Genome-Wide Association Study for Abscission Failure of Fruit Pericarps (Stick-Tights) in Wild Macadamia Germplasm

Abstract

Macadamia pericarps that fail to abscise (‘stick-tights’) are an important trait to select against in breeding as they can harbour pests and diseases. Traditional macadamia breeding cycles are lengthy and expensive due to long juvenilities and large tree sizes. Thus, genome-wide association studies (GWAS) are an important investigative tool to identify candidate trait-linked markers to enable potential reductions in evaluation and selection cycles via marker-assisted selection (MAS) in young seedlings. This study assessed 199 wild macadamia germplasm accessions for stick-tight prevalence across two years. As the number of stick-tights per tree is limited by the number of nuts per tree, we conducted association analyses to identify SNPs linked with the number of stick-tights per tree, and examined whether such SNPs were also associated with, and thus confounded with, the number of nuts per tree. We also assessed associations with the proportion of stick-tights per total number of nuts. Thirty-two SNPs were associated with at least one of the stick-tight traits in one year (p < 0.001). Of all such SNPs, only one was associated with the number of nuts per tree (p < 0.001), indicating that most associations were not confounded with yield.