RNA-seq-based SNP discovery and functional characterization reveal genetic variation and evolutionary insights in Cinnamomum species

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Genli G., Furan M. A.

Advances in Agriculture and Biology, cilt.8, sa.1, ss.1-13, 2025 (Hakemli Dergi)

• Yayın Türü: Makale / Tam Makale
• Cilt numarası: 8 Sayı: 1
• Basım Tarihi: 2025
• Doi Numarası: 10.63072/aab.25001
• Dergi Adı: Advances in Agriculture and Biology
• Sayfa Sayıları: ss.1-13
• Van Yüzüncü Yıl Üniversitesi Adresli: Evet

Özet

Abstract 

 

Genetic differences are essential for the adaptability, 

resilience, and evolutionary success of plant species. 

Cinnamomum, a genus of commercial and therapeutic 

significance, remains little studied at the genomic level. In 

this study, we conducted a comprehensive RNA-Seq-based 

single nucleotide polymorphism (SNP) analysis on six 

transcriptome samples from C. camphora and C. verum, 

aligned with the C. kanehirae reference genome. We 

identified a total of 184,532 high-confidence SNPs, 

comprising 410,247 missense SNPs and 397,053 

synonymous SNPs, yielding a missense-to-synonymous 

ratio of 1.03. Chromosome-wide analysis revealed that 

chromosome QPKB01000001.1 contained the highest SNP 

count (12,458 SNPs), whereas QPKB01000005.1 exhibited 

the strongest population differentiation, with a mean FST 

value of 0.342. A strong positive correlation (r = 0.79, p < 

0.001) was observed between SNP density and 

chromosomal length. Functional enrichment analysis 

demonstrated that SNP-associated genes were significantly 

enriched (FDR < 0.05) in metabolic processes, cellular 

architecture, and regulatory pathways. KEGG annotation 

linked SNPs to significant metabolic pathways, including 

purine metabolism, phenylpropanoid biosynthesis (-

log10(p) > 5), and lignin biosynthesis. Analysis of linkage 

disequilibrium (LD) decay showed that the mean r² value 

dropped below 0.2 within approximately 50 kilobases, 

indicating high recombination rates and low genome-wide 

LD. The allele frequency spectrum revealed a 

predominance of low-frequency variants (MAF < 0.1), 

constituting over 60% of all SNPs, which suggests the 

influence of genetic drift and recent population expansion. 

Notably, over 20 genes exhibited an accumulation of more 

than 50 missense SNPs, highlighting potential targets of 

evolutionary selection. These results clarify the molecular 

and evolutionary dynamics of Cinnamomum species and 

provide a robust basis for additional research into plant 

adaptation, genetic conservation, and trait-based selection 

in non-model plant genomes.