Analysis of genetic variation within clonal lineages of grape phylloxera (Daktulosphaira vitifoliae Fitch) using AFLP fingerprinting and DNA sequencing

Genome ◽  
2007 ◽  
Vol 50 (7) ◽  
pp. 660-667 ◽  
Author(s):  
S. Vorwerk ◽  
A. Forneck
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Chloroplast Dna ◽  
Aflp Fingerprinting ◽  
Daktulosphaira Vitifoliae ◽  
Banding Patterns ◽  
Grape Phylloxera ◽  
Noncoding Regions ◽  
Polymorphic Bands ◽  
Fingerprinting Methods

Two AFLP fingerprinting methods were employed to estimate the potential of AFLP fingerprints for the detection of genetic diversity within single founder lineages of grape phylloxera ( Daktulosphaira vitifoliae Fitch). Eight clonal lineages, reared under controlled conditions in a greenhouse and reproducing asexually throughout a minimum of 15 generations, were monitored and mutations were scored as polymorphisms between the founder individual and individuals of succeeding generations. Genetic variation was detected within all lineages, from early generations on. Six to 15 polymorphic loci (from a total of 141 loci) were detected within the lineages, making up 4.3% of the total amount of genetic variation. The presence of contaminating extra-genomic sequences (e.g., viral material, bacteria, or ingested chloroplast DNA) was excluded as a source of intraclonal variation. Sequencing of 37 selected polymorphic bands confirmed their origin in mostly noncoding regions of the grape phylloxera genome. AFLP techniques were revealed to be powerful for the identification of reproducible banding patterns within clonal lineages.

scholarly journals Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wen-Wen Li ◽  
Li-Qiang Liu ◽  
Qiu-Ping Zhang ◽  
Wei-Quan Zhou ◽  
Guo-Quan Fan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Chloroplast Dna ◽  
Population Expansion ◽  
Prunus Armeniaca ◽  
River Valley ◽  
Nuclear Ribosomal Dna ◽  
Glacial Refugium ◽  
Ili River Valley ◽  
Wild Apricot

AbstractTo clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: HT = 0.499; ITS: HT = 0.876) and a low level of genetic differentiation (cpDNA: FST = 0.1628; ITS: FST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

Short Communication: Genetic variation of Coelogyne pandurate, C. rumphii and their hybrids based on RAPD markers

2020 ◽  
Vol 21 (10) ◽  
Author(s):  
Sri Hartati ◽  
ENDANG S. MULIAWATI
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Rapd Markers ◽  
Short Communication ◽  
F1 Hybrids ◽  
Polymorphic Bands ◽  
Large Clusters

Abstract. Hartati S, Muliawati ES. 2020. Short Communication: Genetic variation of Coelogyne pandurata, C. rumphii and their hybrids based on RAPD markers. Biodiversitas 21: 4709-4713. One effort to increase the genetic diversity of orchids is by crossing. This research aims to assess the genetic variation of a hybrid orchid obtained by crossing Coelogyne pandurata and C. rumphii and their hybrids based on RAPD markers. In this research, both parents were analyzed in three replications, while the hybrid was done in 10 replications. The study was conducted by analyzing DNA bands using RAPD markers with six primers, i.e. OPA 02, OPA 07, OPA 13, OPB 12, OPB 17, and OPD 08. Identification of the parents and their F1 hybrids showed 95.83% polymorphic bands with 43 bands measuring 200-2100 bp. The parents of C. rumphii, C. pandurata, and their hybrids showed similarity range of 0.16-1.00. The crossing of C. rumphii and C. pandurata resulted in a similarity of 0.5, shown in two large clusters. The first cluster consisted only of C. pandurata males and the second cluster consisted of C. rumphii females, together with all hybrid individuals. This study succeeded in creating new hybrids of orchids that have different characters from their parents, having a genetic variation of 23%.

scholarly journals Unusually Low Levels of Genetic Variation among Giardia lamblia Isolates

2007 ◽  
Vol 6 (8) ◽  
pp. 1421-1430 ◽  
Author(s):  
Smilja Teodorovic ◽  
John M. Braverman ◽  
Heidi G. Elmendorf
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Giardia Lamblia ◽  
Diarrheal Disease ◽  
Regulation Of Gene Expression ◽  
Genetic Exchange ◽  
Disease Etiology ◽  
Noncoding Regions ◽  
Low Genetic Diversity ◽  
Low Levels

