Population genetic diversity of Phytophthora infestans from China as revealed by SSRs and RAPDs

AbstractSimple sequence repeats (SSR) and random amplification of polymorphic DNA (RAPD) molecular markers were used to assess the genetic diversity of 80 isolates of Phytophthora infestans in potato (Solanum tuberosum) from Fujian, Heilongjiang, Hebei and Inner Mongolia Provinces in China. Polymorphism was identified by 13 SSR primers and 14 RAPD primers in the isolates of P. infestans in potato. A total of 76 bands were amplified by SSRs, with the percentage of polymorphic bands (PPB) being 78.9% and the similarity coefficient ranging between 0.00 and 0.42. A total of 189 bands were amplified by RAPDs, with the percentage of polymorphic bands being 95.2% and the similarity coefficient ranging between 0.04 and 0.66. Analysis of genetic diversity showed that there exists higher genetic variation in the Fujian population in comparison to the populations of Heilongjiang, Hebei and Inner Mongolia. Nei's genetic identity analysis indicates that the genetic similarity between populations of Heilongjiang and Inner Mongolia is the highest and that between Fujian and Hebei is the lowest. A cluster analysis revealed that isolates from Fujian, in the south of China, are distantly related to those from Heilongjiang, Hebei and Inner Mongolia in the north, and the Fujian population is distributed among more groups than the other three, exhibiting a higher genetic diversity.

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Genetic Diversity of Vitis davidii Accessions Revealed Using Microsatellite and Sequence-related Amplified Polymorphism Markers

HortScience ◽

10.21273/hortsci12506-17 ◽

2018 ◽

Vol 53 (3) ◽

pp. 283-287

Author(s):

Xiu Cai Fan ◽

Hai Sheng Sun ◽

Ying Zhang ◽

Jian Fu Jiang ◽

Min Li ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Genetic Similarity ◽

Similarity Coefficient ◽

Srap Markers ◽

Average Percentage ◽

Allele Number ◽

Ssr Primers ◽

Vitis Davidii ◽

Simple Sequence

In this study, simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers were used to analyze the genetic diversity of 48 wild Vitis davidii accessions. A total of 78 distinct alleles were amplified by 11 SSR primers, and the average allele number was 8.8. The average observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.785 and 0.814, respectively. The effective allele numbers ranged from 3.92 to 9.61. The average polymorphism information content (PIC) was 0.798. Twelve of 169 SRAP primer combinations were selected for SRAP analysis. A total of 188 bands were produced, and the average was 15.7 bands per primer combination; the average percentage of polymorphic bands was 84.0%. The average PIC was 0.76. The results of the clustering analysis based on SSR markers showed that the 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient level of 0.68. The dendrogram obtained from the SRAP data showed that 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient of 0.72. SSR and SRAP markers differentiated all accessions studied including those with a similar pedigree. We speculated on the origin of Ciputao 0941♀, Ciputao 0940♂, and Fu’an-ci-01 using SSR markers and used both SSR and SRAP markers to resolve homonymy. The result will be valuable for further management and protection of V. davidii germplasm resources.

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Genetic Diversity of Local Maize Germplasm of Tana Toraja South Sulawesi Using SSR (Simple Sequence Repeat) Markers

Ilmu Pertanian (Agricultural Science) ◽

10.22146/ipas.33085 ◽

2018 ◽

Vol 2 (3) ◽

pp. 144

Author(s):

Ramlah Ramlah ◽

Isna Rasdianah Aziz ◽

Cut Muthiadin ◽

Mashuri Masri ◽

Muhammad Khalifah Mustami ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Simple Sequence Repeat ◽

Genetic Similarity ◽

Agricultural Research ◽

Similarity Coefficient ◽

Sequence Repeat ◽

Maize Germplasm ◽

South Sulawesi ◽

Simple Sequence

Plant genetic diversity is an emerging variation in a crop group caused by its genetic factors. Local corn germplasm as a source of plant genes that are able to adapt to the local environment. The purpose of this research is to obtain information on genetic variation of Tana Toraja local maize germ plasm using SSR (Simple Sequence Repeat) marker. This research was conducted at Balitsereal Molecular Biology Laboratory, Agricultural Research Agency in Maros Regency, South Sulawesi. A total of 4 local maize populations were analyzed by laboratory experimental method with observation with NTSYS pc 2.1 program. The results showed that the average number of alleles was 3.72 alleles per locus and the polymorphism rate of 0.53 with the genetic similarity coefficient was in the range of 0.47 to 0.85. 2 main clusters formed in the genetic similarity coefficient 0.47. Klaster I is Local DallePondan and Local Purple. Klaster II is Local Bebo and Kandora. The genetic distance is in the range of 0.15 to 0.74 with an average genetic distance of 0.46. From the data obtained shows that the 4th germplasm of the population of Tana Toraja Local maize diteleti has a very informative level of genetic diversity. Genetic diversity of local maize germplasm of Tana Toraja, can be used as a source of genes in the assembly of improved varieties in the future.

