scholarly journals Phenetic Characterization of Plum Cultivars by High Multiplex Ratio Markers: Amplified Fragment Length Polymorphisms and Inter-simple Sequence Repeats

2001 ◽  
Vol 126 (1) ◽  
pp. 72-77 ◽  
Author(s):  
Luís Goulão ◽  
Luisa Monte-Corvo ◽  
Cristina M. Oliveira
Keyword(s):  
Fragment Length ◽  
Simple Sequence Repeats ◽  
Group Method ◽  
Similarity Coefficients ◽  
Pair Group ◽  
Multiple Loci ◽  
Inter Simple Sequence Repeats ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Simple Sequence

Variability of commercial plum (Prunus L. sp.) cultivars is unknown since breeding often involves intercrossing hybrids with several species but has been based on a low number of parents. Molecular markers like amplified fragment length polymorphisms (AFLP) and inter-simple sequence repeats (ISSR), which sample multiple loci simultaneously, have become increasingly popular, and were used to characterize 24 diploid and four hexaploid cultivars of plum. Seven AFLP and six ISSR primers were used, and resulted in amplification of 379 and 270 products, respectively. Unweighted pair-group method with arithmetic averages (UPGMA) dendrograms, based on similarity coefficients, reflected a clear separation between diploid and hexaploid plums. Among diploid plums, two pairs of cultivars were relatively distinct from the rest, namely `Golden Japan' and `Methley' and `Ozark Premier' and `Songold'. Furthermore, several cultivars were grouped together both with AFLP and ISSR analysis: 1) `Ambra', `Red Beaut', and `Black Beaut', 2) `Black Diamond' and `Royal Diamond', 3) `June Rose', `Santa Rosa', and `Royal Red', and iv) `Freedom', `Larry Ann', and `Queen Rosa'. Although the phenetic classification obtained by the two methods were similar (r = 0.73, for the diploid group), ISSR had a higher reproducibility and percentage of polymorphisms (87.4% vs. 62.8%) than AFLP. Methodological aspects of both markers systems are discussed. Results obtained suggest that the AFLP and ISSR approaches are valuable tools for identification of specific genotypes and analysis of phenetic relationships in plum.

scholarly journals Use of Inter-Simple Sequence Repeats and Amplified Fragment Length Polymorphisms to Analyze Genetic Relationships Among Small Grain-Infecting Species of Ustilago

2003 ◽  
Vol 93 (2) ◽  
pp. 167-175 ◽  
Author(s):  
J. G. Menzies ◽  
G. Bakkeren ◽  
F. Matheson ◽  
J. D. Procunier ◽  
S. Woods
Keyword(s):  
Fragment Length ◽  
Simple Sequence Repeats ◽  
Genetic Relationships ◽  
Molecular Techniques ◽  
Smut Fungi ◽  
Inter Simple Sequence Repeats ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Dna Profiles ◽  
Simple Sequence

In the smut fungi, few features are available for use as taxonomic criteria (spore size, shape, morphology, germination type, and host range). DNA-based molecular techniques are useful in expanding the traits considered in determining relationships among these fungi. We examined the phylogenetic relationships among seven species of Ustilago (U. avenae, U. bullata, U. hordei, U. kolleri, U. nigra, U. nuda, and U. tritici) using inter-simple sequence repeats (ISSRs) and amplified fragment length polymorphisms (AFLPs) to compare their DNA profiles. Fifty-four isolates of different Ustilago spp. were analyzed using ISSR primers, and 16 isolates of Ustilago were studied using AFLP primers. The variability among isolates within species was low for all species except U. bullata. The isolates of U. bullata, U. nuda, and U. tritici were well separated and our data supports their speciation. U. avenae and U. kolleri isolates did not separate from each other and there was little variability between these species. U. hordei and U. nigra isolates also showed little variability between species, but the isolates from each species grouped together. Our data suggest that U. avenae and U. kolleri are monophyletic and should be considered one species, as should U. hordei and U. nigra.

scholarly journals Lemons: Diversity and Relationships with Selected Citrus Genotypes as Measured with Nuclear Genome Markers

2001 ◽  
Vol 126 (3) ◽  
pp. 309-317 ◽  
Author(s):  
O. Gulsen ◽  
M.L. Roose
Keyword(s):  
Simple Sequence Repeats ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Ssr Loci ◽  
High Level ◽  
Simple Sequence

