Genetic linkage mapping and QTL analysis of sweet basil (Ocimum basilicum L.) to identify genomic regions associated with cold tolerance and major volatiles

Chilling sensitivity is one of the greatest challenges affecting the profitability of sweet basil (Ocimum basilicum L.) in the US and worldwide. Currently, there are no sweet basils commercially available with significant chilling tolerance and traditional aroma profiles. This study was conducted to identify quantitative trait loci (QTL) responsible for chilling tolerance and aroma compounds in a biparental mapping population, including the chilling tolerant parent, "CB15", the chilling sensitive parent, "Rutgers Obsession DMR" and 200 F2 individuals. Chilling tolerance was assessed by percent necrosis using machine learning and aroma profiling was evaluated using gas chromatography (GC) mass spectrometry (MS). Single nucleotide polymorphism (SNP) markers were generated from genomic sequences derived from double digestion restriction-site associated DNA sequencing (ddRADseq) and converted to genotyping data using a reference genome alignment. A genetic linkage map was constructed and five significant QTL were identified in response to chilling temperatures with possible interactions between QTL. Ch-24 represented the QTL with the largest effect and was significant in all three replicates. No QTL was identified for linalool, as the population did not segregate enough to detect this trait. Two significant QTL were identified for estragole (also known as methyl chavicol) with only est-01 being significant after multiple-QTL model (MQM). Euc-26 was identified as a significant QTL for eucalyptol (also known as 1,8-cineole). These QTL may represent key mechanisms for chilling tolerance and aroma compounds in basil, providing critical knowledge for future investigation of these phenotypic traits and molecular breeding.