Transcription factor retention through multiple polyploidization steps in wheat.
Transcription factor retention through multiple polyploidization steps in wheat.
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DOI：
10.1093/g3journal/jkac147
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发表时间：
2022-07-29
影响因子：
2.6
通讯作者：
Borrill, Philippa
中科院分区：
文献类型：
--
作者：
Evans, Catherine E. B.;Arunkumar, Ramesh;Borrill, Philippa
关键词：
全基因组复制在植物进化史上广泛存在，随后是非随机基因丢失以返回二倍体状态。在多个被子植物物种中，保留的基因往往是剂量敏感的调节基因，例如转录因子，但较年轻的多倍体物种的数据很少。在这里，我们分析了最近异源六倍体面包小麦（Triticum aestivum L.）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，在每次杂交和全基因组复制事件之后，基因组中转录因子的比例都会增加。在四倍体和六倍体小麦中，转录因子比其他基因优先保留为同源组。在各个品种中，转录因子同源物比非转录因子含有更少的有害错义突变，这表明转录因子在六倍体小麦群体中保持为三种功能同源物。转录因子同源物比非转录因子更强烈地共表达，表明同源物之间的功能保守。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种同源物，这与低表达水平和高水平串联复制有关。总之，我们的结果表明，尽管科之间存在差异，但转录因子优先保留在多倍体小麦基因组中。使用 TILLING 或 CRISPR 敲除一种转录因子同源物来改变基因剂量，可以产生用于小麦育种的新表型。
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.
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WGCNA：用于加权相关网络分析的 R 包。
影响因子：
3
作者：
Langfelder P;Horvath S
通讯作者：
Horvath S
差异同源物对面包小麦中叶基因表达的差异贡献的基因组分布。
影响因子：
13.8
作者：
Harper AL;Trick M;He Z;Clissold L;Fellgett A;Griffiths S;Bancroft I
通讯作者：
Bancroft I
DOI：
10.1534/g3.117.043679
发表时间：
2017-09-07
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Borrill P;Harrington SA;Uauy C
通讯作者：
Uauy C
影响因子：
56.9
作者：
Avni, Raz;Nave, Moran;Distelfeld, Assaf
通讯作者：
Distelfeld, Assaf
影响因子：
4.5
作者：
Chen A;Dubcovsky J
通讯作者：
Dubcovsky J