ABSTRACT Giardia lamblia, an intestinal pathogen of mammals, including humans, is a significant cause of diarrheal disease around the world. Additionally, the parasite is found on a lineage which separated early from the main branch in eukaryotic evolution. The extent of genetic diversity among G. lamblia isolates is insufficiently understood, but this knowledge is a prerequisite to better understand the role of parasite variation in disease etiology and to examine the evolution of mechanisms of genetic exchange among eukaryotes. Intraisolate genetic variation in G. lamblia has never been estimated, and previous studies on interisolate genetic variation have included a limited sample of loci. Here we report a population genetics study of intra- and interisolate genetic diversity based on six coding and four noncoding regions from nine G. lamblia isolates. Our results indicate exceedingly low levels of genetic variation in two out of three G. lamblia groups that infect humans; this variation is sufficient to allow identification of isolate-specific markers. Low genetic diversity at both coding and noncoding regions, with an overall bias towards synonymous substitutions, was discovered. Surprisingly, we found a dichotomous haplotype structure in the third, more variable G. lamblia group, represented by a haplotype shared with one of the homogenous groups and an additional group-specific haplotype. We propose that the distinct patterns of genetic-variation distribution among lineages are a consequence of the presence of genetic exchange. More broadly, our findings have implications for the regulation of gene expression, as well as the mode of reproduction in the parasite.

scholarly journals Morphological Characterization and Genetic Diversity of Rice Blast Fungus, Pyricularia oryzae, from Thailand Using ISSR and SRAP Markers

2020 ◽  
Vol 6 (1) ◽  
pp. 38 ◽  
Author(s):  
Apinya Longya ◽  
Sucheela Talumphai ◽  
Chatchawan Jantasuriyarat
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Rice Blast ◽  
Rice Blast Fungus ◽  
Pyricularia Oryzae ◽  
Blast Disease ◽  
Host Recognition ◽  
Srap Markers ◽  
Blast Fungus ◽  
Polymorphic Bands

Rice blast disease is caused by the ascomycete fungus Pyricularia oryzae and is one of the most destructive rice diseases in the world. The objectives of this study were investigating various fungal morphological characteristics and performing a phylogenetic analysis. Inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers were used to examine the genetic variation of 59 rice blast fungus strains, including 57 strains collected from different fields in Thailand and two reference strains, 70-15 and Guy11. All isolates used in this study were determined to be P. oryzae by internal transcribed spacer (ITS) sequence confirmation. A total of 14 ISSR primers and 17 pairs of SRAP primers, which produced clear and polymorphic bands, were selected for assessing genetic diversity. A total of 123 polymorphic bands were generated. The similarity index value for the strains ranged from 0.25 to 0.95. The results showed that the blast fungus population in Thailand has both morphological and genetic variations. A high level of genetic variation, or genome adaptation, is one of the fungal mechanisms that could overcome host resistance to avoid host recognition. Results from this research study could bring substantial benefits and ultimately help to understand the blast fungal pathogen genome and the population structure in Thai blast fungus.

scholarly journals Phylogeography of Prunus Armeniaca L. By Chloroplast DNA and Nuclear Ribosomal Sequences

2021 ◽  
Author(s):  
Wen-Wen Li ◽  
Li-Qiang Liu ◽  
Qiu-Ping Zhang ◽  
Wei-Quan Zhou ◽  
Guo-Quan Fan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Chloroplast Dna ◽  
Sequence Data ◽  
Population Expansion ◽  
Prunus Armeniaca ◽  
River Valley ◽  
Nuclear Ribosomal Dna ◽  
Ili River Valley ◽  
Wild Apricot

Abstract To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess the genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed that the level of genetic diversity in P. armeniaca was high (cpDNA: HT=0.499; ITS: HT=0.876), and the level of genetic differentiation was low (cpDNA: FST=0.1628; ITS: FST=0.0297). An analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating a genealogical structure in P. armeniaca. P. armeniaca shared the same genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugiume for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

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 Genetic diversity of strawberry cultivars in Banyuroto, Magelang, Indonesia based on Cleaved Amplified Polymorphic Sequence

2019 ◽  
Vol 20 (6) ◽  
Author(s):  
MUHAMMAD FAUZI ARIF ◽  
GANIES RIZA ARISTYA ◽  
RINA SRI KASIAMDARI
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Dna Amplification ◽  
Molecular Study ◽  
Cleaved Amplified Polymorphic Sequence ◽  
Central Java ◽  
Ctab Method ◽  
Polymorphic Bands ◽  
Caps Markers ◽  
Strawberry Cultivars

