Chinese Academy of Tropical Agricultural Sciences/Zhanjiang Rubber Forest Economic Engineering Technology Research Center, Zhanjiang Experimental Station, Zhanjiang, Guangdong, China.
Huazhong Agricultural University, Wuhan, Hubei, China.
PLoS One. 2024 Aug 5;19(8):e0306806. doi: 10.1371/journal.pone.0306806. eCollection 2024.
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.
阳春砂（Amomum villosum Lour.）是一种有价值的草本植物，它产生著名的中药砂仁。鉴定与阳春砂生长相关的分子标记可以促进该植物的分子标记辅助育种。本研究以 75 份阳春砂为试验材料，利用 71 对多态性简单重复序列（SSR）分子标记对群体进行基因型分析。通过连锁不平衡和群体结构分析，研究分析了 SSR 标记与表型性状的关联。还鉴定了与分子标记相关的候选基因。结果表明，12 个农艺性状的表型多样性指数范围为 4.081-4.312，符合正态分布。此外，在 75 个品系中检测到 293 个等位基因变异，每个位点平均有 5.32 个扩增等位基因，范围为 3-8。AVL12 的扩增等位基因最多为 8 个。群体结构和聚类分析表明，供试品系可分为 2 个亚群。利用群体结构（Q）+亲缘关系矩阵（K）的混合线性模型（MLM）进行关联分析，检测到 3 个与农艺性状显著相关的 SSR 分子标记。采用荧光定量方法分析 6 个候选基因的表达水平，发现其中 3 个基因在表型不同的品系中差异表达。本研究首次利用 SSR 标记进行阳春砂全基因组关联研究（GWAS）作图和相关农艺性状鉴定。本研究结果为阳春砂生长性状的遗传标记辅助选择提供了依据。
