1 Introduction

Potato (Solanum tuberosum L.) is a staple food crop with significant economic and nutritional value worldwide. The improvement of potato varieties through breeding is essential to meet the increasing demand for higher yields, disease resistance, and stress tolerance. Genetic mapping and marker-assisted selection (MAS) have emerged as pivotal tools in modern potato breeding, enabling the precise identification and selection of desirable traits at the genetic level. These techniques facilitate the development of new potato cultivars with enhanced characteristics, thereby accelerating the breeding process and improving crop performance (Beketova et al., 2021).

The primary objective of MAS in potato breeding is to enhance the efficiency and accuracy of selecting plants with desirable traits, such as disease resistance, stress tolerance, and improved yield. This is achieved by identifying molecular markers linked to specific genes or quantitative trait loci (QTLs) and using these markers to screen breeding populations. Various methodologies are employed in MAS, including bulked segregant analysis (BSA), genotyping-by-sequencing (GBS), and the development of single nucleotide polymorphism (SNP) markers (Caruana et al., 2019; Meng et al., 2021; Tu et al., 2023). For instance, the use of high-throughput transcriptome sequencing has been shown to be effective in identifying a large number of SNP markers, which can be used for genomic selection and improving genetic progress in potato breeding. The integration of high-density SSR genetic linkage maps and kompetitive allele-specific PCR (KASP) assays further enhances the precision of MAS (Meade et al., 2019).

Despite the advancements in genetic mapping and MAS, several challenges remain in their application to potato breeding. These include the complexity of the potato genome, the polyploid nature of the crop, and the need for high-quality phenotypic data to validate marker-trait associations. Moreover, the development of cost-effective and reliable markers that can be routinely used in breeding programs is crucial. This study will provide a comprehensive overview of the advancements in genetic mapping and MAS in potato breeding, highlighting the importance of these technologies in enhancing potato yield and stress resistance. It will cover the methodologies adopted in MAS, as well as the practical applications and outcomes of these approaches in breeding programs. The focus will be on the current status of MAS in potato breeding, identifying future research and application directions to improve the efficiency and effectiveness of potato breeding programs.

2 Advancements in Genetic Mapping Technologies for Potato Breeding

2.1 Development and evolution of mapping techniques

The development of genetic mapping techniques has significantly evolved over the years, particularly in the context of potato breeding. Initially, traditional methods such as linkage mapping were employed to identify genetic markers associated with desirable traits. These methods, although foundational, were often labor-intensive and time-consuming. The advent of molecular markers, such as simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), marked a significant leap forward, enabling more precise and efficient mapping of genetic traits (Ahmad et al., 2022).

2.2 Incorporation of next-generation sequencing (NGS) and genomics

The incorporation of Next-Generation Sequencing (NGS) technologies has revolutionized genetic mapping in potato breeding. NGS allows for the rapid sequencing of entire genomes, facilitating the development of ultra-high-density genetic linkage maps. This has enabled the fine mapping of quantitative trait loci (QTLs) and the identification of candidate genes with unprecedented accuracy (Figure 1) (Jaganathan et al., 2020; Saidi and Hajibarat, 2020). Techniques such as genome-wide association studies (GWAS), whole genome resequencing (WGRS), and RNA sequencing (RNA-seq) have become powerful tools for analyzing complex traits and developing molecular markers for traits such as drought tolerance (Yamakawa et al., 2021). The use of NGS-based forward genetic approaches has further streamlined the identification and mapping of causal mutations, enhancing the resolution of QTL mapping and enabling the precise determination of functional variations in genes.

Figure 1 Various techniques followed for fine mapping during the pre- and post-NGS era and their impact on fine mapping (Adopted from Jaganathan et al., 2020)

2.3 Impact on potato genetic improvement

The advancements in genetic mapping technologies, particularly the integration of NGS and genomics, have had a profound impact on potato genetic improvement. These technologies have facilitated the rapid development of tightly linked DNA markers, which are crucial for marker-assisted selection (MAS) in breeding programs. The ability to accurately identify and select for desirable traits has accelerated the breeding process, leading to the development of potato varieties with improved yield, nutritional value, and stress tolerance (Hameed et al., 2018; Sahu et al., 2020). Moreover, the application of new breeding technologies such as CRISPR/Cas9 and TALENs has enabled the generation of transgene-free products, addressing consumer and regulatory concerns while enhancing the agronomic profile of potatoes.

