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Abstract Background 14–3-3 proteins are essential in regulating various biological processes and abiotic stress responses in plants. Although 14–3-3 proteins have been studied in model plants such as Arabidopsis thaliana and Oryza sativa, there is a lack of research on the 14–3-3 gene family in potatoes (Solanum tuberosum L.). Results A total of 18 14–3-3 genes encoding proteins containing a typical conserved PF00244 domain were identified by genome-wide analysis in potatoes. The St14–3-3 gene family members were unevenly distributed across the chromosomes, and gene structure analysis showed that gene length and intron number varied greatly among the members. Phylogenetic analysis of 14–3-3 proteins in potatoes and other plant species showed that they could be divided into two distinct groups (ε and non-ε). Members in the ε group tended to have similar exon-intron structures and conserved motif patterns. Promoter sequence analysis showed that the St14–3-3 gene promoters contained multiple hormone-, stress-, and light-responsive cis-regulatory elements. Synteny analysis suggested that segmental duplication events contributed to the expansion of the St14–3-3 gene family in potatoes. The observed syntenic relationships between some 14–3-3 genes from potato, Arabidopsis, and tomato suggest that they evolved from a common ancestor. RNA-seq data showed that St14–3-3 genes were expressed in all tissues of potatoes but that their expression patterns were different. qRT-PCR assays revealed that the expression levels of nearly all tested St14–3-3 genes were affected by drought, salt, and low-temperature stresses and that different St14–3-3 genes had different responses to these stresses. Conclusions In summary, genome-wide identification, evolutionary, and expression analyses of the 14–3-3 gene family in potato were conducted. These results provide important information for further studies on the function and regulation of St14–3-3 gene family members in potatoes. more...

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. more...

Early tuberization, a short period from stolon occurrence to tuber formation, is one of the major characteristics of a good early-maturing potato cultivar, while the regulatory mechanism of tuberization time (TT) is still unclear. In this study, two tetraploid cultivars, Zhongshu 3 (Z3) and Zhongshu 18 (Z18), with short and long TT respectively, were examined to reveal regulatory genes related to TT using RNA sequencing of tissue samples taken during stolon occurrence, stolon swelling and tuber formation. Cluster analysis showed that the gene expression patterns at the stolon swelling and tuber formation stages were significantly different from those at stolon occurrence in both Z3 and Z18. Therefore, we screened the differentially expressed genes (DEGs) at stolon swelling and tuber formation and compared them to those at stolon occurrence. A total of 3 085 DEGs were specifically identified and analyzed according to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment, and DEGs involved in starch and sucrose metabolism, plant hormone signal transduction and plant circadian clock were significantly enriched. The circadian clock genes were significantly differentially expressed between Z3 and Z18, revealing an important role for the plant circadian pathway in regulating TT. Furthermore, three candidate genes, StGI, StPRR and StEFM involved in circadian regulation and significantly differentially expressed between Z3 and Z18, were discovered and confirmed by qRT-PCR. The results provide valuable information for understanding the regulatory mechanisms of potato TT and represent a step toward breeding early-maturing potato cultivars. more...

Phenotypic evaluation and molecular biotechnology are both important in the identification and utilization of crop germplasm resources. In this study, the phenotypic variation and genetic diversity of 149 main potato cultivars in China were investigated with 12 phenotypic traits and 24 SSR markers. The coefficient of variation of 12 phenotypic traits ranged from 12.11% to 156.93%. The results of SSR markers exhibited a relatively high level of genetic variation (Na =5.458 ± 1.499, Ne =3.300 ± 1.087, I =1.397 ± 0.298, Ho =0.797 ± 0.178, He = 0.660 ± 0.117, and PIC=0.702 ± 0.087). Population structure and phylogenetic tree analysis divided the varieties into three subgroups. The results indicated that ninety percent of the molecular variance was attributed to within-group differences, and the remaining 10% was attributed to variation among groups. Consistent with previous report, alleles of the STI032 marker were significantly associated with tuber starch content and growth period traits in the population. The results of this study could facilitate the utilization of potato germplasm resources, molecular genetic breeding and improvement. more...

