Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat

Abstract

BackgroundBread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoloci, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution ‘nullisomic-tetrasomic’ lines) with next generation deep sequencing of gene transcripts (RNA-Seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative contribution of individual homoeoloci to gene expression.ResultsWe discover, based on a sample comprising ~5-10% of the total wheat gene content, that at least 45% of wheat genes are expressed from all three distinct homoeoloci. Most of these genes show strikingly biased expression patterns in which expression is dominated by a single homoeolocus. The remaining ~55% of wheat genes are expressed from either one or two homoeoloci only, through a combination of extensive transcriptional silencing and homoeolocus loss.ConclusionsWe conclude that wheat is tending towards functional diploidy, through a variety of mechanisms causing single homoeoloci to become the predominant source of gene transcripts. This discovery has profound consequences for wheat breeding and our understanding of wheat evolution.

Nonadditive Gene Expression in Polyploids

“…However, no global bias in homeolog expression toward one parent was detected, although B-genome homeologs tended to contribute more to gene expression (98). Consistent with a previous study (19), Leach et al (98) suggested that T. aestivum has undergone extensive functional diploidization through homeolog loss and silencing.…”

“…Based on RNA-Seq data (98), 650 of 2,356 genes on chromosomes 1 and 5 exhibited differential expression among the three parental homeologs; 55% of those genes showed predominant expression of one homeolog, whereas 45% of the genes were co-upregulated by the other two homeologs (98). However, no global bias in homeolog expression toward one parent was detected, although B-genome homeologs tended to contribute more to gene expression (98).…”

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

“…Another consequence of polyploidization is unequal expression of homoeologous genes in allopolyploids [30][31][32] Table 16). Although the average expression levels and numbers of expressed genes varied among different tissues and developmental stages (Supplementary Fig.…”

Homoeologous copy-specific expression patterns of MADS-box genes for floral formation in allopolyploid wheat

“…These studies indicate that up to 20% of genes show non-additive expression with homoeolog-specific upor down-regulation. Leach et al (2014) performed RNAseq analysis using next generation sequencing with nullisomic-tetrasomic lines of chromosome groups 1 and 5 in hexaploid wheat to identify homoeolog-specific expression patterns. They assessed 2354 genes from homoeologous chromosomes and showed that at least 45% are expressed from all three homoeologs, but that most of the genes have strikingly biased expression patterns among the homoeologs.…”