@article{ZHENG2026, 
author = {Mingmin ZHENG and Xiaowei LIU and Qiuyu YU and Yang LI and Rui ZENG and Yunhong GAO and Min YANG},
title = {Genome-wide analysis of simple sequence repeats and development of molecular markers in Toona sinensis},
year = {2026},
journal = {Journal of Central South University of Forestry & Technology},
volume = {46},
number = {5},
pages = {149-157},
keywords = {Toona sinensis, genome, SSR, marker development},
url = {https://www.sciopen.com/article/10.14067/j.cnki.1673-923x.2026.05.015},
doi = {10.14067/j.cnki.1673-923x.2026.05.015},
abstract = {【Objective】A systematic analysis of SSR loci in the genome and the development of efficient molecular markers was accomplished to provide a theoretical basis and technical support for further research on germplasm identification, genetic diversity analysis, linkage map construction, and molecular marker-assisted breeding in T. sinensis.【Method】Based on the published reference genome of the cultivar ‘Heiyouchun’, genome-wide SSR loci containing 1-6 nucleotide repeats were identified using the MISA software, and the distribution patterns and characteristics of SSR types were comprehensively analyzed. SSR primers were developed using Primer3.0 in combination with in silico PCR. Subsequently, 20 pairs of SSR primers were randomly selected for PCR amplification using genomic DNA from six T. sinensis samples. The validity and polymorphism of these primers were evaluated using polyacrylamide gel electrophoresis (PAGE).【Result】A total of 308 421 SSR loci were identified in the genome of T. sinensis, with an average of one locus per 1.92 kb. The distribution frequency of SSRs was relatively uniform across the chromosomes. Mononucleotide and dinucleotide repeats were the predominant types, accounting for 59.23% and 31.08% of the total SSRs, respectively. Across the entire genome, 979 distinct SSR motif types were identified. Among these, A/T, AT/TA, and AAT/ATT motifs occurred most frequently, indicating that A and T bases were predominant in the SSR sequences of the T. sinensis genome. The length of SSR sequences in the T. sinensis genome ranged from 10 to 1 218 bp, and the number of SSR loci decreased with increasing repeat length across all nucleotide repeat motifs. A total of 104 813 pairs of SSR primers were designed based on the flanking sequences of the SSR loci. Among the 20 pairs of primers synthesized, 18 pairs of primers amplified the target bands with an amplification efficiency of 90.0%. Additionally, products from nine primer pairs exhibited polymorphism, and the polymorphism rate reached 50.0%.【Conclusion】This study elucidated the distribution characteristics of SSRs in the T. sinensis genome and developed a large set of genome-wide SSR markers, providing valuable molecular tools for future genetic studies and breeding applications in T. sinensis.}
}