Christophe Montagnon

Genetics of coffee quality

Coffee quality, in the present context of overproduction worldwide, has to be considered as a main selection criterion for coffee improvement. After a definition of quality, and an overview of the non genetic factors affecting its variation, this review focuses on the genetic factors involved in the control of coffee quality variation. Regarding the complexity of this trait, the different types of quality are first presented. Then, the great variation within and between coffee species is underlined, mainly for biochemical compounds related to quality (caffeine, sugars, chlorogenic acids, lipids). The ways for breeding quality traits for cultivated species, Coffea arabica and Coffea canephora are discussed, with specific challenges for each species. For C. arabica, maintaining a good quality in F 1 intraspecific hybrids, introgressed lines from Timor hybrid, and grafted varieties are the main challenges. For C. canephora, the improvement is mainly based on intraspecific and interspecific hybrids, using the whole genetic variability available within this species. An improvement is obtained for bean size, with significant genetic gains in current breeding programmes. The content in biochemical compounds related to cup quality is another way to improve Robusta quality. Finally, ongoing programmes towards the understanding of the molecular determinism of coffee quality, particularly using coffee ESTs, are presented.

Yield stability in clones of Coffea canephora in the short and medium term: longitudinal data analyses and measures of stability over time

In perennial crops like coffee, genetic improvement efficiency is limited by several factors. These include determining the acceptable minimum observation period for yield traits, and also variation of the traits over time, in order to develop breeding objectives that incorporate stability and persistence of the desired traits. Yield data from a trial comparing 20 Coffea canephora clones in Ivory Coast, monitored over nine production years, were analyzed by two different methods. (1) After studying genetic correlations between yields in successive years, longitudinal data analyses were applied to understand relationships between years. Several models were tested and the Compound Symmetry model, with heterogeneous variances (CSH model), best described the data structure. For instance, at tree level, correlations between yields of the different years were moderately stable, which revealed a major tree effect within clones. (2) Subsequently, derived index traits were considered, characterizing yield distribution over the different years. The traits involved were earliness, alternation, and the intensity of variations between years. Despite a marked tendency towards biennial cropping, especially in the early years, the estimated genetic correlations between years, and between individual years and cumulative yield were generally high. The intensity of the relative differences between yields in successive years was heritable only in the second production cycle. Despite some clonal differences in yield-stability variables, clonal yields in single years or groups of years evidently reflected both cumulative yields and comparative yield stability.

Performance of Coffea arabica F1 hybrids in agroforestry and full-sun cropping systems in comparison with American pure line cultivars

Coffea arabica F1 hybrids derived from crosses between wild Sudan-Ethiopian and American cultivars and propagated by somatic embryogenesis have been obtained in Central America. These new hybrids considerably enhanced the genetic diversity of coffee in the region. We conducted 15 trials to assess whether using hybrids represents substantial genetic progress in terms of productivity in agroforestry and full-sun cropping systems. The new germplasm was grown in the same conditions as the best American cultivar (homozygous pure lines). The results showed that yields of hybrids were earlier and superior to those of American cultivars. The hybrids were also more stable than the American cultivars in all environments. In the agroforestry system, the mean yield of hybrids was 58% higher than that of the American cultivars, while the mean yield of hybrids in the full-sun system was 34% higher. Coffee-based agroforestry systems (AS) are considered effective in protecting the environment in the volcanic cordilleras of Central America. We found that introducing hybrids in coffee-based AS can considerably increase productivity. This finding could be a convincing argument to encourage coffee growers who have adopted the full-sun cropping system to return to agroforestry cropping systems. Finally, the conditions for large-scale dissemination of those new hybrids—which represent a major innovation for C. arabica cropping—was analysed.

