Transcriptome analysis reveals DNA repair-related clues associated with divergent leaf nuclear DNA diversity in...

Intraorganismal genetic heterogeneity (IGH) arises from the accumulation of somatic mutations during plant growth. Although leaves of Leymus chinensis exhibit pronounced IGH, its molecular basis remains unclear. Under strictly controlled growth conditions, this study compared a wild population (LC-W) with the cultivated cultivar Zhongke No. 2 (LC-ZK2) to search for DNA repair-related clues associated with leaf nuclear DNA diversity. Genomic DNA amplification and Sanger sequencing of three nuclear loci (MCM7, PsaE, and PsaL) showed that, compared with LC-W, LC-ZK2 exhibited fewer polymorphic sites and lower haplotype diversity, indicating a more restricted leaf-scale sequence heterogeneity. De novo leaf transcriptome analysis identified 3,833 differentially expressed genes (DEGs; |log₂FC| ≥ 1, FDR < 0.05; log₂FC = log₂[LC-W/LC-ZK2]). GO and KEGG analyses indicated that DEGs were significantly enriched in DNA damage response and DNA repair pathways, with particularly prominent enrichment of base excision repair (BER) and homologous recombination (HR). The BER scaffold gene XRCC1 plays an important role in these pathways and was significantly upregulated in LC-ZK2 (~2.6-fold), suggesting transcriptional differences in repair-related genes between the two materials. Further Sanger sequencing of the XRCC1 BRCT domain indicated that LC-ZK2 possessed a more concentrated haplotype spectrum and exhibited distinct amino acid substitution combinations, providing candidate sites for subsequent functional validation. Overall, this study links differences in nuclear DNA diversity with repair-associated transcriptomic signatures and provides an interpretive framework for understanding leaf-scale heterogeneity divergence in L. chinensis.