Li Xiaoxia, Dai Xiaofan, He Huiying, Chen Wu, Qian Qian, Shang Lianguang, Guo Longbiao, He Wenchuang
Rice Research Institute, Shenyang Agricultural University, Shenyang, China.
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Front Plant Sci. 2025 Apr 14;16:1573546. doi: 10.3389/fpls.2025.1573546. eCollection 2025.
The rice improvement process, driven by modern breeding techniques, represents the second revolutionary advancement in rice agronomic traits, following domestication. Advances in pan-genomes and enhanced capacity for analyzing structural variations have increasingly highlighted their role in rice genetic improvement. Transposable element (TE) variants have been previously reported to influence rice genomic diversity during the domestication, but their contribution to the improvement from landraces to improved varieties remains unclear.
Here, we combined a high-quality pan-TE variation map, transcriptome profiles, and phenotypic data for 100 landraces and 92 improved varieties to investigate the contribution of TE variations to phenotypic improvement in rice.
The total number and length of TE variations in improved varieties were significantly greater than those in rice landraces, particularly for Ty3-retrotransposons, LTR and elements. Comparing landraces and improved varieties, 4,334 selective TEs were detected within or near 3,070 genes that were enriched in basic metabolism and development and stress resistance. Among the 14,076 differentially expressed genes between the two groups, the expression level of 3,480 (24.7%) genes were significantly associated with TE variations. Combining with haplotype analysis, we demonstrated potential patterns of how TEs affect gene expression variation and thereby participate in the improvement of important agronomic traits in rice.
Collectively, our results highlight the contributions of TE variations to rice improvement in shaping the genetic basis of modern rice varieties and will facilitate the exploration of superior genes and advance molecular breeding efforts in rice.
由现代育种技术推动的水稻改良过程，是继驯化之后水稻农艺性状的第二次革命性进步。泛基因组研究的进展以及分析结构变异能力的增强，越来越凸显了它们在水稻遗传改良中的作用。转座元件（TE）变体先前已被报道在驯化过程中影响水稻基因组多样性，但其对从地方品种到改良品种的改良贡献仍不清楚。
在此，我们结合了100个地方品种和92个改良品种的高质量泛TE变异图谱、转录组图谱和表型数据，以研究TE变异对水稻表型改良的贡献。
改良品种中TE变异的总数和长度显著大于水稻地方品种，特别是Ty3反转录转座子、长末端重复序列（LTR）和元件。比较地方品种和改良品种，在3070个基因内部或附近检测到4334个选择性TE，这些基因富集于基础代谢、发育和抗逆性。在两组之间的14076个差异表达基因中，3480个（24.7%）基因的表达水平与TE变异显著相关。结合单倍型分析，我们展示了TE影响基因表达变异从而参与水稻重要农艺性状改良的潜在模式。
总体而言，我们的结果突出了TE变异在塑造现代水稻品种遗传基础方面对水稻改良的贡献，并将有助于探索优良基因，推动水稻分子育种工作。
