Molecular Pathogens, 2025, Vol.16, No.1, 36-44 http://microbescipublisher.com/index.php/mp 37 2 Overview of Potato Genomics 2.1 Advances in genome sequencing In recent years, genome sequencing technology has become more advanced. In the past, people used short read sequencing, but now more and more people are starting to use long read sequencing. This new approach can help us understand the entire genetic information of the Solanum plants more clearly, including their genetic diversity (Tiwari et al., 2022). There is also a method called dRenSeq which is also very popular. It can be used to find disease-resistant genes in potatoes, especially in tetraploid potatoes. Compared with whole genome sequencing, dRenSeq is cheaper and has a high efficiency (Armstrong et al., 2018). In addition, gene editing tools like CRISPR are also being used in potato breeding. Everyone hopes to use these technologies to breed new varieties that are more resistant to disease and perform better (Berindean et al., 2024). 2.2 Genetic diversity and resources The genetic resources of the nightshade are abundant, but only a small part of potato breeding in the past has been used (Tiwari et al., 2022). Now, scientists are trying to make full use of these resources. Technologies like Genome-wide Association Research (GWAS) and genome selection have helped us find many key genes related to disease resistance. For example, some genes can make potatoes better resist late blight and potato cyst nematodes. In addition, the researchers also combined the analysis methods of the transcriptome and metabolomic group to study the anti-disease mechanism of potatoes more deeply. They found that a class of proteins called LRR-RLK plays an important role in recognizing pathogens and initiating defense responses (Yogendra and Kushalappa, 2016a). 2.3 Databases and bioinformatics tools Current potato research is inseparable from bioinformatics. Researchers use tools and databases to analyze genes so that they can find mutation points in genes, such as SNP (single nucleotide polymorphism), which is very useful for breeding (Caruana et al., 2019). These tools can also help predict the combination of different alleles in a breed and judge its breeding potential, which can make breeding more efficient (Caruana et al., 2019). In addition, some new DNA markers have been developed to screen out better potato varieties. These techniques allow us to better combine genomic research with actual breeding (Gebhardt, 2013). 3 Identification of Disease-Resistance Genes 3.1 Major Resistance (R) Genes in Potatoes Finding disease-resistant genes in potatoes is very important for breeding. Most of these R genes are single dominant genes that can help plants fight against a variety of pathogens such as viruses, nematodes, and fungi. Currently, researchers have found 19 such genes with DNA markers. Many of them are concentrated in certain “hot spots” regions on the potato genome (Gebhardt and Valkonen, 2001). These genes are particularly critical to resistance to severe diseases such as late blight (Gebhardt and Valkonen, 2001; De La Cruz et al., 2023). There is also a method called dRenSeq, which can also be used to detect these disease-resistant genes. Compared with whole genome sequencing, it is faster, more cost-effective and has good results (Armstrong et al., 2018). 3.2 Genome-wide association studies (GWAS) Genome-wide association research, referred to as GWAS, is a common method to find disease-resistant genes. For example, scientists used GWAS to find SNP markers related to potato wart disease. This disease is caused by a pathogen called Synchytrium endobioticum (Prodhomme et al., 2020). This technique is also used to study potatoes' genes that resist late blight and nematodes. It was found that there were several obvious marker points on chromosomes 5, 10 and 11. These places are considered areas with relatively concentrated disease-resistant genes (Sood et al., 2023). These findings not only help us better understand how resistance is inherited, but also provide a reference for molecular markers used in breeding (Prodhomme et al., 2020; Sood et al., 2023). 3.3 Functional characterization of resistance genes It is not enough to just know that there are disease-resistant genes, and we also need to understand how they work. There is a method called “effect genomics”, which can find the non-toxic genes in pathogens. Through these
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