Thanthirige Hiruni A, Wimalarathna Nilni A, Wickramasuriya Anushka M
Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka.
BMC Genomics. 2025 Mar 17;26(1):256. doi: 10.1186/s12864-025-11414-2.
Single nucleotide polymorphisms (SNPs) have emerged as the marker of choice in breeding and genetics, particularly in non-model organisms such as black pepper (Piper nigrum L.), a globally recognized spice crop. This study presents a comprehensive catalog of SNPs in the black pepper genome using data from 30 samples obtained from RNA sequencing and restriction site-associated DNA sequencing, retrieved from the Sequence Read Archive, and their consequences at the sequence level.
Three SNP calling and filtering pipelines, namely BCFtools, Genome Analysis Toolkit (GATK)-soft filtering, and GATK-hard filtering, were employed. Results revealed 498,128, 396,003, and 312,153 SNPs respectively identified by these pipelines, with 260,026 SNPs commonly detected across all methods. Analysis of SNP distribution across the 45 scaffolds of the black pepper genome showed varying densities, with pseudo-chromosomes Pn25 (0.86 SNPs/kb), Pn8 (0.74 SNPs/kb), and Pn7 (0.72 SNPs/kb) exhibiting the highest densities. Conversely, scaffolds Pn27 to Pn43 exhibited minimal SNP distribution, except Pn45. Approximately 34.80% of SNPs exhibited stronger genetic linkage (r > 0.7). Moreover, SNPs predominately mapped to downstream (≈ 32.54%), upstream (≈ 22.52%), and exonic (≈ 16.20%) regions of genes. Transition substitution accounted for the majority (≈ 57.42%) of identified SNPs, resulting in an average transition-to-transversion ratio of 1.36. Notably, 56.09% of SNPs were non-synonymous, with a significant proportion (≈ 53.59%) being missense mutations. Additionally, 12,491 SNPs with high or moderate impacts were identified, particularly in genes associated with secondary metabolism and alkaloid biosynthesis pathways. Furthermore, the expression of 675 genes was potentially influenced by local (cis-acting) SNPs, while 554 genes were affected by distal (trans-acting) SNPs.
The findings of the present study underscore the utility of identified SNPs and their targets, especially those impacting important pathways, for future genetic investigations and crop improvement efforts in black pepper. The characterization of SNPs in genes related to secondary metabolism and alkaloid biosynthesis highlights their potential for targeted breeding aimed at enhancing the yield, quality, and resilience of this economically important crop in diverse environmental conditions.
单核苷酸多态性（SNP）已成为育种和遗传学领域的首选标记，尤其是在非模式生物中，如全球知名的香料作物黑胡椒（Piper nigrum L.）。本研究利用从序列读取档案库中检索到的30个样本的RNA测序和限制性位点关联DNA测序数据，展示了黑胡椒基因组中SNP的全面目录，以及它们在序列水平上的影响。
采用了三种SNP检测和过滤流程，即BCFtools、基因组分析工具包（GATK）-软过滤和GATK-硬过滤。结果显示，这些流程分别鉴定出498,128、396,003和312,153个SNP，所有方法共检测到260,026个SNP。对黑胡椒基因组45个支架上的SNP分布分析表明，密度各不相同，假染色体Pn25（0.86个SNP/kb）、Pn8（0.74个SNP/kb）和Pn7（0.72个SNP/kb）密度最高。相反，除Pn45外，支架Pn27至Pn43的SNP分布最少。约34.80%的SNP表现出较强的遗传连锁（r>0.7）。此外，SNP主要映射到基因的下游（约32.54%）、上游（约22.52%）和外显子（约16.20%）区域。转换替代占已鉴定SNP的大多数（约57.42%），导致平均转换与颠换比为1.36。值得注意的是，56.09%的SNP是非同义的，其中很大一部分（约53.59%）是错义突变。此外，还鉴定出12,49个具有高或中等影响的SNP，特别是在与次生代谢和生物碱生物合成途径相关的基因中。此外，675个基因的表达可能受局部（顺式作用）SNP影响，而554个基因受远端（反式作用）SNP影响。
本研究结果强调了已鉴定SNP及其靶点的实用性，特别是那些影响重要途径的靶点，对未来黑胡椒的遗传研究和作物改良工作具有重要意义。对与次生代谢和生物碱生物合成相关基因中的SNP进行表征，突出了它们在定向育种中的潜力，旨在提高这种经济作物在不同环境条件下产量、品质和抗逆性。
