中国水稻科学 ›› 2026, Vol. 40 ›› Issue (5): 598-606.DOI: 10.16819/j.1001-7216.2026.250213
李笑霞1,2,#, 张天驰1,2,#, 贺文闯2, 贺慧英2, 盘楠2, 刘祎凡2, 钱前1,2,3, 商连光2,3,*(
)
收稿日期:2025-02-25
修回日期:2025-03-11
出版日期:2026-09-10
发布日期:2026-09-16
通讯作者:
*email: shanglianguang@caas.cn作者简介:#共同第一作者
基金资助:
LI Xiaoxia1,2,#, ZHANG Tianchi1,2,#, HE Wenchuang2, HE Huiying2, PAN Nan2, LIU Yifan2, QIAN Qian1,2,3, SHANG Lianguang2,3,*()
Received:2025-02-25
Revised:2025-03-11
Online:2026-09-10
Published:2026-09-16
About author:#These authors contributed equally to this work
摘要：
【目的】转座子(TE)是水稻遗传多样性的重要来源，在亚洲栽培稻(Oryza sativa)的驯化过程中发挥了关键作用。然而，由于TE序列的高度重复性，其鉴定通常依赖于高质量的基因组序列。目前，非洲栽培稻(Oryza glaberrima，Og)的基因组资源有限，导致对其TE的多样性及其在驯化过程中的贡献仍然缺乏系统性研究。【方法】本研究基于11份Og和10份短舌野生稻(Oryza barthii，Ob)的染色体级别的基因组序列，构建了Og和Ob群体的高精度泛TE变异图谱。通过对该图谱进行选择性分析，鉴定了854个在Og驯化过程中受到选择的TE变异。【结果】该泛TE图谱共包含17,097个高质量的TE变异，覆盖基因组总长度39.1 Mb，其中61.7%的TE变异长度超过1 kb。Ob群体的TE变异总数高于Og群体。在Og驯化过程中，共鉴定出658个含受选择TE变异的基因，这些基因显著富集于基础代谢相关的生物过程，其中包括30个在Og独立驯化过程中发挥作用的已知功能基因。【结论】本研究揭示了TE变异是Og驯化过程中表型变异的重要来源，构建的高质量泛TE变异图谱不仅丰富了水稻育种的可用变异库，也为Og种质资源的遗传改良提供了重要的理论依据和资源支持。
李笑霞, 张天驰, 贺文闯, 贺慧英, 盘楠, 刘祎凡, 钱前, 商连光. 泛基因组图谱揭示转座子在非洲栽培稻驯化中的作用[J]. 中国水稻科学, 2026, 40(5): 598-606.
LI Xiaoxia, ZHANG Tianchi, HE Wenchuang, HE Huiying, PAN Nan, LIU Yifan, QIAN Qian, SHANG Lianguang. A Pan-genome Map Reveals the Contribution of Transposable Elements to Domestication of Oryza glaberrima[J]. Chinese Journal OF Rice Science, 2026, 40(5): 598-606.
图1 21份非洲稻材料的群体结构分析 A: 主成分分析(PCA)；B: 群体结构分布。
Fig. 1. Population structure analysis of 21 African rice accessions A, Principal component analysis(PCA); B, Population structure distribution.
图2 泛TE变异图谱的构建 A：21个材料中不同TE家族的TE数目。X轴表示每个TE家族在单个材料中TE数目差异，以变异系数（CV）评估；Y轴表示每个TE家族在单个材料中总TE数目的差异，以标准差（SD）评估；Z轴表示每个TE家族在单个材料中平均TE数目的差异；B：21个样品构建的泛TE图谱，Og和Ob分别指非洲栽培稻和短舌野生稻。
Fig. 2. Construction of pan-TE variation map A, Number of TE for each TE family in 21 African accessions. X axis represents the number of TE for each TE family across accessions, evaluated as coefficient of variation (CV); Y axis represents the differences in total TE number for each family among accessions, evaluated as standard deviation (SD); Z axis represents the average number of TEs for each family; B, Landscape of TE variations across the 21 African accessions.
