Population structure and genetic relationships between Ethiopian and Brazilian Coffea arabica genotypes revealed by SSR markers

Coffea canephora: Heterotic Crosses Indicated by Molecular Approach

The genus Coffea comprises more than 100 species, of which the most commercially important are Coffea arabica and Coffea canephora. The latter is a self-incompatible plant with high natural genetic variability. The detection of polymorphism at the DNA level by molecular markers allowed significant progress with the selection of superior plants. The objective of this study was the molecular characterization of C. canephora using microsatellite markers. To this end, a population of forty-four C. canephora genotypes and one C. arabica genotype, was evaluated with 21 primers. These primers identified 61 alleles in the population and between 2 and 5 alleles per locus. The information index indicated a high level of polymorphism of the analyzed markers. According to the observed and expected heterozygosity, the genetic diversity in the population is high. The overall inbreeding coefficient of the population detected high heterozygosity and zero inbreeding within this population. Genetic diversity among the accessions was also evaluated by the unweighted pair-group method based on arithmetic averages (UPGMA). Six groups were formed based on Mojena's cutting rule and three using the Bayesian approach. These results confirmed the existence of genetic diversity, genetic variability and a potential for selection in future breeding efforts involving the 45 genotypes studied.

Validating South Sudan as a Center of Origin for Coffea arabica: Implications for Conservation and Coffee Crop Improvement

Cultivated Arabica coffee outside Ethiopia is plagued by low genetic diversity, compromising disease resistance, climate resiliency and sensory potential. Access to the wider genetic diversity of this species may circumvent some of these problems. In addition to Ethiopia, South Sudan has been postulated as a center of origin for Arabica coffee, but this has never been genetically confirmed. We used simple sequence repeat (SSR) markers to assess the genetic diversity of wild and cultivated populations of Arabica coffee from the Boma Plateau in South Sudan, against farmed accessions (of wild origin) from Ethiopia, Yemen, and global cultivars. Our results not only validate Boma Plateau as part of the natural distribution and as a center of origin for Arabica coffee but also indicate that wild populations in South Sudan are genetically distinct from Ethiopian Arabica. This newly identified genetic diversity within Arabica could have the potential for crop improvement through selection and use in breeding programs. Observations and analyses show that the extent and health of the wild population of Arabica in South Sudan have declined. Urgent action should be taken to conserve (in situ and ex situ) the unique, remaining genetic diversity of wild Arabica populations in South Sudan.

Coffee (Coffea arabica L.): Methods, Objectives, and Future Strategies of Breeding in Ethiopia—Review

Coffea arabica L. belongs to the Rubiaceae family, and the genus Coffea is believed to have a primary center of origin and genetic variability in the highlands of southwestern Ethiopia. It is a vital beverage commodity across the world and a valuable export product, ranking second in international trade after petroleum. Ethiopia is among the top five major coffee-producing countries and is Africa’s leading producer. However, its full production capacity has not yet been exploited, and research efforts to reduce biotic and abiotic factors through reproduction have been extremely limited. Hence, improvement through different breeding methods is essential to overcome the constraints in its production. Thus, the objective of this study is to review the different breeding methods applied for different traits in Ethiopia. Breeding methods depend on the type and the source of traits and the final breeding objectives. The main breeding objectives are production, resistance/tolerance to diseases, and cup quality. The commonly applied breeding methods are selected and intra-specific hybridization, germplasm enhancement, and the development of improved varieties with wider adaptability. There is also a practice of crossing parental lines selected for certain desirable traits for the development of hybrid varieties. Accordingly, some promising success has been obtained. Forty-one coffee varieties have been released so far. Because conventional breeding methods are time-consuming, integrating conventional breeding methods with biotechnological techniques could have an instrumental role in the rapid development of suitable varieties for the changing climate.

Combining Ability and Molecular Marker Approach Identified Genetic Resources to Improve Agronomic Performance in Coffea arabica Breeding

Plant breeding aims to develop cultivars with good agronomic traits through gene recombination and elite genotype selection. To support Coffea arabica breeding programs and assist parent selection, molecular characterization, genetic diversity (GD) analyses, and circulating diallel studies were strategically integrated to develop new cultivars. Molecular markers were used to assess the GD of 76 candidate parents and verify the crossing of potential F1 hybrids. Based on the complementary agronomic traits and genetic distance, eight elite parents were selected for circulating diallel analysis. The parents and 12 hybrids were evaluated based on 10 morpho-agronomic traits. For each trait, the effects of general and specific combining abilities, as well as the averages of the parents, hybrids, and predicted hybrids, were estimated. Crosses that maximize the genetic gains for the main agronomic traits of C. arabica were identified. Joint analysis of phenotypic and molecular data was used to estimate the correlation between molecular GD, phenotypic diversity (PD), phenotypic mean, and combining ability. The selection of parents that optimize the allele combination for the important traits of C. arabica is discussed in detail.

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.

Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers

Akebia trifoliata (Lardizabalaceae) is an important medicinal plant with multiple pharmacological effects. However, the lack of genomic information had limited the further excavation and utilization of this plant. An initial survey of the genome A. trifoliata was performed by next-generation sequencing, and then the genome size was inferred by flow cytometry. The whole genome survey of A. trifoliata generated 61.90 Gb of sequence data with approximately 95.51 × coverage. The genome size, heterozygosity and GC content obtained by k-mer analysis were almost 648.07 Mb, 0.72% and 36.11%, respectively. The genome size calculated by flow cytometry was 685.77 Mb, which was consistent with the results of genome survey. A total of 851,957 simple sequence repeats (SSR) were identified in the A. trifoliata genome. Twenty-eight phenotypic traits and thirty pairs of SSR primers were selected for the analysis of the genetic diversity of 43 accessions of cultivated A. trifoliata. The results showed that 216 bands were generated by 30 pairs of SSR primers, of which 189 (87.5%) were polymorphic. In addition, the phenotypes and SSR markers were used for cluster analysis of 43 cultivated accessions. The results of the two clustering methods were partially consistent. The genome survey of A. trifoliata demonstrated that the genome size of this plant was about 648.07 Mb. In the present study, the size and characteristics of the genome of A. trifoliata were reported for the first time, which greatly enriched the genomic resources of A. trifoliata for the further research and utilization.