Research Article ISSR and SSR markers for determining genetic relationships among three wild species of <i>Passiflora</i>

In this study, SRAP and SSR markers were employed to determine genetic relationships among 42 persimmon genotypes (Diospyros kaki Thunb) obtained from Hatay province and 3 persimmon cultivars, 2 of which belong to Diospyros kaki Thunb and one belongs to Diospyros oleifera Cheng. Genetic relationships were determined by using a total of 29 molecular DNA primers (SRAP and SSR). Of these primers, 21 SRAP primer combinations produced a total of 107 bands and 77.6% of them were polymorphic; 8 SSR primers produced 26 polymorphic bands with an average polymorphism ratio of 84.6%. The SRAP and SSR markers produced 4.6 bands as average and the number of bands produced per marker was calculated as 3.6. The lowest similarity was observed between MK-113 (Diospyros oleifera Cheng) and the other genotypes all belongs to Diospyros kaki Thunb (with similarity ratios of 0.41-0.69 for SRAP primers, between 0.25-0.67 for SSR primers). The genotypes/cultivars belongs to Diospyros kaki had similarity ratio between 0.98-1.00 according to SRAP and SSR markers. This synonym or similarity could be results of clonal propagation rather than autogamy.

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Determination of genetic relationships among elite thermosensitive genic male sterile lines (TGMS) of rice (Oryza sativa L.) employing morphological and simple sequence repeat (SSR) markers

Journal of Genetics ◽

10.1007/s12041-011-0018-5 ◽

2011 ◽

Vol 90 (1) ◽

pp. 11-19 ◽

Cited By ~ 8

Author(s):

VIKAS KUMAR SINGH ◽

PRITI UPADHYAY ◽

PALLAVI SINHA ◽

ASHISH KUMAR MALL ◽

SANJAY KUMAR JAISWAL ◽

...

Keyword(s):

Oryza Sativa ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Oryza Sativa L ◽

Genetic Relationships ◽

Sequence Repeat ◽

Male Sterile ◽

Simple Sequence

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Analysis of genetic relationships of genotypes of the genus Rosa L. from the collection of Nikita Botanical Gardens using ISSR and IRAP DNA markers

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj20.639 ◽

2020 ◽

Vol 24 (5) ◽

pp. 474-480

Author(s):

I. I. Suprun ◽

S. A. Plugatar ◽

I. V. Stepanov ◽

T. S. Naumenko

Keyword(s):

Genetic Diversity ◽

Bayesian Methods ◽

Dna Markers ◽

Wild Species ◽

Genetic Similarity ◽

Genetic Relationships ◽

Issr Markers ◽

The Other ◽

Clustering Methods ◽

Botanical Gardens

In connection with the development of breeding and the creation of new plant varieties, the problem of their genotyping and identification is becoming increasingly important, therefore the use of molecular methods to identify genetic originality and assess plant genetic diversity appears to be relevant. As part of the work performed, informative ISSR and IRAP DNA markers promising for the study of genetic diversity of the Rosa L. genus were sought and applied to analysis of genetic relationships among 26 accessions of the genus Rosa L. from the gene pool collection of Nikita Botanical Gardens. They included 18 cultivated varieties and 8 accessions of wild species. The species sample included representatives of two subgenera, Rosa and Platyrhodon. The subgenus Platyrhodon was represented by one accession of the species R. roxburghii Tratt. Cultivated roses were represented by varieties of garden groups hybrid tea, floribunda, and grandiflora. The tested markers included 32 ISSRs and 13 IRAPs. Five ISSR markers (UBC 824, ASSR29, 3A21, UBC 864, and UBC 843) and three IRAPs (TDK 2R, Сass1, and Сass2) were chosen as the most promising. They were used for genotyping the studied sample of genotypes. In general, they appeared to be suitable for further use in studying the genetic diversity of the genus Rosa L. The numbers of polymorphic fragments ranged from 12 to 31, averaging 19.25 fragments per marker. For markers UBC 864 and UBC 843, unique fingerprints were identified in each accession studied. The genetic relationships of the studied species and varieties of roses analyzed by the UPGMA, PCoA, and Bayesian methods performed on the basis of IRAP and ISSR genotyping are consistent with their taxonomic positions. The genotype of the species R. roxburghii of the subgenus Platyrhodon was determined genetically as the most distant. According to clustering methods, the representative of the species R. bengalensis did not stand out from the group of cultivated varieties. When assessing the level of genetic similarity among the cultivated varieties of garden roses, the most genetically isolated varieties were ‘Flamingo’, ‘Queen Elizabeth’, and ‘Kordes Sondermeldung’; for most of the other varieties, groups of the greatest genetic similarity were identified. This assessment reflects general trends in phylogenetic relationships, both among the studied species of the genus and among cultivated varieties.

