Development and characterization of EST-SSR markers from Jatropha curcas EST database and their transferability across jatropha-related species/genus

Biologia ◽  
2013 ◽  
Vol 68 (1) ◽  
Author(s):  
Kularb Laosatit ◽  
Patcharin Tanya ◽  
Chatree Saensuk ◽  
Peerasak Srinives
Keyword(s):  
Ssr Markers ◽  
Jatropha Curcas ◽  
Related Species ◽  
High Efficiency ◽  
Genetic Relatedness ◽  
Ricinus Communis ◽  
Raw Material ◽  
Breeding Programs ◽  
New Varieties

AbstractJatropha curcas (jatropha) is a multipurpose plant with potential as a raw material for biofuel. In the present study, a total of 43,349 expressed sequence tags (ESTs) from J. curcas were searched for type and frequency of simple sequence repeat (SSR) markers. Five thousand one hundred and seventy-five sequences were indentified to contain 6,108 SSRs with 90.8% simple and 9.2% compound repeat motifs. One hundred and sixty-three EST-SSRs were developed and used to evaluate the transferability and genetic relatedness among 4 accessions of J. curcas from China, Mexico, Thailand and Vietnam; 5 accessions of congeneric species, viz. J. gossypiifolia, dwarf J. integerrima, normal J. integerrima, J. multifida, J. podagrica; and Ricinus communis. The polymorphic markers showed 75.56–85.19% transferability among four species of Jatropha and 26.67% transferability across genera in Ricinus communis. Investigation of genetic relatedness showed that J. curcas and J. integerrima are closely related. EST-SSRs used in this study demonstrate a high efficiency of cross species/genera amplification and are useful for identifying genetic diversity of jatropha and its close taxa and to choose the desired related species for wide crossing to improve new varieties of jatropha. The markers can also be further exploited for genetic resource management and genetic improvement of related species/genera through marker-assisted breeding programs.

scholarly journals Development and Characterization of Genic SSR Markers from Indian Mulberry Transcriptome and Their Transferability to Related Species of Moraceae

PLoS ONE ◽  
2016 ◽  
Vol 11 (9) ◽  
pp. e0162909 ◽  
Author(s):  
B. Mathi Thumilan ◽  
R. S. Sajeevan ◽  
Jyoti Biradar ◽  
T. Madhuri ◽  
Karaba N. Nataraja ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Related Species ◽  
Genic Ssr ◽  
Indian Mulberry

scholarly journals Characterization of 23 Polymorphic SSR Markers in Salix humboldtiana (Salicaceae) Using Next-Generation Sequencing and Cross-Amplification from Related Species

2015 ◽  
Vol 3 (4) ◽  
pp. 1400120 ◽  
Author(s):  
Jorge A. Bozzi ◽  
Sascha Liepelt ◽  
Sebastian Ohneiser ◽  
Leonardo A. Gallo ◽  
Paula Marchelli ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ssr Markers ◽  
Related Species ◽  
Next Generation ◽  
Cross Amplification ◽  
Generation Sequencing

Development of interspecific and intergeneric hybrids among jatropha-related species and verification of the hybrids using EST–SSR markers

2014 ◽  
Vol 12 (S1) ◽  
pp. S58-S61 ◽  
Author(s):  
Kularb Laosatit ◽  
Patcharin Tanya ◽  
Narathid Muakrong ◽  
Peerasak Srinives
Keyword(s):  
Related Species ◽  
Oil Content ◽  
Expressed Sequence Tag ◽  
Ricinus Communis ◽  
Fruit Size ◽  
Intergeneric Hybrids ◽  
Raw Material ◽  
Biofuel Production ◽  
Intergeneric Hybridization ◽  
Oilseed Crop

Jatropha curcas (jatropha) is an important non-edible oilseed crop with potential as a raw material for biofuel production. Although J. curcas has 30–35% oil content in its seeds, it has low seed yield ( < 2 ton/ha) and thus cannot become an economically viable crop. However, jatropha has many related species and genera such as J. integerrima, J. multifida, J. podagrica and Ricinus communis that are suitable for interspecific and intergeneric hybridization. The desirable features that can be obtained from these species are high number of inflorescences from J.integerrima, large fruit size from J. multifida, high oil content from J. podagrica and raceme-type inflorescence from R. communis. We were initially successful in producing hybrids between J. curcas and these related species. Hybridity was confirmed using expressed sequence tag (EST)–simple sequence repeat markers developed from the J. curcas EST database.

