Genome-wide differences in gene expression and alternative splicing in developing embryo and endosperm, and between F1 hybrids and their parental pure lines in sorghum.

Ning Li,Weiguang Yang,Meishan Zhang,Bao Liu

doi:10.1007/s11103-021-01196-y

Abstract

Developing embryo and endosperm of sorghum show substantial and multifaceted differences in gene expression and alternative splicing, which are potentially relevant to heterosis. Differential regulation of gene expression and alternative splicing (AS) are major molecular mechanisms dictating plant growth and development, as well as underpinning heterosis in F1 hybrids. Here, using deep RNA-sequencing we analyzed differences in genome-wide gene expression and AS between developing embryo and endosperm, and between F1 hybrids and their pure-line parents in sorghum. We uncover dramatic differences in both gene expression and AS between embryo and endosperm with respect to gene features and functions, which are consistent with the fundamentally different biological roles of the two tissues. Accordingly, F1 hybrids showed substantial and multifaceted differences in gene expression and AS compared with their pure-line parents, again with clear tissue specificities including extents of difference, genes involved and functional enrichments. Our results provide useful transcriptome resources as well as novel insights for further elucidation of seed yield heterosis in sorghum and related crops.

Highlights

Sorghum (Sorghum bicolor L.) ranks fifth in global cereal production, and its seeds provide important resources for food, feed and biofuel worldwide (Mace et al 2013)
We performed high-throughput RNA-seq using the Illumina HiSeq 2500 platform for embryo and endosperm tissues dissected from sorghum seeds at 14 days after pollination (DAP) of four genotypes
Gene and transcript expression levels were estimated with Ballgown and measured as transcript per million base pairs (TPM)

Summary

Introduction

Sorghum (Sorghum bicolor L.) ranks fifth in global cereal production, and its seeds provide important resources for food, feed and biofuel worldwide (Mace et al 2013). Endosperm and embryo are major components of seeds and are direct determinants of yield. Sorghum seed development is initiated following double fertilization, which gives rise to diploid embryo and triploid endosperm, respectively, with the two tissues exhibiting dramatic differences in many respects. In flowering plants, developing endosperm is the primary tissue of imprinted gene expression, i.e., unequal expression of maternal and paternal alleles depending on parent of origin (Gehring and Satyaki 2017; Zhang et al 2011). We identified 101 sorghum imprinted genes (≥ 5-fold allelic expression difference) including 85 maternally expressed imprinted genes (MEGs) and 16 paternally expressed imprinted genes (PEGs) from 14 DAP (days after pollination) sorghum endosperm based on RNA-sequencing (Zhang et al 2016)

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