Simple sequence repeats (SSRs) are important sources of genetic diversity and are widely used as markers in genetics and molecular breeding. In this study, we examined four potato genomes of DM1-3 516 R44 (DM) from Solanum phureja, RH89039-16 (RH) from Solanum tuberosum, M6 from Solanum chacoense and Solanum commersonii to determine SSR abundance and distribution and develop a larger list of polymorphic markers for a potentially wide range of uses for the potato community. A total of 1,734,619 SSRs were identified across the four genomes with an average of 433,655 SSRs per genome and 2.31kb per SSR. The most abundant repeat units for mono-, di-, tri-, and tetra-nucleotide SSRs were (A/T)n, (AT/AT)n, (AAT/ATT)n, and (ATAT/ATAT)n, respectively. The SSRs were most abundant (78.79%) in intergenic regions and least abundant (3.68%) in untranslated regions. On average, 168,069 SSRs with unique flanking sequences were identified in the four genomes. Further, we identified 16,245 polymorphic SSR markers among the four genomes. Experimental validation confirmed 99.69% of tested markers could generate target bands. The high-density potato SSR markers developed in this study will undoubtedly facilitate the application of SSR markers for genetic research and marker-pyramiding in potato breeding.

Hormones play an important role in plant disease resistance and defense. Transcriptome data of late blight resistant potato genotype SD20 treated by ethylene (ET), jasmonate (JA), salicylic acid (SA), and Phytophthora infestans CN152 was analyzed to assess the role of the ET/JA/SA regulatory network in plant disease resistance and defense and predict key resistant genes. The results show that there was significant crossover of differentially expressed genes (DEGs) between all treatments, and common and specific plant disease interaction genes for the ET, JA, and SA treatments were differentially expressed in the CN152 treatment. The resistance and defense genes of the potato genotype SD20 could be induced to regulate metabolic and hormone signaling pathways by alternative splicing in all treatments. Further analysis found that JA and ET pathways can work together synergistically, JA/ET and SA pathways antagonize each other to initiate the expression of calmodulin-domain protein kinases (CDPK), calmodulin/calmodulin-like (CaM/CML), and RPM1-interacting protein 4 (RIN4) genes, and activate HSP-mediated HR response and defense-related genes. Meanwhile nine defense genes, including wound-responsive AP2 like factor, glutathione-s-transferase, serine/threonine-protein kinase BRI1, and Avr9/Cf-9 rapidly elicited protein genes were obtained using WGCNA, which provided reliable targets for functional verification. This study provides a theoretical reference for the comprehensive application of plant hormones to improve resistance to potato late blight disease.

High temperatures delay tuberization and decrease potato (Solanum tuberosum L.) yields. However, the molecular mechanisms and regulatory networks underlying tuberization under high temperatures remain largely unknown. Here, we performed the mRNA and miRNA sequencing of leaves and stems to identify genes and regulatory networks involved in tuberization under high temperatures. A total of 2804 and 5001 differentially expressed genes (DEGs) under high-temperature stress were identified in leaves and stems, respectively. These genes were significantly enriched in gene ontology terms regarding meristem development, the sucrose biosynthetic process, and response to heat. Meanwhile, 101 and 75 differentially expressed miRNAs (DEmiRNAs) were identified in leaves and stems, respectively. We constructed an interaction network between DEmiRNAs and DEGs, identifying 118 and 150 DEmiRNA–DEG pairs in leaves and stems, respectively. We found three miRNA–mRNA candidate modules involved in tuberization under high temperatures, including stu-miR8030-5p/StCPY714, stu-miR7981f-p5/StAGL8a, and stu-miR10532A/StAGL8b. Our study constructed an interaction network between miRNAs and target genes and proposes candidate miRNA–gene modules that regulate tuber formation under high temperatures. Our study provides new insights for revealing the regulatory mechanism of the high-temperature inhibition of tuberization and also provides gene resources for improving the heat tolerance in potatoes.

Water and nitrogen are essential for potato growth and development. We aim to understand how potato adapts to changes in soil water and nitrogen content. Potato plant adaptations to changes in soil moisture and nitrogen levels were analyzed at the physiological and transcriptomic levels in four treatment groups: adequate nitrogen under drought, adequate nitrogen under sufficient irrigation, limited nitrogen under drought, and limited nitrogen under sufficient irrigation. Many light-capture pigment complex genes and oxygen release complex genes were differentially expressed in leaves when nitrogen levels were increased under drought conditions, and several genes encoding rate-limiting enzymes in the Calvin–Benson–Bassham cycle were up-regulated; furthermore, leaf stomatal conductance decreased, whereas the saturated vapor pressure difference and relative chlorophyll content in the chloroplasts increased. StSP6A, a key gene in potato tuber formation, was down-regulated in response to increased nitrogen application, and the stolon growth time was prolonged. Genes related to root nitrogen metabolism were highly expressed, and protein content in the tuber increased. Weighted gene co-expression network analysis (WGCNA) revealed 32 gene expression modules that responded to changes in water and nitrogen levels. A total of 34 key candidate genes were identified, and a preliminary molecular model of potato responses to alterations in soil water and nitrogen content was constructed.

Maturity is a key trait for breeders to identify potato cultivars suitable to grow in different latitudes. However, the molecular mechanism regulating maturity remains unclear. In this study, we performed a grafting experiment using the early-maturing cultivar Zhongshu 5 (Z5) and the late-maturing cultivar Zhongshu 18 (Z18) and found that abscisic acid (ABA) and salicylic acid (SA) positively regulate the early maturity of potato, while indole-3-acetic acid (IAA) negatively regulated early maturity. A total of 43 long-distance transport mRNAs are observed to be involved in early maturity, and 292 long-distance transport mRNAs involved in late maturity were identified using RNA sequencing. Specifically, StMADS18, StSWEET10C, and StSWEET11 are detected to be candidate genes for their association with potato early maturity. Metabolomic data analysis shows a significant increase in phenolic acid and flavonoid contents increased in the scion of the early-maturing cultivar Z5, but a significant decrease in amino acid, phenolic acid, and alkaloid contents increased in the scion of the late-maturing cultivar Z18. This work reveals a significant association between the maturity of tetraploid cultivated potato and long-distance transport signal molecules and provides useful data for assessing the molecular mechanisms underlying the maturity of potato plants and for breeding early-maturing potato cultivars.