Excessive use of chemical fertilizers deteriorates the soil environment and limits the normal growth of Arabica coffee trees. In order to identify the optimal coupling mode of chemical fertilizer application and biomass return that enhances the soil ecological environment and promotes the photosynthetic efficiency of Arabica coffee, this study investigated the impacts of three levels of inorganic fertilizers (F_L: 360 kg·ha⁻¹, F_M: 720 kg·ha⁻¹, and F_H: 1080 kg·ha⁻¹) and three types of coffee husk returning methods (C_B: coffee husk biochar, C_C: coffee husk compost, C_A: coffee husk ash) on the soil fertility, microbial amount, enzyme activity, and photosynthetic characteristics of the Arabica coffee root zone. The entropy weight-TOPSIS method was employed to evaluate the comprehensive benefits. The results showed that F_M had the biggest effect on improving soil fertility, microorganisms, and enzyme activities compared with F_L and F_H. Moreover, compared to C_A, C_C significantly increased soil organic carbon, organic matter, and total nitrogen content. C_C significantly enhanced the activities of soil phosphatase and urease, respectively, by 29.84% and 96.00%, and significantly increased the amount of bacteria, fungi, and actinomycetes by 62.15%, 68.42%, and 46.21%, respectively. The net photosynthetic rate (Pn), transpiration rate (Tr), and stomatal conductance (Gs) of F_MC_C were significantly higher than those of other treatments. The comprehensive benefit evaluation of the soil environment and photosynthetic characteristics by the entropy weight-TOPSIS method ranked F_MC_C first. Therefore, F_MC_C was the optimal coupling mode for fertilizer application and the coffee husk returning method. The findings of this study not only provide scientific guidance for fertilizing Arabica coffee but also clarify the proper approach to returning coffee husk to the field, thereby improving soil ecology and promoting green and efficient production of specialty crops.

Coffea arabica L. (C. arabica) is an economically important agricultural crop and the most popular beverage worldwide. To analyze genetic diversity and provide genetic resources for the selection and breeding of superior varieties of C. arabica, 61 cultivated Arabica coffee accessions were analyzed in the study, including 12 resequencing accessions from previous research and 49 accessions that were resequenced in this study. Single nucleotide polymorphisms (SNPs) and insertion–deletions (InDels) were statistically analyzed. Based on SNP variations, a genetic structure analysis, phylogenetic tree construction, and principal component analysis were performed for the 61 coffee accessions. The results showed that a total of 805.46 Gb of raw whole-genome resequencing data was obtained from the 61 coffee accessions, with 781.29 Gb of high-quality sequencing data after filtering. In total, 7,013,820 SNP sites and 1,074,329 InDel sites were detected. The average sequencing depth ranged from 6.69× to 19.35×, and the coverage ranged from 85.49% to 96.43%. The population genetic structure and phylogenetic analysis of the 61 coffee accessions revealed four lineages, suggesting that they had at least four ancestral genetic components. Catimor exhibited the highest genetic diversity, while Geisha had the lowest genetic diversity. The selective sweep analysis indicated that among the selected genes in Catimor, disease-resistance genes were significantly more numerous than in other coffee varieties. The genome resequencing data and genetic markers identified from the 61 cultivated Arabica coffee materials provided insights into the genetic variation in Arabica coffee germplasm and facilitated extensive genetic research.

Background: The Orah mandarin is an economically important variety of Citrus reticulata for citrus growers in Yunnan Province, China. Generally, the fruit peel is smooth, an attractive feature for consumer preferences. Recently, rough peels have been observed in several orchards, making the fruit aesthetically less desirable. Little is known about the mechanism of rough skin development. Methods: In this study, we used global metabolomics and a comparative transcriptomic approach to characterize the differences between smooth (CK) and rough (CP) Orah mandarin peels. Results: Our results indicate that CP fruits have a significantly larger diameter, peel weight and thickness, total soluble solids, and titratable acid content compared to CK. Metabolomic analysis detected 810 metabolites, of which 192 were differentially accumulated in CP and CK. CP is characterized by higher levels of flavonoids, amino acids and derivatives, terpenoids, and alkaloids. We also report nine compounds detected exclusively in CP, including dambonitol, 3-methyl-L-histidine, deacetylnomilinic acid, obacunoic acid, and 6-O-acetylarbutin. The transcriptome results showed that the expression of genes enriched in flavonoids, lipid, and amino acid metabolism and related pathways were consistent with the metabolome profiles. We also discuss the possible involvement of phytohormones in peel roughening. Conclusions: Overall, we present, for the first time, a detailed comparative metabolome and transcriptome profile in smooth and rough Orah mandarin peels. Our data and discussion highlight the potential mechanisms and provide a theoretical basis for the improvement of rough peel Orah mandarins.