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.
Highlights
Theobroma cacao L. is a small understory tree native to the Amazon estuary (Motamayor et al, 2008)
The higher pest and disease incidence is reflected in the percentage of healthy pods (%HP), which was more than 80% for PT07 and PT02 but the percentage decreased to 53.6 and 56.8% for PT03 and PT08, respectively
Four trials were analyzed in a multisite analysis to evaluate the genetic architecture of 10 traits, and make selections from the trial PT08 using a weighted index
Summary
Theobroma cacao L. is a small understory tree native to the Amazon estuary (Motamayor et al, 2008). Seventy-five percent of global production comes from West African countries, where farmers achieve a yield of 300 kg/ha on average (Lim and Pang, 1990; CacaoNet, 2012). The estimated yield potential based on the cultivation of improved clonal material in intensified farming systems has been estimated to be 2.7 t/ha, and has been demonstrated in high-density production environments in Southeast Asia and Latin America (Lim and Pang, 1990; Schnell et al, 2005; Laliberté and End, 2015). The use and dissemination of improved genetic material in the form of high-yielding clones with resistance to a range of pests and diseases constitute the primary objective for future cacao breeding efforts to continue meeting demand, and buffering fluctuations in supply (Phillips et al, 2009)
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