Inter-simple sequence repeats (ISSR), simple sequence repeats (SSR) and isozymes were used to measure genetic diversity and phylogenetic relationships among 95 Citrus L. accessions including 57 lemons [C. limon (L.) Burm. f.], related taxa, and three proposed ancestral species, C. maxima (Burm.) Merrill (pummelo), C. medica L. (citron), and C. reticulata Blanco (mandarin). The ancestry of lemons and several other suspected hybrids was also studied. Five isozyme and five SSR loci revealed relatively little variation among most lemons, but a high level of variation among the relatively distant Citrus taxa. Eight ISSR primers amplified a total of 103 polymorphic fragments among the 83 accessions. Similarity matrices were calculated and phylogenetic trees derived using unweighted pair-group method, arithmetic average cluster analysis. All lemons, rough lemons, and sweet lemons, as well as some other suspected hybrids, clustered with citrons. Most lemons (68%) had nearly identical marker phenotypes, suggesting they originated from a single clonal parent via a series of mutations. Citrons contributed the largest part of the lemon genome and a major part of the genomes of rough lemons, sweet lemons, and sweet limes. Bands that characterize C. reticulata and C. maxima were detected in lemons, suggesting that these taxa also contributed to the pedigree of lemon.

Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers

2013 ◽  
Vol 93 (6) ◽  
pp. 1089-1096 ◽  
Author(s):  
Shiyong Chen ◽  
Xinquan Zhang ◽  
Xiao Ma ◽  
Linkai Huang
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Tibet Plateau ◽  
Group Method ◽  
Similarity Coefficients ◽  
Arithmetic Average ◽  
Pair Group ◽  
Elymus Nutans ◽  
Qinghai Tibet Plateau ◽  
Simple Sequence

Chen, S., Zhang, X., Ma, X. and Huang, L. 2013. Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers. Can. J. Plant Sci. 93: 1089–1096. Elymus nutans Griseb., an important alpine forage grass, is widely distributed in the Qinghai–Tibet Plateau. A total of 50 E. nutans accessions from the eastern Qinghai–Tibet Plateau were analyzed using simple sequence repeats (SSR) markers from wheat and Elymus species. Our results show that a total of 144 reliable bands were generated, of which 132 (91.38%) were found to be polymorphic. Nei-Li's genetic similarity coefficients ranged from 0.515 to 0.870 with an average of 0.719, which shows a high level of genetic diversity and a broad genetic base among accessions. There was a low correlation between genetic distance and geographical distance (r=0.121, P=0.088) in the region, which is consistent with the unweighted pair group method with arithmetic average cluster analysis of accessions. The mountain ridges and river valleys in the eastern Qinghai–Tibet region could serve as genetic barriers for pollinator movement and seed dispersal. The rule of the most genetic diversity at medium altitude of E. nutans in the Qinghai–Tibet Plateau was also validated in the study. The implications of these results for the conservation of E. nutans are discussed.

scholarly journals Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 143
Author(s):  
Lei Zhu ◽  
Huayu Zhu ◽  
Yanman Li ◽  
Yong Wang ◽  
Xiangbin Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Group Method ◽  
Motif Length ◽  
Pair Group ◽  
Ssr Loci ◽  
Ssr Frequency ◽  
Basic And Applied Research ◽  
Simple Sequence

Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.

scholarly journals Kemiripan genetik klon karet (Hevea brasiliensis Muell. Arg.) berdasarkan metode Amplified Fragment Length Polymorphisms (AFLP) Genetic similarity of rubber clones (Hevea brasiliensis Muell. Arg) based on Amplified Fragment Length Polymorphisms (AFLP) method

2016 ◽  
Vol 71 (1) ◽  
Author(s):  
. NURHAIMI-HARIS ◽  
Hajrial ASWIDINNOOR ASWIDINNOOR ◽  
Nurita TORUAN-MATHIUS ◽  
Agus PURWANTARA
Keyword(s):  
Fragment Length ◽  
Genetic Similarity ◽  
Numerical Taxonomy ◽  
Group Method ◽  
Corynespora Cassiicola ◽  
Resistant Clone ◽  
Expression Study ◽  
Multivariate System ◽  
Pair Group ◽  
Length Polymorphisms

