Genetic Parameters and the Impact of Off-Types for Theobroma cacao L. in a Breeding Program in Brazil

Abstract

Breeding programs of cacao (Theobroma cacao L.) trees share the many challenges of breeding long-living perennial crops, and genetic progress is further constrained by both the limited understanding of the inheritance of complex traits and the prevalence of technical issues, such as mislabeled individuals (off-types). To better understand the genetic architecture of cacao, in this study, 13 years of phenotypic data collected from four progeny trials in Bahia, Brazil were analyzed jointly in a multisite analysis. Three separate analyses (multisite, single site with and without off-types) were performed to estimate genetic parameters from statistical models fitted on nine important agronomic traits (yield, seed index, pod index, % healthy pods, % pods infected with witches broom, % of pods other loss, vegetative brooms, diameter, and tree height). Genetic parameters were estimated along with variance components and heritabilities from the multisite analysis, and a trial was fingerprinted with low-density SNP markers to determine the impact of off-types on estimations. Heritabilities ranged from 0.37 to 0.64 for yield and its components and from 0.03 to 0.16 for disease resistance traits. A weighted index was used to make selections for clonal evaluation, and breeding values estimated for the parental selection and estimation of genetic gain. The impact of off-types to breeding progress in cacao was assessed for the first time. Even when present at <5% of the total population, off-types altered selections by 48%, and impacted heritability estimations for all nine of the traits analyzed, including a 41% difference in estimated heritability for yield. These results show that in a mixed model analysis, even a low level of pedigree error can significantly alter estimations of genetic parameters and selections in a breeding program.

Keywords: REML; SNP; breeding values; cacao; genetic gains; heritability.

Figure 1

The number of families corresponding to different proportions of off-types in PT08.

Figure 2

The percent change in genetic gains by trait resulting from the exclusion of off-types in the single site analysis. For blue traits, the estimated gains increase once off-types are removed but for red traits, the estimated gains decrease with the removal of off-types.

Figure 3

(A) Population structure of 3,358 progeny from the trial PT08. (B) The proportions of ancestry in the genetic background of individuals with the top 1% breeding values per trait.