3 Diverse Marker Types and Their Utility in Potato Breeding

3.1 Overview of marker types

In potato breeding, various molecular markers are employed to facilitate the identification and selection of desirable traits. These markers include simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), sequence-characterized amplified regions (SCARs), and kompetitive allele-specific PCR (KASP) markers. SSR markers are highly polymorphic and have been extensively used for genetic diversity studies and association mapping (Meng et al., 2021; Bhardwaj et al., 2023). SNP markers, on the other hand, offer high-throughput and dense genome coverage, making them suitable for genomic selection and QTL mapping (Massa et al., 2015). SCAR markers are particularly useful for tracking specific resistance genes, such as those conferring resistance to late blight. KASP markers provide a cost-effective and efficient platform for genotyping, especially when consolidated from various marker types.

3.2 Selection of marker types based on breeding objectives

The choice of marker type in potato breeding largely depends on the specific breeding objectives. For instance, SSR markers are preferred for evaluating genetic diversity and population structure due to their high polymorphism and informativeness. When the goal is to rapidly develop tightly linked DNA markers for traits such as disease resistance, SNP markers identified through whole-genome resequencing and QTL-seq are highly effective (Caruana et al., 2019; Yamakawa et al., 2021). For early-stage screening of breeding populations, SCAR markers are advantageous as they can halve the workload by efficiently tracking resistance genes. KASP markers are ideal for integrating various marker types into a single platform, thus streamlining the genotyping process in commercial breeding programs (Meade et al., 2019).

3.3 Case studies of marker utility

Several case studies highlight the practical applications of these markers in potato breeding. One study demonstrated the use of SCAR markers to track Rpi genes for late blight resistance, significantly reducing the screening workload in early breeding stages (Beketova et al., 2021). Another study utilized SSR markers to analyze genetic diversity and identify markers associated with late blight resistance, providing valuable tools for marker-assisted selection (MAS) (Figure 2) (Bhardwaj et al., 2023). The development of SNP markers through QTL-seq has been shown to facilitate the rapid identification of markers linked to important traits such as nematode resistance and anthocyanin content in storage roots. Additionally, the implementation of KASP markers has enabled the consolidation of various resistance markers into a single genotyping platform, enhancing the efficiency of MAS in commercial breeding programs.

Figure 2 Boxplots representing variations for late blight resistance in four subpopulations generated from the diversity panel of 353 potato accessions through structure software based on the 25 SSR markers: (a) Pop-1; (b) Pop-2; (c) Pop-3; (d) Pop-4 (Adopted from Bhardwaj et al., 2023)

4 Marker-Assisted Selection in Trait Improvement through MAS

4.1 MAS for disease resistance and agronomic traits

Late blight, caused by Phytophthora infestans, is a significant threat to potato crops worldwide. Marker-assisted selection (MAS) has been effectively utilized to enhance resistance to this disease. For instance, the use of SCAR markers to track Rpi genes has shown promise in early-stage breeding programs, significantly reducing the workload by half when screening F1 offspring for late blight resistance (Beketova et al., 2021; Markel and Shih, 2021). SSR markers have been employed to evaluate genetic diversity and population structure, identifying specific markers associated with late blight resistance, which can be used in MAS breeding. SNP-based genetic maps have also been developed to locate QTLs contributing to late blight resistance, enabling the introgression of multiple resistance sources through MAS. PCR-based assays for Rpi-blb1 and Rpi-bt1 genes have been validated to distinguish between resistant and susceptible progeny, further supporting the utility of MAS in breeding for late blight resistance (Chen et al., 2017).

Potato virus Y (PVY) is another major concern for potato breeders. MAS has been applied to develop PVY-resistant cultivars by identifying and utilizing DNA markers linked to resistance genes from different species. For example, markers such as RYSC3, Ry364, and RAPD38-530 have been used to genotype breeding lines, facilitating the selection of lines with combined resistance genes from different species (Voronkova et al., 2020). In Australia, the RYSC3, M45, and STM0003 markers have been validated for their effectiveness in identifying PVY-resistant cultivars, demonstrating the potential of these markers in MAS for PVY resistance (Slater et al., 2020).

MAS has also been employed to improve agronomic traits such as drought tolerance. The development of functional markers (FMs) associated with specific phenotypic traits allows for precise selection in breeding programs. These markers facilitate the direct selection of genes linked to desirable traits, thereby increasing the efficiency of breeding for complex traits like drought tolerance. The integration of MAS with advanced genomic tools has enabled the identification of QTLs associated with agronomic traits, further enhancing the potential for improving these traits through targeted breeding strategies (Kadirvel et al., 2015).

