Development of KASP markers, SNP fingerprinting and population genetic analysis of Cymbidium ensifolium (L.) Sw. germplasm resources in China

• DOI: 10.3389/fpls.2024.1460603
• Publication Date: 2025-01-08T06:22:20Z
• Authors: Baoming Shen; Airong Shen; Yun Tan; Lina Liu; Sainan Li; Zhuming Tan
• Keywords: Germ plasm; DNA profiling; SNP

Cymbidium ensifolium (L.) Sw. is a valuable ornamental plant in the genus Cymbidium, family Orchidaceae, with high economic and ecological significance. However, lack of population genetic information molecular markers has hindered development sales market breeding C. despite abundance commercial cultivars available. In this study, we aimed to develop set single nucleotide polymorphism (SNP) distinguish main cultivated China provide technical support for domestic cultivar protection, registration, rights protection. A total 1,280,516 high-quality loci were identified from 10,021,591 SNPs obtained by sequencing 50 using double digest restriction site-assisted DNA technology. 7,599 selected kompetitive allele-specific PCR (KASP) primer design, 4,360 successfully designed as KASP markers. Population structure analysis revealed that best divided into four populations, some correlation between group distribution morphological geographical characteristics germplasm. Using genotyping results 28 screened cultivars, minimum 11 was could 83 completely, remaining 17 serving extended The average PIC value 0.345, which considered medium polymorphism. fingerprints constructed on basis markers, providing new approach mapping efficiency, accuracy, low cost compared traditional methods.