Determination of intra-specific genetic variation of Phlomis kurdica and Phlomis oppositiflora and investigation for the hybridity of P. x melitenense (Lamiaceae) by means of molecular markers

Biologia ◽  
2015 ◽  
Vol 70 (9) ◽  
pp. 1159-1171
Author(s):  
Özay Hasan Evren ◽  
Ertuǧrul Yüzbaşıoǧlu ◽  
Mehmet Yaşar Dadandı
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Distance ◽  
Issr Markers ◽  
Morphological Data ◽  
Quantitative Characters ◽  
Wilks Lambda ◽  
Molecular Aspects ◽  
Species Specific ◽  
Rapd And Issr

Abstract In this study, intra-specific genetic variation and inter-specific genetic relation were investigated among Phlomis oppositiflora, P. kurdica, P. × melitenense (P. kurdica × oppositiflora), P. capitata and P. kurdica × capitata by using RAPD and ISSR markers. The hybridity of P. × melitenense and P. kurdica × capitata samples was also surveyed in terms of morphological and molecular aspects. Except for two, all bands obtained from RAPD (707 bands) and ISSR (651 bands) analyses were polymorphic. The lowest genetic distance values obtained from RAPD and ISSR analyses were 0.0156 (between P. × melitenense and P. kurdica) and 0.0142 (between P. × melitenense and P. kurdica) respectively. The highest genetic distance values obtained from RAPD and ISSR analyses were 0.0866 (between P. kotschyana and P. oppositiflora) and 0.1237 (between P. kotschyana and P. kurdica × capitata) respectively. While P. kurdica indicated the highest genetic diversity (H = 0.1572; I = 0.2646) in RAPD analysis, P. capitata displayed the highest genetic diversity (H = 0.1403; I = 0.2329) in ISSR analysis. AMOVA results showed that 86% and 75% of the total variance resided within groups based on RAPD and ISSR markers, respectively. Based on the RAPD and ISSR results, both P. × melitenense and P. kurdica × capitata samples inherited species specific bands from their parental species, which confirms their hybridity. Although both P. × melitenense and P. kurdica × capitata hybrids showed a morphological mosaic between their parental phenotypes in terms of the majority of the quantitative characters examined, P. × melitenense and P. kurdica × capitata exceeded their parental phenotypes in terms of the three and 11 quantitative characters respectively. MANOVA results from the morphological data showed significant distinction among P. kurdica, P. oppositiflora, P. × melitenense, P. capitata and P. kurdica × capitata (Wilks’ Lambda = 0.003; df = 112; P < 0.01). Average pollen fertilities of P. oppositiflora, P. × melitenense, P. capitata, P. kurdica and P. kurdica × capitata were 93.44%, 68.42%, 93.28 %, 90.12% and 92.77% respectively.

Genetic diversity in Cinnamomum tamala Nees. accessions through DNA fingerprinting using molecular markers

2016 ◽  
Author(s):  
S Zafar Haider ◽  
Ujjwal . Bhandari ◽  
Gaurav . Naik ◽  
Nirpendra . Chauhan
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Rapd Markers ◽  
Issr Markers ◽  
Initial Screening ◽  
Cinnamomum Tamala ◽  
Upgma Cluster Analysis ◽  
Polymorphic Bands ◽  
Rapd And Issr ◽  
Uttarakhand Himalaya

The present study aims to investigate the genetic variation in Cinnamomum tamala Nees. (Lauraceae) accessions collected from different locations of Uttarakhand Himalaya. The leaves samples were analyzed by using RAPD and ISSR markers. A total 22 primers were used for initial screening in order to select the ones giving good amplification. Seven primers (OPA-12, OPA-18, OPB-10, OPB-17, ISSR-21, ISSR-24 and ISSR-30) were found to be polymorphic in eight accessions. Based on combined profile of ISSR and RAPD markers the dendrogram was constructed by using UPGMA cluster analysis and all the accessions showed discrimination from one another. All the accessions were clustered into two major groups, one containing T1-T4 and second T5-T8. The percentage of polymorphic bands was 86.3 % for three ISSR markers and 70.5 % for four RAPD markers. This emphasize that ISSR markers were found to be the best for genetic variation in the species.

scholarly journals Does marine geospatial/environmental variation affect genetic variation? A meta-analysis

2021 ◽  
Author(s):  
◽  
Daniel Cárcamo
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
New Zealand ◽  
Genetic Variability ◽  
Genetic Distance ◽  
Meta Analysis ◽  
Environmental Variation ◽  
Environmental Data ◽  
Seascape Genetics ◽  
Species Specific

