 1-11
Author(s):  
Rezq Basheer-Salimia
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Vitis Vinifera L ◽  
Similarity Matrix ◽  
Breeding Programs ◽  
Local Varieties ◽  
Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

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