SNP fingerprint database and makers screening for current Phalaenopsis cultivars
SNP fingerprint database and makers screening for current Phalaenopsis cultivars
Blog Article
The Moth orchid is globally recognized as one of the most popular and important ornamental species.However, due bar drain board to the complicated history of hybridization, long growth cycles, and industrial vegetative propagation, there are huge challenges in cultivar identification and protection leading to market issues.Consequently, it is important to develop effective and stable markers to identify and preserve core Phalaenopsis cultivar resources.In this study, we collected 53 commercially prevalent Phalaenopsis cultivars in China.
Through detailed phenotypic observations, morphological genetic diversity was measured in 19 quantitative and 15 qualitative traits.By genome skimming and the subsequent SNP calling pipeline, we discovered 5,984 high-quality single nucleotide polymorphisms (SNPs) and constructed a comprehensive Phalaenopsis SNP database of cultivars.These SNPs got a high correlation with variation for quantitative traits ranging from 16.09% to 154.
60%, while those for qualitative traits spanned from 20.54% to 130.81%.This database demonstrated a high degree of genetic diversity and a robust capacity for identifying polymorphisms and distinguishing among current varieties.
These discovered SNPs consist of 12 types, C/T (23.86%), G/A roneverhart.com (22.31%), A/G (8.89%), and T/C (7.
84%).The ratio of transition to transversion was approximately 1.70.70.
91% of the SNP loci were in intergenic regions, 9.61% in upstream regions, and 9.37% within intronic regions.Fifty three cultivar PCAs could serve as three groups, which was matched with trait clusters.
Based on 5,984 SNP sites, we conducted secondary screening and screened out 14 core sites.The clustering results of the NJ tree based on 14 core SNP loci and the NJ tree based on 5,984 whole genome SNP loci were consistent among 53 Phalaenopsis cultivars.Besides, each variety was then encoded with a unique barcode by 14 core SNP markers.This preliminary approach offers a putative and effective tool for variety identification, genetic analysis, and further development of Phalaenopsis germplasm resources.