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

Haifeng Yan,Jianming Wu,Hanmin Luo,Lihang Qiu,Xujuan Li,Zhongfeng Zhou,Rongfa Chen,Yangrui Li,Ting Luo,Yegeng Fan,Xinlong Liu,Huiwen Zhou

doi:10.1186/s12870-021-02989-5

Haifeng Yan, Jianming Wu + Show 10 more

Open Access

https://doi.org/10.1186/s12870-021-02989-5

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Abstract

BackgroundAlthough 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.ResultsHerein, 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.ConclusionsCollectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.

Highlights

Extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential
A total of 570, 055 and 357,140 circular consensus sequence (CCS) were identified in F01 and F02, respectively, and classified as FL based on the presence of 5′ primers, 3′ primers and poly(A) tail (Table 1)
By merging full-length nonchimeric Reads (FLNC) transcript lists from the two libraries, we identified 41,109 unique FLNC transcripts in S. officinarum spanning 91,227,518 bp

Summary

Introduction

Extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Sugarcane (Saccharum officinarum L.) is an important economic crop of the grass family. It is cultivated in the tropic and subtropic regions and represents the main source of world’s sucrose [1]. Worldwide sugarcane average yield (84 t/ha) is far below the theoretical potential (384 t/ ha), considerable efforts are still needed to increase the crop productivity [3]. Tillering is the sprouting of lateral buds, which can subsequently develop into mature stalks, it is an important component of sugarcane yield. Elucidating the molecular mechanism of tiller development is critical for sugarcane productivity

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