Genome-wide identification of copy number variation in diverse black pepper accessions.

Abstract

Main conclusion: A genome-wide resequencing analysis reveals the involvement of copy-number variation in black pepper accessions influencing advantageous agronomic traits and the evolution of elite genotypes with specific attributes. Black pepper (Piper nigrum L.) is renowned as a versatile seasoning, offers numerous health benefits, and possesses historical significance in the global spice trade. Variations in advantageous agronomic traits among diverse black pepper genotypes underscore the potential value of understanding their underlying genetic regulation. One emerging genetic component of interest is copy number variation (CNV), which represents a significant source of intra-varietal genetic diversity by altering the dosage of DNA segments, thereby influencing phenotypic characteristics. In this study, we conducted genome-wide resequencing of thirty-nine black pepper germplasm accessions to identify high-confidence CNVs and explore their functional impact on agronomic traits. Our analysis identified a total of 159,390 CNVs and delineated 11,360 CNV regions (CNVRs) with an average length of 87,106 base pairs. Among these, we observed 82,027 deletion and 77,363 duplication events across the 26 chromosomes of black pepper. Notably, deletions were more frequent than duplications. Enrichment analysis of genes harbored within CNVRs revealed their involvement primarily in piperine biosynthesis and immune response pathways. Principal component analysis demonstrated varietal differentiation and highlighted intra-varietal evolutionary linkage among tested genotypes, suggesting that CNVRs play a significant role in shaping the evolution of elite black pepper genotypes. For instance, genotype IISR-Malabar Excel exhibited the highest number of deletions, whereas genotype Acc:7211 showed the most duplications. Chromosome 1 exhibited the highest frequency of deletions, while chromosome 3 showed the highest frequency of duplications. While the overall number of CNVRs did not significantly differ among genotypes, 33 CNVRs contained genes crucial for phenylpropanoid biosynthesis, with 14 genes undergoing deletions and 19 genes showing duplications. Additionally, we developed a web resource BPCNVDb, which could be retrieved ( https://bpcnvdb.daasbioinfromaticsteam.in/index.php ) to facilitate access to genotype-specific CNVs and CNVRs, aiming to enhance breeding efforts in black pepper.