4.2 Enhancements in root and tuber quality

MAS has been instrumental in improving root and tuber quality in potatoes. By identifying markers linked to quality traits, breeders can select for desirable characteristics such as tuber size, shape, and nutritional content. The use of genome-scanning marker platforms like PotatoMASH allows for the efficient survey of genetic variation throughout the potato genome, facilitating the selection of superior lines with enhanced tuber quality (Leyva-Pérez et al., 2022). The application of MAS in this context ensures that breeding programs can rapidly and accurately develop cultivars with improved root and tuber quality.

4.3 MAS strategies for polygenic traits

Polygenic traits, controlled by multiple genes, present a challenge for traditional breeding methods. However, MAS strategies such as marker-assisted recurrent selection (MARS) and genome-wide association studies (GWAS) have shown potential in improving these complex traits. MARS allows for the accumulation of favorable alleles over successive generations, while GWAS enables the identification of QTLs associated with polygenic traits (Hasan et al., 2021; Huang and Hong, 2024). These strategies, combined with the use of functional markers, provide a robust framework for the enhancement of polygenic traits in potato breeding programs (Salgotra and Stewart, 2020).

5 Challenges and Limitations in Implementing MAS and Genetic Mapping

5.1 Technical and genetic challenges

Implementing marker-assisted selection (MAS) and genetic mapping in potato breeding faces several technical and genetic challenges. One significant issue is the complexity of the potato genome, which is highly heterozygous and polyploid, making it difficult to identify and utilize genetic markers effectively (Sandhu et al., 2022). The development of reliable markers is also hindered by the need for high-throughput phenotyping and genotyping technologies, which are not always accessible or cost-effective for all breeding programs.

Moreover, the genetic diversity within potato species can complicate the identification of consistent markers across different cultivars. For instance, the study on late blight resistance in a diverse panel of potato accessions revealed high levels of polymorphism, which, while beneficial for diversity, poses a challenge for uniform marker application (Bhardwaj et al., 2023). The integration of various types of molecular markers into a single, unified platform remains a technical hurdle, as highlighted by the need for consolidating different marker types into SNP-based platforms for more streamlined genotyping (Meade et al., 2019).

5.2 Economic and resource barriers

Economic and resource barriers also play a critical role in the implementation of MAS and genetic mapping. The cost of developing and validating molecular markers can be prohibitive, especially for smaller breeding programs. For example, while the PotatoMASH system offers a low-cost genotyping solution, the initial setup and validation still require significant investment (Kumawat et al., 2020). Furthermore, the cost-effectiveness of MAS compared to traditional breeding methods is not always clear-cut. Although MAS can reduce the breeding cycle and workload, as demonstrated in the development of late blight-resistant cultivars, the upfront costs and resource requirements can be substantial (Beketova et al., 2021).

Additionally, the economic feasibility of MAS is influenced by the scale of the breeding program. Large-scale programs may benefit from economies of scale, whereas smaller programs might struggle with the high costs of high-throughput technologies and the need for specialized equipment and expertise (Slater et al., 2017). The integration of advanced technologies such as genomic selection, which combines MAS with high-throughput phenotyping and genotyping, further adds to the resource demands, making it challenging for resource-limited programs to adopt these methods.

6 Applications of Genetic Mapping and MAS in Developing Disease-Resistant Potato Varieties

6.1 Identification of resistance genes

Genetic mapping has been instrumental in identifying resistance genes in potatoes. For instance, the study by Beketova et al. (2021) utilized sequence-characterized amplified region (SCAR) markers to track Rpi genes effective against Phytophthora infestans, the pathogen responsible for late blight. Similarly, Bhardwajet al. (2023) employed simple sequence repeat (SSR) markers to analyze genetic diversity and identify markers associated with late blight resistance. These markers are crucial for understanding the genetic basis of resistance and for developing molecular tools for breeding programs. Prodhomme et al. (2020) conducted a genome-wide association study (GWAS) to identify haplotype-specific SNP markers linked to wart disease resistance, further illustrating the power of genetic mapping in pinpointing resistance loci.

6.2 Use of MAS in resistance breeding

Marker-assisted selection (MAS) has become a cornerstone in breeding disease-resistant potato varieties. The study by Meade et al. (2019) demonstrated the development of kompetitive allele-specific PCR (KASP) markers for resistance genes, which streamline the genotyping process and enhance the efficiency of breeding programs. Tu et al. (2023) highlighted the use of MAS in a diallel population to map frost tolerance loci and develop SNP markers for early screening. The integration of MAS in breeding programs allows for the rapid selection of resistant genotypes, reducing the reliance on labor-intensive phenotypic screening. The comprehensive review by Pathania et al. (2017) underscores the various strategies of MAS, including marker-assisted backcrossing and gene pyramiding, which are pivotal in developing robust disease-resistant varieties.

