Genomic studies of biochemical compounds determining arabica coffee (Coffea arabica L.) quality

Abstract

Coffee is an important crop globally. Improving coffee quality is a primary breeding target that would benefit from understanding of trait inheritance and ancestral genetic information. However, comparatively little information exists on the genetics of quality and the relationships between wild and cultivated coffee genotypes, especially arabica coffee (Coffea arabica L.) which accounts for almost 60% of coffee production globally. The complex polyploidy genome and limited genomic information for C. arabica have impeded the progress of genetic studies. Arabica coffee is among the major organisms that do not have a reference genome. This project aimed to develop and utilise genomic resources in genetic studies of arabica coffee quality. The relationship between coffee species and the position of arabica within the Coffeeae tribe were investigated using complete chloroplast genome sequences to determine the value of these genetic resources in breeding. A draft genome sequence of arabica coffee was developed. Marker-trait associations were studied for caffeine and trigonelline, the two principal compounds known to be related to coffee quality, paving the way for developing new improved varieties with preferred levels of these compounds in the coffee beans.Chloroplast genomes of 16 coffee species were sequenced and their phylogeny constructed. Results support distinct Psilanthus and Coffea clades. It is likely that C. canephora is a hybrid that has a Psilanthus maternal genome but received much of its nuclear genome from Coffea. The maternal genomes of C. arabica and C. canephora are divergent. This result is in agreement with the fact that the chloroplast genome of arabica should be that of the maternal parent i.e. C. eugenioides. There were two species (C. humblotiana and C. tetragona) close to C. arabica and one species (P. ebracteolatus) close to C. canephora containing almost no caffeine. They could serve as important materials in arabica quality breeding and research.For the association study, 232 diverse arabica coffee accessions originating from 27 countries were harvested from the germplasm collection at CATIE (Tropical Agricultural Research and Higher Education Centre), Costa Rica. Substantial variation between genotypes was observed for bean morphology attributes. Non-volatiles including caffeine and trigonelline showed larger variation in range than was previously reported. Results of targeted analysis of 18 volatiles from 35 accessions also showed significant variation. No strong correlation was found between bean morphology and the levels of non-volatile or volatile compounds, implying that it is difficult to select for low or high non-volatile and volatile compounds based on bean physical characteristics. However, it also indicates that breeding for desirable combinations of traits (i.e. large bean size, low caffeine, high trigonelline, and favourable volatiles) is possible.ii The genome of the most popular arabica variety (K7) in Australia was sequenced. Genome assembly was performed using b...

Genetic Diversity and Population Structure Analysis of Arabica Coffee (Coffea arabica L.) Germplasm Collections in Burundi Based on DArTseq

“…This low level of genetic diversity can be attributed to two reasons. First, due to its recent origins, limited geographical distribution and self-fertilisation, C. arabica accessions generally contain fewer polymorphic sites compared to the more diverse C. canephora accessions [6,25,57,59]. The intraspecific breeding between a low number of plants that were initially distributed worldwide was reported as the source of low polymorphism for C. arabica [2,55,60,61].…”