Molecular Plant Breeding 2025, Vol.16, No.1, 55-62 http://genbreedpublisher.com/index.php/mpb 59 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 8. 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.
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