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Analysis of genetic diversity among different tomato genotypes using ISSR DNA marker

Genetika ◽

10.2298/gensr1701031s ◽

2017 ◽

Vol 49 (1) ◽

pp. 31-42

Author(s):

Saida Sharifova ◽

Sabina Mehdiyeva ◽

Mehraj Abbasov

Keyword(s):

Genetic Diversity ◽

Dna Marker ◽

Diversity Index ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Similarity Coefficient ◽

Variation Analysis ◽

A Value ◽

Polymorphic Bands ◽

Simple Sequence

Inter simple sequence repeat (ISSR) markers were used for variation analysis among 41 tomato accessions. A total of 50 scorable bands were obtained, where 32 were polymorphic, representing 63.3% of all the amplified loci. Polymorphism percentage ranged from 50 to 90% and an average number of polymorphic bands of 4.0 were observed. An average genetic diversity index was 0.61. Primer UBC860 and UBC825 generated the greatest diversity index with a value of 0.89 and 0.85 respectively. The smallest diversity identified by primer UBC808, with an index of 0.34. The genetic similarity among studied genotypes ranged from 0.52 to 0.98. The cluster analysis based on Jaccard?s similarity coefficient divided genotypes into 6 distinct clusters on a value of 0.74. The lowest genetic distance was found between ?Gronastiy? and ?AG1224? (0.52), ?Orange? and ?AG1224? (0.54), and ?Evgeniya? and ?AG1224? (0.55) accessions. The highest similarity of 0.98 was determined between ?Zafar? and ?Azerbaijan-94?, ?Khachmaz-1? and ?Azerbaijan-94?, ?Khachmaz-1? and ?Severyanka?, and ?Shakar? and ?Absheron-1? accessions.

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GENETIC DIVERSITY EEL Anguilla marmorata BY RAPD IN THUA THIEN HUE PROVINCE, VIETNAM

HUE UNIVERSITY JOURNAL OF SCIENCE TECHNIQUES AND TECHNOLOGY ◽

10.26459/hueunijtt.v130i2b.6132 ◽

2021 ◽

Vol 130 (2B) ◽

Author(s):

Kiều Thị Huyền ◽

Hà Thị Huệ ◽

Nguyễn Quang Linh

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Molecular Marker ◽

Genetic Similarity ◽

Economic Value ◽

Similarity Coefficient ◽

Similarity Coefficients ◽

Random Primer ◽

Anguilla Marmorata ◽

Random Amplification

Anguilla marmorata is a species with high economic value and increasingly interested by organizations and scientists. So far, many of the eel's biological characteristics remain mysterious, and they are often classified according to morphological features such as pigmentation patches, number of vertebrae, ... It is even difficult to distinguish one individual from another in some species, especially in the larval stage. In this study, the Random amplification of polymorphic DNA (RAPD) molecular marker was used to evaluate the genetic diversity of 48 eels collected in Thua Thien Hue province. Results showed that the genetic diversity of individuals in the Eel population studied is quite high. With 8 random primers via PCR, 77 DNA tapes with 76 polymorphic tapes were obtained, the tape size ranged from 170-2,500 bp, in which primer S10 showed the highest diversity with an average Ho value of 0.563, followed by primer S8 (Ho = 0.558). The lowest diversity was in the OPD5 primer (Ho = 0.300). The OPG17 primer is the primer that produces the most polymorphic tapes (13/13 tapes) and the S3 primer for the least amplified tapes polymorphism (9/10 DNA tapes). The diversity coefficient in each random primer ranged from about 0.300 to 0.563, with an average of 0.433. The genetic variation in the Eel population is random. Genetic variation can be attributed mainly to different eel breeding conditions and origins. Genetic similarity coefficients among the Eels varied from 0.660 to 0.910 and were divided into two main groups in genetic similarity coefficient 0.660.

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Genetic Diversity of Castor Bean (Ricinus communis L.) Revealed by ISSR and RAPD Markers

Agronomy ◽

10.3390/agronomy11030457 ◽

2021 ◽

Vol 11 (3) ◽

pp. 457

Author(s):

HyokChol Kim ◽

Pei Lei ◽

Aizhi Wang ◽

Shuo Liu ◽

Yong Zhao ◽

...

