Microsatellite-based evaluation of Ribes spp. germplasm

Genome ◽  
2009 ◽  
Vol 52 (10) ◽  
pp. 839-848 ◽  
Author(s):  
M. Cavanna ◽  
D. Torello Marinoni ◽  
G. L. Beccaro ◽  
G. Bounous
Keyword(s):  
Genetic Variability ◽  
Simple Sequence Repeat ◽  
Initial Study ◽  
Microsatellite Analysis ◽  
Sequence Repeat ◽  
Microsatellite Data ◽  
Breeding Programs ◽  
Plant Collections ◽  
Ribes Spp ◽  
Simple Sequence

There is a lack of published microsatellite data which characterizes Ribes spp. To address this, an initial study of simple sequence repeat (SSR) variation was undertaken in 41 cultivars belonging to four species of the genus Ribes to evaluate its genetic variability. The cultivars were collected in Piedmont, northwest Italy, together with one cultivar from Switzerland. Twenty SSRs were screened for amplification and polymorphism. Seven failed to amplify, and therefore the remaining 13 were selected and used to fingerprint all the cultivars. Microsatellite analysis resulted in the identification of 38 genotypes, suggesting the existence of possible clonal genotypes and synonyms. Among the cultivars analyzed, two tetraploid accessions were found. The evaluation of genetic variability in Ribes is of fundamental importance for future nutritional breeding programs and to preserve genetic resources, as cultivar characterization permits better management of plant collections.

scholarly journals 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

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.

scholarly journals Genetic Relationships among 10 Prunus Rootstock Species from China, Based on Simple Sequence Repeat Markers

2016 ◽  
Vol 141 (5) ◽  
pp. 520-526 ◽  
Author(s):  
Qijing Zhang ◽  
Dajun Gu
Keyword(s):  
Phylogenetic Analysis ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Banding Patterns ◽  
Simple Sequence Repeat Markers ◽  
Ssr Primers ◽  
Relationship Of ◽  
Simple Sequence

To improve the efficiency of breeding programs for Prunus rootstock hybrids in China, we analyzed the subgenus status and relationship of 10 Chinese rootstock species, by using 24 sets of simple sequence repeat (SSR) primers. The SSR banding patterns and phylogenetic analysis indicated that subgenus Cerasus is more closely related to subgenus Prunophora than to subgenus Amygdalus, and that subgenus Lithocerasus is more closely related to subgenus Prunophora and subgenus Amygdalus than to subgenus Cerasus. In addition, Prunus triloba was more closely related to Prunus tomentosa than to the members of subgenus Amygdalus. Therefore, we suggest that P. tomentosa and P. triloba should be assigned to the same group, either to subgenus Lithocerasus or Prunophora, and we also propose potential parent combinations for future Prunus rootstock breeding.

scholarly journals Evaluation and Pre-selection of New Grapevine Genotypes Resistant to Downy and Powdery Mildew, Obtained by Cross-Breeding Programs in Spain

2021 ◽  
Vol 12 ◽  
Author(s):  
Leonor Ruiz-García ◽  
Pilar Gago ◽  
Celia Martínez-Mora ◽  
José Luis Santiago ◽  
Diego J. Fernádez-López ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Powdery Mildew ◽  
Simple Sequence Repeat ◽  
Selection Process ◽  
Sequence Repeat ◽  
Sources Of Resistance ◽  
Breeding Programs ◽  
Phenotypic Resistance ◽  
Simple Sequence ◽  
Selection Of