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Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

10.21203/rs.3.rs-673512/v1 ◽

2021 ◽

Author(s):

Varun Hiremath ◽

Kanwar Pal Singh ◽

Neelu Jain ◽

Kishan Swaroop ◽

Pradeep Kumar Jain ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Structure Analysis ◽

Genetic Relationships ◽

Crop Improvement ◽

Test Analysis ◽

Average Value ◽

Population Structure Analysis ◽

Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

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Molecular Diversity Analysis in Boro Rice (Oryza sativa L.) Landraces using SSR Markers

Asian Journal of Biology ◽

10.9734/ajob/2021/v12i130156 ◽

2021 ◽

pp. 36-48

Author(s):

Farhana Afrin Vabna ◽

Mohammad Zahidul Islam ◽

Md. Ferdous Rezwan Khan Prince ◽

Md. Ekramul Hoque

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Molecular Diversity ◽

Genetic Relationships ◽

Group Method ◽

Diversity Analysis ◽

Average Value ◽

Rice Landraces ◽

Boro Rice ◽

Research Institute

Aims: The aim of the study was to determine the genetic diversity of twenty four Boro rice landraces using rice genome specific twelve well known SSR markers. Study Design: Genomic DNA extraction, PCR amplification, Polyacrylamide gel electrophoresis (PAGE) and data analysis-these steps were followed to perform the research work. Data was analysed with the help of following software; POWERMAKER version 3.25, AlphaEaseFC (Alpha Innotech Corporation) version 4.0. UPGMA dendrogram was constructed using MEGA 5.1 software. Place and Duration of Study: The study was conducted at the Genetic Resources and Seed Division (GRSD), Bangladesh Rice Research Institute (BRRI), Joydebpur, Gazipur, Bangladesh during the period of November 2017 to March 2018. Methodology: Simple Sequence Repeat (SSR) markers were used to assay 24 landraces of Boro rice collected from the Gene Bank of Bangladesh Rice Research Institute (BRRI). Results: A total fifty four (54) alleles were detected, out of which forty five (45) polymorphic alleles were identified. The Polymorphic Information Content (PIC) of SSR markers ranged from 0.08 (RM447) to 0.84 (RM206) with an average value of PIC = 0.49. Gene diversity ranges from 0.08 (RM447) to 0.86 (RM206) with an average value of 0.52. The RM206 marker can be considered as the best marker among the studied markers for 24 rice landraces. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Mean (UPGMA) indicated the segregation of 24 genotypes into three main clusters. Conclusion: The result revealed that SSR markers are very effective tools in the study of genetic diversity and genetic relationships and this result can be conveniently used for further molecular diversity analysis of rice genotypes to identify diverse parent for the development of high yielding variety in rice.

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A search for diagnostic AFLP markers in Cichorium species with emphasis on endive and chicory cultivar groups

Genome ◽

10.1139/g00-024 ◽

2000 ◽

Vol 43 (3) ◽

pp. 470-476 ◽

Cited By ~ 24

Author(s):

A M Kiers ◽

T HM Mes ◽

R van der Meijden ◽

K Bachmann

Keyword(s):

Wild Species ◽

Genetic Relationships ◽

Group Method ◽

Specific Marker ◽

Pair Group ◽

Cultivar Groups ◽

Average Analysis ◽

Species Analysis ◽

Cultivated Species ◽

Unique Markers

The genus Cichorium consists of two widely cultivated species C. intybus (chicory) and C. endivia (endive) and four wild species, C. bottae, C. spinosum, C. calvum, and C. pumilum. A multivariate and an UPGMA (unweighted pair group method average) analysis based on AFLP (amplified fragment length polymorphism) markers were used to establish the genetic relationships among the species and cultivar groups of C. intybus and C. endivia. At the species level, the results correspond with previously obtained phylogenetic relationships in that C. bottae is the most divergent species, and C. intybus and C. spinosum, as well as C. endivia, C. pumilum, and C. calvum formed clusters. Based on the congruence between phylogenetic and genetic analyses, unique markers were expected for all species, however, hardly any specific marker was found except for C. bottae. The analysis of cultivar groups of C. intybus resembled the species analysis in two respects: (i) grouping of cultivars according to cultivar groups, and (ii) lack of markers unique to cultivar groups. In contrast to C. intybus, the cultivar series of C. endivia do not form distinct groups, which would reflect that crosses have been made among the various cultivar groups. The relationships among Cichorium species and cultivars will be useful for setting up a core collection of Cichorium, and stress the importance of inclusion of the wild species in the collection.Key words: Cichorium, AFLP, diagnostic markers, cultivar relationships, genetic resources.

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Genetic diversity among silkworm (Bombyx mori L., Lep., Bombycidae) germplasms revealed by microsatellites

Genome ◽

10.1139/g05-053 ◽

2005 ◽

Vol 48 (5) ◽

pp. 802-810 ◽

Cited By ~ 30

Author(s):

Muwang Li ◽

Li Shen ◽

Anying Xu ◽

Xuexia Miao ◽

Chengxiang Hou ◽

...