Keyword(s):

Genetic Diversity ◽

Castor Bean ◽

Genetic Similarity ◽

Rapd Markers ◽

Ricinus Communis ◽

Similarity Coefficient ◽

Morphological Data ◽

Oilseed Crop ◽

Ricinus Communis L ◽

Polymorphic Bands

Castor (Ricinus communis L.), known as castor oil plant or castor bean, is a non-edible oilseed crop. In the present study, the genetic diversity among 54 samples (3 wild and 51 cultivated) collected worldwide was evaluated using inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPD) markers. A total of 9 ISSR primers produced 83 high-resolution bands with 61 (74.53%) as polymorphic. The percentage of polymorphic bands per primer and the genetic similarity coefficient ranged from 54.55% (UBC-836) to 100% (UBC-808) and from 0.74 to 0.96, respectively. A total of 11 out of 20 RAPD primers amplified unique polymorphic products with an average percentage of polymorphic bands of 60.98% (56 polymorphic bands out of a total of 90 bands obtained). The percentage of polymorphic bands per primer ranged from 25% (OPA-02 and B7) to 90.91% (B21) with the genetic similarity coefficient ranging from 0.73 to 0.98. The unweighted pair group method with arithmetic averages (UPGMA) dendrogram using two molecular markers divided 54 castor genotypes into three groups. Furthermore, based on morphological data, all 54 castor varieties were grouped into three main clusters. The genetic diversity analysis based on two molecular makers showed that most varieties from China were closely related to each other with three varieties (GUANGDONGwild, ZHEJIANGWild, and HANNANWild) belonging to a wild group separated from most of the cultivated castor samples from China, India, France, and Jordan. These results suggested that the cultivated castor contains a narrow genetic base. Accordingly, we recommend that wild castor genetic resources be introduced for breeding novel castor varieties. Furthermore, the Vietnam, Malaysia, Indonesia, and Nigeria accessions were clustered into the same group. The results of principal coordinate analysis (PCoA) and UPGMA cluster analysis were consistent with each other. The findings of this study are important for future breeding studies of castor.

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Study of Genetic Diversity Among Crataegus Species (Hawthorn) Using ISSR Markers in Northwestern of Iran

Pharmaceutical and Biomedical Research ◽

10.18502/pbr.v7i1.7357 ◽

2021 ◽

Author(s):

Mina Beigmohamadi ◽

Fatemeh Rahmani ◽

Leila Mirzaei

Keyword(s):

Genetic Similarity ◽

Genetic Relationships ◽

Issr Markers ◽

Similarity Coefficient ◽

Species Relationships ◽

Important Data ◽

Inter Simple Sequence Repeats ◽

Medicinal Properties ◽

Polymorphic Bands ◽

Simple Sequence

Background: Crataegus spp. (Hawthorn) are used for horticultural and medicinal purposes. Objectives: In the present study, the genetic relationships among the five Iranian Crataegus species were evaluated by Inter Simple Sequence Repeats (ISSR) molecular marker Methods: PCR reactions were performed using six primers (811, 827, 834, 845, 856, and 868) and genetic similarity was calculated based on Jacquard’s similarity coefficient. Results: Six primers generated 79 products in total, of which 71 were polymorphic (89.9%), with an average of 13.1 bands per primer. The percentage of polymorphic bands ranged from 77 to 100. Primer 856 produced the highest number of bands, while the lowest was generated by primer 845. The Jacquard’s similarity coefficient, derived from ISSR marker analysis, ranged from 0.164 to 0.337, indicating high genetic variation among Crataegus species in Iran. Conclusion: This study provides important data for identifying species relationships and helps develop plant breeding strategies to improve the medicinal properties of this genus in the future.

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Genetic Diversity of Phalaris arundinacea Linn Germplasm Detected by SRAP Markers

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.726-731.4494 ◽

2013 ◽

Vol 726-731 ◽

pp. 4494-4503

Author(s):

Kai Kai Cheng ◽

Juan Du ◽

Yan Hua Huang ◽

Casler Michael ◽

Yun Wei Zhang

Keyword(s):

Genetic Diversity ◽

Molecular Marker ◽

Information Content ◽

Polymorphism Information Content ◽

Genetic Similarity ◽

Phalaris Arundinacea ◽

Similarity Coefficient ◽

Ecological Environment ◽

The Usa ◽

Polymorphic Bands

Sequence-related amplified polymorphism (SRAP) molecular marker was used to detect the genetic diversity of 25 accessions of Phalaris arundinacea Linn that collected from the USA, Russia, Kazakhstan, Canada, LanZhou and HuBei. The following results were obtained: 1) Sixteen primer pairs produced 131 polymorphic bands, with an average of 8.19 bands per primer pair. The percentage of polymorphic bands on average was 89.25%. The polymorphism information content (PIC) ranged from 0.784 to 0.9069, with an average of 0.8696. 2) The Neis genetic similarity coefficient of the tested accessions ranged from 0.5959 to 0.8425, and the average of Neis coefficient was 0.7422. These results suggested that there was rich genetic diversity among the resources of Phalaris arundinacea Linn. 3) Twenty-five accessions were clustered into five groups. Moreover, the accessions from the same or similar origin frequently clustered into one group. The findings implied that the correlation among the resources, geographical and ecological environment.