The need to develop an environmentally friendly, sustainable viticulture model has led to numerous grapevine improvement programmes aiming to increase resistance to downy and powdery mildew. The success of such programmes relies on the availability of protocols that can quantify the resistance/susceptibility of new genotypes, and on the existence of molecular markers of resistance loci that can aid in the selection process. The present work assesses the degree of phenotypic resistance/susceptibility to downy and powdery mildew of 28 new genotypes obtained from crosses between “Monastrell” and “Regent.” Three genotypes showed strong combined resistance, making them good candidates for future crosses with other sources of resistance to these diseases (pyramiding). In general, laboratory and glasshouse assessments of resistance at the phenotype level agreed with the resistance expected from the presence of resistance-associated alleles of simple sequence repeat (SSR) markers for the loci Rpv3 and Ren3 (inherited from “Regent”), confirming their usefulness as indicators of likely resistance to downy and powdery mildew, respectively, particularly so for downy mildew.

scholarly journals Genetic Diversity and Population Structure of Traditional Greek and Cypriot Melon Cultigens (Cucumis melo L.) Based on Simple Sequence Repeat Variability

HortScience ◽  
2009 ◽  
Vol 44 (7) ◽  
pp. 1820-1824 ◽  
Author(s):  
Emmanouil N. Tzitzikas ◽  
Antonio J. Monforte ◽  
Abdelhak Fatihi ◽  
Zacharias Kypriotakis ◽  
Tefkros A. Iacovides ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Simple Sequence Repeat ◽  
Cucumis Melo ◽  
Sequence Repeat ◽  
Population Structure Analysis ◽  
Simple Sequence

Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure among traditional Greek and Cypriot melon cultigens (Cucumis melo L.). All SSR markers were polymorphic with a total number of 81 alleles, whereas all cultigens could be distinguished with at least one SSR, except cultigens 43 and 41. Reference accessions showed larger genetic variability with an average of four alleles per locus and 0.65 gene of diversity compared with an average of 2.47 alleles per locus and 0.30 of gene diversity for the Greek/Cypriot cultigens. Observed heterozygosity was very low, indicating a lack of outcrossing, at least in recent times. Unrooted neighbor-joining tree analysis and population structure analysis clustered the cultigens and the reference genotypes into five groups. All cultigens could be distinguished; the Cypriot cultigens were more closely related to the inodorus ‘Piel de Sapo’, whereas the Greek cultigens were located in an intermediate position between the inodorus ‘Piel de Sapo’ and the cantalupensis ‘Védrantais’. The cultigen ‘Kokkini’ was the most divergent among the Greek and Cypriot cultigens. This association between geographic origin and genetic similarity among Greek and Cypriot cultigens indicates geographic isolation. Most of the cultivars from the same cultivar group (i.e., inodorus, cantalupensis) clustered together, but some exceptions were found, suggesting that former inodorus landraces would have been transformed to cantalupensis as a result of intercrossing and further selection by farmers. Results of population structure analysis support mixing between cantalupensis and inodorus. ‘Agiou Basileiou’, an inodorus cultigen, was assigned to the subpopulation IV/II of which II is a pure cantalupensis subpopulation. Greek and Cypriot melon cultigens were developed from a broader germplasm base than western Mediterranean cultivars and exhibited useful for melon breeding programs genetic variability.

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

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.

scholarly journals Characterisation and genetic diversity analysis of selected chickpea cultivars of nine countries using simple sequence repeat (SSR) markers

2011 ◽  
Vol 62 (2) ◽  
pp. 177 ◽  
Author(s):  
Tadesse Sefera ◽  
Bekele Abebie ◽  
Pooran M. Gaur ◽  
Kebebew Assefa ◽  
Rajeev K. Varshney
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Dna Fingerprint ◽  
Pedigree Information ◽  
Sequence Repeat ◽  
Dissimilarity Matrix ◽  
Breeding Programs ◽  
Simple Sequence ◽  
Chickpea Cultivars

