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Potato is considered a key component of the global food system and plays a vital role in strengthening world food security. A major constraint to potato production worldwide is the Potato Virus Y (PVY), belonging to the genus Potyvirus in the family of Potyviridae. Selective breeding of potato with resistance to PVY pathogens remains the best method to limit the impact of viral infections. Understanding the genetic diversity and population structure of potato germplasm is important for breeders to improve new cultivars for the sustainable use of genetic materials in potato breeding to PVY pathogens. While, genetic diversity improvement in modern potato breeding is facing increasingly narrow genetic basis and the decline of the genetic diversity. In this research, we performed genotyping-by-sequencing (GBS)-based diversity analysis on 10 commercial potato cultivars and weighted gene co-expression network analysis (WGCNA) to identify candidate genes related to PVY-resistance. WGCNA is a system biology technique that uses the WGCNA R software package to describe the correlation patterns between genes in multiple samples. In terms of consumption, these cultivars are a high rate among Iranian people. Using population structure analysis, the 10 cultivars were clustered into three groups based on the 118343 single nucleotide polymorphisms (SNPs) generated by GBS. Read depth ranged between 5 and 18. The average data size and Q30 of the reads were 145.98 Mb and 93.63%, respectively. Based on the WGCNA and gene expression analysis, the StDUF538, StGTF3C5, and StTMEM161A genes were associated with PVY resistance in the potato genome. Further, these three hub genes were significantly involved in defense mechanism where the StTMEM161A was involved in the regulation of alkalization apoplast, the StDUF538 was activated in the chloroplast degradation program, and the StGTF3C5 regulated the proteins increase related to defense in the PVY infected cells. In addition, in the genetic improvement programs, these hub genes can be used as genetic markers for screening commercial cultivars for PVY resistance. Our survey demonstrated that the combination of GBS-based genetic diversity germplasm analysis and WGCNA can assist breeders to select cultivars resistant to PVY as well as help design proper crossing schemes in potato breeding. [ABSTRACT FROM AUTHOR]

Biotic and abiotic stresses are among major factors limiting crop yields, and Filamentation temperature-sensitive (FtsH) genes are one of the key regulators of plant response to these stresses. The FtsH is an ATP-dependent metalloprotease in prokaryotes and eukaryotes. Due to the economic importance and cultivation of potato grown in the biotic and abiotic stress prone areas, identification and characterization of FtsH family members are crucially important. The present research was conducted to investigate FtsH family members in potato under stressful regime. To detect the FtsH genes in potato, we performed genome-wide analysis of FtsH genes in the Solanum tuberosum genome using the Ensemble Plant. All putative sequences were approved with the Pfam. Bioinformatics analysis was conducted using phylogenetic tree, gene structure, Transcription factor-binding site (TFBS) analysis, protein–protein interaction, and gene expression. The members of FtsH were categorized into eight groups. Some of the FtsH proteins were subcellularly located in the nucleus and chloroplast. The number of introns was ranged from 3 to 14 in gene family members. Totally, 33 TFBS including biotic and abiotic stress-responsive elements were found in FtsH promoter sequences. MYB and WRKY were the highest number among TFBS which were involved in abiotic and biotic stresses. Gene expression analysis revealed that the StFtsH2 and StFtsH5 had the highest gene expression, induced by abiotic and biotic stresses in all three tissues of stem, root, and leaves. It is expected that the StFtsH2 and StFtsH5 could be used in plant manipulation and breeding programs aimed for tolerance enhancement to abiotic (cold, heat, and high light) and biotic stresses [Potato virus Y (PVY), Potato virus X (PVX), Potato virus A (PVA), Potato virus X (PVA), and Potato virus S (PVS)]. [ABSTRACT FROM AUTHOR]

GF14 proteins are a family of conserved proteins involved in many cellular processes including transport, growth, metabolism, and stress response. However, only few reports are available regarding the 14-3-3 genes in potato. In this study, twelve 14-3-3 genes were detected in the potato genome. Based on their phylogenetic relationships, the StGF14 family members were categorized into two classes. Gene expression analysis demonstrated that StGF14h, StGF14a, and StGF14k had the highest gene expression, induced by abiotic and biotic stresses in all three tissues. The number of exons in 14-3-3 genes ranged from four to seven and most of these genes in the same subfamily had similar exon-intron patterns. The results of our study showed that the conserved motifs are similar in most of the proteins in each group. The intron-exon patterns and the composition of conserved motifs validated the 14-3-3 gene phylogenetic classification. According to the genome distribution results, 14-3-3 genes were located unevenly on the 12 Solanum tuberosum chromosomes. We find out 97 orthologous gene pairs between potato and Arabidopsis as well as 15 paralogous genes among potato genomes. Our results showed that GF-14 genes have an effective role in functional and molecular mechanisms in response to environmental stresses. [ABSTRACT FROM AUTHOR]