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SSR DNA marker aided genetic diversity assessment of selected willow clones

Genetika ◽

10.2298/gensr1302527s ◽

2013 ◽

Vol 45 (2) ◽

pp. 527-536 ◽

Cited By ~ 3

Author(s):

N.B. Singh ◽

S. Joshi ◽

P. Choudhary ◽

J.P. Sharma

Keyword(s):

Genetic Diversity ◽

Molecular Diversity ◽

Dna Marker ◽

Similarity Coefficient ◽

Gene Pools ◽

Morphometric Traits ◽

Genetic Base ◽

Diversity Assessment ◽

Ssr Primers ◽

Clustering Pattern

Around 100 clones of tree willows were subjected for nursery screening twice on morphometric traits. Genetic diversity was assessed in twenty-five genetically superior willow clones hailing from six countries using 16 SSR primers. Fourteen primers amplified the DNA but only ten showed polymorphism. Total 34 bands were scored, out of that 27 were found to be polymorphic and 7 were monomorphic. Three primers showed 100% polymorphism whereas 79.4% polymorphism was recorded in total. The dendrogram obtained from SSR markers revealed that clone SE-69-002 (S. matsudana) and NZ-1040 (S. matsudana X S. alba) as most similar clones (Jaccards coefficient of 0.97), and clone PN-721(S. matsudana X S. alba) and PN-731 (S. nigra), as most divergent clones (Jaccards coefficient of 0.63). All the genotypes were grouped into 4 distinct clusters. On the basis of similarity coefficient analysis the first cluster comprised of 11 genotypes, the second cluster have 8 genotypes where as third one has only one genotype and fourth cluster retained five genotypes. The clustering pattern further indicated that the geographic distribution may not be the reflection of genetic diversity in willow clones. Genotypes with high molecular diversity could be used in breeding programme in order to obtain heterotic hybrids and development of gene pools with broad genetic base. The genotype specific bands developed by the SSR primers could also be used for identification of cultivar.

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EVALUATION OF GENETIC DIVERSITY IN CACAO COLLECTED FROM KOLAKA, SOUTHEAST SULAWESI, USING SSR MARKERS

Indonesian Journal of Agricultural Science ◽

10.21082/ijas.v16n2.2015.pp.71-78 ◽

2016 ◽

Vol 16 (2) ◽

pp. 71

Author(s):

Rubiyo Rubiyo ◽

Nur Kholilatul Izzah ◽

Indah Sulistiyorini ◽

Cici Tresniawati

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Gel Electrophoresis ◽

Genetic Similarity ◽

Similarity Coefficient ◽

Breeding Program ◽

New Variety ◽

Average Value ◽

The Third ◽

Ctab Method

Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC) resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety.

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Genetic diversity of Czech apple cultivars inferred from microsatellite markers analysis

Horticultural Science ◽

10.17221/218/2011-hortsci ◽

2012 ◽

Vol 39 (No. 4) ◽

pp. 149-157 ◽

Cited By ~ 10

Author(s):

J. Patzak ◽

F. Paprštein ◽

A. Henychová ◽

J. Sedlák

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Simple Sequence Repeat ◽

Cultivar Identification ◽

Genetic Relationships ◽

Similarity Coefficient ◽

Collection Management ◽

Apple Cultivars ◽

Repeat Primer ◽

Simple Sequence

Genetic diversity and genetic relationships of Czech apple cultivars were evaluated. Trees of 33 Czech apple cultivars and 97 reference foreign cultivars were analysed using the set of 10 SSR (simple sequence repeat) primer pairs. The total of 89 polymorphic alleles were amplified, while the number of alleles per locus ranged from 4 to 14. The SSR dendrogram, based on the Jaccard’s similarity coefficient, divided apple cultivars into three major groups: Cox’s Orange Pippin, McIntosh and Golden Delicious ancestries. The clustering highly depended on pedigree and origin of apple cultivars. Spontaneous mutated cultivars were identical with their progenitors. We proved that microsatellite markers were useful for evaluation of genetic resources, collection management and cultivar identification.  

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