Combining phenotypic and SSR markers to characterize genetic diversity, develop a core collection, and identify elite...

Nekemias grossedentata, a perennial woody vine and the primary source of vine tea, is valued for its medicinal and edible properties. Its leaves contain key bioactive compounds, such as flavonoids (notably dihydromyricetin) and polyphenols, which determine the core quality of vine tea. However, overexploitation threatens wild populations, leading to germplasm resource depletion and loss of genetic diversity, underscoring the urgent need for effective conservation and breeding strategies. Therefore, this study aimed to clarify the genetic diversity, construct a core germplasm collection, and screen elite accessions to support the conservation and sustainable utilization of N. grossedentata. Using principal component analysis on 10 leaf phenotypic traits from 190 samples across eight production regions, this study identified total leaf flavonoid content (contribution rate: 0.810) as the key factor influencing phenotypic variation. Based on transcriptome data previously obtained by our group from different tissues, 25,009 EST-SSR primer pairs were developed, from which 18 stable and polymorphic EST-SSR markers were screened. Utilizing these markers to assess population and individual genetic diversity revealed a high level of genetic diversity in N. grossedentata: average Shannon's diversity index (0.880), expected heterozygosity (0.497), and observed heterozygosity (0.194). Based on these analyses, a core germplasm collection comprising 19 representative accessions from eight geographic origins was constructed. Finally, based on the catechin quality index (CQI) of these 19 core accessions, six elite accessions were selected: GD-10, GX-13, GX-15, GX-18, GX-21, and HN-31. These accessions exhibit high genetic diversity, high CQI (>100), and high total flavonoid content (>20%), making them suitable for direct use as core parental materials. This study provides the first systematic evidence of high genetic diversity in N. grossedentata resources, successfully establishing a core germplasm collection while identifying elite accessions to offer a scientific foundation for conservation, evaluation, and breeding utilization.