National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Sanya Institute of China Agricultural University, Sanya, Hainan, China.
Mol Biol Evol. 2022 Jun 2;39(6). doi: 10.1093/molbev/msac078.
Loss of seed shattering was a key step during cereal domestication, and it greatly facilitated seed harvest of the staple cereal foxtail millet (Setaria italica) because the cereal has very small seeds. However, the genetic basis for this loss has been largely unknown. Here, we combined comparative and association mapping to identify an 855-bp Harbinger transposable element insertion in the second exon of the foxtail millet gene shattering1 (sh1) that was responsible for the loss of seed shattering. The sh1 gene encodes zinc finger and YABBY domains. The insert prevents transcription of the second exon, causing partial loss of the zinc finger domain and then loss of natural seed shattering. Specifically, sh1 functions as a transcription repressor and represses the transcription of genes associated with lignin synthesis in the abscission zone, including CAD2. The diversity of sh1 is highly reduced in foxtail millet, consistent with either a severe domestication bottleneck or a selective sweep. Phylogenetic analysis of sh1 further revealed a single origin of foxtail millet in China. Our results support the theories that transposons were the most active factors in genome evolution driving loss of natural seed shattering during foxtail millet domestication and that sh1 underwent parallel selection during domestication across different cereal species.
种子爆裂的丧失是谷物驯化过程中的关键步骤，它极大地方便了主食谷子（Setaria italica）的种子收获，因为这种谷物的种子非常小。然而，这种丧失的遗传基础在很大程度上是未知的。在这里，我们结合比较和关联作图，鉴定了谷子基因 shattering1（sh1）第二外显子中 Harbinger 转座元件插入 855bp，该插入负责丧失种子爆裂。sh1 基因编码锌指和 YABBY 结构域。该插入阻止了第二外显子的转录，导致锌指结构域的部分缺失，从而导致天然种子爆裂的丧失。具体而言，sh1 作为转录抑制剂起作用，并抑制与离层木质素合成相关的基因的转录，包括 CAD2。sh1 在谷子中的多样性高度降低，与严重的驯化瓶颈或选择清除一致。sh1 的系统发育分析进一步表明，中国是谷子的单一起源地。我们的研究结果支持这样的理论，即转座子是驱动谷子驯化过程中天然种子爆裂丧失的最活跃的基因组进化因素，并且 sh1 在不同谷物物种的驯化过程中经历了平行选择。
