Microsatellite markers reveal low breeding system efficacy and pollen contamination can limit production of full-sib avocado progeny

Phytophthora cinnamomi causes a severe root rot in avocado, Persea americana. Breeding tolerant rootstocks is thought to be the most promising method for phytophthora root rot disease control but breeding avocado is challenging. The avocado flowering syndrome (synchronous protogynous dichogamy), combined with high flowering and low fruit set, render controlled pollination exceedingly difficult. Juxtaposing complementary flowering types of elite parent cultivars (cultivars that produce progeny with tolerance to phytophthora root rot) was performed in an effort to increase the number of full-sib progeny for elite maternal parents and, hypothetically, the number of phytophthora root rot tolerant progeny. Although high outcrossing rates were achieved (estimated ∼93%), the majority of progeny had a non-elite paternal parent (56% of progeny were offtypes) implying maternal trees were pollinated by non-elite distant trees. Among progeny that could be confidently genotyped, a high number of cross types were detected (33). Contrary to our hypothesis, a significant portion of the progeny were the result of crosses between like, and not complementary, flowering types. The spatial distribution of productive trees and grafts helped to explain these data, as productive grafts were directly adjacent to grafts of the same flowering type more often than that of the complementary flowering type. Selfed progeny were significantly less tolerant to phytophthora root rot than outcrossed progeny. Progeny resulting from crosses between an elite maternal parent and non-elite pollen donor (offtypes) were less tolerant than full-sib progeny resulting from crosses between elite parents. Maternal effects may interfere with identifying truly disease tolerant selections. Thus, to reduce maternal effects and non-elite pollen donor contamination, removal of seedling cotyledons before screening for disease tolerance and better isolation of elite parent trees and windbreaks may improve breeding efficacy. This study also demonstrates the usefulness of microsatellite markers in parentage analysis where a high proportion of the putative parents are closely related.