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

作者：J Chen, Shuai Guo, Xueli Hu, Rui Wang, Donghai Jia, Qiang Li, Xianmei Yin, Xuejiao Liao, Zunhong Hu, Peiqi Wang, Chaoxiang Ren, Shuai Dong, Chao Chen, Shilin Chen, Jiang Xu, Jin Pei · 发表于：Horticulture Research · 年份：2023 · DOI：10.1093/hr/uhad197 · 被引用次数：26 · 研究领域：Sunflower and Safflower Cultivation、Peanut Plant Research Studies、Lipid metabolism and biosynthesis

Abstract 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. ...