PDF(Pubmed)
Abstract：
Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited, with diversity assessments often relying on only a few samples or DNA markers. Here we employed restriction-site associated DNA sequencing to analyze 175 P. nigrum accessions from eight main black pepper growing regions in Sri Lanka. The sequencing effort resulted in 1,976 million raw reads, averaging 11.3 million reads per accession, revealing 150,356 high-quality single nucleotide polymorphisms (SNPs) distributed across 26 chromosomes. Population structure analysis revealed two subpopulations (K = 2): a dominant group consisting of 152 accessions sourced from both home gardens and large-scale cultivations, and a smaller group comprising 23 accessions exclusively from native collections in home gardens. This clustering was further supported by principal component analysis, with the first two principal components explaining 35.2 and 12.1% of the total variation. Genetic diversity analysis indicated substantial gene flow (Nm = 342.21) and a low fixation index (FST = 0.00073) between the two subpopulations, with no clear genetic differentiation among accessions from different agro-climatic regions. These findings demonstrate that most current black pepper genotypes grown in Sri Lanka share a common genetic background, emphasizing the necessity to broaden the genetic base to enhance resilience to biotic and abiotic stresses. This study represents the first attempt at analyzing black pepper genetic diversity using high-resolution SNP markers, laying the foundation for future genome-wide association studies for SNP-based gene discovery and breeding.
摘要：
尽管黑胡椒（黑胡椒）的经济重要性，全世界的高价值作物，基因组资源的开发和利用仍然有限，多样性评估通常只依赖于少数样本或DNA标记。在这里，我们使用限制性位点相关的DNA测序来分析来自斯里兰卡八个主要黑胡椒生长区的175种黑胡椒。测序工作产生了19.76亿条原始读数，平均每次加入1,130万次读取，揭示了150,356个高质量的单核苷酸多态性（SNP）分布在26条染色体上。种群结构分析揭示了两个亚群（K=2）：一个由152个来自家庭花园和大规模种植的种质组成的优势群，和一个较小的群体，包括23种专门来自家庭花园的本地收藏的种质。主成分分析进一步支持了这种聚类，前两个主成分解释了总变异的35.2%和12.1%。遗传多样性分析表明两个亚群之间的基因流量很大（Nm=342.21）和固定指数较低（FST=0.00073），不同农业气候地区的种质之间没有明显的遗传分化。这些发现表明，目前在斯里兰卡种植的大多数黑胡椒基因型具有共同的遗传背景，强调必须扩大遗传基础，以增强对生物和非生物胁迫的抵抗力。这项研究代表了使用高分辨率SNP标记分析黑胡椒遗传多样性的首次尝试，为基于SNP的基因发现和育种奠定了未来全基因组关联研究的基础。