The genomic DNA profiles of 48 chickpea cultivars released in nine countries and of historical significance to the chickpea breeding programs at ICRISAT and in Ethiopia were evaluated using 48 simple sequence repeat (SSR) markers. Across the cultivars, a total of 504 alleles representing the 48 SSR loci were detected with frequencies ranging from three to 22 (mean 10.5) alleles per locus. The polymorphism information content (PIC) for the SSR markers varied from 0.37 to 0.91 (mean 0.77). A subset of only three highly informative SSR markers (TA176, TA2, TA180) enabled complete discrimination among all 48 chickpea cultivars tested. Hierarchical neighbour-joining UPGMA cluster analysis based on simple matching dissimilarity matrix resolved the 48 cultivars into two major clusters representing desi and kabuli types. These cluster groupings of the cultivars were consistent with the pedigree information available for the cultivars as to the phenotypic classes of chickpea types. Analysis of the temporal patterns of the SSR diversity by classifying 48 chickpea cultivars into four periods of release revealed increasing tendencies in the overall genetic diversity from 0.42 for the earliest varieties developed in the 1970s to 0.62 for those released in the 1980s, and reached a maximum and equivalent level of 0.72 for the varieties developed in the 1990s and 2000s. Overall, the study ascertained that SSRs provide powerful marker tools in revealing genetic diversity and relationships in chickpeas, thereby proving useful for selection of parents in breeding programs and also for DNA fingerprint identification of cultivars.

scholarly journals Genetic variability analysis of faba bean accessions using Inter-simple sequence repeat (ISSR) markers

2015 ◽  
Vol 75 (1) ◽  
pp. 122-130 ◽  
Author(s):  
María E Salazar-Laureles ◽  
Delfina de J. Pérez-López ◽  
Andrés González-Huerta ◽  
Luis M Vázquez-García ◽  
Ernestina Valadez-Moctezuma
Keyword(s):  
Genetic Variability ◽  
Faba Bean ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
Variability Analysis ◽  
Simple Sequence

scholarly journals Genetic Diversity of Arabica Coffee (Coffea arabicaL.) in Nicaragua as Estimated by Simple Sequence Repeat Markers

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Mulatu Geleta ◽  
Isabel Herrera ◽  
Arnulfo Monzón ◽  
Tomas Bryngelsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Simple Sequence Repeat ◽  
Significant Contribution ◽  
Gene Diversity ◽  
Ex Situ ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Arabica Coffee ◽  
Simple Sequence

Coffea arabicaL. (arabica coffee), the only tetraploid species in the genusCoffea, represents the majority of the world’s coffee production and has a significant contribution to Nicaragua’s economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR) markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei’s gene diversity (HT) and the within-population gene diversity (HS) were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA) revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (FST=0.13;P<0.001). The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved throughex situconservation of a low number of populations from each variety.

scholarly journals Genetic variability of Brazilian rice landraces determined by SSR markers

2009 ◽  
Vol 44 (7) ◽  
pp. 706-712 ◽  
Author(s):  
Tereza Cristina de Oliveira Borba ◽  
Clistiane dos Anjos Mendes ◽  
Élcio Perpétuo Guimarães ◽  
Tuliana Oliveira Brunes ◽  
Jaime Roberto Fonseca ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Molecular Data ◽  
Factorial Correspondence Analysis ◽  
Rice Cultivars ◽  
Market Demand ◽  
Breeding Programs ◽  
Rice Landraces ◽  
Simple Sequence

The objective of this study was to evaluate the genetic variability of rice (Oryza sativa) landraces collected in Brazilian small farms. Twelve simple sequence repeat (SSR) markers characterized 417 landraces collected in 1986, 1987 and 2003, in the state of Goiás, Brazil. The number of landraces with long and thin grain type increased in the evaluated period, probably due to market demand. Based on the molecular data, the genetic variability increased during this period and, as per to the factorial correspondence analysis, most of the accessions were grouped according to the year of collection. The incorporation of modern rice cultivars in landrace cultivation areas and the selection carried out by small farmers are the most probable factors responsible for increasing landrace genetic variability, during the evaluated period. Genotype exchange between farmers, selection practice and local environmental adaptation are able to generate novel adapted allele combinations, which can be used by breeding programs, to reinitiate the process.

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