Stansell Zachary, Hyma Katie, Fresnedo-Ramírez Jonathan, Sun Qi, Mitchell Sharon, Björkman Thomas, Hua Jian
1School of Integrative Plant Science, Horticulture Section, Cornell University, Geneva, NY 14456 USA.
2Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853 USA.
Hortic Res. 2018 Jul 1;5:38. doi: 10.1038/s41438-018-0040-3. eCollection 2018.
forms a diverse and economically significant crop group. Improvement efforts are often hindered by limited knowledge of diversity contained within available germplasm. Here, we employ genotyping-by-sequencing to investigate a diverse panel of 85 landrace and improved broccoli, cauliflower, and Chinese kale entries. Ultimately, 21,680 high-quality SNPs were used to reveal a complex and admixed population structure and clarify phylogenetic relationships among groups. Each broccoli landrace contained, on average, 8.4 times as many unique alleles as an improved broccoli and landraces collectively represented 81% of all broccoli-specific alleles. Commercial broccoli hybrids were largely represented by a single subpopulation identified within a complex population structure. Greater allelic diversity in landrace broccoli and 96.1% of SNPs differentiating improved cauliflower from landrace cauliflower were common to the larger pool of broccoli germplasm, supporting a parallel or later development of cauliflower due to introgression events from broccoli. Chinese kale was readily distinguished by principal coordinate analysis. Genotyping was accomplished with and without reliance upon a reference genome producing 141,317 and 20,815 filtered SNPs, respectively, supporting robust SNP discovery methods in neglected or unimproved crop groups that lack a reference genome. This work clarifies the population structure, phylogeny, and domestication footprints of landrace and improved broccoli using many genotyping-by-sequencing markers. Additionally, a large pool of genetic diversity contained in broccoli landraces is described which may enhance future breeding efforts.
构成了一个多样化且具有重要经济意义的作物群体。由于对现有种质中所含多样性的了解有限，改良工作常常受到阻碍。在此，我们采用简化基因组测序来研究由85个地方品种以及改良的西兰花、花椰菜和芥蓝材料组成的多样化样本。最终，利用21,680个高质量单核苷酸多态性（SNP）来揭示一个复杂且混合的群体结构，并厘清各群体之间的系统发育关系。每个西兰花地方品种平均所含的独特等位基因数量是改良西兰花的8.4倍，且地方品种共同代表了所有西兰花特异性等位基因的81%。商业西兰花杂交种在很大程度上由在复杂群体结构中鉴定出的一个单一亚群体所代表。地方品种西兰花具有更高的等位基因多样性，并且区分改良花椰菜和地方品种花椰菜的SNP中有96.1%在更大的西兰花种质库中是常见的，这支持了由于西兰花的基因渗入事件导致花椰菜平行或较晚发育的观点。通过主坐标分析很容易区分芥蓝。分别在依赖和不依赖参考基因组的情况下完成了基因分型，分别产生了141,317个和20,815个经过筛选的SNP，这支持了在缺乏参考基因组的被忽视或未改良作物群体中强大的SNP发现方法。这项工作利用许多简化基因组测序标记厘清了地方品种和改良西兰花的群体结构、系统发育和驯化印记。此外，还描述了西兰花地方品种中所含的大量遗传多样性，这可能会加强未来的育种工作。
