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Pattern and variation in simple sequence repeat (SSR) at different genomic regions and its implications to maize
Meiqi Zhao1,2, Guoping Shu1,3, Yanhong Hu1,3
1Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China.
BMC Genomics
|March 22, 2023
Summary
Simple sequence repeats (SSRs) are crucial DNA markers in maize. This study reveals their distribution and polymorphism patterns in high-quality maize genomes, highlighting their potential for genetic research and breeding.
Area of Science:
- Genomics
- Molecular Biology
- Plant Genetics
Background:
- Repetitive DNA constitutes over 80% of the maize genome.
- Simple sequence repeats (SSRs), though a small fraction, are vital codominant DNA markers for maize research and breeding.
- Genome-wide SSR distribution and polymorphism require high-quality sequence data for comprehensive study.
Purpose of the Study:
- To investigate the genome-wide distribution and polymorphism of SSRs in maize.
- To analyze SSR abundance in genic versus intergenic regions and specific sequence elements (CDS, UTR).
- To explore SSR density in relation to Long Terminal Repeat Retrotransposons (LTR-RTs) of varying ages and their evolutionary dynamics.
Main Methods:
- Utilized high-quality de novo-sequenced maize genomes from five inbred lines.
- Analyzed SSR distribution patterns, including density in telomeric vs. centromeric regions and genic vs. intergenic sequences.
- Examined SSR motif composition in coding sequences (CDS) and untranslated regions (UTR).
- Assessed SSR polymorphism across different genomic regions and motifs.
Main Results:
- SSRs are more concentrated in telomeric regions and genic sequences than centromeric and intergenic regions, respectively.
- Tri- and hexanucleotide SSR motifs are prevalent in CDS, while mono- and dinucleotide motifs are more common in UTRs.
- SSR median length (14-18 bp) and density (3355.77 bp/Mbp) showed narrow ranges, with higher density observed in younger LTR-RTs.
- Significant genome-specific and motif-specific SSR polymorphisms were identified.
Conclusions:
- SSR length and density appear to be regulated by unknown evolutionary forces, with consistent median lengths across motifs.
- Higher SSR density in genic regions and consistent density across LTR-RTs of different ages were observed.
- Identified SSR polymorphisms offer a valuable resource for developing advanced genome and gene markers in maize genetic research and molecular breeding.
Keywords:
BreedingEvolutionLong terminal repeat-retrotransposons (LTR-RTs)Maize genomeMolecular markerSimple sequence repeat (SSR)More Related Videos
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