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<p><i>Azadirachta indica</i> (Neem) is a multipurpose tree species mainly used for its pesticidal compound azadirachtin, a key ingredient in eco-friendly biopesticides. However, the genetic basis underlying variation in azadirachtin content remains poorly understood, hindering efforts to breed high-yielding cultivars. This study addresses this critical research gap by performing comparative whole-genome based single-nucleotide polymorphism (SNP) analysis of two contrasting neem genotypes as VKAF-75 (high azadirachtin content) and VKAF-99 (low azadirachtin content). Growth and yield traits, including tree height, DBH, seed and oil characteristics, and azadirachtin content, were assessed. Using a genotyping-by-sequencing approach, we identified 4,63,273 SNPs in VKAF-75 and 6,18,669 SNPs in VKAF-99, with intronic variants being more frequent than exonic ones. VKAF-99 exhibited a higher frequency of potentially disruptive mutations, including nonsynonymous, stop-gain, and frameshift-inducing variants, particularly in key genes involved in azadirachtin biosynthesis such as squalene monooxygenase, terpene cyclase, cytochrome P450, and NADPH-cytochrome P450 reductase. These findings suggest that functional SNPs in VKAF-99 may impair biosynthetic pathways, contributing to its lower azadirachtin yield. This is the first genomic study to associate SNP variation with azadirachtin content, thus&#xa0;offering critical insights for the development of marker-assisted selection and genetic improvement programs in neem.</p>

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Functional single nucleotide polymorphisms (SNPs) in terpene cyclase genes contribute to variability in Azadirachtin biosynthesis in neem germplasm

  • 期刊论文

  • 发表日期：

    2025年8月10日

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  • K. Rajarajan,
  • Shreishtha Singh,
  • A. Arunachalam,
  • A. K. Handa,
  • S. K. Dhyani

摘要

Azadirachta indica (Neem) is a multipurpose tree species mainly used for its pesticidal compound azadirachtin, a key ingredient in eco-friendly biopesticides. However, the genetic basis underlying variation in azadirachtin content remains poorly understood, hindering efforts to breed high-yielding cultivars. This study addresses this critical research gap by performing comparative whole-genome based single-nucleotide polymorphism (SNP) analysis of two contrasting neem genotypes as VKAF-75 (high azadirachtin content) and VKAF-99 (low azadirachtin content). Growth and yield traits, including tree height, DBH, seed and oil characteristics, and azadirachtin content, were assessed. Using a genotyping-by-sequencing approach, we identified 4,63,273 SNPs in VKAF-75 and 6,18,669 SNPs in VKAF-99, with intronic variants being more frequent than exonic ones. VKAF-99 exhibited a higher frequency of potentially disruptive mutations, including nonsynonymous, stop-gain, and frameshift-inducing variants, particularly in key genes involved in azadirachtin biosynthesis such as squalene monooxygenase, terpene cyclase, cytochrome P450, and NADPH-cytochrome P450 reductase. These findings suggest that functional SNPs in VKAF-99 may impair biosynthetic pathways, contributing to its lower azadirachtin yield. This is the first genomic study to associate SNP variation with azadirachtin content, thus offering critical insights for the development of marker-assisted selection and genetic improvement programs in neem.