Potato is the most widely grown non-grain crop and ranks as the third most significant global food crop following rice and wheat. Despite its long history of cultivation over vast areas, slow breeding progress and environmental stress have led to a scarcity of high-yielding potato varieties. Enhancing the quality and yield of potato tubers remains the ultimate objective of potato breeding. However, conventional breeding has faced challenges due to tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression. Recent advancements in molecular biology and functional genomic studies of potato have provided valuable insights into the regulatory network of physiological processes and facilitated trait improvement. In this review, we present a summary of identified factors and genes governing potato growth and development, along with progress in potato genomics and the adoption of new breeding technologies for improvement. Additionally, we explore the opportunities and challenges in potato improvement, offering insights into future avenues for potato research.

Leaf inclination, a component of crop architecture, influences photosynthetic efficiency and planting density. Various factors, particularly the phytohormones auxin and brassinosteroids (BRs), function in regulating lamina joint bending, and understanding of the genetic control of leaf inclination will help to elucidate the relevant regulatory network. Screening a rice T-DNA insertion population revealed a mutant that was insensitive to auxin and displayed an enlarged leaf angle due to increased cell length on the adaxial side of the lamina joint. Genetic analysis revealed that the increased leaf inclination was caused by T-DNA insertion in the promoter region of OsIAA6, resulting in elevated OsIAA6 expression. Further study showed that OsIAA6 interacts with OsARF1 to suppress auxin signaling and regulates leaf inclination. OsIAA6 mediates the BR effects on lamina joint development, and OsBZR1, the key transcription factor in BR signaling, binds directly to the promoter of OsIAA6 to stimulate its transcription. These results indicate the roles of the OsIAA6–OsARF1 module in regulating rice leaf inclination and suggest the synergistic effects of the phytohormones auxin and BR.

Potato is the fourth most important food crop in the world. Although with a long history for breeding approaches, genomic information and association between genes and agronomic traits remain largely unknown particularly in autotetraploid potato cultivars, which limit the molecular breeding progression. By resequencing the genome of 108 main cultivar potato accessions with rich genetic diversity and population structure from International Potato Center, with approximate 20-fold coverage, we revealed more than 27 million Single Nucleotide Polymorphisms and ~ 3 million Insertion and Deletions with high quality and accuracy. Domestication analysis and genome-wide association studies (GWAS) identified candidate loci related to photoperiodic flowering time and temperature sensitivity as well as disease resistance, providing informative insights into the selection and domestication of cultivar potato. In addition, GWAS with GWASploy for 25 agronomic traits identified candidate loci by association signals, especially those related to tuber size, small-sized tuber weight and tuber thickness that was also validated by transcriptome analysis. Our study provides a valuable resource that facilitates the elucidation of domestication process as well as the genetic studies and agronomic improvement of autotetraploid potato.

Soil inorganic phosphate (Pi) levels are frequently suboptimal for the growth and development of crop plants. Although MADS-box genes participate in diverse plant developmental processes, their involvement in phosphate starvation responses (PSRs) remains unclear. We identified a type I MADS-box transcription factor gene, TaMADS2-3D, which was rapidly induced under low-Pi stress in roots of wheat (Triticum aestivum). A TaMADS2-3D-GFP fusion protein was found located in the nucleus. Transgenic Arabidopsis plants overexpressing TaMADS2-3D (TaMADS2-3DOE) showed shortened primary roots, increased lateral root density, and retarded seedling growth under high-Pi (HP) conditions, accompanied by increased Pi contents in their shoots and roots. The Arabidopsis TaMADS2-3DOE plants showed similar PSR phenotypes under low Pi (LP) conditions. These results indicate constitutive activation of PSRs by overexpression of TaMADS2-3D in Arabidopsis. Reactive oxygen species (ROS), H₂O₂ and O₂⁻, levels were increased in root tips of Arabidopsis TaMADS2-3DOE plants under HP conditions. Transcriptome analysis of Arabidopsis TaMADS2-3DOE plants under different Pi regimes revealed expression changes for a variety of PSR genes including AtZAT6. Overexpression of TaMADS2-3D in wheat also led to constitutive activation of PSRs. We propose that TaMADS2-3D regulates plant PSRs probably by modulating ROS homeostasis, root development, PSR gene expression, and Pi uptake. This study increases our understanding of plant PSR regulation and provides a valuable gene for improving phosphorus-use efficiency in wheat and other crops.

Heterosis is an important biological phenomenon and widely applied in agriculture. Although many studies have been performed by using vegetative organs of F₁ hybrid plants, how heterosis (or hybrid vigor) is initiated and formed, particularly the underlying molecular mechanism, remain elusive. Hybrid contemporary seeds of rice indica varieties 9311 and PA64 were innovatively used and analysis of DNA methylome of embryo and endosperm at early developing stages revealed the globally decreased DNA methylation. Genes, especially those relate to hormones function and transcriptional regulation present non-additive methylation. Previously identified heterosis-related superior genes are non-additively methylated in early developing hybrid contemporary seeds, suggesting that key genes/loci responsible for heterosis are epigenetically modified even in early developing hybrid seeds and hypomethylation of hybrid seeds after cross-pollination finally result in the long-term transcriptional change of F₁ hybrid vegetative tissues after germination, demonstrating that altered DNA methylation in hybrid seeds is essential for initiation regulation and maintenance of heterosis exhibiting in F₁ hybrid plants. Notably, a large number of genes show non-additive methylation in the endosperm of reciprocal hybrids, suggesting that endosperm might also contribute to heterosis.