Revealing the Genetic Diversity and Population Structure of Garlic Resource Cultivars and Screening of Core Cultivars Based on Specific Length Amplified Fragment Sequencing (SLAF-Seq)

Garlic is an important vegetable and condiment that has good medical and health care effects. At present, the origin of Chinese garlic and its association with other types of quality are limited to the molecular marker level, and there are few reports at the genome level. Therefore, this study is based on the specific length amplified fragment sequencing (SLAF-seq) of 102 copies of garlic germplasm resources, the group structure, and further screening of the core germplasm. SLAF-seq of 102 garlic cultivars yielded 1949.85 Mb of clean data and 526,432,275 SNPs. Through principal component analysis, evolutionary tree, population structure, and genetic relationship analysis, all garlic cultivars were divided into 3 groups. Among them, Group 1 contains 45 Chinese cultivars and 1 Egyptian cultivar, which are distributed mainly in the coastal and central areas of China. Group 2 contains 36 Chinese cultivars and 1 U.S. cultivar, which are distributed mainly in Northwest China. Group 3 contains 19 Chinese cultivars, which are distributed mainly in Xinjiang, China. The genetic diversity results indicate that the fixation index (Fst) values of Group 1 and Group 2 are lower than those of Group 1 and Group 3 and that the diversity of nucleotides (π) of Group 3 is greater than those of Group 2 and Group 1. Finally, the 30 parts of the cultivars were used as the core germplasms, and there was no difference between the two cultivars in terms of core quality. In summary, this study provides tags for the determination of garlic molecular markers and genotypes and provides a theoretical basis for subsequent resource protection and utilization, genetic positioning of important agronomic traits, and molecular marking agglomeration breeding.