Genomic estimates of inbreeding and inbreeding depression in a self-pollinated population of eucalyptus

Abstract This research aims to investigate the patterns of inbreeding depression in an $S_{0:1}$ population of Eucalyptus spp., by examining autozygosity and genetic parameters, and studying the impact of an unequal number of selfed and crossed individuals within families on inbreeding depression estimations. Inbreeding has been less investigated in forest species, including eucalyptus, than in annual crops, largely because of their extended reproductive cycles, substantial genetic load, and the practical difficulties of performing controlled selfing. In this study, we self-pollinated 20 elite Eucalyptus spp. genotypes. From each self-pollinated genotype, 30 seeds were collected, resulting in seedlings that were subsequently planted in a field trial. A total of 600 individuals were established in a randomized complete block design trial and evaluated for growth traits at 3 years of age. Both the progenies and the 20 parent were genotyped using Single Nucleotide Polymorphisms chips. Inbreeding depression was evident, as indicated by a decline in diameter at breast height from 13.88 to 9.73 cm in selfed individuals compared with crossed ones. Moreover, the autozygosity observed in the most inbred individuals was primarily due to recent inbreeding, whereas in the best-performing individuals, it mainly resulted from ancient inbreeding events. Simulations highlighted that unbalanced sample sizes of selfed and crossed individuals within families could bias estimates of inbreeding depression. By integrating genomic data and advanced quantitative methods, this study provides new insights into the genetic consequences of self-pollinating eucalyptus, offering a foundation for managing inbreeding and enhancing genetic gains in perennial crops.