6.3 Case studies in disease-resistant potato breeding

Several case studies exemplify the successful application of genetic mapping and MAS in breeding disease-resistant potatoes. For instance, Beketova et al. (2021) reported the use of SCAR markers to select clones with Rpi genes, significantly reducing the workload in early-stage breeding. Another study focused on breeding lines with resistance to Potato virus Y (PVY), using DNA markers to identify and combine resistance genes from different wild species. This approach led to the development of breeding lines with enhanced resistance profiles (Voronkova et al., 2020). Bali et al. (2021) identified SNP, SSR, and INDEL markers linked to nematode resistance, facilitating the selection of resistant clones through MAS (Figure 3). These case studies highlight the practical benefits of integrating genetic mapping and MAS in breeding programs, leading to the development of disease-resistant potato varieties with improved agronomic traits.

Figure 3 New ICT based fertility management model in private dairy farm India as well as abroad

7 Future Prospects for Genetic Mapping and MAS in Potato Breeding

7.1 Innovations in genomic and bioinformatics tools

The future of genetic mapping and marker-assisted selection (MAS) in potato breeding is poised for significant advancements due to innovations in genomic and bioinformatics tools. High-throughput sequencing techniques, such as next-generation sequencing (NGS), have revolutionized the ability to analyze the complex potato genome, which is characterized by high heterozygosity and polyploidy (Bykova et al., 2017). The development of high-resolution melting (HRM) DNA markers and kompetitive allele-specific PCR (KASP) assays has streamlined the identification of single nucleotide polymorphisms (SNPs) associated with desirable traits, enhancing the precision of MAS (Meiyalaghan et al., 2019). The integration of transcriptome sequencing for dense marker discovery has shown promise in accelerating genomic selection by providing a comprehensive SNP dataset that covers the entire genome (Caruana et al., 2019). These advancements are supported by improved computational power and bioinformatics pipelines, which facilitate the analysis and interpretation of large genomic datasets, ultimately accelerating the breeding process.

7.2 Research directions in polygenic and complex traits

Research in potato breeding is increasingly focusing on polygenic and complex traits, which are controlled by multiple genes and influenced by environmental factors. Traditional biparental mating designs and QTL mapping have limitations in capturing the full genetic architecture of these traits. Genomic selection (GS) has emerged as a powerful approach to address these challenges by predicting the breeding values of lines based on high-density marker scores and phenotypic data. This method incorporates all marker information into the prediction model, capturing the effects of small-effect QTLs and providing more accurate estimates of genetic potential. Studies have demonstrated the potential of GS to enhance genetic gain and reduce the breeding cycle, making it a valuable tool for improving complex traits such as disease resistance, yield, and tuber quality (Slater et al., 2017). Furthermore, the application of genome editing technologies, such as CRISPR-Cas9, offers new avenues for precise manipulation of polygenic traits, enabling the development of potato varieties with enhanced agronomic performance (Ahmad et al., 2022; Ma, 2024).

7.3 Enhancing efficiency in breeding programs

The efficiency of potato breeding programs can be significantly enhanced through the integration of MAS and genomic selection with traditional breeding methods. The use of MAS for early-stage selection has been shown to reduce the workload and increase the efficiency of breeding programs by enabling the rapid identification of desirable genotypes. For instance, the application of MAS for frost tolerance and late blight resistance has demonstrated practical advantages in screening early breeding offspring, thereby accelerating the development of resistant cultivars (Beketova et al., 2021; Tu et al, 2023). High-throughput phenotyping systems, equipped with automated imaging sensors and ground- or aerial-based vehicles, further complement these efforts by providing accurate and rapid phenotypic data. The combination of these advanced tools and methodologies allows for a more streamlined and cost-effective breeding process, ultimately leading to the faster release of improved potato varieties with multiple desirable traits (Meade et al., 2019).

Acknowledgments

Thanks to Dr. Li from the Hainan Institution of Biotechnology for her assistance in references collection and discussion for this work completion.

Funding

This research received funding from the Ningbo Public Welfare Research Technology Project(2024S014); Breeding of New Dry Grain Varieties in Zhejiang Province(2021C02064-1-5) and Ningbo Key Laboratory of Testing and Control for Characteristic Agro-Product Quality and Safety.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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