Department of Agronomy and Plant Breeding, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran.
Dryland Agricultural Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Kermanshah, 1164-67145, Iran.
Mol Biol Rep. 2020 Mar;47(3):2123-2135. doi: 10.1007/s11033-020-05312-x. Epub 2020 Feb 15.
Safflower (Carthamus tinctorius L.) is one of the most important oilseed crops for its seed oil rich in unsaturated fatty acids. Precise utilization of diverse genetic resources is fundamental in breeding programs to improve high yield genotypes with desirable traits. In this study, for the first time we report successful application of DArTseq technology; an efficient genotyping-by-sequencing (NGS); to analysis genetic diversity and population structure of 89 safflower accessions from worldwide origins. Totally, 19,639 DArTseq markers (10,130 SilicoDArTs and 9509 SNPs) generated through DArTseq genotyping. After filtering the data, 3431 polymorphic DArTseq markers (1136 SilicoDArTs and 2295 SNPs) used for genetic diversity, population structure and linkage disequilibrium analysis in safflower genotypes. All the SilicoDArT and SNP markers showed high reproducibility and call rate. Polymorphism information content (PIC) values ranged from 0.1 to 0.5, while ≥ 0.50% of SilicoDArTs and ≥ 0.64% SNPs showed PIC values more than median. Genotypes grouping using DArTseq markers resulted in three distinct clusters. Results showed weak correlation between safflower diversity pattern and origins. Analysis of molecular variance revealed that the majority of genetic variation was attributed to the differences among varieties within cluster populations and there was no significant molecular variance between origins. However, safflower of accessions belonged to Iran, Turkey, Pakistan and India indeed appear to be genetically similar and grouped close in referred cluster, while the accessions from Near East (Afghanistan, China) being distinct. Our results were in agreement with hypothesis that safflower domesticated in somewhere west of Fertile Crescent and then expanded through Africa and Europe. Present study using a panel of globally diverse safflower accessions and large number of DArTseq markers set the stage for future analysis of safflower domestication using large germplasm from proposed domestication centers. Also, studied germplasm in this study can be used as a valuable source for future genomic studies in safflower for mapping desirable traits through genome-wide association mapping studies.
红花（Carthamus tinctorius L.）是最重要的油料作物之一，其种子油富含不饱和脂肪酸。在育种计划中，精确利用多样化的遗传资源是培育具有理想特性的高产量基因型的基础。在这项研究中，我们首次成功应用 DArTseq 技术；一种高效的测序基因分型（NGS）；对来自世界各地的 89 个红花品种的遗传多样性和种群结构进行分析。总共通过 DArTseq 基因分型生成了 19639 个 DArTseq 标记（10130 个 SilicoDArTs 和 9509 个 SNPs）。在数据过滤后，3431 个多态性 DArTseq 标记（1136 个 SilicoDArTs 和 2295 个 SNPs）用于红花基因型的遗传多样性、种群结构和连锁不平衡分析。所有的 SilicoDArT 和 SNP 标记都表现出很高的重现性和标记率。多态性信息含量（PIC）值范围从 0.1 到 0.5，而 SilicoDArTs 的≥0.50%和 SNPs 的≥0.64%显示出高于中位数的 PIC 值。使用 DArTseq 标记对基因型进行分组，结果产生了三个不同的聚类。结果表明，红花的多样性模式与起源之间存在弱相关性。分子方差分析表明，大部分遗传变异归因于聚类群体内品种之间的差异，起源之间没有显著的分子方差。然而，来自伊朗、土耳其、巴基斯坦和印度的红花品种确实在遗传上相似，在参考聚类中分组较近，而来自近东（阿富汗、中国）的红花品种则不同。我们的结果与红花在肥沃月湾的某个地方驯化，然后通过非洲和欧洲扩张的假说一致。本研究使用一组全球多样化的红花品种和大量的 DArTseq 标记为未来利用拟议的驯化中心的大种质资源对红花驯化进行分析奠定了基础。此外，本研究中研究的种质资源可作为未来在红花中进行基因组研究的宝贵资源，通过全基因组关联图谱研究来映射理想的特性。
