Analysis of Genetic Relationships in Germplasms of Mugua in China Revealed by Internal Transcribed Spacer and its Taxonomic Significance Analysis of Genetic Relationships in Germplasms of Mugua in China Revealed by Internal Transcribed Spacer and its Taxonomic Signifi cance

2010 ◽  
Vol 65 (7-8) ◽  
pp. 495-500 ◽  
Author(s):  
Bangxing Han ◽  
Huasheng Peng ◽  
Qin Yao ◽  
Yang Zhou ◽  
Ming’en Cheng ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Related Species ◽  
Internal Transcribed Spacer ◽  
Genetic Relationships ◽  
Distance Matrix ◽  
Its Sequences ◽  
Taxonomic Significance ◽  
Significance Analysis ◽  
Its Analysis ◽  
Genetic Distance Matrix

Genetic relationships were studied among eight species of three taxa in the genus Chaenomeles by nuclear ribosomal internal transcribed spacer (ITS) analysis. A genetic distance matrix based on ITS sequences was estimated according to the formula of Kimura-2 parameter and a neighbour-joining phenogram, which were obtained with Clustalx4.1 software. The results showed that the germplasms of Mugua originate from Ch. speciosa (Sweet) Nakai, not including Ch. sinensis (Thouin) Kochne and Ch. cathayensis (Hemsl.) Schneid. The results also showed that ‘Yao Mugua’ and ‘Ornamental Mugua’ are the most distantly related species in germplasms.

Comparative analysis of genetic diversity in Canadian barley assessed by SSR, DarT, and pedigree data

Genome ◽  
2013 ◽  
Vol 56 (6) ◽  
pp. 351-358 ◽  
Author(s):  
Mebarek Lamara ◽  
Li Yi Zhang ◽  
Suzanne Marchand ◽  
Nicholas A. Tinker ◽  
François Belzile
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Relationships ◽  
Distance Matrix ◽  
Estimation Methods ◽  
Pedigree Data ◽  
Barley Cultivars ◽  
Genetic Distance Matrix ◽  
Ssr Loci ◽  
Good Agreement

The aim of this study was to measure genetic diversity and population structure among 92 Canadian barley cultivars using two types of molecular markers (SSRs and DArTs) and pedigree data. A total of 368 alleles were identified at 50 SSR loci. The number of alleles per locus ranged between 2 and 13 ([Formula: see text] = 7.36) and PIC values ranged from 0.34 to 0.86 ([Formula: see text] = 0.69). For the biallelic DArT markers, the genetic distance matrix was based on 971 markers whose PIC values ranged between 0.06 and 0.50 ([Formula: see text] = 0.39). A third distance matrix was computed based on the kinship coefficient. Clustering of genotypes was performed based on the genetic distance matrix and the three dendrograms obtained showed the genetic relationships among barley cultivars. The topological similarity of the three dendrograms was estimated using a congruence index and showed the three dendrograms to be in very good agreement. Statistical analysis also showed a highly significant correlation between the SSR and DArT matrices (r = 0.80, p < 0.002) compared with lower yet significant correlations of the pedigree data with both marker types (r = 0.46, p < 0.002; r = 0.52, p < 0.002). Finally, we assessed linkage disequilibrium in this germplasm and found it to be quite extensive, as the mean distance between marker pairs with significant (P < 0.001) r2 values >0.5 was 3.8 cM. Information obtained from comparing results of different genetic diversity estimation methods should be useful for the improvement and conservation of barley genetic resources.

Agromorphological and molecular analysis discloses wide genetic variability in sunflower breeding lines from USDA, USA

2019 ◽  
Vol 79 (02) ◽  
Author(s):  
K. T. Ramya ◽  
A. Vishnuvardhan Reddy ◽  
M. Sujatha
Keyword(s):  
Genetic Distance ◽  
Polymorphic Information Content ◽  
Distance Matrix ◽  
Coefficient Matrix ◽  
Male Sterile ◽  
Breeding Lines ◽  
Genetic Distance Matrix ◽  
Ssr Primers ◽  
Fertility Restorers ◽  
Simple Sequence