Abstract. Arif MF, Aristya GR, Kasiamdari RS. 2019. Genetic diversity of strawberry cultivars in Banyuroto, Magelang, Indonesia based on Cleaved Amplified Polymorphic Sequence. Biodiversitas 20: 1721-1728. Banyuroto Village, Magelang, Central Java is the center of strawberry (Fragaria spp.) development and cultivation program. The mild climate makes the location very suitable for developing sub-tropic horticulture such as strawberry. Various kinds of cultivars have been developed as part of the agrotourism program. However, genetic variation research of those cultivars is still rarely done. Therefore, the molecular study of strawberry was conducted to determine the genetic variation using CAPS markers. DNA of Five strawberry cultivars from Banyuroto and seven strawberry cultivars from Indonesian Citrus and Subtropical Fruits Research Institute, Malang were isolated using the CTAB method. DNA amplification was performed by PCR using four pairs of primers named APx, OLP, F3H2, and CTI2. The amplification results were cut with three kinds of restriction endonuclease enzymes named MboI, MluI, and TaqI. Restriction product was used to analyze the genetic variation of twelve cultivars and to construct the dendrogram using MVSP software with the UPGMA algorithm. The result showed that the percentage of polymorphic was 45% from 9 polymorphic bands. Dendrogram result showed that there were four clusters. Cluster A consists of Stroberi Hitam, Cluster B consists of Californica Cultivars, cluster C consists of Osso Grande and Osso Purbalingga cultivars, and cluster D consists of Rosalinda, Deeprose, Dorit, Earlibrite, Tristar, Festival, Brastagi, and Aerut. This research concluded that CAPS markers can be used as a method for study genetic diversity of strawberries.

scholarly journals High Genetic Diversity and Insignificant Interspecific Differentiation inOpisthopappusShih, an Endangered Cliff Genus Endemic to the Taihang Mountains of China

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Rongmin Guo ◽  
Lihua Zhou ◽  
Hongbo Zhao ◽  
Fadi Chen
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Species Level ◽  
Endangered Plants ◽  
High Genetic Diversity ◽  
Fragmented Distribution ◽  
Polymorphic Bands ◽  
Genetic Structures ◽  
Different Levels

OpisthopappusShih is endemic to the Taihang Mountains, China. It grows in the crevice of cliffs and is in fragmented distribution. This genus consists of two species, namely,O. taihangensis(Ling) Shih andO. longilobusShih, which are both endangered plants in China. This study adopted intersimple sequence repeat markers (ISSR) to analyze the genetic diversity and genetic structure from different levels (genus, species, and population) in this genus. A total of 253 loci were obtained from 27 primers, 230 of which were polymorphic loci with a proportion of polymorphic bands (PPB) of up to 90.91% at genus level. At species level, bothO. taihangensis(PPB=90.12%,H=0.1842, andI=0.289) andO. longilobus(PPB=95.21%,H=0.2226, andI=0.3542) have high genetic diversity. Their respective genetic variation mostly existed within the population. And genetic variation inO. longilobus(84.95%) was higher than that inO. taihangensis(80.45%). A certain genetic differentiation among populations inO. taihangensiswas found (Gst=0.2740,Φst=0.196) and genetic differentiation inO. longilobuswas very small (Gst=0.1034,Φst=0.151). Gene flow in different degrees (Nm=1.325and 4.336, resp.) and mating system can form the existing genetic structures of these two species. Furthermore, genetic differentiation coefficient (Gst=0.0453) between species and the clustering result based on the genetic distance showed that interspecific differentiation betweenO. taihangensisandO. longilobuswas not significant and could occur lately.

Genetic Variation of Erigeron breviscapus (Vant.) Hand-Mazz in Yunnan under Heavy Metals Stress

2013 ◽  
Vol 726-731 ◽  
pp. 378-381
Author(s):  
Xin Xiang A ◽  
Hua Bin Xiong ◽  
Ming Hong Chen
Keyword(s):  
Heavy Metals ◽  
Genetic Diversity ◽  
Genetic Variation ◽  
Raw Materials ◽  
Scientific Basis ◽  
Inter Simple Sequence Repeat ◽  
Variation Characteristics ◽  
Polymorphic Bands ◽  
Erigeron Breviscapus ◽  
Growing Conditions

Erigeron breviscapus (Vant.) Hand-Mazz is the raw materials to product Health drugs and injectable formulations. Study the genetic diversity of Erigeron breviscapus under harmful substances stress provides insight into their genetic variation characteristics under stress. In this research, genetic diversity of Erigeron breviscapus under heavy metals (Cr, Cd, Hg, Cu, Pb) stress with different concentrations were analyzed by using 8 inter-simple sequence repeat markers (ISSR). The results showed that Erigeron breviscapus had rich genetic variation under five different kinds heavy metals stress. A total of 96 bands were amplified, of which 80 polymorphic bands were discovered and the percentage of polymorphic bands (PPB) was 83.33%. Their indexes of Na, Ne, H, I and PPB were calculated. Richer genetic diversity was discovered under Cu stress, followed by Cd, Cr, Pb and Hg stress in order. This study will be provide a scientific basis to improve the quality Erigeron breviscapus and optimize its growing conditions.

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