Transcription factor retention through multiple polyploidisation steps in wheat

Abstract

Whole genome duplication (WGD) is widespread in plant evolutionary history, but the mechanisms of non-random gene loss after WGD are debated. The gene balance hypothesis proposes that dosage-sensitive genes such as regulatory genes are retained in polyploids. To test this hypothesis, we analysed the retention of transcription factors (TFs) in the recent allohexaploid bread wheat (Triticum aestivum). We annotated TFs in hexaploid, tetraploid and diploid wheats; compared the co-expression of homoeologous TF and non-TF triads; and analysed single nucleotide variation in TFs across cultivars. We found that, following each of two hybridisation and WGD events, the proportion of TFs in the genome increased. TFs were preferentially retained over other genes as homoeologous groups in tetraploid and hexaploid wheat. Across cultivars, TF triads contain fewer deleterious missense mutations than non-TFs. TFs are preferentially retained as three functional homoeologs in hexaploid wheat, in support of the gene balance hypothesis. High co-expression between TF homoeologs suggests that neo- and sub-functionalisation are not major drivers of TF retention in this young polyploid. Knocking out one TF homoeolog to alter gene dosage, using TILLING or CRISPR, could be a way to further test the gene balance hypothesis and generate new phenotypes for wheat breeding.

CRISPR/Cas9‐targeted mutagenesis of TaDCL4, TaDCL5 and TaRDR6 induces male sterility in common wheat

“…To investigate the divergence of PHAS genes among three sub‐genomes of wheat, we merged all PHAS loci into one dataset and yielded 2924 21‐nt (21‐ PHAS ) and 1736 24‐nt (24‐ PHAS ) non‐redundant PHAS loci. Aligning these PHAS loci to the genomes with stringent criterion of 80% identity and 80% length, we found that only a small fraction of PHAS loci, 2.6% for 21‐ PHAS and 1.7% for 24‐ PHAS , had additional homologues in other sub‐genome(s), significantly less than protein‐coding genes, of which 56% genes were triads with three homologues in all the subgenomes (Evans et al ., 2022). In other words, 81.22% 21‐ PHAS and 86.52% 24‐ PHAS were singleton, significantly more than that of the coding genes, that is, 25.97% (Figure 6a,b).…”