Evolutionary rate variation among genes involved in galactomannan biosynthesis in Coffea canephora

A Systematic Mapping Study of Coffee Quality throughout the Production-to-Consumer Chain

Coffee is one of the most consumed beverages in the world and is crucial in the economy of many developing countries. The search to improve coffee quality comes from many fronts, as do the many ways to measure quality and the factors that affect it. Several techniques are used to measure the different metrics to assess coffee quality, across different types of coffee samples and species, and throughout the entire process from farm to cup. In this work, we conducted a systematic mapping study of 1,470 articles to identify the aspects of quality that are the most important in the scientific literature to evaluate coffee throughout the processing chain. The study revealed that cup quality and biochemical composition are the most researched quality attributes. The main objective of the reviewed studies is the correlation between different quality measurements. The most used techniques are the analytical chemistry methods. The most studied species is Coffea arabica. The most used sample presentation is green coffee. The postharvest stage is the most researched, in which quality control receives more attention. In the preharvest stage, management practices stand out. Finally, the most used type of research was the evaluation research.

Revealing Distinctions in Genetic Diversity and Adaptive Evolution Between Two Varieties of Camellia sinensis by Whole-Genome Resequencing

Camellia sinensis var. sinensis (CSS) and C. sinensis var. assamica (CSA) are the two most economically important tea varieties. They have different characteristics and geographical distribution. Their genetic diversity and differentiation are unclear. Here, we identified 18,903,625 single nucleotide polymorphisms (SNPs) and 7,314,133 insertion-deletion mutations (indels) by whole-genome resequencing of 30 cultivated and three wild related species. Population structure and phylogenetic tree analyses divided the cultivated accessions into CSS and CSA containing 6,440,419 and 6,176,510 unique variations, respectively. The CSS subgroup possessed higher genetic diversity and was enriched for rare alleles. The CSA subgroup had more non-synonymous mutations and might have experienced a greater degree of balancing selection. The evolution rate (dN/dS) and KEGG enrichment indicated that genes involved in the synthesis and metabolism of flavor substances were positively selected in both CSS and CSA subpopulations. However, there are extensive genome differentiation regions (2959 bins and approximately 148 M in size) between the two subgroups. Compared with CSA (141 selected regions containing 124 genes), the CSS subgroup (830 selected regions containing 687 genes) displayed more selection regions potentially related to environmental adaptability. Fifty-three pairs of polymorphic indel markers were developed. Some markers were located in hormone-related genes with distinct alleles in the two cultivated subgroups. These identified variations and selected regions provide clues for the differentiation and adaptive evolution of tea varieties. The newly developed indel markers will be valuable in further genetic research on tea plants.