Keyword(s):

Genetic Diversity ◽

Bombyx Mori ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Group Method ◽

Sequence Repeat ◽

Bombyx Mori L ◽

Simple Sequence ◽

Silkworm Bombyx Mori

To determine genetic relationships among strains of silkworm, Bombyx mori L., 31 strains with different origins, number of generations per year, number of molts per generation, and morphological characters were studied using simple sequence repeat (SSR) markers. Twenty-six primer pairs flanking microsatellite sequences in the silkworm genome were assayed. All were polymorphic and unambiguously separated silkworm strains from each other. A total of 188 alleles were detected with a mean value of 7.2 alleles/locus (range 2–17). The average heterozygosity value for each SSR locus ranged from 0 to 0.60, and the highest one was 0.96 (Fl0516 in 4013). The mean polymorphism index content (PIC) was 0.66 (range 0.12–0.89). Unweighted pair group method with arithmetic means (UPGMA) cluster analysis of Nei's genetic distance grouped silkworm strains based on their origin. Seven major ecotypic silkworm groups were analyzed. Principal components analysis (PCA) for SSR data support their UPGMA clustering. The results indicated that SSR markers are an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in the silkworm.Key words: silkworm, Bombyx mori L., microsatellites, simple sequence repeat (SSR), genetic diversity.

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Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb) Lindl) assessed by SSR markers

Genome ◽

10.1139/g04-101 ◽

2005 ◽

Vol 48 (1) ◽

pp. 108-114 ◽

Cited By ~ 35

Author(s):

José Miguel Soriano ◽

Carlos Romero ◽

Santiago Vilanova ◽

Gerardo Llácer ◽

María Luisa Badenes

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Malus Domestica ◽

Genetic Relationships ◽

Germplasm Collection ◽

Mean Value ◽

Eriobotrya Japonica ◽

Fixation Index ◽

Group Method ◽

Malus Domestica Borkh

Genetic relationships among 40 loquat (Eriobotrya japonica (Thunb) Lindl) accessions that originated from different countries and that are part of the germplasm collection of the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were evaluated using microsatellites. Thirty primer pairs flanking microsatellites previously identified in Malus × domestica (Borkh.) were assayed. Thirteen of them amplified polymorphic products and unambiguously distinguished 34 genotypes from the 40 accessions analyzed. Six accessions showing identical marker patterns were Spanish local varieties thought to have been derived from 'Algerie' by a mutational process very common in loquat species. A total of 39 alleles were detected in the population studied, with a mean value of 2.4 alleles per locus. The expected and observed heterozygosities were 0.46 and 51% on average, respectively, leading to a negative value of the Wright's fixation index (–0.20). The values of these parameters indicate a smaller degree of genetic diversity in the set of loquat accessions analyzed than in other members of the Rosaceae family. Unweighted pair-group method (UPGMA) cluster analysis, based on Nei's genetic distance, generally grouped genotypes according to their geographic origins and pedigrees. The high number of alleles and the high expected heterozygosity detected with SSR markers developed in Malus × domestica (Borkh.) make them a suitable tool for loquat cultivar identification, confirming microsatellite marker transportability among genera in the Rosaceae family.Key words: Eriobotrya japonica, SSR markers, microsatellites, genetic diversity.

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Genetic diversity and relationships among Prunus cerasifera (cherry plum) clones

Botany ◽

10.1139/b08-097 ◽

2008 ◽

Vol 86 (11) ◽

pp. 1311-1318 ◽

Cited By ~ 12

Author(s):

Aniko Horvath ◽

Hélène Christmann ◽

Frédéric Laigret

Keyword(s):

Ssr Markers ◽

Genetic Relationships ◽

Molecular Data ◽

Mean Value ◽

Factorial Correspondence Analysis ◽

Prunus Cerasifera ◽

Statistical Parsimony ◽

Natural Forms ◽

Cpdna Markers ◽

Morphological And Molecular Data

Prunus cerasifera (Ehrh.) (cherry or Myrobalan plum) is a diverse species with several recognized subspecies and natural forms. It is used as rootstock or as an ornamental tree, and is considered to be one progenitor of the garden plum ( Prunus domestica L.). This study considers the genetic relationships among different P. cerasifera clones, including horticultural cultivars. Twenty nine P. cerasifera accessions of the Prunus Genetic Resources Collection of INRA were analysed using morphological traits, maternally inherited chloroplastic DNA (cpDNA) markers, and biparentally inherited microsatellite (SSR) markers. Ploidy information was obtained by flow cytometry. Multiple factorial correspondence analysis of morphological descriptors shows important differences between some clones, but most of the samples are grouped. Fifteen haplotypes of cpDNA were identified and clustered into three groups after statistical parsimony analysis. SSR markers revealed a total of 74 alleles, with a mean value of 10.6 alleles per locus. After analysis of ploidy level, P. cerasifera subsp. caspica was shown to have a hexaploid genome. Morphological and molecular data suggest that the taxonomic classification of some subspecies and of P. cerasifera subsp. caspica may need to be revised after analysis of additional individuals.

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