<p>Genetic information is important to inform management and conservation. However, few studies have tested the relationship between genetic variation and geospatial/environmental variation across marine species. Here, I test two genetics-based ideas in evolutionary theory using data from 55 New Zealand coastal marine taxa. The Core-Periphery Hypothesis (CPH) states that populations at the centre of a species’ distribution exhibit greater genetic variability than populations at the periphery (the ‘normal’ model). Variants of this model include the ‘ramped north’ (greatest variation in the north), the ‘ramped south’ (greatest variation in the south), and the ‘abundant edge’ (greatest variation at the distributional edges, least variation at the centre). The Seascape Genetics Test (SGT) null hypothesis predicts no association between genetic variation and environmental variation. I conducted a meta-analysis of published/unpublished material on population genetic connectivity and diversity and marine environmental data to test both hypotheses. To assess the CPH, genetic data were fitted to four models (Normal, Ramped North, Ramped South, Abundant Edge). I also conducted a descriptive analysis between the genetic outcomes of the CPH and abundance records for a subset of species. The SGT involved GLM analyses using eleven geospatial/environmental variables and species-specific FST-ΦST (genetic distance) estimates plus a smaller subset of genetic diversity data. The CPH results showed that 55 of 249 tests (evaluating on average 2.9 ± 1.3 genetic indices in each of the 84 studies) fitted at least one of the four models: Ramped North (10%), Ramped South (8%), Normal (2%) and Abundant Edge (2.4%). Species-specific abundance records followed the same patterns detected by the CPH. These results indicate that edge populations (Ramped North, Ramped South, Abundant Edge) exhibit greater genetic variability than central populations amongst marine taxa from New Zealand, but that most taxa do not conform to any model (~78% of all tests were not statistically significant). For the seascape genetics multi-species analysis (comprising 498 individual tests), the FST-ΦST estimates (genetic distance estimates between pairs of populations) were mostly affected by four factors related to sea surface temperature. For genetic diversity indices the most significant predictors were latitude and longitude. Whilst different factors (e.g., physical oceanography, food availability, life-history traits and harvesting), either acting alone or acting synergistically, are likely to be important in explaining patterns of genetic diversity in New Zealand’s marine coastal species, my results indicate that variables including SST and to a lesser extent the geospatial variables (latitude and longitude) explain much of the variation in the genetic indices tested here.</p>

scholarly journals Does marine geospatial/environmental variation affect genetic variation? A meta-analysis

2021 ◽  
Author(s):  
◽  
Daniel Cárcamo
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
New Zealand ◽  
Genetic Variability ◽  
Genetic Distance ◽  
Meta Analysis ◽  
Environmental Variation ◽  
Environmental Data ◽  
Seascape Genetics ◽  
Species Specific

<p>Genetic information is important to inform management and conservation. However, few studies have tested the relationship between genetic variation and geospatial/environmental variation across marine species. Here, I test two genetics-based ideas in evolutionary theory using data from 55 New Zealand coastal marine taxa. The Core-Periphery Hypothesis (CPH) states that populations at the centre of a species’ distribution exhibit greater genetic variability than populations at the periphery (the ‘normal’ model). Variants of this model include the ‘ramped north’ (greatest variation in the north), the ‘ramped south’ (greatest variation in the south), and the ‘abundant edge’ (greatest variation at the distributional edges, least variation at the centre). The Seascape Genetics Test (SGT) null hypothesis predicts no association between genetic variation and environmental variation. I conducted a meta-analysis of published/unpublished material on population genetic connectivity and diversity and marine environmental data to test both hypotheses. To assess the CPH, genetic data were fitted to four models (Normal, Ramped North, Ramped South, Abundant Edge). I also conducted a descriptive analysis between the genetic outcomes of the CPH and abundance records for a subset of species. The SGT involved GLM analyses using eleven geospatial/environmental variables and species-specific FST-ΦST (genetic distance) estimates plus a smaller subset of genetic diversity data. The CPH results showed that 55 of 249 tests (evaluating on average 2.9 ± 1.3 genetic indices in each of the 84 studies) fitted at least one of the four models: Ramped North (10%), Ramped South (8%), Normal (2%) and Abundant Edge (2.4%). Species-specific abundance records followed the same patterns detected by the CPH. These results indicate that edge populations (Ramped North, Ramped South, Abundant Edge) exhibit greater genetic variability than central populations amongst marine taxa from New Zealand, but that most taxa do not conform to any model (~78% of all tests were not statistically significant). For the seascape genetics multi-species analysis (comprising 498 individual tests), the FST-ΦST estimates (genetic distance estimates between pairs of populations) were mostly affected by four factors related to sea surface temperature. For genetic diversity indices the most significant predictors were latitude and longitude. Whilst different factors (e.g., physical oceanography, food availability, life-history traits and harvesting), either acting alone or acting synergistically, are likely to be important in explaining patterns of genetic diversity in New Zealand’s marine coastal species, my results indicate that variables including SST and to a lesser extent the geospatial variables (latitude and longitude) explain much of the variation in the genetic indices tested here.</p>

Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 769-777 ◽  
Author(s):  
Melanie Mehes-Smith ◽  
Paul Michael ◽  
Kabwe Nkongolo
Keyword(s):  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Pinus Monticola ◽  
The Family ◽  
Species Specific ◽  
Rapd And Issr ◽  
Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

scholarly journals Molecular analysis of genetic diversity in population of Silybum marianum (L.) Gaertn in Egypt

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Marwa Hamouda
Keyword(s):  
Genetic Diversity ◽  
Electrophoretic Pattern ◽  
Issr Markers ◽  
Silybum Marianum ◽  
Inter Simple Sequence Repeats ◽  
Sds Page ◽  
Dna Pattern ◽  
Pharmaceutical Properties ◽  
High Level ◽  
Rapd And Issr

Abstract Background Silybum marianum L. Gaertn is a medicinal plant of unique pharmaceutical properties in the treatment of liver disorders and diabetic nephropathy. Biochemical (SDS-PAGE) and molecular markers such as randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) technologies were used in this work to detect genetic diversity of 14 collections of Silybum marianum population in Egypt. Results The electrophoretic pattern of seed protein gave different molecular weight bands, ranging from 24 to 111 KDa with the presence of unique bands. RAPD results revealed a high level of polymorphism (73.2%) using 12 RAPD primers, but only eight of them gave reproducible polymorphic DNA pattern. Sixteen primers were used in the ISSR method; only ten of them yielded clearly identifiable bands. The percentage of polymorphism is about 80% of the studied samples. Conclusion The obtained data confirmed that SDS-protein, RAPD, and ISSR markers are important tools for genetic analysis for Silybum marianum and recommended to give accurate results.

scholarly journals Efficiency of improved RAPD and ISSR markers in assessing genetic diversity and relationships in Angelica sinensis (Oliv.) Diels varieties of China

2015 ◽  
Vol 18 (2) ◽  
pp. 96-102 ◽  
Author(s):  
Zhiqiang Mei ◽  
Chun Zhang ◽  
Md. Asaduzzaman Khan ◽  
Ye Zhu ◽  
Mousumi Tania ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Issr Markers ◽  
Angelica Sinensis ◽  
Rapd And Issr

scholarly journals Measurement of Genetic Diversity of Chinese Seashore Paspalum Resources through Morphological and Sequence-related Amplified Polymorphism Analysis

2019 ◽  
Vol 144 (6) ◽  
pp. 379-386
Author(s):  
Yan Liu ◽  
Hailin Guo ◽  
Yi Wang ◽  
Jingang Shi ◽  
Dandan Li ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Distance ◽  
Morphological Characteristics ◽  
The United States ◽  
Germplasm Resources ◽  
Seashore Paspalum ◽  
Chinese Germplasm

Seashore paspalum (Paspalum vaginatum) is a notable warm-season turfgrass. Certain germplasm resources are distributed in the southern regions of China. The objectives of this study were to investigate the genetic diversity and genetic variation of Chinese seashore paspalum resources. Morphological characteristics and sequence-related amplified polymorphism (SRAP) markers were used to assess genetic relationships and genetic variation among 36 germplasm resources from China and six cultivars from the United States. The results showed significant variation for 13 morphological characteristics among 42 tested seashore paspalum accessions, and that the phenotypic cv was, in turn, turf height > turf density > internode length > inflorescence density > leaf width > reproductive branch height > spikelet width > leaf length > spikelet number > inflorescence length > internode diameter > inflorescence width > spikelet length. According to the morphological characteristics and cluster analysis, 42 seashore paspalum accessions were divided into six morphological types. In total, 374 clear bands were amplified using 30 SRAP primer combinations; among these bands, 321 were polymorphic with 85.83% polymorphism. SRAP marker cluster analysis showed that 42 seashore paspalum accessions were grouped into seven major groups, with a genetic similarity coefficient ranging from 0.4385 to 0.9893 and genetic distance values ranging from 0.0108 to 0.8244. The high level of genetic diversity occurred among Chinese germplasm, and the genetic distance was relatively high between Chinese germplasm and cultivars introduced from the United States. The patterns in morphological trait variations and genetic diversity will be useful for the further exploitation and use of Chinese seashore paspalum resources.

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