Stable resistance against the leaf miner #Leucoptera coffeella# expressed by genetically transformed #Coffea canephora# in a pluriannual field experiment in French Guiana

SummaryA pluriannual field trial of transgenic clones of Coffea canephora (the Robusta coffee tree) transformed for resistance to the lepidopteran coffee leaf miner Leucoptera coffeella was installed in French Guiana. Fifty-eight transformed clones produced by transformation of the C. canephora clone 126 were planted. They were harbouring the pEF1α constitutive promoter of Arabidopsis thaliana controlling either the Bacillus thuringiensis native gene for the cry1Ac insecticidal protein (eight clones) or a synthetic cry1Ac gene (53 clones). The vectors for the transformation were a strain of the bacterium Agrobacterium tumefaciens and one of Agrobacterium rhizogenes. The transformed clones were generally independent, presenting different integration patterns of the genetic construct. Four randomly distributed groups of five plants per transformed clone were planted along with 60 untransformed control trees. Over a 4-year period after plantation six releases of L. coffeella were performed. Mines on the leaves are the marks of larvae development and were counted on plants. A majority of the independent transformed clones harbouring the synthetic gene and transformed by the strain of A. tumefaciens displayed constantly much less mines than the control, therefore expressing a stable resistance. The need for complementary research is presented.

Competition effects in cocoa (Theobroma cacao L.) hybrid trials

A method developed in coffee tree breeding to assess family competitioneffects (partner effects) in comparative variety trials was applied to thecocoa tree (Theobroma cacao L.). The study was conducted in ahybrid comparative trial planted in French Guiana, involving twelve familiesof 50 trees in a totally randomized single-tree plot design, at a density of1,667 trees per hectare. The trial was thinned at 10 years, at a rate of twoout of four rows. Competition was studied with reference to juvenile andadult vegetative vigour, and to periodic and cumulative yields (number ofpods, potential weight, average weight of one pod, and the production:vigour ratio). At the end of the trial, after thirteen years of monitoring,competition effects were revealed which explained 8 to 10% of theresidual variance after removal of the hybrid and micro-environment effects.These effects, which were detected as early as 18 months, occurred earlierthan generally acknowledged. Under the trial conditions, the families couldbe classed as aggressive, stimulating or passive for their neighbours.Vegetative vigour (trunk cross-section) explained 34% of the competitioneffects (partner effects), which, with hindsight, vindicated the use of theproduction : vigour ratio as the main selection criterion in cocoa breeding.The partner effects noted on the production variables were never explainedby any production variable, hence non-aggressive high-yielding families canbe selected.

Characterization and evaluation of two genetic groups and value of intergroup hybrids of #Cola nitida# (Vent.) Schott and Endlicher

The collection of Cola nitida in Côte d’Ivoire was previously classified, based on isozyme markers, into three groups named A, B and C, based on isozymic differences. In this study, morphological traits and several yield components as well as genotypic and phenotypic variabilities for vigour were investigated in groups A and B. We found that group A was characterized by a low vigour and high yield components. In contrast, group B expressed high vigour and low yield components. Intergroup hybrids were more vigorous and high yielder than intragroup hybrids. The vigour of intergroup hybrids was comparable to that of half sib commercial hybrids. Value of heterosis obtained for the yield of intergroup hybrids was 350%. It was concluded, based on our findings, that reciprocal recurrent selection in Cola nitida using plant materials of groups A and B should lead to significant improvement.

Transformation of a nonnormal distribution of quantitative traits for breeding purposes

Some continuous quantitative traits such as yield are not always normally distributed. This article proposes an underlying normal distribution—called the equivalent normal distribution—to help analyze and interpret the distribution of such data. The mean and standard deviation of this distribution are estimated through the regression of the theoretical (assuming normality) selection intensity on the corresponding observed standardized selection differential at each selection rate that may be applied (as many selection rates as individuals in the distribution). This simple and pragmatic transformation does not require scale transformations, which sometimes obscure biological interpretation. A possible biological interpretation of the Equivalent Normal Distribution is presented; it considers the difference between the potential and the eventually observed performance. This method allows comparisons between distributions of apparently different shapes. Simulations furthermore indicated that Equivalent statistics, compared with observed statistics, allowed an improved prediction of genetic values and estimation of realised heritability.