Construction of SNP fingerprint and population genetic analysis of honeysuckle germplasm resources in China

Abstract

IntroductionThe flower buds of Lonicera japonica Thunb. are widely used in Chinese medicine for their anti-inflammatory properties, and they have played an important role in the fight against SARS COVID-19 and other major epidemics. However, due to the lack of scientific and accurate variety identification methods and national unified standards, scattered and non-standardized management in flower bud production has led to mixed varieties that have caused significant difficulties in the cataloging and preservation of germplasm resources and the identification, promotion, and application of new L. japonica varieties.MethodsIn this study, we evaluated the population structure, genetic relationships, and genetic fingerprints of 39 germplasm resources of Lonicera in China using simplified genome sequencing technology.ResultsA total of 13,143,268 single nucleotide polymorphisms (SNPs) were identified. Thirty-nine samples of Lonicera were divided into four subgroups, and the population structure and genetic relationships among existing Lonicera germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Through several stringent selection criteria, 15 additional streamlined, high-quality DNA fingerprints were filtered out of the validated 50 SNP loci and verified as being able to effectively identify the 39 Lonicera varieties.DiscussionTo our knowledge, this is the first comprehensive study measuring the diversity and population structure of a large collection of Lonicera varieties in China. These results have greatly broadened our understanding of the diversity, phylogeny, and population structure of Lonicera. The results may enhance the future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding by providing a scientific basis and reference data for these efforts.

Genetic diversity analysis and core germplasm bank construction in cold resistant germplasm of rubber trees (Hevea brasiliensis)

“…It is not affected by the environment or its own growth status, and can provide a direct and effective theoretical basis for the improvement and protection of varieties. At present, fingerprint maps of cotton 28 , moss 29 , and honeysuckle 30 have been constructed, providing important basis for the breeding of new plant varieties. In this study, the DNA fingerprint library of 195 rubber trees was constructed by 20 highly differentiated SNP, assigning each test material a unique code.The DNA fingerprint library can be directly used for the selection of rubber tree hybrid parents, better exerting heterosis, and promoting the breeding process of rubber trees.…”

Successful development of molecular diagnostic technology combining mini-barcoding and high-resolution melting for traditional Chinese medicine agarwood species based on single-nucleotide polymorphism in the chloroplast genome

“…SNP molecular marker technology can be used to identify abundant loci and has been applied to the analysis of germplasm resource evolution and species identification (Li et al, 2023;Palasciano et al, 2023). Chloroplasts are maternally inherited, and the genetic information of each species can be stably inherited.…”

Efficacy of botanical lozenges in the treatment of chronic pharyngitis: a randomized controlled trial

“…As one of the main bioactive metabolites of Siraitia grosvenorii, Mogroside V has the function of regulating immunity ( Duan et al, 2023 ). Lonicera japonica Thunb [Caprifoliaceae; Lonicerae japonicae flos] is a liana and native to China Southeast, Japan, Korea, Manchuria and Taiwan ( Li et al, 2023 ). It is widely used to treat upper respiratory inflammation symptoms, such as cough and sore throat ( Guo et al, 2021 ).…”