Analysis of genetic diversity, population structure and its association with quality traits in germplasm of Blumea balsamifera (L.) DC. based on EST-SSR markers
Authors: Li Xin , Huang Mei , Chen Zhenxia , Wang Dan , Wang Kai , Hu Xuan , Chen Xiaolu , Guan Lingliang , Zhang Hongrui , Pang Yuxin , Yu Fulai 
Published: March 2023

Abstract
Background
In order to establish the link between quality traits and genotypes of Blumea balsamifera and specific allele variations, 51 B. balsamifera germplasm resources were used to evaluate the quality traits, EST-SSR markers were used to analyze the genetic diversity, population structure and the correlation between main quality traits and EST-SSR molecular markers.
Results
(1) There were abundant variations in the main quality traits of the tested materials. The highest coefficient of variation was Eriodictyol (85.5%), followed by carotenoid 3,3’,5,7-tetrahydroxy-4’-methoxyflavanone and Sakuranetin, 11 excellent B. balsamifera germplasms were selected by principal component analysis; (2) Genetic diversity analysis showed that a total of 102 alleles were amplified from 22 pairs of primers, of which the effective alleles accounted for 53.52%, and the average polymorphism information content was 0.488, 9 pairs of primers had high polymorphism (PIC > 0.5), 11 pairs of primers had moderate polymorphism (0.25 < PIC < 0.5), and the proposed primers had strong effectiveness and good polymorphism; The average gene flow Nm was 0.203, which was far less than 1, indicating that there was almost no inbreeding between germplasms; The average Nei diversity index and Shannon information index were 0.542 and 1.023, which showed that the population had a high level of genetic diversity; (3) UPGMA cluster analysis and population structure analysis divided the 51 germplasms into 4 groups, and the germplasms from the same source were often gathered in a group. UPGMA cluster analysis showed that geographic distance affected the genetic relationship of germplasm to some extent; PCA analysis indicated that the genetic background of germplasm with similar geographical distance was similar, and the genetic relationship was closer; The analysis of population structure showed that the geographical origin of germplasm was closely related to the genetic relationship of germplasm, and again confirmed the accuracy of UPGMA cluster analysis; (4) The result of linkage disequilibrium(LD) analysis showed that the markers with D '>0.5 accounted for more than 50%, and the recombination probability between germplasm genes was low, indicating that the level of genetic diversity of the population was high, suggesting that the experimental materials were suitable for association analysis, and (5) The result of correlation analysis between quality traits and EST-SSR markers showed that 23 markers significantly correlated with 6 quality traits were detected, and the variance interpretation rate was 19.33% − 57.86%. Among them, the character Blumeatin had the best correlation with EST-SSR loci, and showed a very significant correlation with Bbf377 marker primer.
Conclusion
The results could lay a theoretical foundation for the selection and genetic improvement of excellent germplasm of B. balsamifera in the future.