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<p>To enhance genetic resource development in&#xa0;<i>Idesia polycarpa</i>, an emerging woody oil crop, we established a dual PCR-based marker system combining genome-derived simple sequence repeats (SSRs) and inter-retrotransposon amplified&#xa0;polymorphisms (IRAPs). The system was validated using 24 geographically diverse accessions, selecting 54 high-polymorphism markers (24 SSR, 30 IRAP) from 120 candidates. SSRs showed 100% polymorphism (163 loci; 6.79 loci/primer; Na = 2.00, Ne = 1.25, H = 0.17, I = 0.29). IRAPs demonstrated superior performance: 99.44% polymorphism (367 loci; 12.17 loci/primer; Na = 1.99, Ne = 1.41, H = 0.26, I = 0.41). The primer pair IpRT15 + IpRT30 uniquely identified all accessions. Comparative analysis confirmed IRAP dominance: higher Polymorphism Information Content (PIC: 0.71–0.91 vs. 0.32–0.90), Effective Multiplex Ratio (EMR: 12.17 vs. 6.79), Resolving Power (Rp: 5.87 vs. 1.94), and Marker Index (MI: 10.48 vs. 4.77). Unweighted pair group method with arithmetic mean (UPGMA) clustering using combined SSR + IRAP data (similarity threshold: 0.54) resolved 8 distinct groups, significantly enhancing discrimination over single-marker analyses (5 groups each). Genetic similarity correlated with geographical proximity, exemplified by Group IV containing all accessions from adjacent Yinjiang/Jiangkou sites. The Liupanshui provenance remained distinct, while SY1 emerged as a unique outlier. Increased geographical distance predicted genetic divergence. We conclude that IRAP markers offer unprecedented efficacy for germplasm identification and diversity analysis in&#xa0;<i>I. polycarpa</i>, though integrated SSR-IRAP approaches provide the highest resolution for deciphering population structure and biogeographical patterns. These findings directly inform conservation and breeding strategies for this valuable species.</p>

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Development and application of simple sequence repeat (SSR) and inter-retrotransposon amplified polymorphism (IRAP) markers based on the genome of Idesia polycarpa: a new woody oil plant species

  • 期刊论文

  • 发表日期：

    2025年12月16日

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  • Huang Yang,
  • Fuhua Fan

摘要

To enhance genetic resource development in Idesia polycarpa, an emerging woody oil crop, we established a dual PCR-based marker system combining genome-derived simple sequence repeats (SSRs) and inter-retrotransposon amplified polymorphisms (IRAPs). The system was validated using 24 geographically diverse accessions, selecting 54 high-polymorphism markers (24 SSR, 30 IRAP) from 120 candidates. SSRs showed 100% polymorphism (163 loci; 6.79 loci/primer; Na = 2.00, Ne = 1.25, H = 0.17, I = 0.29). IRAPs demonstrated superior performance: 99.44% polymorphism (367 loci; 12.17 loci/primer; Na = 1.99, Ne = 1.41, H = 0.26, I = 0.41). The primer pair IpRT15 + IpRT30 uniquely identified all accessions. Comparative analysis confirmed IRAP dominance: higher Polymorphism Information Content (PIC: 0.71–0.91 vs. 0.32–0.90), Effective Multiplex Ratio (EMR: 12.17 vs. 6.79), Resolving Power (Rp: 5.87 vs. 1.94), and Marker Index (MI: 10.48 vs. 4.77). Unweighted pair group method with arithmetic mean (UPGMA) clustering using combined SSR + IRAP data (similarity threshold: 0.54) resolved 8 distinct groups, significantly enhancing discrimination over single-marker analyses (5 groups each). Genetic similarity correlated with geographical proximity, exemplified by Group IV containing all accessions from adjacent Yinjiang/Jiangkou sites. The Liupanshui provenance remained distinct, while SY1 emerged as a unique outlier. Increased geographical distance predicted genetic divergence. We conclude that IRAP markers offer unprecedented efficacy for germplasm identification and diversity analysis in I. polycarpa, though integrated SSR-IRAP approaches provide the highest resolution for deciphering population structure and biogeographical patterns. These findings directly inform conservation and breeding strategies for this valuable species.