Genetic diversity and population structure analysis in Asparagus officinalis

Abstract

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.