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Identification of lncRNAs involved in wheat tillering development in two pairs of near-isogenic lines

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Abstract

Emerging evidence demonstrates that lncRNAs participate in various developmental processes in plants via post-transcription regulation. However, few lncRNAs have been identified as regulators of tiller development in wheat (Triticum aestivum L.). In this study, high-throughput ribosomal depleted RNA sequencing was performed on the tillering nodes of two pairs of near-isogenic lines that differed only in the tillering trait. We identified 5399 lncRNA transcripts using bioinformational analyses. KEGG pathway analysis revealed 74 common differentially expressed lncRNAs substantially enriched in photosynthesis-related, phenylpropanoid biosynthesis, phosphatidylinositol signaling, brassinosteroid biosynthesis, zeatin biosynthesis, and carotenoid biosynthesis pathways. Detailed functional annotations of target genes were used to identify 27 tillering-associated lncRNAs. Among these, 10 were in photosynthesis-related pathways; 15 were in secondary metabolite pathways; and 8 were in plant hormone pathways, with 6 enriched in two kinds of pathways. These findings contribute to identifying tillering-associated lncRNAs in wheat and enable further investigation into the functions and roles of key candidate lncRNAs, and more experimental evidence was also needed if breeders wanted to utilize these candidate lncRNAs in wheat crop yield improvement in the future.

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Funding

This study was supported by the National Natural Science Foundation of China (31771794 and 91731305), the National Key Research and Development Program of China (2016YFD0101004 and 2017YFD0100900), the outstanding Youth Foundation of the Department of Science and Technology of Sichuan Province (2016JQ0040), and the International Science and Technology Cooperation Program of the Bureau of Science and Technology of Chengdu China (No. 2015DFA306002015-GH03-00008-HZ).

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  1. Wanlin Zhou and Haoran Shi contributed equally to this work.

Authors and Affiliations

  1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China

    Wanlin Zhou, Haoran Shi, Zhiqiang Wang, Yueting Zhao, **angjian Gou, Caixia Li, Shihang Liu, Mei Deng, Youliang Zheng, Yuming Wei & Yaxi Liu

  2. College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China

    Guangdeng Chen

  3. State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu, 611130, China

    Jian Ma, Youliang Zheng, Yuming Wei & Yaxi Liu

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  1. Wanlin Zhou
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Contributions

WLZ and HRS conducted data analysis and drafted the manuscript.

ZQW, YTZ, XJG, CXL, GDC, SHL, and MD performed the phenotypic evaluation and field sampling and helped with data analysis.

JM helped to draft the manuscript.

YLZ helped to coordinate the study.

YMW participated in the design of the study and partially revised the manuscript.

YXL designed and coordinated this study and revised the manuscript.

All authors have read and approved the final manuscript.

Corresponding authors

Correspondence to Yuming Wei or Yaxi Liu.

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Figure S1.

a Tillering phenotypes of NIL7 at grain-filling stage (NIL7B, left; NIL7A, right). b Tillering phenotypes of NIL11 at grain-filling stage (NIL11B, left; NIL11A, right) (PNG 2343 kb)

High resolution image (TIF 10558 kb)

Figure S2.

a Sampling periods of NIL7A (From Z20 to Z23). b Sampling periods of NIL7B (From Z20 to Z23). c Sampling periods of NIL11A (From Z20 to Z23). d Sampling periods of NIL11B (From Z20 to Z23) (PNG 1556 kb)

High resolution image (TIF 1409 kb)

Figure S3.

Length distribution of 5399 identified lncRNA transcripts (PNG 1538 kb)

High resolution image (TIF 6153 kb)

Figure S4.

Exon number of 5399 identified lncRNA transcripts (PNG 2192 kb)

High resolution image (TIF 9509 kb)

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Zhou, W., Shi, H., Wang, Z. et al. Identification of lncRNAs involved in wheat tillering development in two pairs of near-isogenic lines. Funct Integr Genomics 20, 669–679 (2020). https://doi.org/10.1007/s10142-020-00742-z

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