Related Experiment Video
Updated: Jul 11, 2025
08:55
Author Spotlight: Harnessing DNA Barcode Technology to Enhance the Efficiency of Medicinal Plant Identification
Published on: November 1, 2024
1.6K
Development of simple sequence repeat markers for sugarcane from data mining of expressed sequence tags
Huahao Jiang1, Muhammad Waseem2,3, Yong Wang1
1College of Agriculture, Guangxi University, Nanning, China.
Frontiers in Plant Science
|November 8, 2023
Summary
This study developed expressed sequence tag-simple sequence repeat (EST-SSR) markers for sugarcane, identifying numerous SSRs within unigenes. These markers aid in sugarcane genetic characterization and breeding for improved varieties.
Area of Science:
- Plant genetics and breeding
- Molecular biology
- Agricultural science
Background:
- Sugarcane (Saccharum spp. hybrids) is a vital global crop for sugar and biofuel, but its genetic complexity hinders variety improvement.
- Molecular breeding offers potential for developing enhanced sugarcane varieties, necessitating effective genetic tools.
- Simple sequence repeats (SSRs) are powerful molecular markers for crop genetic studies.
Purpose of the Study:
- To develop and characterize expressed sequence tag-simple sequence repeat (EST-SSR) markers in sugarcane.
- To analyze the genetic diversity and relationships among sugarcane accessions using the developed markers.
- To provide valuable molecular resources for sugarcane genetic characterization and breeding programs.
Main Methods:
- Mining of 285,216 expressed sequence tags (ESTs) to identify unigenes and SSRs.
- Design and validation of 173 EST-SSR primers using PAGE analysis on 10 sugarcane accessions.
- Functional annotation of unigenes using UniProt, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases.
- Cluster analysis to assess genetic relationships among sugarcane accessions.
Main Results:
- Identified 4,960 SSRs within 4,120 unigenes, with monomeric, trimeric, and dimeric repeats being most abundant.
- PAGE analysis revealed distinct banding patterns, indicating the utility of EST-SSR markers.
- Functional annotation provided insights into the roles of identified unigenes across molecular, cellular, and biological pathways.
- Cluster analysis delineated four distinct genetic clusters among the studied sugarcane accessions.
Conclusions:
- The developed EST-SSR markers are effective for analyzing genetic diversity in sugarcane.
- These markers represent a valuable resource for future genetic characterization, species identification, and marker-assisted breeding in sugarcane.
- The findings contribute to advancing molecular breeding strategies for developing improved sugarcane varieties.
Related Concept Videos
03:21RNA-seq
10.0K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.0K
01:29Modern Molecular Taxonomy
23
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
23
03:00Next-generation Sequencing
89.0K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
89.0K
01:57Sanger Sequencing
754.6K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
754.6K