Molecular phylogeny of genus Musa determined by simple sequence repeat markers

Musa L. was previously separated into five sections (Eumusa, Rhodochlamys, Callimusa, Australimusa and Ingentimusa) based on basic chromosome numbers and morphological characters. However, several molecular analyses currently support restructuring of Musa species into two sections, Musa and Callimusa. The application of simple sequence repeat molecular marker analysis to Musa phylogeny provided valuable, supplemental information about the classification of, and relationships between, Musa species and subspecies. Totally, 28 accessions of Musa acuminata Colla subspecies and varieties and 25 accessions of other Musa species were evaluated; 12 primers produced 91 polymorphic bands, polymorphic information content ranged from 0.4473 to 0.8394 (average = 0.7226), indicating that the primers showed a high level of polymorphism. Our results generally agreed with previous phylogenetic analyses based on molecular data. One clade comprised species of sections Australimusa and Callimusa (X= 10/9); most species of sections Eumusa and Rhodochlamys (X= 11) formed the other clade. The relationships between most species were as expected; however, some species did not conform to findings of previous studies. A wide range of variability was observed in the M. acuminata complex. M. acuminata var. chinensis and M. acuminata subsp. 522 showed the most distant relationships to other subspecies: Musa laterita, Musa ornata and Musa velutina clustered with M. acuminata var. chinensis, suggesting that they may constitute a secondary gene pool for the improvement of cultivated bananas. Molecular data indicated that Musa tongbiguanensis Chen You & Yao-Ting Wu, which was observed and described by our research group in Yunnan, China, was a distinct, new species.

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Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽

10.21273/hortsci.50.8.1143 ◽

2015 ◽

Vol 50 (8) ◽

pp. 1143-1147 ◽

Cited By ~ 8

Author(s):

Benard Yada ◽

Gina Brown-Guedira ◽

Agnes Alajo ◽

Gorrettie N. Ssemakula ◽

Robert O.M. Mwanga ◽

...

Keyword(s):

Genetic Diversity ◽

Linkage Analysis ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Polymorphic Information Content ◽

Genetic Distances ◽

Sequence Repeat ◽

Population Improvement ◽

High Level ◽

Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

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Inter Simple Sequence Repeat markers for analysis of molecular diversity and genetic structure of eighteen Dendrobium cultivars in Sri Lanka

International Journal for Innovation Education and Research ◽

10.31686/ijier.vol6.iss3.975 ◽

2018 ◽

Vol 6 (3) ◽

pp. 91-102

Author(s):

Thanuja Dilrukshi Dharmarathna ◽

H.M.D.A.K. Herath ◽

P.A. Weerasinghe ◽

H.M.V.G. Herath

Keyword(s):

Information Content ◽

Simple Sequence Repeat ◽

Polymorphic Information Content ◽

Morphological Characters ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Sequence Repeat ◽

Information Index ◽

Expected Heterozygosity ◽

Simple Sequence

The genus Dendrobium is one of the largest genera in the family Orchidaceae having more than thousand species over the world with diverse morphological characters. Dendrobium is a popular ornamental plant with complex genetic background which emphasize on the species identification at molecular level. The present study was aimed to identify Inter-Simple Sequence Repeat (ISSR) markers capable of detecting genetic polymorphism to characterize 18 hybrid, commercially available Dendrobium cultivars. Genomic DNA of each cultivar was extracted using CTAB method. A total of 17 different ISSR primers were evaluated. Only the reproducible bands were scored and number of different alleles (Na), number of effective alleles (Ne), Shannon’s Information Index (I), Expected heterozygosity (He), Unbiased expected heterozygosity (UHe), polymorphic percentage and polymorphic information content (PIC) of each primer were calculated. The highest Shannon’s Information Index (0.537±0.08) was recorded by the primer UBC 826 while the highest polymorphic information content (PIC) was generated by primer UBC 807. The PIC values of the primers were ranged from 0.0068 to 0.451, indicating that primers are moderately informative. In total, 631 bands representing 120 loci were amplified showing 85.71% - 100% polymorphism. The genetic similarities between individuals were compiled in the Nei’s genetic identity matrix in order to construct the UPGMA dendrogram. Principle component analysis (PCA) and clustering analysis were done to divide different cultivars into groups. The analysis revealed the presence of four major clusters and two minor clusters among the cultivars. The study suggested that the ISSR markers originated from eight primers 12, 155, UBC 807, UBC 812, UBC 826, UBC 835, UBC 841 and UBC 842 can be used in the detection of molecular variation among cultivars in the genus Dendrobium.

