Transcriptome shock in an interspecific F1 triploid hybrid of Oryza revealed by RNA sequencing

Abstract

Interspecific hybridization is a driving force in evolution and speciation of higher plants. Interspecific hybridization often induces immediate and saltational changes in gene expression, a phenomenon collectively termed "transcriptome shock". Although transcriptome shock has been reported in various plant and animal taxa, the extent and pattern of shock-induced expression changes are often highly idiosyncratic, and hence entails additional investigations. Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica (2n ¼ 2x ¼ 24, genome AA) and the tetraploid form of O. punctata (2n ¼ 4x ¼ 48, genome, BBCC), and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico "hybrids" (parental mixtures). We found that approximately 16% (2,541) of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the transcriptome response to interspecific hybridization and heterosis.Keywords: Cis-and trans-regulation; homeolog expression rewiring; interspecific hybrid; Oryza; promoter divergence; transcriptome shock Citation: Wu Y, Sun Y, Wang X, Lin X, Sun S, Shen K, Wang J, Jiang T, Zhong S, Xu C, Liu B (2016) Transcriptome shock in an interspecific F1 triploid hybrid of Oryza revealed by RNA sequencing.

Transcriptome analysis of neo-tetraploid rice reveals specific differential gene expressions associated with fertility and heterosis

“…Moreover, about 3% of total genes displayed nonadditive expressions, which might be regulated by trans -acting factors33. These results are consistent with the previous studies, who also found nonadditive genes in rice121429. All of these results demonstrated complex regulatory mechanisms associated with heterosis, and differential gene expression was involved in fertility of neo-tetraploid rice hybrids.…”

“…Moreover, RNA-seq-based transcriptome profiling analysis has revealed that polyploidy level is greatly associated with genome-wide disruption of gene expression and ultimately altered phenotypes in the polyploid rice hybrids ( indica × japonica )28. Transcriptome analysis revealed that about 16% of the 16,112 expressed genes showed nonadditive expressions in leaf tissue of an interspecific F 1 triploid hybrid29. The differential gene expressions for cell growth and functional secondary metabolites were found in induced autotetraploid of Chinese Woad ( Isatis indigotica Fort.)…”

Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq

“…Since then, next-generation high-throughput RNA sequencing (RNA-seq) has been developed to discover, profile, and quantify RNA transcripts [14, 15]. It has also been used to study the mechanisms of heterosis in interspecific F1 triploids or F1 hybrids of cotton [16], wheat [17], and rice [18, 19], but few studies have investigated heterosis in soybean using RNA-seq.…”

Creating new interspecific hybrid and polyploid crops

“…RNASeq data have been used to quantify genomic changes occurring as a consequence of polyploidisation in coffee [52]: homoeologous exchange events shared by all accessions confirmed that a single polyploidisation event had occurred. RNASeq was likewise used to investigate 'transcriptome shock' in interspecific rice hybrids [53]. The genomes of species that have originated via natural interspecific hybridisation, such as many citrus crops, can also be characterised to identify the chromosomal fragments that are contributed by the different ancestral genomes.…”