Sidhu Gurleen, Banks Travis, Wolyn David
Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada.
Vineland Research and Innovation Centre, Vineland, Ontario, Canada.
J Genet Eng Biotechnol. 2025 Jun;23(2):100491. doi: 10.1016/j.jgeb.2025.100491. Epub 2025 Apr 26.
Asparagus cultivars grown worldwide are thought to have originated from a limited genetic base, however, selection has resulted in variation for climatic adaptation and other traits. Understanding genetic diversity of the crop is important to guide breeding decisions. The objectives of this research were to identify SNPs among 64 cultivated lines from different geographic areas and assess genetic variation, population structure and linkage disequilibrium. More than 55,000 SNPs were identified by GBS and subjected to filtration for minor allele frequency and missing data, resulting in 12,886 markers for all subsequent analysis. Markers exhibited a wide range of Expected Heterozygosity (He), Polymorphic Information Content (PIC) and Observed Heterozygosity (Ho) with mean values of 0.370, 0.310, and 0.450 respectively. Population STRUCTURE analysis indicated that the 64 lines were grouped into two, four, seven, and nine subpopulations. For K = 4, four distinct groups were defined: (1) New Zealand, New Jersey, France, and California; (2) Canada; (3) China, The Netherlands, and Germany; and (4) England, Denmark, Spain, Turkey, and India. The results were further confirmed by PCA, and a phylogenetic tree. LD declined rapidly with an increase in physical distance. A considerable amount of genetic diversity was observed, despite previous suggestions that asparagus cultivars may have originated from one open-pollinated population.
全世界种植的芦笋品种被认为起源于有限的遗传基础，然而，选择已导致其在气候适应性和其他性状方面产生了变异。了解该作物的遗传多样性对于指导育种决策很重要。本研究的目的是鉴定来自不同地理区域的64个栽培品系中的单核苷酸多态性（SNP），并评估遗传变异、群体结构和连锁不平衡。通过简化基因组测序（GBS）鉴定出超过55,000个SNP，并对次要等位基因频率和缺失数据进行过滤，从而得到12,886个标记用于所有后续分析。这些标记显示出广泛的期望杂合度（He）、多态信息含量（PIC）和观察杂合度（Ho），平均值分别为0.370、0.310和0.450。群体结构分析表明，这64个品系被分为两个、四个、七个和九个亚群。当K = 4时，定义了四个不同的组：（1）新西兰、新泽西州、法国和加利福尼亚州；（2）加拿大；（3）中国、荷兰和德国；（4）英国、丹麦、西班牙、土耳其和印度。主成分分析（PCA）和系统发育树进一步证实了结果。连锁不平衡随着物理距离的增加而迅速下降。尽管之前有观点认为芦笋品种可能起源于一个开放授粉群体，但仍观察到了相当数量的遗传多样性。