The present study investigates genetic divergence among 84 fertility restorers and 32 cytoplasmic male sterile (CMS) lines of sunflower augmented from USDA, USA along with the popular Indian parental lines using simple sequence repeats (SSR). Thirty-nine polymorphic SSR primers produced 139 alleles with an average of 3.56 alleles per locus. The polymorphic information content ranged from 0.23 to 0.69 with an average of 0.45. The average genetic distance was 0.45 and 0.42 for the R and CMS lines, respectively. Dendrogram based on the dissimilarity coefficient matrix grouped the CMS and R lines into separate clusters except for Cluster A which consisted of all CMS lines along with five R lines. Genetic distance matrix estimated from three sets of mitochondrial primers (BOX, ERIC and REP) grouped the 32 CMS lines into eight clusters. The results suggest the existence of considerable genetic diversity among the restorer and CMS lines of sunflower obtained from USDA, USA.

scholarly journals Molecular characterization of papaya genotypes using AFLP markers

2011 ◽  
Vol 33 (3) ◽  
pp. 849-858 ◽  
Author(s):  
Eder Jorge de Oliveira ◽  
Juliana Leles Costa ◽  
Lucas Ferraz dos Santos ◽  
Fabiana Moraes de Carvalho ◽  
Aline dos Santos Silva ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Genetic Distance ◽  
Carica Papaya ◽  
Fragment Length Polymorphism ◽  
Distance Matrix ◽  
Inbred Lines ◽  
Genetic Distance Matrix ◽  
Pair Method ◽  
Polymorphic Bands

Due to the low genetic variability reported in the commercial plantations of papaya (Carica papaya L.), the objective of this study was analyze the genetic diversity of 32 genotypes including cultivars, landraces, inbred lines, and improved germplasm using the AFLP technique (Amplified Fragment Length Polymorphism). The genetic distance matrix was obtained using the Nei and Li genetic distance and clustering was performed using the unweighted pair-method with arithmetic mean (UPGMA). Using 11 combinations of EcoRI/MseI primers, 383 polymorphic bands were obtained. On average, 34.8 polymorphic bands were obtained per primer combination. Five clusters were formed. The traditional cultivar 'Sunrise' and the inbred line CMF-L30-08 were the closest genotypes, and the improved germplasm (CMF041) and landrace (CMF233) the most distant. The main papaya cultivars commercially grown in Brazil, as well as four inbred lines and three improved germplasm, were clustered together, however, were not grouped in the same branch. The genetic distance between the Sunrise and Golden cultivars was 0.329, and even arising from mutation and selection within the Sunrise variety, the Golden stores considerable genetic variability. Additional variability was observed in the inbred lines derived from papaya breeding program at Embrapa Cassava and Fruits.

Genetic and morphological evidence for a new cryptic species of Ectinogonia (Coleoptera: Buprestidae) from central Chile

Zootaxa ◽  
2017 ◽  
Vol 4303 (2) ◽  
pp. 284 ◽  
Author(s):  
SIMÓN ANGUITA-SALINAS ◽  
RODRIGO M. BARAHONA-SEGOVIA ◽  
ELIE POULIN ◽  
ALVARO ZÚÑIGA-REINOSO
Keyword(s):  
New Species ◽  
Genetic Distance ◽  
Cryptic Species ◽  
Distance Matrix ◽  
Morphological Evidence ◽  
Mountain Range ◽  
Central Chile ◽  
The Andes ◽  
Genetic Distance Matrix ◽  
Coi Sequences

The genus Ectinogonia Spinola, 1837 is a genus mainly found in Chile; it currently contains 17 species. Recent exploration in the Andes Mountain Range of the Bio Bio Region in Chile have resulted in the collection of specimens slightly different morphologically from all previously described species. The aim of this paper is to describe this new species of Ectinogonia using morphological and genetic evidence. To establish differences between species we described the external morphology and compared it to species that are morphologically similar (i.e. E. buqueti Spinola 1837 and E. intermedia Kerremans 1903). We also measured the genetic differences in COI sequences, constructing a distance matrix in which we compared it to species that are morphologically similar (E. buqueti and E. intermedia) and other species found in the same region (E. speciosa oscuripennis Moore 1994). We found that E. cryptica sp. n. differs from E. buqueti (which previously contained E. cryptica sp. n.) in pronotum and elytral patterns. The genetic distance matrix shows that E. cryptica sp. n. differs by 4.6% from all other Ectinogonia species compared, supporting the morphological evidence. 

scholarly journals Molecular characterization of elephantgrass accessions through RAPD markers

2005 ◽  
Vol 29 (3) ◽  
pp. 568-574 ◽  
Author(s):  
Leônidas Paixão Passos ◽  
Marco Antonio Machado ◽  
Maria Coletta Vidigal ◽  
Ana Lúcia Campos
Keyword(s):  
Genetic Variability ◽  
Genetic Distance ◽  
Binary Data ◽  
Rapd Markers ◽  
Dna Amplification ◽  
Distance Matrix ◽  
Genetic Distances ◽  
Average Genetic Distance ◽  
Genetic Distance Matrix

