Natural Variation of a PPR Coding Gene SST1 Confers Salt Tolerance During Soybean Domestication

Soil salinity is one of the constraints that adversely affect seedling growth and limit soybean yield. Identifying salt tolerance genes and profiling their allele variants are crucial for elucidating the mechanisms underlying salt tolerance in soybean and enabling the genetic improvement of salt-tolerant cultivars. Here, we developed a salt-induced leaf senescence-based screening system to assess salt tolerance and identified a key salt tolerance gene, SST1, which encodes a pentatricopeptide repeat (PPR) protein, via genome-wide association analysis. We showed that the truncated allele SST1^HapT, which has a nonsense mutation, increases salt tolerance in soybean, whereas the full-length allele SST1^HapC does not. Located in mitochondria, SST1 regulates RNA editing of the mitochondrial genes cob, nad3 and atp6-1, thereby influencing mitochondrial morphology and H₂O₂ homeostasis in root cells. SST1 is an adaptive domestication-related gene; the truncated SST1^HapT allele is exclusively fixed in cultivated soybean but absent in wild soybean, indicating selection under increasing soil salinity during domestication. Furthermore, our results revealed that SST1 regulates salt tolerance by synergistic interaction with GmCHX1, a pivotal salt tolerance gene unselected during domestication. Our findings provide valuable insights into soybean domestication and offer targets for enhancing soybean salt tolerance.