As a key tropical economic tree species, the girth of the rubber tree (Hevea brasiliensis) not only reflects its growth rate and timber yield but also determines tapping schedules and non-productive periods. This trait critically influences both the species’ economic value and latex production potential. Despite recent advances in genetic analyses of girth driven by genomic technologies, the number of identified key genes remains insufficient to support molecular breeding programs. This study focuses on 138 samples of rubber tree natural accessions, integrating phenotypic data analysis, population genetic structure analysis, and genome-wide association analysis (GWAS) to identify genetic loci and candidate genes associated with girth. Population stratification divides the tested accessions into four genetic groups: Groups Ⅰ and Ⅳ exhibit high genetic purity, while Groups Ⅱ and Ⅲ display hybrid characteristics. GWAS based on a mixed linear model detects 7 and 23 SNPs significantly associated with girth at p = 4.4 × 10⁻⁸ and p = 2.22 × 10⁻⁷, respectively. The most significant SNP is located at position 44994744 on chromosome CM021229.1. Under the highly significant association threshold, 27 candidate genes were identified, 4 of which are directly related to girth. Gene Ontology (GO) annotation of these 27 candidate genes reveals their primary involvement in metabolic regulation, signal transduction, and cell component construction. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis shows they are primarily enriched in the “aminoacyl-tRNA biosynthesis” and “glycolysis/gluconeogenesis” pathways. These findings provide significant theoretical support for genetic enhancement and mechanistic analysis of rubber tree growth traits. They reveal novel SNP markers and genes that complement existing genetic resources, refining breeding strategies for elite genotype selection and ultimately contributing to enhanced rubber production.

Amomum villosum Lour. (A. villosum) is a valuable herbaceous plant that produces the famous traditional Chinese medicine Amori Fructus. Identifying molecular markers associated with the growth of A. villosum can facilitate molecular marker-assisted breeding of the plant. This study employed 75 A. villosum accessions as the test material and utilized 71 pairs of polymorphic simple sequence repeat (SSR) molecular markers to genotype the population. The study analyzed the association between SSR markers and phenotypic traits through the linkage imbalance and population structure analysis. Candidate genes associated with the molecular markers were also identified. The results showed that the phenotypic diversity index range of the 12 agronomic traits was 4.081–4.312 and conformed to a normal distribution. Moreover, 293 allelic variations were detected in the 75 accessions, with an average of 5.32 amplified alleles per loci, ranging from 3 to 8. The maximum number of amplified alleles for AVL12 was 8. The population structure and cluster analysis indicated that the accessions could be divided into two subgroups. Using the mixed linear model (MLM) model of population structure (Q)+kinship matrix (K) for association analysis, three SSR molecular markers significantly associated with the agronomic traits were detected. Fluorescence quantification was used to analyze the expression levels of six candidate genes, and it was found that three of the genes were differentially expressed in phenotypically different accessions. This study is the first to use SSR markers for genome-wide association study (GWAS) mapping and identification of the associated agronomic traits in A. villosum. The results of this study provide a basis for identifying genetic markers for growth traits for marker-assisted breeding in A. villosum.