Molecular Plant Breeding 2025, Vol.16, No.2, 125-132 http://genbreedpublisher.com/index.php/mpb 126 2 Germplasm Collections of Chieh-Qua 2.1 Importance of germplasm in crop breeding Germplasm collections are vital for crop breeding as they provide a reservoir of genetic diversity necessary for the development of new cultivars with improved traits (Upadhyaya et al., 2014; Mondal et al., 2023). The genetic diversity within these collections allows breeders to select for traits such as disease resistance, drought tolerance, and yield improvement. Molecular markers, such as single nucleotide polymorphisms (SNPs), have been instrumental in elucidating the genetic structure of these collections, thereby enhancing their utility in breeding programs (Glaszmann et al., 2010; Reeves et al., 2020; Abady et al., 2021). For instance, the use of SNP markers has enabled the identification of genetic variations that are crucial for crop adaptation and improvement, as demonstrated in crops like groundnut and common bean (Nkhata et al., 2020; Abady et al., 2021). 2.2 Conservation and collection efforts The conservation and collection of germplasm are essential to safeguard the genetic diversity of crops. Efforts to conserve germplasm involve the establishment of gene banks and the development of core collections that represent the genetic diversity of the entire collection (Dar et al., 2015; Li, 2024). These core collections facilitate the efficient use of germplasm in breeding programs by providing a manageable subset of the total collection that captures the maximum genetic diversity (Jansky et al., 2015; Wang et al., 2021). For example, the development of a core SNP marker set in bottle gourd has enabled the creation of a core population that represents the full genetic variation of the species, thus aiding in its preservation and utilization (Wang et al., 2021). 2.3 Current status of Chieh-Qua germplasm collections The current status of Chieh-Qua germplasm collections reflects ongoing efforts to characterize and utilize genetic diversity for crop improvement. Advances in genomic technologies, such as whole-genome resequencing and SNP genotyping, have significantly enhanced the ability to assess genetic diversity and population structure within these collections (Khazaei et al., 2016; Zhang et al., 2016; Reeves et al., 2020). Studies on various crops, including maize and lentil, have shown that germplasm collections often exhibit considerable genetic diversity, which can be harnessed for breeding purposes (Lu et al., 2009; Khazaei et al., 2016; Zhang et al., 2016). However, challenges remain in efficiently accessing and utilizing this diversity due to the large size and heterogeneous nature of the collections. The application of bioinformatic approaches to extract functional genetic diversity from heterogeneous germplasm collections has been proposed as a solution to these challenges, as demonstrated in sorghum (Reeves et al., 2020). 3 SNP Markers in Genetic Diversity Analysis 3.1 SNP markers and their applications in genetic studies Single nucleotide polymorphisms (SNPs) are a type of genetic marker that have become increasingly valuable in genetic studies due to their abundance and distribution throughout the genome. SNP markers are used for various applications, including genetic diversity studies, genetic mapping, and association studies. For instance, in a study on pea germplasm, a custom 384-SNP set was used to genotype a Pisum germplasm collection and a genetic mapping population, demonstrating the utility of SNP markers in generating genetic maps and identifying new gene markers (Deulvot et al., 2010). Similarly, SNP markers have been employed to analyze the genetic diversity and population structure of common bean germplasm collections, revealing significant variability and delineating genotypes into distinct groups (Nkhata et al., 2020). 3.2 Advantages of SNP markers in germplasm analysis SNP markers offer several advantages in germplasm analysis. Firstly, they provide high-resolution data due to their widespread presence across the genome. This allows for a detailed assessment of genetic diversity and population structure. In the case of common bean germplasm, SNP markers revealed considerable genetic variation, with mean gene diversity and polymorphic information content values indicating substantial genetic diversity among the genotypes (Nkhata et al., 2020). Additionally, SNP markers facilitate high-throughput genotyping, as demonstrated by the successful genotyping of over 92% of SNPs in a pea germplasm collection using the Illumina GoldenGate assay (Deulvot et al., 2010). This high-throughput capability simplifies genotyping procedures and enhances the efficiency of genetic studies.
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