Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning
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| Publicat a: | Plants vol. 13, no. 18 (2024), p. 2619 |
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| Autor principal: | |
| Altres autors: | , , , , |
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MDPI AG
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| Accés en línia: | Citation/Abstract Full Text + Graphics Full Text - PDF |
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| 022 | |a 2223-7747 | ||
| 024 | 7 | |a 10.3390/plants13182619 |2 doi | |
| 035 | |a 3110667828 | ||
| 045 | 2 | |b d20240101 |b d20241231 | |
| 084 | |a 231551 |2 nlm | ||
| 100 | 1 | |a Subramaniam Geethanjali |u Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; <email>geethanjalitnau@yahoo.com</email> (S.G.); <email>sadhanariya17@gmail.com</email> (N.H.S.) | |
| 245 | 1 | |a Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning | |
| 260 | |b MDPI AG |c 2024 | ||
| 513 | |a Journal Article | ||
| 520 | 3 | |a Genetic markers are powerful tools for understanding genetic diversity and the molecular basis of traits, ushering in a new era of molecular breeding in crops. Over the past 50 years, DNA markers have rapidly changed, moving from hybridization-based and second-generation-based to sequence-based markers. Simple sequence repeats (SSRs) are the ideal markers in plant breeding, and they have numerous desirable properties, including their repeatability, codominance, multi-allelic nature, and locus specificity. They can be generated from any species, which requires prior sequence knowledge. SSRs may serve as evolutionary tuning knobs, allowing for rapid identification and adaptation to new circumstances. The evaluations published thus far have mostly ignored SSR polymorphism and gene evolution due to a lack of data regarding the precise placements of SSRs on chromosomes. However, NGS technologies have made it possible to produce high-throughput SSRs for any species using massive volumes of genomic sequence data that can be generated fast and at a minimal cost. Though SNP markers are gradually replacing the erstwhile DNA marker systems, SSRs remain the markers of choice in orphan crops due to the lack of genomic resources at the reference level and their adaptability to resource-limited labor. Several bioinformatic approaches and tools have evolved to handle genomic sequences to identify SSRs and generate primers for genotyping applications in plant breeding projects. This paper includes the currently available methodologies for producing SSR markers, genomic resource databases, and computational tools/pipelines for SSR data mining and primer generation. This review aims to provide a ‘one-stop shop’ of information to help each new user carefully select tools for identifying and utilizing SSRs in genetic research and breeding programs. | |
| 653 | |a Evolution | ||
| 653 | |a Gene polymorphism | ||
| 653 | |a Genetic markers | ||
| 653 | |a Plant breeding | ||
| 653 | |a Genomics | ||
| 653 | |a Data mining | ||
| 653 | |a Hybridization | ||
| 653 | |a Knobs | ||
| 653 | |a Adaptability | ||
| 653 | |a Codominance | ||
| 653 | |a Crops | ||
| 653 | |a Genomes | ||
| 653 | |a Nucleotide sequence | ||
| 653 | |a Genes | ||
| 653 | |a Genetic diversity | ||
| 653 | |a Artificial chromosomes | ||
| 653 | |a Genotyping | ||
| 653 | |a Polymorphism | ||
| 653 | |a Chromosomes | ||
| 653 | |a Pipelines | ||
| 653 | |a Gene sequencing | ||
| 653 | |a Cloning | ||
| 653 | |a Deoxyribonucleic acid--DNA | ||
| 653 | |a Simple sequence repeats | ||
| 653 | |a Single-nucleotide polymorphism | ||
| 653 | |a Information processing | ||
| 653 | |a Breeding | ||
| 653 | |a Algorithms | ||
| 653 | |a Software | ||
| 700 | 1 | |a Kadirvel, Palchamy |u Crop Improvement Section, ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad 500030, India; <email>kadirvel.palchamy@gmail.com</email> | |
| 700 | 1 | |a Anumalla, Mahender |u Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños 4031, Laguna, Philippines; <email>m.anumalla@irri.org</email>; IRRI South Asia Hub, Patancheru, Hyderabad 502324, India | |
| 700 | 1 | |a Nithyananth Hemanth Sadhana |u Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; <email>geethanjalitnau@yahoo.com</email> (S.G.); <email>sadhanariya17@gmail.com</email> (N.H.S.) | |
| 700 | 1 | |a Anandan Annamalai |u Indian Council of Agricultural Research (ICAR), Indian Institute of Seed Science, Bengaluru 560065, India | |
| 700 | 1 | |a Jauhar, Ali |u Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños 4031, Laguna, Philippines; <email>m.anumalla@irri.org</email> | |
| 773 | 0 | |t Plants |g vol. 13, no. 18 (2024), p. 2619 | |
| 786 | 0 | |d ProQuest |t Agriculture Science Database | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/3110667828/abstract/embedded/09EF48XIB41FVQI7?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text + Graphics |u https://www.proquest.com/docview/3110667828/fulltextwithgraphics/embedded/09EF48XIB41FVQI7?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/3110667828/fulltextPDF/embedded/09EF48XIB41FVQI7?source=fedsrch |