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Characterization of full-length transcriptome in Saccharum officinarum and molecular insights into tiller development

文献类型： 外文期刊

作者： Yan, Haifeng 1 ; Zhou, Huiwen 1 ; Luo, Hanmin 1 ; Fan, Yegeng 1 ; Zhou, Zhongfeng 1 ; Chen, Rongfa 1 ; Luo, Ting 1 ; Li, 1 ;

作者机构： 1.Guangxi Acad Agr Sci, Sugarcane Res Inst, Guangxi Key Lab Sugarcane Genet Improvement, East Daxue Rd 172, Nanning 530004, Guangxi, Peoples R China

2.Minist Agr, Key Lab Sugarcane Biotechnol & Genet Improvement, East Daxue Rd 172, Nanning 530004, Guangxi, Peoples R China

3.Yunnan Acad Agr Sci, Sugarcane Res Inst, East Lingquan Rd 172, Kaiyun 661600, Yunnan, Peoples R China

关键词： Crop productivity; Genomic data; C-4 plant; Carbon fixation; Linoleic acid; Gene expression

期刊名称：BMC PLANT BIOLOGY （ 影响因子：4.215； 五年影响因子：4.96 ）

ISSN： 1471-2229

年卷期： 2021 年 21 卷 1 期

页码：

收录情况： SCI

摘要： Background Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies. Results Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development. Conclusions Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.

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