Alternative splicing (AS) occurs extensively in eukaryotes as an important mechanism for regulating transcriptome complexity and proteome diversity, but variation in the AS landscape in response to domestication and polyploidization in crops is unclear. Hexaploid wheat (AABBDD, Triticum aestivum) has undergone two separate allopolyploidization events, providing an ideal model for studying AS changes during domestication and polyploidization events. In this study, we performed high-throughput transcriptome sequencing of roots and leaves from wheat species with varied ploidies, including wild diploids (A^bA^b, Triticum boeoticum) and tetraploids (AABB, Triticum dicoccoides), domesticated diploids (A^mA^m, Triticum monococcum) and tetraploids (AABB, Triticum dicoccum), hexaploid wheat (AABBDD, T. aestivum), as well as newly synthesized hexaploids together with their parents. Approximately 22.1% of genes exhibited AS, with the major AS type being intron retention. The number of AS events decreased after domestication in both diploids and tetraploids. Moreover, the frequency of AS occurrence tended to decrease after polyploidization, consistent with the functional sharing model that proposes AS and duplicated genes are complementary in regulating transcriptome plasticity in polyploid crops. In addition, the subgenomes exhibited biased AS responses to polyploidization, and ~87.1% of homeologs showed AS partitioning in hexaploid wheat. Interestingly, substitution of the D-subgenome modified 42.8% of AS patterns of the A- and B-subgenomes, indicating subgenome interplay reprograms AS profiles at a genome-wide level, although the causal–consequence relationship requires further study. Conclusively, our study shows that AS variation occurs extensively after polyploidization and domestication in wheat species.

替代剪接（AS）广泛存在于真核生物中，是调节转录组复杂性和蛋白质组多样性的重要机制，但是尚不清楚农作物的驯化和多倍化对AS格局的影响。六倍体小麦（AABBDD，普通小麦）经历了两次单独的同种多倍体化事件，为研究驯化和多倍体化事件中AS变化提供了理想模型。在这项研究中，我们对具有不同倍性的小麦物种的根和叶进行了高通量转录组测序，包括野生二倍体（AbAb，Triticum boeoticum）和四倍体（AABB，Triticum dicoccoides），驯化二倍体（AmAm，Triticum monococcum）和四倍体（AABB，Triticum dicoccum），六倍体小麦（AABBDD，Triticum aestivum L.），以及新合成的六倍体及其父母。大约22.1％的基因表现出AS，主要的AS类型是内含子保留。驯化后，二倍体和四倍体的AS事件数量均减少。此外，多倍体化后AS的发生频率趋于降低，这与提出AS的功能共享模型一致，并且重复的基因在调节多倍体作物的转录组可塑性中是互补的。另外，亚基因组对多倍体化表现出偏向的AS反应，约87.1％的同源同源物在六倍体小麦中显示AS分配。有趣的是，D亚基因组的替换修饰了A和B亚基因组的AS模式的42.8％，表明亚基因组相互作用在全基因组水平上重新编程了AS配置文件，尽管因果关系需要进一步研究。总之，我们的研究表明，在小麦中多倍体化和驯化后，AS变异广泛发生。