An Altered Circadian Clock Coupled with a Higher Photosynthesis Efficiency Could Explain the Better Agronomic Performance of a New Coffee Clone When Compared with a Standard Variety.

In a context where climate change is threatening coffee productivity, the management of coffee leaf rust is a challenging issue. Major resistant genes, which have been used for many years, are systematically being overcome by pathogens. Developing healthy plants, able to defend themselves and be productive even when attacked by the pathogen, should be part of a more sustainable alternative approach. We compared one hybrid (GPFA124), selected for its good health in various environments including a reduced rust incidence, and the cv. 'Caturra', considered as a standard in terms of productivity and quality but highly susceptible to rust, for phenotypic variables and for the expression of genes involved in the circadian clock and in primary photosynthetic metabolism. The GPFA124 hybrid showed increased photosynthetic electron transport efficiency, better carbon partitioning, and higher chlorophyll content. A strong relationship exists between chlorophyll a fluorescence and the expression of genes related to the photosynthetic electron transport chain. We also showed an alteration of the amplitude of circadian clock genes in the clone. Our work also indicated that increased photosynthetic electron transport efficiency is related to the clone's better performance. Chlorophyll a fluorescence measurement is a good indicator of the coffee tree's physiological status for the breeder. We suggest a connection between the circadian clock and carbon metabolism in coffee tree.

A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm.

In order to better understand the mechanisms generating genetic diversity in the recent allotetraploid species Coffea arabica, here we present a chromosome-level assembly obtained with long read technology. Two genomic compartments with different structural and functional properties are identified in the two homoeologous genomes. The resequencing data from a large set of accessions reveals low intraspecific diversity in the center of origin of the species. Across a limited number of genomic regions, diversity increases in some cultivated genotypes to levels similar to those observed within one of the progenitor species, Coffea canephora, presumably as a consequence of introgressions deriving from the so-called Timor hybrid. It also reveals that, in addition to few, early-occurring exchanges between homoeologous chromosomes, there are numerous recent chromosomal aberrations including aneuploidies, deletions, duplications and exchanges. These events are still polymorphic in the germplasm and could represent a fundamental source of genetic variation in such a lowly variable species.

A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids.

Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops.

Authentication of Coffea arabica Varieties through DNA Fingerprinting and its Significance for the Coffee Sector.

BACKGROUND: Locating the optimal varieties for coffee cultivation is increasingly considered a key condition for sustainable production and marketing. Variety performance varies when it comes to susceptibility to coffee leaf rust and other diseases, adaptation to climate change and high cup quality for specialty markets. But because of poor organization and the lack of a professional coffee seed sector, most existing coffee farms (and even seed lots and nurseries) do not know which varieties they are using. DNA fingerprinting of coffee planting material will contribute to professionalize the coffee seed sector. OBJECTIVE: The objective of this paper is i) to check in a large scale the robustness of the existing coffee DNA fingerprinting method based on eight Single Sequence Repeats markers (SRR) and ii) to describe how it can help in moving the needle towards a more professional seed sector. METHOD: 2533 samples representing all possible genetic background of Arabica varieties were DNA fingerprinted with 8 SRR markers. The genetic diversity was analyzed and the genetic conformity to varietal references was assessed. RESULTS: The DNA fingerprinting method proved to be robust in authenticating varieties and trace back the history of C. arabica breeding and of the movement of C. arabica varieties. The genetic conformity of two important coffee varieties, Marseillesa and Gesha, proved to be 91% and 39% respectively. CONCLUSIONS: DNA fingerprinting provides different actors in the coffee sector with a powerful new tool-farmers can verify the identity of their cultivated varieties, coffee roasters can be assured that marketing claims related to varieties are correct, and most of all, those looking to establish the a more professional and reliable coffee seed sector have a reliable new monitoring tool to establish and check genetic purity of seed stock and nursery plants. HIGHLIGHTS: While C. arabica is primarily self-pollinating, even fixed line varieties appear to be drifting away from their original genetic reference due to uncontrolled cross pollination. A set of 8 SSR markers applied to the largest possible genetically diverse set of samples prove to discriminate between a wide range of varieties Figures confirm that genetic non conformity of coffee varieties can represent up to 61% of checked samples.

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm.

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.

Influence of Environmental Conditions and Genetic Background of Arabica Coffee (C. arabica L) on Leaf Rust (Hemileia vastatrix) Pathogenesis.

Global warming is a major threat to agriculture worldwide. Between 2008 and 2013, some coffee producing countries in South and Central America suffered from severe epidemics of coffee leaf rust (CLR), resulting in high economic losses with social implications for coffee growers. The climatic events not only favored the development of the pathogen but also affected the physiological status of the coffee plant. The main objectives of the study were to evaluate how the physiological status of the coffee plant modified by different environmental conditions impact on the pathogenesis of CLR and to identify indicators of the physiological status able to predict rust incidence. Three rust susceptible genotypes (one inbred line and two hybrids) were grown in controlled conditions with a combination of thermal regime (TR), nitrogen and light intensity close to the field situation before being inoculated with the rust fungus Hemileia vastatrix. It has been demonstrated that a TR of 27-22°C resulted in 2000 times higher sporulation than with a TR of 23-18°C. It has been also shown that high light intensity combined with low nitrogen fertilization modified the CLR pathogenesis resulting in huge sporulation. CLR sporulation was significantly lower in the F1 hybrids than in the inbred line. The hybrid vigor may have reduced disease incidence. Among the many parameters studied, parameters related to photosystem II and photosynthetic electron transport chain components appeared as indicators of the physiological status of the coffee plant able to predict rust sporulation intensity. Taken together, these results show that CLR sporulation not only depends on the TR but also on the physiological status of the coffee plant, which itself depends on agronomic conditions. Our work suggests that vigorous varieties combined with a shaded system and appropriate nitrogen fertilization should be part of an agro-ecological approach to disease control.

Juvenile Coffee Leaves Acclimated to Low Light Are Unable to Cope with a Moderate Light Increase.

The understorey origin of coffee trees and the strong plasticity of Coffea arabica leaves in relation to contrasting light environments have been largely shown. The adaptability of coffee leaves to changes in light was tested under controlled conditions by increasing the illumination rate on C. arabica var. Naryelis seedlings acclimated to low light conditions and observing leaf responses at three different developmental stages (juvenile, growing and mature). Only mature leaves proved capable of adapting to new light conditions. In these leaves, different major mechanisms were found to contribute to maintaining a good photosynthetic level. With increased illumination, a high photosynthetic response was conserved thanks to fast nitrogen remobilization, as indicated by SPAD values and the photorespiration rate. Efficient photoprotection was accompanied by a great ability to export sucrose, which prevented excessive inhibition of the Calvin cycle by hexose accumulation. In contrast, in younger leaves, increased illumination caused photodamage, observable even after 9 days of treatment. One major finding was that young coffee leaves rely on the accumulation of chlorogenic acids, powerful antioxidant phenolic compounds, to deal with the accumulation of reactive oxygen species rather than on antioxidant enzymes. Due to a lack of efficient photoprotection, a poor ability to export sucrose and inadequate antioxidant protection, younger leaves seemed to be unable to cope with increased illumination. In these leaves, an absence of induced antioxidant enzyme activity was accompanied, in growing leaves, by an absence of antioxidant synthesis or, in juvenile leaves, inefficient synthesis of flavonoids because located in some epidermis cells. These observations showed that coffee leaves, at the beginning of their development, are not equipped to withstand quick switches to higher light levels. Our results confirm that coffee trees, even selected for full sunlight conditions, remain shade plants possessing leaves able to adapt to higher light levels only when mature.