Summary   Genetic similarity among ten rubber clones originating from the Wickham collection was studied by Amplified Fragment Length Polymorphism (AFLP) markers.  These clones have different levels of resistance to Corynespora cassiicola, one of the major pathogens in rubber plantations.  The information resulted from this study will be used to determine resistant and susceptible clones which will be used in expression study of the genes encoding plant resistance to C. cassiicola.  Genetic similarity values of clones were calculated from all AFLP markers and used to produce a dendrogram using Unweight Pair-Group Method Arithmetic (UPGMA) based on Numerical Taxonomy and Multivariate System (NTSYS) version  1.8 pc.  A total of 481 fragments were detected by using ten pairs of selective AFLP primers, and 233 fragments (48,4 %) of them were polymorphic.  The results clearly demonstrated that genetic background of these ten clones were 85.5% similar.  At 88.0% similarity level, the clones could be divided into three clusters.  Genetic similarity of IRR 100 (resistant clone) with RRIC 103, PPN 2444 and IAN 873 (susceptible clones) was 90.5, 89.5 and 89.0% respectively, while genetic similarity of other three resistant clones (AVROS 2037, PR 255 and BPM 1) to those susceptible clones was 88.0%.  The lowest genetic similarity (85.5%) was found between RRIC 100 (resistant clone) and those three susceptible clones. By considering the distribution and the source of clones, AVROS 2037 (resistant) and PPN 2444 (susceptible) clones which have 88.0% genetic similarity  will finally  be selected for the expression study of the genes.  Kemiripan genetik sepuluh klon karet yang berasal dari koleksi Wickham dipelajari dengan menggunakan marka Amplified Fragment Length Polymorphism (AFLP).  Kesepuluh klon tersebut memiliki tingkat resistensi berbeda terhadap Corynespora cassiicola, salah satu cendawan patogen penting pada daun tanaman karet. Informasi yang diperoleh dalam penelitian ini akan digunakan untuk menetapkan klon resisten dan klon rentan untuk digunakan dalam mempelajari ekspresi gen yang menyandikan ketahanan tanaman karet terhadap C. cassiicola.  Nilai kemiripan genetik kesepuluh klon karet dihitung berdasarkan semua marka AFLP yang diperoleh dan selanjutnya digunakan untuk. membuat dendrogram dengan menggunakan Unweight Pair-Group Method Arithmetic (UPGMA) berdasarkan Numerical Taxonomy and Multivariate System (NTSYS) version 1.8 pc.  Dengan menggunakan 10 pasang primer AFLP selektif diperoleh sebanyak 481 fragmen DNA, S 2037, PR 255 and BPM 1) to those susceptible clones was 88.0%.  The lowest genetic similarity (85.5%) was found between RRIC 100 (resistant clone) and those three susceptible clones. By considering the distribution and the source of clones, AVROS 2037 (resistant) and PPN 2444 (susceptible) clones which have 88.0% genetic similarity  will finally  be selected for the expression study of the genes. 233 fragmen (48,4 %) di antaranya polimorfik    Dendrogram  dengan nyata menunjukkan bahwa 85,5% latar belakang genetik kesepuluh klon karet tersebut adalah sama, dan pada tingkat 88,0% kesepuluh klon terpisah dalam tiga kelompok.  Kemiripan genetik klon IRR 100 (resisten) dengan klon rentan RRIC 103, PPN 2444 dan IAN 873 masing-masing adalah 90,5, 89,5 dan 89,0%,  sedangkan kemiripan genetik tiga klon resisten lainnya (AVROS 2037, PR 255 dan BPM 1) dengan ketiga klon rentan yang sama adalah 88,0%.  Kemiripan genetik terendah (85,5%) terdapat antara klon RRIC 100 (resisten) dengan ketiga klon rentan tersebut.  Dengan mempertimbangkan distribusi penyebaran klon dan asal klon maka klon resisten AVROS 2037 dan klon rentan PPN 2444 yang memiliki kemiripan genetik 88,0% akan dipilih untuk digunakan dalam studi ekspresi gen tanaman karet. acerun:yes'>  Kesepuluh klon tersebut memiliki tingkat resistensi berbeda terhadap Corynespora cassiicola, salah satu cendawan patogen penting pada daun tanaman karet. Informasi yang diperoleh dalam penelitian ini akan digunakan untuk menetapkan klon resisten dan klon rentan untuk digunakan dalam mempelajari ekspresi gen yang menyandikan ketahanan tanaman karet terhadap C. cassiicola.  Nilai kemiripan genetik kesepuluh klon karet dihitung berdasarkan semua marka AFLP yang diperoleh dan selanjutnya digunakan untuk. membuat dendrogram dengan menggunakan Unweight Pair-Group Method Arithmetic (UPGMA) berdasarkan Numerical Taxonomy and Multivariate System(NTSYS) version 1.8 pc.  Dengan menggunakan 10 pasang primer AFLP selektif diperoleh sebanyak 481 fragmen DNA, S 2037, PR 255 and BPM 1) to those susceptible clones was 88.0%.  The lowest genetic similarity (85.5%) was found between RRIC 100 (resistant clone) and those three susceptible clones. By considering the distribution and the source of clones, AVROS 2037 (resistant) and PPN 2444 (susceptible) clones which have 88.0% genetic similarity  will finally  be selected for the expression study of the genes.   

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