Background: The Plant U-box (PUB), ubiquitin ligase gene, has a highly conserved domain in potato. However, little information is available about U-box genes in potato (Solanum tuberosum). In this study, 62 U-box genes were detected in the potato genome using bioinformatics methods. Further, motif analysis, gene structure, gene expression, TFBS, and synteny analysis were performed on the U-box genes. Results: Based on in silico analysis, most of StU-boxs included a U-box domain; however, some of them lacked harbored domain the ARM, Pkinase_Tyr, and other domains. Based on their phylogenetic relationships, the StU-box family members were categorized into four classes. Analysis of transcription factor binding sites (TFBS) in the promoter region of StU-box genes revealed that StU-box genes had the highest and the lowest number of TFBS in MYB and CSD, respectively. Moreover, based on in silico and gene expression data, variable frequencies of TFBS in StU-box genes could indicate that these genes control different developmental stages and are involved in complex regulatory mechanisms. The number of exons in U-box genes ranged from one to sixteen. For most U-box genes, the exon–intron compositions and conserved motifs composition in most proteins in each group were similar. The intron–exon patterns and the composition of conserved motifs validated the U-box genes phylogenetic classification. Based on the results of genome distribution, StU-box genes were distributed unevenly on the 12 S. tuberosum chromosomes. The results showed that gene duplication may possess a significant role in genome expansion of S. tuberosum. Furthermore, genome evolution of S. tuberosum was surveyed using identification of orthologous and paralogous. We identified 40 orthologous gene pairs between S. tuberosum with Solanum lycopersicum, Oryza sativa, Triticum aestivum, Gossypium hirsutum, Zea maize, Coriaria mytifolia, and Arabidopsis thaliana as well as eight duplicated genes (paralogous) in S. tuberosum. StU-box 51 gene is one of the important gene among other StU-boxes in S. tuberosum under drought stress which was expressed in tuber and leaf under drought stress. Furthermore, StU-box 51 gene has the highest expression levels in four tissue-specific (stem, root, leaf, and tuber) in potato as well as it had the highest number of TFBS in promoter region. Based on our results, StU-box 51 can introduce to researcher to utilize in breeding program and genetic engineering in potato. Conclusions: The results of this survey will be useful for further investigation of the probable role and molecular mechanisms of U-box genes in response to different stresses. [ABSTRACT FROM AUTHOR]

Background: Potato is one of the most important food crops worldwide, contributing key nutrients to the human diet. Plant hormones act as vital switchers in the regulation of various aspects of developmental and growth stages in potato. Due to the broad impacts of hormones on many developmental processes, their role in potato growth and developmental stages has been investigated. This review presents a description of hormonal basic pathways, various interconnections between hormonal network and reciprocal relationships, and clarification of molecular events underlying potato growth. In the last decade, new findings have emerged regarding their function during sprout development, vegetative growth, tuber initiation, tuber development, and maturation in potato. Hormones can control the regulation of various aspects of growth and development in potato, either individually or in combination with other hormones. The molecular characterization of interplay between cytokinins (CKs), abscisic acid (ABA), and auxin and/or gibberellins (GAs) during tuber formation requires further undertaking. Recently, new evidences regarding the relative functions of hormones during various stages and an intricate network of several hormones controlling potato tuber formation are emerging. Although some aspects of their functions are widely covered, remarkable breaks in our knowledge and insights yet exist in the regulation of hormonal networks and their interactions during different stages of growth and various aspects of tuber formation. Short conclusion: The present review focuses on the relative roles of hormones during various developmental stages with a view to recognize their mechanisms of function in potato tuber development. For better insight, relevant evidences available on hormonal interaction during tuber development in other species are also described. We predict that the present review highlights some of the conceptual developments in the interplay of hormones and their associated downstream events influencing tuber formation. [ABSTRACT FROM AUTHOR]

