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

生物 红花属 基因组 遗传学 参考基因组 顺序装配 基因 候选基因 转录组 医学 基因表达 传统医学
作者
J Chen,Shuai Guo,Xueli Hu,Rui Wang,Jia DongHai,Qiang Li,Xianmei Yin,Xuejiao Liao,Zunhong Hu,Peiqi Wang,Chaoxiang Ren,Shuai Dong,Chao Chen,Shilin Chen,Jiang Xu,Jin Pei
出处
期刊:Horticulture research [Springer Nature]
卷期号:10 (11) 被引量:2
标识
DOI:10.1093/hr/uhad197
摘要

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 eudicot γ-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.
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