scholarly journals Molecular characterization of Moroccan grapevine germplasm using SSR markers for the establishment of a reference collection

OENO One ◽  
2009 ◽  
Vol 43 (3) ◽  
pp. 135 ◽  
Author(s):  
Aicha El Oualkadi ◽  
Mohammed Ater ◽  
Zerhoune Messaoudi ◽  
Valérie Laucou ◽  
Jean-Michel Boursiquot ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Core Collection ◽  
Genetic Relatedness ◽  
Geographical Origin ◽  
Molecular Data ◽  
Small Sample ◽  
Reference Collection ◽  
Nuclear Ssr ◽  
High Diversity

<p style="text-align: justify;"><strong>Aims</strong>: This study aims to characterize the SODEA ampelographic collection in Meknès, the only germplasm repository in Morocco. To assess the usefulness of this germplasm, a study was conducted to verify the trueness to type of the genotypes and to provide the first database for a reference collection in Morocco. A core collection was then established to define a small sample easier to handel further characterization.</p><p style="text-align: justify;"><strong>Methods and results</strong>: Ninety-four grapevine samples from the collection were analyzed using 20 nuclear SSR markers. From these samples, we identified 67 grapevine genotypes. The nuclear SSRs revealed a high diversity within the SODEA collection: 202 alleles were detected with a mean of 10.1 alleles per locus. Analysis of molecular data with the software DARwin was used to classify the genotypes into six groups according to their origin or their genetic relatedness. The 18 autochthonous cultivars were differentiated according to geographical origin (North vs. South). We established a core collection among this germplasm using MSTRAT: the complete diversity present in the collection was captured with only 34 individuals. Nevertheless, an optimal core collection representing 89% of the diversity was constituted by only 17 cultivars. Among these 17 individuals, 5 are autochthonous.</p><p style="text-align: justify;"><strong>Conclusion</strong>: The collection of SODEA represents a unique resources of grapevines for Morocco. It contains several important autochthonous cultivars in terms of diversity and agronomic utilisation.</p><p style="text-align: justify;"><strong>Significance and impact of the study</strong>: The study showed potential and interest of the cultivars present in the collection of SODEA, suggesting that their utilisation may be important for the farmers.</p>

scholarly journals Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.)

2010 ◽  
Vol 10 (1) ◽  
pp. 278 ◽  
Author(s):  
Lijun Qiu ◽  
Chun Yang ◽  
Bo Tian ◽  
Jun-Bo Yang ◽  
Aizhong Liu
Keyword(s):  
Ssr Markers ◽  
Castor Bean ◽  
Ricinus Communis ◽  
Ricinus Communis L

Molecular Characterization of Parental Lines and Validation of Snp Markers for Disease Resistance in Common Bean

2021 ◽  
Author(s):  
Lucas Matias Gomes-Messias ◽  
Rosana Pereira Vianello ◽  
Joney Pereira Monteiro-Júnior ◽  
Luana Alves Rodrigues ◽  
Ana Paula Simplício Mota ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Common Bean ◽  
Molecular Characterization ◽  
High Efficiency ◽  
Snp Markers ◽  
Molecular Tools ◽  
Breeding Programs ◽  
Efficiency Of Selection ◽  
Selection Of

Abstract The implementation of molecular tools that help the early selection of genotypes carrying target alleles increases efficiency and reduces the time and costs of breeding programs. The present study aimed the molecular characterization and validation of SNPs targeting disease resistance alleles for assisted selection. A total of 376 common bean lines with contrasting responses for anthracnose and angular leaf spot resistance were used, as well as 149 F2 plants from the cross between BRS Cometa x SEL 1308 (carrying the Anthracnose resistance gene Co-42). Seven of the ten SNP markers evaluated showed potential for assisted breeding: snpPV0025 (Phg-2), snpPV0027 (Phg-5), snpPV0079 (Phg-5), snpPV0046 (Co-u), snpPV0068 (Co-42), snpPV0070 (Co-42) and snpP8282v3-817 (Co-42). Markers snpPV0070 and snpP8282v3-817 showed high efficiency of selection (99.7 and 99.8%, respectively). These markers exhibit great potential to assist in the selection at different stages of the breeding program and may be readily incorporated into marker-assisted selection.

scholarly journals Development and Use of miRNA-derived SSR Markers to Study Genetic Diversity, Population Structure and Characterization of Genotypes for Heat Tolerance Breeding in Bread Wheat (Triticum aestivum L.)

