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Heterosis is a fundamental biological phenomenon characterized by the superior performance of hybrids over their parents. Although tremendous progress has been reported in seed crops, the molecular mechanisms underlying heterosis in clonally propagated crops are largely unknown. Potato (Solanum tuberosum L.) is the most important tuber crop and an ongoing revolution is transforming potato from a clonally propagated tetraploid crop into a seed‐propagated diploid hybrid potato. In our previous study, we developed the first generation of highly homozygous inbred lines of potato and hybrids with strong heterosis. Here, we integrated transcriptome, metabolome, and DNA methylation data to explore the genetic and molecular basis of potato heterosis at three developmental stages. We found that the initial establishment of heterosis in diploid potato was mainly due to dominant complementation. Flower color, male fertility, and starch and sucrose metabolism showed obvious gene dominant complementation in hybrids, and hybrids devoted more energy to primary metabolism for rapid growth. In addition, we identified ~2 700 allele‐specific expression genes at each stage, which likely function in potato heterosis and might be regulated by CHH allele‐specific methylation level. Our multi‐omics analysis provides insight into heterosis in potato and facilitates the exploitation of heterosis in potato breeding.

Increasing soil salinization seriously impairs plant growth and development, resulting in crop loss. The Salt-Overly-Sensitive (SOS) pathway is indispensable to the mitigation of Na⁺ toxicity in plants under high salinity. However, whether natural variations of SOS2 contribute to salt tolerance has not been reported. Here a natural variation in SlSOS2 promoter region was identified to be associated with root Na⁺/K⁺ ratio and the loss of salt resistance during tomato domestication. This natural variation contains an ABI4 binding cis-element and plays an important role in the repression of SlSOS2 expression. Genetic evidence revealed that SlSOS2 mutations increase root Na⁺/K⁺ ratio under salt stress conditions and thus attenuate salt resistance in tomato. Together, our findings uncovered a critical but previously unknown natural variation of SOS2 in salt resistance, which provides valuable natural resources for genetic breeding for salt resistance in cultivated tomatoes and other crops.

Cold stress adversely affects crop growth and productivity. Resolving the genetic basis of freezing tolerance is important for crop improvement. Wild potato (Solanum commersonii) exhibits excellent freezing tolerance. However, the genetic factors underlying its freezing tolerance remain poorly understood. Here, we identified flavonoid 3′-hydroxylase (F3′H), a key gene in the flavonoid biosynthesis pathway, as highly expressed in S. commersonii compared with cultivated potato (S. tuberosum L.). Loss of ScF3′H function impaired freezing tolerance in S. commersonii, while ScF3′H overexpression in cultivated potato enhanced its freezing tolerance. Metabolic analysis revealed that F3′H generates more downstream products by adding hydroxyl (−OH) groups to the flavonoid ring structures. These flavonoids enhance reactive oxygen species scavenging, thereby contributing to freezing tolerance. Furthermore, the W-box element in the F3′H promoter plays a critical role in cold responses. Cold-induced transcription factor ScWRKY41 directly binds to the ScF3′H promoter region and recruits histone acetyltransferase 1 (ScHAC1), which enhances histone acetylation at the F3′H locus and activates its transcription. Overall, we identified the cold-responsive WRKY41–F3′H module that enhances freezing tolerance by augmenting the antioxidant capacity of flavonoids. This study reveals a valuable natural gene module for breeding enhanced freezing tolerance in potato and other crops.