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Simple Sequence Repeat Markers from Cercis canadensis Show Wide Cross-species Transfer and Use in Genetic Studies

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.137.3.189 ◽

2012 ◽

Vol 137 (3) ◽

pp. 189-201 ◽

Cited By ~ 4

Author(s):

Phillip A. Wadl ◽

Robert N. Trigiano ◽

Dennis J. Werner ◽

Margaret R. Pooler ◽

Timothy A. Rinehart

Keyword(s):

Simple Sequence Repeat ◽

Polymorphic Information Content ◽

Genetic Relationships ◽

Tree Breeding ◽

The United States ◽

Morphological Characters ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Simple Sequence ◽

Botanical Varieties

There are 11 recognized Cercis L. species, but identification is problematic using morphological characters, which are largely quantitative and continuous. Previous studies have combined morphological and molecular data to resolve taxonomic questions about geographic distribution of Cercis species, identifying botanical varieties, and associations between morphological variation and the environment. Three species have been used in ornamental plant breeding in the United States, including three botanical varieties of C. canadensis L. from North America and two Asian species, C. chingii Chun and C. chinensis Bunge. In this article, 51 taxa were sampled comprising eight species of Cercis and a closely related species, Bauhinia faberi Oliv. Sixty-eight polymorphic simple sequence repeat markers were used to assess genetic relationships between species and cultivars. For all samples the number of alleles detected ranged from two to 20 and 10 or more alleles were detected at 22 loci. Average polymorphic information content was 0.57 and values ranged from 0.06 to 0.91 with 44 loci 0.50 or greater. Cross-species transfer within Cercis was extremely high with 55 loci that amplified at 100%. Results support previously reported phylogenetic relationships of the North American and western Eurasian species and indicate suitability of these markers for mapping studies involving C. canadensis and C. chinensis. Results also support known pedigrees from ornamental tree breeding programs for the widely cultivated C. canadensis and C. chinensis species, which comprised the majority of the samples analyzed.

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Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

Biochemical Genetics ◽

10.1007/s10528-021-10090-7 ◽

2021 ◽

Author(s):

Júlia Halász ◽

Noémi Makovics-Zsohár ◽

Ferenc Szőke ◽

Sezai Ercisli ◽

Attila Hegedűs

Keyword(s):

Simple Sequence Repeat ◽

Principal Component ◽

Sequence Repeat ◽

Breeding Programs ◽

Allele Number ◽

Genetic Potential ◽

Ssr Loci ◽

High Level ◽

Diversity Studies ◽

Simple Sequence

AbstractPolyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

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Screening of homokaryotic protoclones of Agaricus bisporus (J. Lge) Imbach by colony characters and ISSR markers

Bangladesh Journal of Botany ◽

10.3329/bjb.v39i1.5537 ◽

2010 ◽

Vol 39 (1) ◽

pp. 119-122 ◽

Cited By ~ 2

Author(s):

Mahmudul Islam Nazrul ◽

Fan Xiao Lin ◽

Bian Yin-Bing

Keyword(s):

Simple Sequence Repeat ◽

Agaricus Bisporus ◽

Morphological Characters ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Fruiting Bodies ◽

Sequence Repeat ◽

Slow Growing ◽

Simple Sequence ◽

Issr Primers

Among ten slow-growing protoclones of Agaricus bisporus (J. Lge) Imbach, all appressed colonies showed slower growth rate and spawn run, and inability to produce fruiting bodies in substrate. Seven of 40 inter-simple sequence repeat (ISSR) primers amplified 78 reproducible fragments, 48.93% were polymorphic, each producing 7 to 16 bands ranging from 0.10 to 2.10 kbp, sufficient to differentiate the protoclones from each other. Appressed protoclones were homoallelic at a number of loci that were heteroallelic in the parent, suggesting that they represented rare homokaryons. Thus, using morphological characters along with ISSR, polymorphisms could be useful for quick, easy, and accurate in distinguishing homo- and heterokaryotic isolates. Key words: Agaricus bisporus (J. Lge) Imbach; Homokaryon; ISSR; Protoclone DOI: 10.3329/bjb.v39i1.5537Bangladesh J. Bot. 39(1): 119-122, 2010 (June)

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Using Morphological Characters and Simple Sequence Repeat (SSR) Markers to Characterize Tunisian Fig (Ficus Carica L.) Cultivars

Acta Biologica Cracoviensia s Botanica ◽

10.2478/v10182-011-0019-y ◽

2011 ◽

Vol 53 (2) ◽

Cited By ~ 5

Author(s):

Olfa Saddoud ◽

Ghada Baraket ◽

Khaled Chatti ◽

Mokhtar Trifi ◽

Mohamed Marrakchi ◽

...