Elephantgrass pastures are limited by yield variations and reductions in forage quality and availability, thus making the search for genotypes with reduced seasonality a major concern. In order to verify the extent of genetic variability among contrasting cultivars, ten elephantgrass accessions were analyzed through DNA amplification by RAPD technique. A total of 160 DNA bands were generated with the use of 44 random primers and 23% of these bands were monomorphic for all accessions. Gel-obtained binary data (1 for presence and 0 for absence) were used for generating a genetic distance matrix, which was utilized in a UPGMA grouping analysis. Elephantgrass cultivars Cameroon and Vruckwona were the accessions mostly divergent from the others, with an average genetic distance of 0.34. The accessions with the lowest average genetic distances from the others were Pioneiro and CNPGL 27-5, both with a distance of 0.25. Overall, genetic distances ranged from 0.06 to 0.43, indicating little genetic variability for the set of accessions, despite the contrasting morphology of the studied genotypes.

Genetic Relationships among Cultivated Species of Rhododendron L. Section Pentanthera G.Don Based on DNA Sequence Variation of the Internal Transcribed Spacer (ITS) Region

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 505f-506
Author(s):  
S.M. Scheiber ◽  
R.L. Jarret ◽  
C.D. Robacker
Keyword(s):  
Internal Transcribed Spacer ◽  
Direct Sequencing ◽  
Genetic Relationships ◽  
Morphological Characteristics ◽  
Sequence Divergence ◽  
Its Region ◽  
Distance Matrix ◽  
Sequence Comparisons ◽  
Additional Species ◽  
Bootstrap Analysis

Rhododendron section Pentanthera has traditionally been viewed as a group of closely related species due to the relative lack of distinctive morphological characteristics separating species and numerous reports in the literature of artificial and natural fertile hybrids that produce fertile progeny. Significant variation within species has created difficulties in efforts to assemble these taxa into well-defined groups. Genetic relationships among cultivated specimens of the 15 currently recognized species in Rhododendron section Pentanthera were derived from sequence comparisons of the internal transcribed spacer (ITS) region. Sequences of the entire ITS region including ITS1, ITS2, and the 5.8S subunit were generated by direct sequencing of polymerase chain reaction (PCR) amplified fragments. Rhododendron vaseyi A.Gray, Rhododendron section Rhodora (L.) G.Don was used as an outgroup. Aligned sequences of the 16 taxa resulted in 690 characters. A distance matrix of sequence divergence was calculated using Kimura's two parameter model. A bootstrap analysis was performed and a phenogram was constructed using MEGA. A phenetic assay rather than a phylogenetic analysis was performed because the ITS region contained only eight (1.16%) phylogenetically informative sites. The entire ITS region contained 41 variable sites (5.94%). Five species had identical ITS sequences. Seven additional species differed only by one or two base pair substitutions and/or the addition or deletion of one or two base pairs. R. luteum Sweet, R. occidentale A. Gray, R. molle (Blume) G.Don, and the outgroup, R. vaseyi had noticeable variation (base substitutions, additions, and deletions) compared to the other species. Divergence values among the taxa were extremely low, ranging from 0.00% to 3.51%. This molecular data, and previous hybridization studies, do not support the accepted taxonomic treatment of the section.

scholarly journals Elit Domuz Ayrığı (Dactylis glomerata L.) Genotiplerinde Genetik Çeşitliliğin SSR Markörleri ile Belirlenmesi

2019 ◽  
Vol 7 (1) ◽  
pp. 127
Author(s):  
Gonul Cömertpay ◽  
Hüseyin Özpınar
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Agricultural Research ◽  
Dactylis Glomerata ◽  
Distance Matrix ◽  
Breeding Lines ◽  
Genetic Distance Matrix ◽  
Group A ◽  
Dactylis Glomerata L