2020 ◽  
Author(s):  
Sandhya Tyagi ◽  
Anuj Kumar ◽  
Tinku Gautam ◽  
Renu Pandey ◽  
Reyazul Rouf Mir
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Heat Tolerance ◽  
Triticum Aestivum L ◽  
Breeding Programs ◽  
Mirna Genes ◽  
Novel Mirna ◽  
The World

AbstractWheat is one of the most important cereal crop in the world. Heat stress is an important abiotic stress limiting wheat production and productivity in the world including south-east Asia. The importance of miRNAs in gene expression under various biotic and abiotic stresses is well documented. Molecular markers, especially SSR markers, plays an important role for the success in molecular plant breeding programs. The discovery of SSRs from non-coding regions has been a challenging task. Therefore, development of novel miRNA-based SSRs from the conserved portions of the genome will prove useful for the study of genetic diversity of heat-responsive miRNA-genes in wheat. In the present study, efforts are made to mine SSR markers from 96 members of heat-responsive miRNA-genes of wheat followed by their validation using 37 contrasting (heat tolerance/susceptible) wheat genotypes. Among a set of 13 miRNA-SSRs used,7 SSRs were found polymorphic. Among these polymorphic SSR markers, three found to be very informative SSRs (HT-169j, HT-160a and HT-160b) and could largely discriminate heat tolerant genotypes from the heat susceptible ones. Further analysis based on Polymorphism Information Content (PIC) revealed that miRNA genes were more diverse in susceptible genotypes compared to tolerant genotypes. Ours is the first report that the genic/miRNA markers could be successfully used to study wheat diversity, population structure and characterization of trait specific germplasm. The important and useful miRNA-based SSRs, therefore, would serve as best markers in the marker-assisted breeding programs aimed at enhancing heat tolerance of Indian wheat.

scholarly journals Functional Analysis of TM6 MADS-box gene in the Octoploid Strawberry by CRISPR/Cas9 directed mutagenesis

2018 ◽  
Author(s):  
Carmen Martín-Pizarro ◽  
Juan Carlos Triviño ◽  
David Posé
Keyword(s):  
Genome Editing ◽  
High Throughput Sequencing ◽  
High Efficiency ◽  
Phenotypic Characterization ◽  
Mads Box ◽  
Breeding Programs ◽  
Mads Box Gene ◽  
Mutant Lines ◽  
First Time

AbstractThe B-class of MADS-box transcription factors has been studied in many plant species, but remain functionally uncharacterized in the Rosaceae family. APETALA3 (AP3), a member of this class, controls the identity of petals and stamens in Arabidopsis thaliana. In this work, we identified two members of the AP3 lineage in the cultivated strawberry (Fragaria × ananassa): FaAP3 and FaTM6. Interestingly, FaTM6, and not FaAP3, shows an expression pattern equivalent to that of AP3 in Arabidopsis. Genome editing using Cluster Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system is becoming a robust tool for targeted and stable mutagenesis of DNA. However, whether it can be efficiently used in an octoploid species such as F. × ananassa is not known. Here we report for the first time the application of CRISPR/Cas9 in F. × ananassa to characterize the function of FaTM6 in flower development. An exhaustive analysis by high-throughput sequencing of the FaTM6 locus spanning the target sites showed a high efficiency genome editing already in the T0 generation. The phenotypic characterization of the mutant lines indicates that FaTM6 plays a key role in petal and especially in anther development in strawberry. in an octoploid species such as F. × ananassa, and offer new opportunities for engineering strawberry to improve traits of interest in breeding programs.

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