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Morphological Characters ◽

Ficus Carica ◽

Sequence Repeat ◽

Simple Sequence

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Assessment of the Genetic Diversity of Joha Rice Germplasms by using Simple Sequence Repeat Markers

Indian Journal of Agricultural Research ◽

10.18805/ijare.a-5689 ◽

2021 ◽

Author(s):

P. Saikia ◽

B. Neog ◽

N. Gogoi ◽

D. Baruah

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Genetic Relationship ◽

Simple Sequence Repeat ◽

Similarity Index ◽

Morphological Characters ◽

Aromatic Rice ◽

Sequence Repeat ◽

Rice Landraces ◽

Simple Sequence

Background: Joha Rice are aromatic rice landraces, having small to medium grain size, indigenous to Assam, India. Due to the introduction of high yielding hybrid varieties, many endemic rice landraces including Joha Rice, are in a verge of extinction, as these can only be conserved and maintained by repetitive cultivation. As there is a conflict of local names for these landraces, many landraces with similar morphological characters have been reported from various parts. Simple sequence repeat (SSR) markers with longer perfect repeats have earlier proved successful and essential in studying the genetic diversity among rice cultivars. The present study is aimed to evaluate the genetic relationship among fifteen (15) aromatic Joha rice landraces endemic to Upper Brahmaputra Valley, Assam.Methods: In the present investigation, different landraces of Joha rice were surveyed during 2016-2019. 15 landraces were selected, based on their morphological characters and local data. The collected germplasm of Joha rice was grown in the experimental plots and DNA from young, healthy leaves were isolated which were further used for determination of genetic diversity using SSR markers. Thirty-eight SSR markers were used to evaluate the genetic relationship among the fifteen aromatic rice landraces.Result: A total of 110 polymorphic alleles were detected by 34 markers across all the landraces, with an average of 3.25 per locus. The Polymorphic Information Content (PIC) ranged from 0.24 to 0.83, with an average of 0.5 for each marker. The marker RM154, RM454 and RM489 produced maximum six alleles showing PIC value of 0.82, 0.82 and 0.83, indicating a high polymorphism. UPGMA cluster analysis using Jaccard’s similarity index produced a dendrogram clustering the rice landraces in three major groups and five subgroups. Group II, which consisted of five sub-groups and 12 landraces, showed diverse genotypes. These landraces showed significant genetic similarities.

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Analysis of the genetic diversity and population structure of Salix psammophila based on phenotypic traits and simple sequence repeat markers

PeerJ ◽

10.7717/peerj.6419 ◽

2019 ◽

Vol 7 ◽

pp. e6419 ◽

Cited By ~ 2

Author(s):

Lei Hao ◽

Guosheng Zhang ◽

Dongye Lu ◽

Jianjun Hu ◽

Huixia Jia

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Simple Sequence Repeat ◽

Phylogenetic Analyses ◽

Group Method ◽

Phenotypic Traits ◽

Germplasm Management ◽

Sequence Repeat ◽

Marginal Populations ◽

Simple Sequence

Salix psammophila (desert willow) is a shrub endemic to the Kubuqi Desert and the Mu Us Desert, China, that plays an important role in maintaining local ecosystems and can be used as a biomass feedstock for biofuels and bioenergy. However, the lack of information on phenotypic traits and molecular markers for this species limits the study of genetic diversity and population structure. In this study, nine phenotypic traits were analyzed to assess the morphological diversity and variation. The mean coefficient of variation of 17 populations ranged from 18.35% (branch angle (BA)) to 38.52% (leaf area (LA)). Unweighted pair-group method with arithmetic mean analysis of nine phenotypic traits of S. psammophila showed the same results, with the 17 populations clustering into five groups. We selected 491 genets of the 17 populations to analyze genetic diversity and population structure based on simple sequence repeat (SSR) markers. Analysis of molecular variance (AMOVA) revealed that most of the genetic variance (95%) was within populations, whereas only a small portion (5%) was among populations. Moreover, using the animal model with SSR-based relatedness estimated of S. psammophila, we found relatively moderate heritability values for phenotypic traits, suggesting that most of trait variation were caused by environmental or developmental variation. Principal coordinate and phylogenetic analyses based on SSR data revealed that populations P1, P2, P9, P16, and P17 were separated from the others. The results showed that the marginal populations located in the northeastern and southwestern had lower genetic diversity, which may be related to the direction of wind. These results provide a theoretical basis for germplasm management and genetic improvement of desert willow.

