Department of Crop Genetics, John Innes Centre, Norwich Research Park NR4 7UH, UK.
School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
G3 (Bethesda). 2022 Jul 29;12(8). doi: 10.1093/g3journal/jkac147.
Whole-genome duplication is widespread in plant evolutionary history and is followed by nonrandom gene loss to return to a diploid state. Across multiple angiosperm species, the retained genes tend to be dosage-sensitive regulatory genes such as transcription factors, yet data for younger polyploid species is sparse. Here, we analyzed the retention, expression, and genetic variation in transcription factors in the recent allohexaploid bread wheat (Triticum aestivum L.). By comparing diploid, tetraploid, and hexaploid wheat, we found that, following each of two hybridization and whole-genome duplication events, the proportion of transcription factors in the genome increased. Transcription factors were preferentially retained over other genes as homoeologous groups in tetraploid and hexaploid wheat. Across cultivars, transcription factor homoeologs contained fewer deleterious missense mutations than nontranscription factors, suggesting that transcription factors are maintained as three functional homoeologs in hexaploid wheat populations. Transcription factor homoeologs were more strongly coexpressed than nontranscription factors, indicating conservation of function between homoeologs. We found that the B3, MADS-M-type, and NAC transcription factor families were less likely to have three homoeologs present than other families, which was associated with low expression levels and high levels of tandem duplication. Together, our results show that transcription factors are preferentially retained in polyploid wheat genomes although there is variation between families. Knocking out one transcription factor homoeolog to alter gene dosage, using TILLING or CRISPR, could generate new phenotypes for wheat breeding.
全基因组复制在植物进化史上广泛存在，并伴随着非随机的基因丢失，以恢复二倍体状态。在多个被子植物物种中，保留下来的基因往往是剂量敏感的调控基因，如转录因子，但对于较年轻的多倍体物种的数据却很少。在这里，我们分析了最近的异源六倍体面包小麦（Triticum aestivum L.）中转录因子的保留、表达和遗传变异。通过比较二倍体、四倍体和六倍体小麦，我们发现，在两次杂交和全基因组复制事件之后，转录因子在基因组中的比例增加了。在四倍体和六倍体小麦中，转录因子作为同源基因组比其他基因更优先保留。在不同品种中，转录因子的同源基因比非转录因子包含更少的有害错义突变，这表明在六倍体小麦群体中，转录因子作为三个功能同源基因被维持。转录因子同源基因的共表达比非转录因子更强，表明同源基因之间功能的保守性。我们发现，B3、MADS-M 型和 NAC 转录因子家族比其他家族更不可能存在三个同源基因，这与低表达水平和串联重复率高有关。总之，我们的研究结果表明，尽管不同家族之间存在差异，但转录因子在多倍体小麦基因组中被优先保留。利用 TILLING 或 CRISPR 敲除一个转录因子同源基因以改变基因剂量，可能会为小麦的育种产生新的表型。
