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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., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Hajibarat et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Plant organelles are highly motile where their movement is significant for fast distribution of material around the cell, facilitation of the plant's ability to respond to abiotic and biotic signals, and for appropriate growth. Abiotic and biotic stresses are among the major factors limiting crop yields, and biological membranes are the first target of these stresses. Plants utilize adaptive mechanisms namely myosin to repair injured membranes following exposure to abiotic and biotic stresses., Objective: Due to the economic importance and cultivation of potato grown under abiotic and biotic stress prone areas, identification and characterization of myosin family members in potato were performed in the present research., Methods: To identify the myosin genes in potato, we performed genome-wide analysis of myosin genes in the S. tuberosum genome using the phytozome. All putative sequences were approved with the interproscan. Bioinformatics analysis was conducted using phylogenetic tree, gene structure, cis-regulatory elements, protein-protein interaction, and gene expression., Result: The majority of the cell machinery contain actin cytoskeleton and myosins, where motility of organelles are dependent on them. Homology-based analysis was applied to determine seven myosin genes in the potato genome. The members of myosin could be categorized into two groups (XI and VIII). Some of myosin proteins were sub-cellularly located in the nucleus containing 71.5% of myosin proteins and other myosin proteins were localized in the mitochondria, plasma-membrane, and cytoplasm. Determination of co-expressed network, promoter analysis, and gene structure were also performed and gene expression pattern of each gene was surveyed. Number of introns in the gene family members varied from 1 to 39. Gene expression analysis demonstrated that StMyoXI-B and StMyoVIII-2 had the highest transcripts, induced by biotic and abiotic stresses in all three tissues of stem, root, and leaves, respectively. Overall, different cis-elements including abiotic and biotic responsive, hormonal responsive, light responsive, defense responsive elements were found in the myosin promoter sequences. Among the cis-elements, the MYB, G-box, ABRE, JA, and SA contributed the most in the plant growth and development, and in response to abiotic and biotic stress conditions., Conclusion: Our results showed that myosin genes can be utilized in breeding programs and genetic engineering of plants with the aim of increasing tolerance to abiotic and biotic stresses, especially to viral stresses such as PVY, PVX, PVA, PVS, high light, drought, cold and heat., (© 2022. The Author(s), under exclusive licence to Springer Nature B.V.)

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., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

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]