Quantitative Traits Loci and candidate gene mapping for Quinones and Phenolic Biosynthesis in Nigella sativa L. using pseudo-chromosome Assembly Arusa Aftab, Zubaida Yousaf, Zill-e-Huma Aftab, Nadia Riaz, Bushra Shamsheer

Abstract Quantitative trait loci (QTL) mapping is a genome-wide inference of the relationship between genotype at various genomic locations and phenotype for a set of quantitative traits in terms of the number, genomic positions, effects, and interaction of QTL. The Quinones and phenolics are the products of Geranyl diphospohate synthase (GPPS). Thymoquinone (TQ), dithymoquinone (DTQ), thymohydroquinone (THQ), and thymol (THY) are the most important pharmacologically active quinone based constituents in Nigella sativa (Black seed oil). Quantitative trait loci, candidate genes and associated morphological markers for these traits have been identified and located in the N.sativa genome. The breeding and genetic improvement of N. sativa is highly restricted due to unexplored high-density genetic map. The study was planned to map the genes linked to quinonens ane phenolics biosynthesis in N. sativa. Two inbred parental lines W626529 and W626530 differing in some phenotypic characters were selected for the study. To construct genetic linkage map and locate QTLs, F1 population of 150 crossed individuals was grown and subsequently produced 50 recombinant inbred lines (RIL). Chromosomal linkage map was constructed using 719 polymorphic pairs; consisted of 14 morphological markers and 705 SSRs through Join Map ver. 3.0. Chromosomal mapping was done using pseudochromosome assembly using Win QTL Cart Software. Single Marker Analysis was done to link QTLs with the morphological and molecular markers. Only 5 morphological traits out of 16 were found to be linked to the QTL. Chromosomal marker linkage was ensured at a minimum likelihood of odds (LOD) > 1.5 and maximum distance 50 cM. Interval mapping led to the detection of eight QTLs on 12 linkage groups; LG1, LG2, LG5, LG6, LG8, LG9 and LG11. The detection of eight QTLs on 12 linkage groups confirmed the influence of both morphological and molecular markers on linked traits and inheritance. The genetic map and improved pseudo-chromosome scale genome provide crucial foundations for marker-assisted selection (MAS) of QTL governing important agronomic traits as well as the accelerated molecular breeding of N. sativa in a cost-effective pattern.