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Genetic variation in Hydrangea macrophylla (Thunb.) Ser. in Russia based on simple sequence repeat markers

Bangladesh Journal of Botany ◽

10.3329/bjb.v47i4.47389 ◽

2018 ◽

Vol 47 (4) ◽

pp. 937-943

Author(s):

Natalia Sukhikh ◽

Valentina Malyarovskaya ◽

Anastasiya Kamionskaya ◽

Lidia Samarina ◽

Svetlana Vinogradova

Keyword(s):

Simple Sequence Repeat ◽

Genetic Relationships ◽

Effective Number ◽

Sequence Repeat ◽

Base Pairs ◽

Breeding Programs ◽

Simple Sequence Repeat Markers ◽

Hydrangea Macrophylla ◽

High Level ◽

Simple Sequence

Genetic diversity and genetic relationships among 39 accessions of Hydrangea macrophylla (Thunb.) Ser. were analyzed using 38 previously developed simple sequence repeat markers (SSRs). A total of 38 polymorphic primers representing 166 bands with an average of 4.53 polymorphic bands per primer were selected. The number of alleles detected per locus ranged from two to eight with a total of 163 alleles amplified. The size of the amplified fragments ranged from 70 to180 base pairs. The effective multiallelic markers with high level of heterozygosity (more than 0.7) and effective number of alleles (more than 3.5) were identified. In this study nine SSR markers showed clear polymorphisms. The dendrogram grouped all hybrids in three major clusters, and two of these clusters included only mophead cultivars. The lacecap cultivars clustered more closely to each other. The results of this research could be used in breeding programs of H. macrophylla.

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ANALYSIS OF GENETIC DIVERSITY IN TWELVE CULTIVARS OF PEA BASED ON MORPHOLOGICAL AND SIMPLE SEQUENCE REPEAT MARKERS

Indonesian Journal of Agricultural Science ◽

10.21082/ijas.v19n2.2018.p57-66 ◽

2018 ◽

Vol 19 (2) ◽

pp. 57

Author(s):

Brijesh Kumar Singh ◽

Monoj Sutradhar ◽

Amit Kumar Singh ◽

Ajay Kumar Singh ◽

Rajendra Prakash Vyas

Keyword(s):

Genetic Diversity ◽

Total Variation ◽

Simple Sequence Repeat ◽

Diversity Index ◽

Polymorphic Information Content ◽

Resolving Power ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Simple Sequence ◽

Number Of Seeds

Pea(Pisum sativum L.)is the second most important legume crop worldwide after chickpea (Cicer arietinum L.) and valuable resources for their genetic improvement. This study aimed to analyze genetic diversity of pea cultivars through morphological and molecular markers. The present investigation was carried out with 12 pea cultivars using 28 simple sequence repeat markers. A total of 60 polymorphic bands with an average of 2.31 bands per primer were obtained. The polymorphic information content, diversity index and resolving power were ranged from 0.50 to 0.33, 0.61 to 0.86 and 0.44 to 1.0 with an average of 0.46, 0.73 and 0.76, respectively. The 12 pea cultivars were grouped into 3 clusters obtained from cluster analysis with a Jaccardd’s similarity coefficient range of 0.47-0.78, indicating the sufficient genetic divergence among these cultivars of pea. The principal component analysis showed that first three principal components explained 86.97% of the total variation, suggesting the contribution of quantitative traits in genetic variability. The contribution of 32.59% for number of seeds per plant, stem circumference, number of pods per plant and number of seeds per pod in the PC1 leads to the conclusion that these traits contribute more to the total variation observed in the 12 pea cultivars and would make a good parental stock material. Overall, this SSR analysis complements morphological characters of initial selection of these pea germplasms for future breeding program.

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