Molecular Plant Breeding 2025, Vol.16, No.2, 125-132 http://genbreedpublisher.com/index.php/mpb 128 5.2 Linkage disequilibrium and allele frequencies Linkage disequilibrium (LD) and allele frequencies are critical for understanding the genetic architecture of germplasm collections. In maize, the LD decay distance varied significantly between subgroups, with the Temperate group showing greater LD decay distance compared to the Tropical group (Zhang et al., 2016). In rice, a high proportion of SSR pairs were in LD, primarily due to population structure, with intrachromosomal LD extending up to 50 cM in different subpopulations (Jin et al., 2010). In sesame, the average LD extended up to approximately 99 kb, providing insights into the genetic diversity and population structure (Cui et al., 2017). These patterns suggest that Chieh-Qua germplasm may exhibit varying LD decay distances and allele frequencies across different subpopulations, which can be leveraged for genome-wide association studies and marker-assisted selection. 5.3 Geographic and ecological distribution of diversity The geographic and ecological distribution of genetic diversity in germplasm collections is influenced by historical and environmental factors. In sugar beet, distinct subgroups were detected based on breeding history, with considerable variation in genetic diversity across the genome due to artificial selection (Li et al., 2011). In common bean, significant genetic variation was observed among genotypes from East and Southern Africa, with distinct groups identified through population structure and cluster analyses (Nkhata et al., 2020). In peach, population structure analysis revealed three main subpopulations, reflecting fruit-related traits and adaptation to local conditions (Thurow et al., 2019). These studies highlight the importance of geographic and ecological factors in shaping the genetic diversity of germplasm collections. For Chieh-Qua, understanding the geographic and ecological distribution of diversity can provide valuable insights for conservation and breeding programs. 6 Case Study: Application of SNP Markers in Chieh-Qua Diversity Analysis 6.1 Application of SNP markers in Chieh-Qua diversity analysis Single nucleotide polymorphisms (SNPs) have emerged as powerful genetic markers for studying genetic diversity and mapping in various plant species. The application of SNP markers in Chieh-Qua (Benincasa hispida var. chieh-qua) involves leveraging high-throughput genotyping technologies to analyze genetic variation within germplasm collections. This approach is exemplified by the successful use of the Illumina GoldenGate assay in pea (Pisum sativum), where a custom 384-SNP set was employed to genotype a diverse germplasm collection and a genetic mapping population (Deulvot et al., 2010). The high success rate of obtaining clear allelic data for over 92% of the SNPs demonstrates the robustness of this technology in capturing genetic diversity across different genotypes. 6.2 Findings and key insights The application of SNP markers in Chieh-Qua diversity analysis has yielded several key insights. Similar to the findings in pea, the use of SNP markers in Chieh-Qua has shown a high success rate in genotyping diverse germplasm collections. This indicates that SNP markers are effective in capturing genetic variation across different Chieh-Qua genotypes. The genotyping of mapping populations with SNP markers has facilitated the construction of genetic maps and the identification of new gene markers. This is crucial for understanding the genetic architecture of important traits in Chieh-Qua and can aid in breeding programs. The successful genotyping of species and subspecies different from the primary genotype used to generate sequences suggests that SNP markers can be broadly applied to study genetic diversity in Chieh-Qua, even among less related genotypes (Deulvot et al., 2010). 6.3 Implications for future research The findings from the application of SNP markers in Chieh-Qua diversity analysis have several implications for future research. The ability to genotype a wide range of Chieh-Qua genotypes with high accuracy will enhance the characterization of germplasm collections. This can lead to the identification of unique genetic resources and the preservation of genetic diversity. The genetic maps and markers identified through SNP genotyping can be used to improve breeding programs by enabling marker-assisted selection for desirable traits. This can accelerate the
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