Terpinolene Synthase (CsTOS/CsTPS14): Chromosomal Localization, Reference-Coordinate Drift, and the Missing Terpene-Synthase Coverage of Published Cannabis sativa SNP Panels

Terpinolene synthase (CsTOS; CsTPS14) defines the terpinolene-dominant chemotype of Cannabis sativa, and its crystal structure recently identified His618 as the residue governing product specificity. Here, the Finola terpinolene synthase cDNA (MK614216.1) whose product was crystallized as PDB 9NO6 was anchored onto both the legacy cs10 and current Pink Pepper (ASM2916894v1) reference coordinate systems, and the chromosomal relationship to the two most widely cited functional markers of the Henry 22-SNP assay, SVIP9 and VSSL_A250D, was tested. NCBI's live annotation anchors the locus only on Pink Pepper (LOC133037760, chromosome 5: 2,896,929–2,905,363), inside a tandem monoterpene-synthase array of fourteen gene models. k-mer mapping of the Finola cDNA against cs10 places the corresponding array at chromosome 5: 2,394,737–2,543,151, comprising at least six paralogous segments at 81–98% nucleotide identity and no single full-length orthologous position. SVIP9 (cs10 chr5: 82,096,056–82,098,831) lies 79.55 Mb distal of the array; its putative gene product (XP_060972072) shows 10.8% protein identity to CsTOS and no terpene-synthase catalytic motifs. VSSL_A250D resides on a different chromosome, and its published "chromosome 9" interval resolves empirically to cs10 NC_044378.1 — chromosome 7 under current NCBI labelling — reflecting the April 2020 cs10 chromosome renumbering. Neither marker tags CsTOS; the 1,504-target HASCH panel and the 18,040-probe CannSelect capture platform place no target inside the array (nearest 13.9 and 11.7 kb, respectively) and jointly contain a single terpene-synthase probe genome-wide, the 2,418-strain Kannapedia repository lists no terpene synthase among its 43 reported genes, and the strongest published myrcene GWAS signals flank these same two chromosome-5 clusters. A parallel audit of 71 acyltransferase-family and 21 cannabinoid-synthase gene records shows the pattern is systemic: 70 of the former carried cs10 coordinates in the May 2020 annotation release and only four still do — none tagged by any panel marker within linkage-disequilibrium range — while 54 sit in tandem arrays that defeat short-read SNP assays. CsTOS therefore remains untagged by every inventoried panel, and His618 emerges as a natural functional-marker target.