Genetic Marker Development and Diversity Analysis in Plant Systems
Summary
Genetic marker development and diversity analysis have become foundational tools in plant science, enabling precise characterisation of germplasm, elucidation of population structure and acceleration of breeding programmes. Molecular markers such as simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) offer codominant resolution, high polymorphism and genome-wide coverage. Advances in next-generation sequencing have dramatically reduced the cost and time required for marker discovery, permitting rapid mining of SSRs from genomic and transcriptomic data and high-throughput SNP genotyping through reduced-representation libraries or whole-genome resequencing. Once developed, markers facilitate the construction of genetic maps, fine-mapping of quantitative trait loci, and marker-assisted selection for agronomic traits. Diversity analysis using these markers provides measures of allelic richness, heterozygosity and population differentiation, informing conservation of wild relatives and management of breeding collections. The integration of marker development with phenotypic evaluation underpins the global endeavour to enhance crop resilience, yield and quality in the face of biotic and abiotic stresses.
Research from Nature Portfolio
Recent studies have exploited genome assemblies and transcriptomic resources to generate highly informative SSR markers. In citrus, a comprehensive survey of two species yielded a catalogue of perfect SSR motifs across all chromosomes. Class I SSRs with long repeat tracts were electronically and experimentally validated in multiple draft genomes, producing a core set of highly polymorphic loci that have been applied to genetic diversity surveys, comparative mapping and QTL discovery in over 180 genotypes. Foundational work in a perennial grass employed deep transcriptome sequencing to identify thousands of expressed sequence tag-derived SSRs. A subset of these EST-SSR primers displayed high transferability across related species and robust polymorphism in genetic diversity assessments, thereby establishing cross-species genotyping tools for pasture grass improvement.
Genetic Marker Development and Diversity Analysis in Plant Systems publication trend
The graph below shows the total number of articles in genetic marker development and diversity analysis in plant systems across all publications each year (not limited to Nature Index journals).
Technical terms
Simple sequence repeat (SSR): Short tandemly repeated DNA motifs used as polymorphic molecular markers.
Expressed sequence tag SSR (EST-SSR): SSR markers developed from transcribed gene sequences, reflecting functional genomic regions.
Next-generation sequencing (NGS): High-throughput DNA sequencing technologies that enable rapid discovery of genetic markers.
Polymorphic information content (PIC): A metric quantifying the discriminatory power of a marker based on the number and frequency of alleles.
Genotyping: The process of determining the allele composition at specific genetic loci in individual samples.
References
- Genome-wide microsatellite characterization and marker development in Diospyros oleifera. Industrial Crops and Products (2023).
- Genetic Diversity Analysis and Fingerprint Construction for 87 Passionfruit (Passiflora spp.) Germplasm Accessions on the Basis of SSR Fluorescence Markers. International Journal of Molecular Sciences (2024).
- Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote. BMC Plant Biology (2024).
- Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species. Scientific Reports (2023).
- Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing. Scientific Reports (2016).
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