Marker-trait association mapping for perpetual flowering habit in an octoploid ancestral strawberry, Fragaria...

Cultivated strawberry Fragaria × ananassa (Duch.) is an economically important small fruit. Flowering habit is a key trait of interest in cultivar development and agricultural production. Two cultivar types are distinguished: seasonal flowering (SF) varieties, which require a sufficiently short day length to initiate flowering; and perpetual flowering (PF) varieties, which are photoperiod-insensitive and continuously flowering at permissive temperatures. Identifying marker-trait associations (MTAs) and genes related to flowering time is an ongoing goal. SF and PF accessions of the ancestral octoploid Fragaria virginiana were used in crossing and backcrossing to generate a BC₁F₁ mapping population, which was genotyped on the IStraw90 SNP array to develop a linkage map using JoinMap 4.1. MTA analysis was done by chi-square test for independence and compared with analyses done using FlexQTL and WinQTLCart. Six MTAs for PF were mapped, suggesting complex genetic regulation. These MTAs were distributed across five linkage groups (LGs) representing four chromosomal homeology groups. Surprisingly, none of these six MTAs were assigned to a member of the F. virginiana subgenome A, the octoploid strawberry subgenome widely agreed to descend from the ancestral diploid Fragaria vesca. This important distinction extended to the strong MTAs on LG14, which our analysis assigned to the same homeology group but not the same homeolog previously assigned to the well-studied FaPFRU locus conferring continuous flowering in F. × ananassa. This alternative localization may help to explain why the gene(s) underlying FaPFRU have remained unidentified in the 13 years since its discovery.