Late blight, caused by Phytophthora infestans (P. infestans), is a devastating disease in potato worldwide. Our previous study revealed that the Solanum andigena genotype 03112-233 is resistant to P. infestans isolate 90128, but susceptible to the super race isolate, CN152. In this study, we confirmed by diagnostic resistance gene enrichment sequencing (dRenSeq) that the resistance of 03112-233 toward 90128 is most likely based on a distinct new R gene(s). To gain an insight into the mechanism that governs resistance or susceptibility in 03112-223, comparative transcriptomic profiling analysis based on RNAseq was initiated. Changes in transcription at two time points (24 h and 72 h) after inoculation with isolates 90128 or CN152 were analyzed. A total of 8,881 and 7,209 genes were differentially expressed in response to 90128 and CN152, respectively, and 1,083 differentially expressed genes (DEGs) were common to both time points and isolates. A substantial number of genes were differentially expressed in an isolate-specific manner with 3,837 genes showing induction or suppression following infection with 90128 and 2,165 genes induced or suppressed after colonization by CN152. Hierarchical clustering analysis suggested that isolates with different virulence profiles can induce different defense responses at different time points. Further analysis revealed that the compatible interaction caused higher induction of susceptibility genes such as SWEET compared with the incompatible interaction. The salicylic acid, jasmonic acid, and abscisic acid mediated signaling pathways were involved in the response against both isolates, while ethylene and brassinosteroids mediated defense pathways were suppressed. Our results provide a valuable resource for understanding the interactions between P. infestans and potato. more...

Late blight, caused by the oomycete Phytophthora infestans, is the most devastating disease in potato-producing regions of the world. Cultivation of resistant varieties is the most effective and environmentally friendly way to control potato late blight disease, and identification of germplasms with late blight resistance and clarification their genetic relationship would promote the development of the resistant varieties. In this study, a diverse population of 189 genotypes with potential late blight resistance, consisting of 20 wild species and cultivated Solanum tuberosum Andigenum group and Chilotanum group, was screened for the presence of late blight resistance by performing challenge inoculation with four Phytophthora infestans isolates including one 13_A2 isolate, CN152. Ten elite resources with broad-spectrum resistance and 127 with isolate-specific resistance against P. infestans were identified. To improve the available gene pool for future potato breeding programs, the population was genotyped using 30 simple sequence repeat (SSR) markers covering the entire potato genome. A total of 173 alleles were detected with an average of 5.77 alleles per locus. Structure analysis discriminated the 189 potato genotypes into five populations based on taxonomic classification and genetic origin with some deviations. There was no obvious clustering by country of origin, ploidy level, EBN (endosperm balance number) value, or nuclear clade. Analysis of molecular variance showed 10.08% genetic variation existed among populations. The genetic differentiation (Fst) ranged from 0.0937 to 0.1764, and the nucleotide diversity (π) was 0.2269 across populations with the range from 0.1942 to 0.2489. Further genotyping of 20K SNP array confirmed the classification of SSRs and could uncover the genetic relationships of Solanum germplasms. Our results indicate that there exits abundant genetic variation in wild and cultivated potato germplasms, while the cultivated S. tuberosum Chilotanum group has lower genetic diversity. The phenotypic and genetic information obtained in this study provide a useful guide for hybrid combination and resistance introgression from wild gene pool into cultivated species for cultivar improvement, as well as for germplasm conservation efforts and resistance gene mining. more...

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. more...

Late blight is a devastating potato disease worldwide, caused by Phytophthora infestans. The P. infestans strain 2013-18-306 from Yunnan is a "supervirulent race" that overcomes all 11 known late blight resistance genes (PI to Pit) from Solanutn clemissum. In a previous study, we identified a diploid wild-type potato JAM 1-4 (S. jamesii) with high resistance to 2013-18-306. dRenSeq analysis indicated the presence of novel R genes in JAM I-4. RNA-Seq was used to analyze the late blight resistance response genes and defense regulatory mechanisms of JAM 1-4 against 2013-18-306. Gene ontology enrichment and KEGG pathway analysis showed that many disease-resistant pathways were significantly enriched. Analysis of differentially expressed genes (DEGs) revealed an active disease resistance mechanism of JAM 1-4, and the essential role of multiple signal transduction pathways and secondary metabolic pathways comprised of SA-JA-ET in plant immunity. We also found that photosynthesis in JAM 1 -4 was inhibited to promote the immune response. Our study reveals the pattern of resistance-related gene expression in response to a super race strain of potato late blight and provides a theoretical basis for further exploration of potato disease resistance mechanisms, discovery of new late blight resistance genes, and disease resistance breeding. [ABSTRACT FROM AUTHOR] more...