Potato, (Solanum tuberosum), is one of the most common and important food sources for humans. It is not only essential as a food source but also has many benefits for human health. Potato is ranked as the world's third non-cereal crop after rice and wheat. Biotic stress, such as viruses, is a common stress in potato-growing areas, leading to reduced tuber yield and quality. This review begins with a description of resistance mechanisms to viruses, historical perspective on potato improvement for virus resistance based on classic and next-generation sequencing (NGS) techniques. Classical breeding has been exploited for improving virus resistant potato. In recent years, plant breeding has quickly changed from phenotypic selection to genotype selection, facilitating the selection process both in terms of time and accuracy. The next-generation sequencing techniques have valuable potential to study the genotype selection through whole-genome re-sequencing (WGRS) and genome-wide association study (GWAS), and RNA-seq has been used to identify markers in virus-resistance potato, facilitating potato breeding for virus resistance. Identification of molecular markers based on new generation sequencing methods and in particular NGS along with bioinformatics tools has facilitated the identification of related markers. The objectives of this review were to better understand virus resistance genes and to recommend the most effective technique and/ or combination approaches for identification of molecular markers in order to breed potato plants resistant to viruses. [ABSTRACT FROM AUTHOR]

The KNOTTED1-LIKE HOMEOBOX (KNOX) transcription factors (TF) play an important role in growth and developmental stages in potato. However, only few reports are available regarding the KNOX gene family in potato. In this study, 17 KNOX genes were detected in the potato genome. The gene structure, protein characteristics, promoter analysis, synthetic regions, gene duplication, gene expression in developmental stages, and chromosomal location were investigated. Based on their phylogenetic relationships, the StKNOX family members were categorized into three classes. Analysis of gene expression showed that the tissue expression patterns of StKNOX genes in the same group were similar but varied among groups. Analysis of transcription factor binding site (TFBS) and microRNA in the promoter region and coding sequence of StKNOX genes revealed the presence of putative TFBS and 49 StmiRNAs. Moreover, variable frequencies of TFSB and miRNA in StKNOX genes could indicate that these genes control different developmental stages and are involved in complex regulatory mechanisms. Our results showed that some members of Class II (StKNOX14) have the highest number of TFBS and are highly expressed in 19 potato tissues. Our findings showed that these genes could be involved in the regulation of plant growth and tuber development in S.tuberosum. The results of this study will be useful in further investigations on the functional role of potato StKNOX genes. • KNOX proteins are homeodomain transcription factors that have a critical role in morphogenesis. • Some members of KNAT2/6 (KNOX6/7/8) have the highest number of TFBS and are highly expressed in plant roots. • KNOX genes could be involved in regulation of plant growth and tuber development in S.tuberosum. [ABSTRACT FROM AUTHOR]

GATA proteins are a group of transcriptional regulators that can detect and bind to GATA motifs by zinc finger domain. The plant GATA family is one of the most significant TFs involved in light-responsive development, nitrogen metabolism, and phyto-hormone signaling. In this study, 20 potatoes and 22 tomato GATA genes were selected. The chromosomal locations, gene structures, phylogenetic tree, and the expression during developmental stages of 42 GATA transcription factors (TFs) in Solanaceae species were analyzed to further investigate the functions of these factors. Also, Gene duplication and synteny between the tomato and potato genomes were also analyzed to provide insights into their evolutionary characteristics. Furthermore, genome evolution of potato and tomato using orthologous and paralogous identification was studied. The results of chromosomal localization revealed that 20 SlGATA genes of tomato were located on 12 chromosomes, except on chromosomes 9 and 11. In potato, all 22 StGATA genes were located on 12 chromosomes. Our results indicated that gene duplication may play an important role in genome expansion of potato and tomato. So far, a complete analysis combining evolutionary analysis and expression of the GATA TFs in the Solanaceae species of tomato and potato has not been reported. A comparative phylogenetic analysis of the GATA factor zinc finger domain sequences in potato and tomato revealed four subfamilies. The conserved motifs and gene structure in most genes in each group was similar, according to the grouping of GATA TFs in phylogenetic tree. The analysis of cis -elements showed that SlGATA26a/26b and StGATA26a/26b can be suggested as candidate genes in response to abiotic and biotic stresses. SlGATA26a/26b and StGATA26a/26b genes were expressed in root, shoot, and inflorescence. Altogether, our resultsshowed diverse roles for StGATA and SlGATA genes under abiotic and biotic stresses. Utilization of cis -elements prediction can faciliate potato and tomato improvement. • GATA proteins are a group of transcriptional regulators that can detect and bind to GATA motifs by zinc finger domain. • We surveyed the phylogenetic relationships, gene structures, chromosomal locations, gene duplications, and genes expression of 42 GATA TFs in three tissue types of tomato and potato. • Our results provide insights into the functional differences, evolutionary relationships and expression profiles of GATA transcription factors in Solanaceae species. [ABSTRACT FROM AUTHOR]