Whole-genome and genome-wide association studies improve key agricultural traits of safflower for industrial and medicinal use

Safflower(Carthamus tinctorius)is widely cultivated around the world for its seeds and flowers.The presence of linoleic acid(LA)in its seeds and hydroxysafflor yellow A(HSYA)in its flowers are the crucial traits that enable safflower to be used for industrial and medicinal purposes.Understanding the genetic control of these traits is essential for optimizing the quality of safflower and its breeding.To further this research,we present a chromosome-scale assembly of the genome of the safflower variety‘Chuanhonghua 1’,which was achieved using an integrated strategy combining Illumina,Oxford Nanopore,and Hi-C sequencing.We obtained a 1.17-Gb assembly with a contig N50 of 1.08 Mb,and all assembled sequences were assigned to 12 pseudochromosomes.Safflower’s evolution involved the core eudicotγ-triplication event and a whole-genome duplication event,which led to large-scale genomic rearrangements.Extensive genomic shuffling has occurred since the divergence of the ancestor of dicotyledons.We conducted metabolite and transcriptome profiles with time-and part-dependent changes and screened candidate genes that significantly contribute to seed lipid biosynthesis.We also analyzed key gene families that participate in LA and HSYA biosynthesis.Additionally,we re-sequenced 220 safflower lines and carried out a genome-wide association study using high-quality SNP data for eight agronomic traits.We identified SNPs related to important traits in safflower.Besides,the candidate gene HH_034464(CtCGT1)was shown to be involved in the biosynthesis of HSYA.Overall,we provide a high-quality reference genome and elucidate the genetic basis of LA and HSYA biosynthesis in safflower.This vast amount of data will benefit further research for functional gene mining and breeding in safflower.

Cloning,expression and activity analysises of chalcone synthase genes in Carthamus tinctorius

Objective:Flavonoids are the bioactive compounds in safflower(Carthamus tinctorius),in which chalcone synthase(CHS)is the first limiting enzyme.However,it is unclear that which chalcone synthase genes(CHSs)are participated in flavonoids biosynthesis in C.tinctorius.In this study,the CHSs in the molecular characterization and enzyme activities were investigated.Methods:Putative chalcone biosynthase genes were screened by the full-length transcriptome sequences data in C.tinctorius.Chalcone biosynthase genes in C.tinctorius(CtCHSs)were cloned from cDNA of flowers of C.tinctorius.The cloned gene sequences were analyzed by bioinformatics,and their expression patterns were analyzed by real-time PCR(RT-PCR).The protein of CtCHS in the development of flowers was detected by polyclonal antibody Western blot.A recombinant vector of CtCHS was constructed.The CtCHS recombinant protein was induced and purified to detect the enzyme reaction(catalyzing the reaction of p-coumaryl-CoA and malonyl-CoA to produce naringin chalcone).The reaction product was detected by HPLC and LC-MS.Results:Two full-length CtCHS genes were successfully cloned from the flowers of safflower(CtCHS1 and CtCHS3),with gene lengths of 1525 bp and 1358 bp,respectively.RT-PCR analysis showed that both genes were highly expressed in the flowers,but the expression of CtCHS1 was higher than that of CtCHS3 at each developmental stage of the flowers.WB analysis showed that only CtCHS1 protein could be detected at each developmental stage of the flowers.HPLC and LC-MS analyses showed that CtCHS1 could catalyze the conversion of p-coumaryl-CoA and malonyl-CoA substrates to naringin chalcone.Conclusion:CtCHS1 is involved in the biosynthesis of naringin chalcone in safflower.