Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm

Abstract

A basic knowledge of linkage disequilibrium and population structure is necessary in order to determine the genetic control and identify significant associations with agronomical and phytochemical compounds in apple (Malus × domestica Borkh). In this study, 186 apple accessions (Pop1), representing both Spanish native accessions (94) and non-Spanish cultivars (92) from the EEAD-CSIC apple core collection, were assessed using 23 SSRs markers. Four populations were considered: Pop1, Pop2, Pop3, and Pop4. The initial Pop1 was divided into 150 diploid (Pop2) and 36 triploid accessions (Pop3), while for the inter-chromosomal linkage disequilibrium and the association mapping analysis, 118 phenotype diploid accessions were considered Pop4. Thus, the average number of alleles per locus and observed heterozygosity for the overall sample set (Pop1) were 15.65 and 0.75, respectively. The population structure analysis identified two subpopulations in the diploid accessions (Pop2 and Pop4) and four in the triploids (Pop3). Regarding the Pop4, the population structure with K = 2 subpopulations segregation was in agreement with the UPGMA cluster analysis according to the genetic pairwise distances. Moreover, the accessions seemed to be segregated by their origin (Spanish/non-Spanish) in the clustering analysis. One of the two subpopulations encountered was quite-exclusively formed by non-Spanish accessions (30 out of 33). Furthermore, agronomical and basic fruit quality parameters, antioxidant traits, individual sugars, and organic acids were assessed for the association mapping analysis. A high level of biodiversity was exhibited in the phenotypic characterization of Pop4, and a total of 126 significant associations were found between the 23 SSR markers and the 21 phenotypic traits evaluated. This study also identified many new marker-locus trait associations for the first time, such as in the antioxidant traits or in sugars and organic acids, which may be useful for predictions and for a better understanding of the apple genome.

Antioxidant, Antidiabetic, and Anti-Obesity Properties of Apple Pulp Extracts (Malus domestica Bork): A Comparative Study of 15 Local and Commercial Cultivars from Spain

“…Some varieties have been demonstrated in vitro inhibitory effects against the enzymes α-glucosidase, lipase, monoamine oxidase A, tyrosinase and acetylcholinesterase [21]. Those biochemical traits, as well as other agronomical characteristics, could also be interesting for a better understanding of apple genomes, particularly to elucidate causal genes associated with human wellness [22]. In this project, twenty-one traits of interest, such as basic fruit quality, antioxidant parameters, individual sugars, and organic acids, were assessed by 23 simple sequence repeat molecular markers; these results showed that the polyphenol content in apples may suggest that breeders may be able to improve the nutritional value of apples through marker assisted breeding (MAB) or gene editing.…”