Genetic dissection of complex traits in citrus: additive and non-additive genetic variances, inbreeding depression, and single-chromosome heritability

Abstract

Genetic evaluation in breeding programs generally considers only additive genetic effects; however, non-additive genetic effects may also contribute to phenotypic and genotypic values. Furthermore, the distributions of causal variants in target traits are associated with the efficiency of accumulation of favorable alleles and are therefore important for plant breeding. Despite this, non-additive effects remain to be fully investigated in citrus. Moreover, although quantitative trait loci in citrus have been previously identified, they cannot adequately explain the genetic variance. Therefore, we attempted to estimate non-additive effects, such as dominance and additive-by-additive effects, together with directional dominance as an indicator of inbreeding depression and with chromosome heritability, which reflects the distributions of causal variants for fruit-quality traits in citrus. Phenotypic records of the fruit weight, sugar content, and acid content of 455 cultivars and their progeny were analyzed. Genomic relationship matrices for non-additive effects and single-chromosome genetic effects were constructed using 2319 genome-wide single nucleotide polymorphism loci, which were also used to evaluate directional dominance. These phenotype and genotype records were analyzed using genomic best linear unbiased prediction models. Through this analysis, we showed (1) overestimation of narrow-sense heritability due to substantial contributions of non-additive effects in the tested traits, (2) evidence of inbreeding depression in fruit weight, and (3) highly polygenic architectures in the tested traits. These findings could contribute to precise evaluation of genotypic values and the development of efficient breeding strategies.