图3 泛TE变异图谱中TE变异特征 A：不同群体中鉴定到的非冗余的TE变异总数和总长度，“All”指本研究中所有材料；B：21个材料构建的泛TE图谱中每个TE变异的频率；C：泛TE图谱中TE变异的长度分布。D：不同亚群中每个材料的TE变异平均长度和平均数目。***P < 0.001, **P < 0.01, *P < 0.05(t检验)；E：泛TE图谱中TE变异的百分比，未知指LTR/未知家族。
Fig. 3. Characteristics of TE variation in pan-TE variation map A, Total length and number of non-redundant TE variations and sequences detected across different subpopulations. All refers to all the accessions in the present study; B, Frequencies of each TE variation in 21 African accessions; C, Length distributions of TE variations in the non-redundant TE dataset for African accessions. D, Average length and number of TE variations for each accession across different subpopulations. ***P < 0.001, **P < 0.01, *P < 0.05 (t-test); E, Percentage of TE variations in the non-redundant TE dataset for African accessions. Unknown refers to LTR/unknown family.
图4 TE变异与基因及邻近区域重叠的百分比 基因及其附近区域包括CDS、3'UTR、5'UTR和内含子，以及上游2 kb（以下称为“启动子”）和下游2 kb（以下称为“下游”）的区域。未知指的是LTR/未知家族。“All”指的是本研究中总泛TE变异图谱中所有TE变异中与基因及其附近区域内重叠的百分比，“NIP”指的是日本晴基因组中TE序列与基因及其附近区域重叠的百分比。
Fig. 4. Percentage of TE variations overlapping with genic regions Genic regions include gene body (CDS, 3’UTR, 5’UTR, and intron), and the regions within 2 kb upstream (henceforth termed “promoter”) and 2 kb downstream (henceforth termed “downstream”) of the gene body. Unknown refers to LTR/unknown family. “All” refers to the percentage of TE variations in the genic regions of all TE loci identified in the present study, and “NIP” refers the percentage of TEs overlapping with genic regions in the Nipponbare genome.
图5 TE对非洲栽培稻驯化过程的影响 A：基于总的泛TE变异图谱构建的系统发生树；B：在Og驯化过程中受选择TE变异的比例，根据TE变异的FST值被认为受选择TE变异；C：根据Fisher检验对每个TE家族中受选择的TE变异进行富集分析，Unknown指LTR/unknown家族。
Fig. 5. Contribution of TE variations to Og domestication A, Phylogeny of 21 African accessions based on pan-TE genotypes; B, Percentage of TE variations showing signatures of selection during Og domestication. FST outlier based on TE variations were indicated as loci showing signatures of selection; C, Fold enrichment of selected TE variations in each TE family by the Fisher’s exact test. Unknown refers to LTR/unknown family.
图6 Og驯化过程含受选择TE变异的基因富集分析
Fig. 6. Enrichment analysis of genes containing selected TE variations during the domestication process of Og accessions
图7 水稻12条染色体上含受选择TE变异的功能基因
Fig. 7. Positions of functional genes harboring selected TEs in their genic regions on chromosomes 1-12
图8 非洲栽培稻驯化过程中已知功能基因中的TE变异 A-B: 在所有Og样品中发现穗发育基因OsYABBY4启动子区域中的Stowaway MITE插入（A）和盐胁迫基因OsHKT2;4启动子区域中的Helitron缺失（B），但在少数Ob样品中未发现。
Fig. 8. TE variations in known functional genes during Og domestication A-B, Stowaway MITE insertion in the OsYABBY4 promoter region (A) and Helitron deletion in the OsHKT2;4 promoter region were found in all Og accessions except a few Ob accessions(B).
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