Inbreeding depression in yield-related traits revealed by high-throughput sequencing in hexaploid persimmon breeding populations

Crossbreeding within narrow genetic resources increases the homozygosity of the offspring. Resultant inbreeding depression can reduce the yield potential of the offspring. Slow progress in breeding programs because of inbreeding has been suggested in persimmon (Diospyros kaki Thunb.), but quantitative evidence has been limited. Here we assessed how inbreeding affects a population's yield-related traits by using sequence-based genotyping. To find a reliable inbreeding estimation method that considers persimmon's hexaploidy, we screened nine marker-based inbreeding estimators (F-M) and various read-depth thresholds for genotype calling; the results suggested that the Loiselle-Huang (LH) F-M and a read-depth threshold of 10 were optimal. After validating 11,379 variant sites selected under the optimal read-depth threshold, we calculated the LH F-M of 97 breeding populations by using the dosage genotypes of 47 cross parents. In these populations, LH F-M successfully identified the less inbred populations and confirmed that the inbreeding level was significantly reduced by a pseudo-backcross strategy designed to widen the genetic diversity of the breeding population. In regression analyses using mean phenotypic value and LH F-M of the 97 populations as response and explanatory variables, respectively, we detected significant reductions of fruit weight, yield, and tree vigor at the first fruit-bearing age, and delay of the first fruit-bearing age itself as inbreeding progressed; the other eight F-M showed similar trends. These results indicate that inbreeding depression occurs in yield-related traits in persimmon and that employing F-M would help breeders increase the chance of developing less inbred cultivars with higher yield potential.