Wang Xiaoming, Liu Yuxiu, Zhao Peng, Hou Wenyang, Cheng Mingzhu, Shi Xue, Simmonds James, Borrill Philippa, Wang Xiaojie, Ji Wanquan, Xu Shengbao
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Engineering Research Center of Wheat Breeding of Ministry of Education, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Genome Biol. 2025 Jul 22;26(1):218. doi: 10.1186/s13059-025-03694-4.
Polyploidy contains multiple gene copies, known as homoeologs. Differential expression of homoeologs confers expression plasticity and facilitates the adaptation and domestication of major polyploid crops. However, how this homoeolog expression bias is produced and genetically regulated remains elusive.
Here we uncover substantial variation in homoeolog expression bias among the root transcriptomes of a natural population of 406 bread wheat (Triticum aestivum ssp. aestivum) accessions collected worldwide. We develop a new model allowing us to identify 14,727 quantitative trait loci regulating the variation in homoeolog expression bias (hebQTLs), indicating that homoeolog expression bias is genetically regulated and can be predicted using genotyping data. The hebQTLs mostly regulate the expression of homoeologs in the same subgenome and downregulate expression to produce homoeolog expression bias, suggesting that intra-subgenomic rather than inter-subgenomic interactions induce homoeolog expression bias. Furthermore, we determine that hebQTL-regulated homoeologs exhibit higher genetic diversity and weaker biological functions than their counterparts. Notably, the downregulation of 38.4% of hebQTL-regulated homoeologs is compensated for by the upregulation of other homoeologs within the triad.
Our findings reveal how homoeolog expression is coordinated at the genetic level and provide an avenue for leveraging homoeolog expression bias to improve polyploid crops.
多倍体包含多个基因拷贝，即同源基因。同源基因的差异表达赋予了表达可塑性，并促进了主要多倍体作物的适应和驯化。然而，这种同源基因表达偏向是如何产生以及如何进行遗传调控的，仍不清楚。
在此，我们揭示了在全球收集的406份普通小麦（Triticum aestivum ssp. aestivum）自然群体的根转录组中，同源基因表达偏向存在显著变异。我们开发了一种新模型，使我们能够鉴定出14727个调控同源基因表达偏向变异的数量性状位点（同源基因表达偏向QTL，hebQTL），这表明同源基因表达偏向受遗传调控，并且可以利用基因分型数据进行预测。hebQTL大多调控同一亚基因组中同源基因的表达，并下调表达以产生同源基因表达偏向，这表明亚基因组内而非亚基因组间的相互作用诱导了同源基因表达偏向。此外，我们确定hebQTL调控的同源基因与其对应基因相比，表现出更高的遗传多样性和更弱的生物学功能。值得注意的是，在三联体中，38.4%的hebQTL调控的同源基因的下调被其他同源基因的上调所补偿。
我们的研究结果揭示了同源基因表达在遗传水平上是如何协调的，并为利用同源基因表达偏向来改良多倍体作物提供了一条途径。
