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.

Phenotypic Description of Theobroma cacao L. for Yield and Vigor Traits From 34 Hybrid Families in Costa Rica Based on the Genetic Basis of the Parental Population

“…Another element that could explain the lower heritabilities for %MO observed is the potential presence of off-type hybrids. In fact, one of the main challenges in cacao breeding programs and other crops is the tendency for mislabeled individuals (off-types; Motilal and Butler, 2003 ; Turnbull et al, 2004 ; Hama-Ali et al, 2015 ; DuVal et al, 2017 ). Genotyping large populations is not always feasible, due to budget, logistical constraints, and other factors specific to a program.…”

“…Genotyping large populations is not always feasible, due to budget, logistical constraints, and other factors specific to a program. In the case of Romero Navarro et al ( 2017 ), the population studied was adjusted for off-type presence using molecular markers, this approach has significantly improved heritabilities for other diseases in cacao (DuVal et al, 2017 ).…”

“…In order to improve analyses based on pedigree and in efforts to gain more information about the 34 families in this trial, the genotyping of L10 (parents of L7) was done on a representative clone from each replication using the 96 SNP off-typing marker described in DuVal et al ( 2017 ). A total of four representative genotypes of the parental clones were compared.…”

“…Several experiments to evaluate genotypes had been established in many countries; however, published results related to genetic architecture of traits are limited. Some recent studies have reported interesting high to moderate narrow-sense heritabilities for traits related to yield (0.37–0.64) and disease traits (0.03–0.16) (DuVal et al, 2017 ); while other studies have reported moderate to low broad-sense heritabilities for yield traits (0.06–0.23) and plant vigor (0.02–0.14) (Ofori et al, 2016 ). In addition, partitioning the genetic signal into an additive (i.e., general combining ability) and a dominant (i.e., specific combining ability) effect has been reported (Dias and Kageyama, 1995 ; Cervantes-martinez et al, 2006 ; DuVal et al, 2017 ), with a strong contribution of the dominance, confirming what is known from this crop, where high levels of heterosis, among specific genetic groups, are found due to genetically diverse origins (Dias, 2001 ).…”

A disease and production index (DPI) for selection of cacao (Theobroma cacao) clones highly productive and tolerant to pod rot diseases

“…The degree to which DPI is an inherited trait for individual clones and therefore selectable as a combined trait is currently unknown. Multiple studies have defined the selection potential of disease and yield‐associated traits in cacao (Ndoumbé et al , ; Cervantes‐Martinez et al , ; DuVal et al , ). Fortunately, the measures contributing to DPI (yield and disease loss) are regular components of these types of studies and with little extra effort provide the data required for determining the heritability and contribution to genetic gain of the combined DPI measure.…”