Effects of forest management on mating patterns, pollen flow and intergenerational transfer of genetic diversity in wild Arabica coffee (Coffea arabica L.) from Afromontane rainforests

Haitian coffee agroforestry systems harbor complex arabica variety mixtures and under-recognized genetic diversity

Though facing significant challenges, coffee (Coffea arabica) grown in Haitian agroforestry systems are important contributors to rural livelihoods and provide several ecosystem services. However, little is known about their genetic diversity and the variety mixtures used. In light of this, there is a need to characterize Haitian coffee diversity to help inform revitalization of this sector. We sampled 28 diverse farms in historically important coffee growing regions of northern and southern Haiti. We performed KASP-genotyping of SNP markers and HiPlex multiplex amplicon sequencing for haplotype calling on our samples, as well as several Ethiopian and commercial accessions from international collections. This allowed us to assign Haitian samples to varietal groups. Our analyses revealed considerable genetic diversity in Haitian farms, higher in fact than many farmers realized. Notably, genetic structure analyses revealed the presence of clusters related to Typica, Bourbon, and Catimor groups, another group that was not represented in our reference accession panel, and several admixed individuals. Across the study areas, we found both mixed-variety farms and monovarietal farms with the historical and traditional Typica variety. This study is, to our knowledge, the first to genetically characterize Haitian C. arabica variety mixtures, and report the limited cultivation of C. canephora (Robusta coffee) in the study area. Our results show that some coffee farms are repositories of historical, widely-abandoned varieties while others are generators of new diversity through genetic mixing.

Genetic composition and diversity of Arabica coffee in the crop's center of origin and its impact on four major fungal diseases

Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the sixty sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels.

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.

Growth and fecundity of colonizing hybrid Raphanus populations are environmentally dependent

PREMISE

Hybrid gene pools harbor more genetic variation than progenitor populations. Thus, we expect hybrid populations to exhibit more dynamic evolutionary responses to environmental variation. We ask how environmental variation experienced by adapted and transplanted populations influence the success of late-generation hybrid populations during invasion.

METHODS

For four generations, 20 wild (Raphanus raphanistrum) and 20 hybrid radish (R. sativus × R. raphanistrum) plant populations evolved under experimentally manipulated moisture conditions (dry, wet, control-sheltered, or control-unsheltered plots; i.e., evolutionary environment) in old fields near Toronto, Canada. We planted advanced-generation wild and hybrid radishes in sheltered plots and exposed them to either an evolutionary or a novel watering environment. To determine how soil moisture would influence invasion success, we compared the phenotype and fecundity of plants grown in these various environments.

RESULTS

Hybridization produced larger plants. In wet environments, hybrid seedlings emerged more frequently and expressed higher photosynthetic activity. Low-moisture, novel conditions delayed and reduced seedling emergence frequency. Hybrid plants and those that evolved under relatively wet environments exhibited higher aboveground biomass. Hybrid plants from control-sheltered plots colonizing novel moisture environments were more fecund than comparable wild plants.

CONCLUSIONS

Dry environments are less likely than other evolutionary environments to contribute colonists. However, relatively wet locations support the evolution of relatively fecund plants, especially crop-wild hybrid populations. Thus, our results provide a strong mechanistic explanation for variation in the relative success of crop-wild hybrids among study locations and a new standard for studies that assess the risk of crop-wild hybridization events.

Organoleptic quality of Ethiopian Arabica coffee deteriorates with increasing intensity of coffee forest management

Arabica coffee (Coffea arabica L.) grows naturally as an understory shrub in the moist evergreen montane forests of Southwest Ethiopia. In response to an increasing local human population pressure and a growing coffee demand on the world market, coffee producing forests are increasingly managed to boost coffee yield. Here we compared organoleptic coffee quality between natural coffee producing forests, large coffee agroforests, and small coffee agroforests. Accounting for variability in Arabica coffee genotype and environment, we found that blind consensus scores, given by a panel of certified Q-Grade cuppers, were negatively affected by increasing forest management intensity. Importantly, only coffee from natural coffee producing forests qualified as specialty coffee following the Specialty Coffee Association of America's standards. We suggest that the most important drivers of deteriorating coffee quality include decreased shade levels and changing micro-climate and biotic interactions. Due to the low yields of coffee in natural coffee producing forests and the lack of quality price premiums, Ethiopian smallholder farmers are inclined to optimize for coffee quantity, rather than for quality, causing a significant challenge for the conservation of Ethiopian natural coffee producing forests.