Data Sheet 1_Uncovering the breeding contribution of transposable elements from landraces to improved varieties through pan-genome-wide analysis in rice.pdf

IntroductionThe 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.
MethodsHere, 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.
ResultsThe total number and length of TE variations in improved varieties were significantly greater than those in rice landraces, particularly for Ty3-retrotransposons, LTR Copia and Helitron 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.
DiscussionCollectively, 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.

引言：由现代育种技术驱动的水稻改良进程，是继驯化之后水稻农艺性状领域的第二次革命性进步。泛基因组（pan-genome）的发展以及结构变异分析能力的提升，日益凸显了其在水稻遗传改良中的关键作用。此前已有研究报道转座因子（transposable element, TE）变异在驯化过程中影响水稻基因组多样性，但这类变异在地方品种向改良品种转变的育种改良过程中所发挥的贡献仍未明确。

方法：本研究整合了100份水稻地方品种与92份改良品种的高质量泛转座因子变异图谱、转录组表达谱与表型数据，以此探究转座因子变异对水稻表型改良的贡献。

结果：改良品种中的转座因子变异总数与总长度均显著高于水稻地方品种，其中尤以Ty3-retrotransposons、LTR Copia元件与Helitron元件最为突出。对比两类品种，我们在3070个基因的内部或其邻近区域检测到4334个选择性转座因子，这些基因显著富集于基础代谢、生长发育以及抗逆相关通路。在两组间共鉴定出的14076个差异表达基因中，3480个（占比24.7%）基因的表达水平与转座因子变异显著相关。结合单倍型分析，我们阐明了转座因子通过影响基因表达变异，进而参与调控水稻重要农艺性状改良的潜在模式。

讨论：综上，本研究结果证实了转座因子变异在塑造现代水稻品种遗传基础过程中对水稻改良的重要贡献，该成果将有助于挖掘水稻优异功能基因，并推进水稻分子育种相关研究工作。