Orchardgrass (Dactylis glomerata L.) is an economically important, and widely cultivated perennial forage grass. The aim of this study was to determine the genetic diversity and genetic relationship among the orchardgrass breeding lines developed in Aegean Agricultural Research Institute, using simple sequence repeat (SSR, microsatellite) molecular markers. The genetic diversity of 32 orchardgrass was assessed using a set of 24 SSR markers. SSR primer pair combinations yielded 126 alleles for all genotypes. The number of alleles per locus ranged from three to seven with an average of 5.25 alleles across 24 loci. The alleles size ranged from 101 to 354 and the polymorphism rate was 100%. Jaccard genetic distance coefficient varied from 0.21 to 0.84 among genotypes. The degree of genetic diversity among the genotypes was high. Total number of rare alleles was 28 alleles across 126 loci. Dendrogram constructed using neighbor-joining analysis based on Jaccard genetic distance matrix were clustered into three main groups A, B and C. Group A was the largest group contained 15 genotypes, while B had 13 genotypes originated mainly from same region. The group C was the smallest group contained genotypes originated from northern part of Turkey. The molecular analysis revealed that a significant genetic variation existed in this orhardgrass collection, and the genotypes studied have potential for ensure rich genetic resources in orchardgrass breeding program. In addition to this, it was concluded that SSR markers are suitable markers for the molecular identification of different orchardgrass genotypes.

scholarly journals Genetic diversity of four cattle breeds using microsatellite markers

2003 ◽  
Vol 32 (1) ◽  
pp. 93-98 ◽  
Author(s):  
Marco Antonio Machado ◽  
Ivan Schuster ◽  
Mário Luiz Martinez ◽  
Ana Lúcia Campos
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Distance Matrix ◽  
Average Heterozygosity ◽  
Informative Locus ◽  
Holstein Breed ◽  
Cattle Breeds ◽  
Genetic Distance Matrix ◽  
Hardy Weinberg Equilibrium ◽  
Nei's Genetic Distance

Four cattle breeds (Gyr, Nellore, Guzerat and Holstein) were analyzed by amplification of genomic DNA using microsatellite loci to evaluate the genetic diversity within and among them. DNA samples of 18 animals from each breed were collected to access the genetic content of them. Allele frequencies were calculated and used to generate a Nei's genetic distance matrix what was used to build a dendrogram following UPGMA clustering. As expected, Holstein breed was the most distinct from the other breeds: 1.15 in relation to Gyr, 1.12 in relation to Nellore and 0.94 in relation to Guzerat. The closest genetic distance was 0.25 between Guzerat and Nellore. A total of 64 alleles in all four breeds were detected using nine microsatellite primers. Each breed showed 53% of the total number of alleles. The average number of alleles per locus was 7.11 ± 3.21. The most informative locus was BMS1237 with 53% of observed heterozygosity and the least informative locus was BMS3004 with 12% only. The average heterozygosity detected for the nine loci were 35% and the expected value for Hardy-Weinberg equilibrium was 53%. This low heterozygosity suggests a high endogamy level among the animals sampled within each breed.

scholarly journals Taxonomic identity of Crepidiastrum ×nakaii recorded on Hongdo Island

2021 ◽  
Vol 51 (3) ◽  
pp. 198-204
Author(s):  
Young-Jong JANG ◽  
Byoung-Hee CHOI
Keyword(s):  
Geographical Distribution ◽  
Related Species ◽  
Internal Transcribed Spacer ◽  
Morphological Traits ◽  
Its Sequences ◽  
Flowering Period ◽  
Morphological Examination

The plant known as “Hong-do-go-deul-ppae-gi” on Hongdo Island, belonging to the genus Crepidiastrum, has been recorded as C. ×nakaii, a hybrid between C. denticulatum and C. platyphyllum. During a survey of the flora of Hongdo Island, we reexamined the taxonomic identity of “Hong-do-go-deul-ppae-gi”. The morphological traits, geographical distribution, and internal transcribed spacer (ITS) sequences of “Hong-do-go-deul-ppae-gi” were compared to related species within the genus. A morphological examination revealed that the plant was similar to C. lanceolatum in that it has subshrub stems with caudex stout, 8 inner involucrals bracts, and 10 to 12 florets. In contrast, similarities to C. denticulatum were observed in terms of radical leaves deciduous in the flowering period, cauline leaves membranous with acute serrations, and beaked achenes. Furthermore, C. denticulatum and C. lanceolatum grew on Hongdo Island and nearby areas, but C. platyphyllum was not distributed in these areas. The results of morphological and distributional investigations revealed that the Hongdo Island plant should be regarded as C. ×muratagenii, a hybrid between C. denticulatum and C. lanceolatum, not C. ×nakaii, which is a hybrid between C. denticulatum and C. platyphyllum. However, the resolution of the ITS sequences was insufficient such that we could not separate the examined species.

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