Characterising the interactions between major nematode pathogens and the host coffee plant

Coffee is a hugely significant agricultural crop, produced by millions of growers worldwide. Production is threatened by numerous pests, pathogens, and increasingly unpredictable climactic conditions such as prolonged periods of drought. Nematode pests, distributed on a global scale, damage production by causing reduced coffee bean yield, and can cause plant death. The work described here investigates the interaction between the two major nematode species Meloidogyne incognita and Pratylenchus coffeae and commercially grown coffee cultivars. Various aspects of plant health under infection were measured in order to characterise the tolerance status of each cultivar to the two nematode species. The effect of drought on these cultivars was also investigated. Variable tolerances to infection and drought were observed between cultivars through photosynthetic rate, fresh weight and leaf water content measurements. Robusta cultivars exhibited strong resistance to nematode infection and reproduction in roots. Drought stress was observed to be a greater limiting factor to plant growth than nematode infection. The Robusta cultivar FRT49 and Arabica both showed stable photosynthetic rate measurements under infection and drought treatments, implying good performance in the field under these stresses. Stronger photosynthetic performance at lower soil moisture was seen in FRT79, suggesting that this cultivar may be useful in selective breeding for a drought tolerant rootstock. Reduced P. coffeae populations in FRT65 roots under drought conditions also suggest that this cultivar may have application in limiting the proliferation of this species in the field, although at the cost of coffee bean yield. The observations made here into the early stages of nematode infection and coffee plant development can be used to inform the application of specific cultivars in breeding programs aimed at producing new nematode and drought tolerant rootstock material

Influence of climate change and variability on Coffea arabica in the East African highlands

A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy (Agroclimatology) at the University of Witwatersrand, 2017.Plant development is inherently linked to meteorological variability. The phenology, distribution and production of crops and wild relatives has already altered in response to climate change. Recent years have produced the warmest mean annual global temperatures since 1880, with 2016 setting the highest record thus far. Such profound changes have sparked investigations into the impact of temperature and rainfall on crop development, particularly those with profound economic importance such as coffee (C. arabica). The crop is a fundamental source of income for smallholder farming communities and governments throughout the tropical highlands. However, the impact of climate change on C. arabica has yet to be quantified using empirical data in East Africa, leaving uncertainty in the cultivable future of the crop. Therefore, the objective of this thesis is to investigate the influence of climate change and variability on C. arabica yields and phenology in East Africa. Using a spatio-temporal approach, trends and relationships between coffee performance and meteorological variables were analysed at different scales and time periods ranging from the macroclimatic national scale (49 year), to the meso- and microclimatic farm level (3 year) scale, and finally to the microclimatic canopy and leaf level (hourly) scales. Data from all three climatic continua reveal for the first time that temperatures, and particularly rapidly advancing night time temperatures, are having a substantial negative impact on C. arabica yields. Forecasting models based on these biophysical relationships indicate that by the year 2050, smallholder farmers would on average harvest approximately 50% of the yield they are achieving today. Warming night time temperatures are also responsible for advancing ripening and harvest phenology. As a result, bean filling and development time is reduced, thereby potentially resulting in lower quality coffee. Trends in precipitation do not appear to have any substantial impact on C. arabica yields or harvest phenology, however, it is proposed that rainfall would act synergistically with temperatures to influence plant development and other phenological phases such as flowering. Finally, thermography is introduced as a novel complementary technique to rapidly analyse the suitability of different agroecological systems on coffee physiology at the leaf level. High temporal resolution (hourly) data, illustrate the success of the method in variable meteorological and environmental conditions. The findings contribute to advancing the protocol for use at the canopy and plantation level on coffee, so that appropriate microenvironment designs and adaptation mechanisms be put in place to accommodate climatic change. Avoiding increments in night time temperatures is key to maintaining or improving yields and fruiting development. Farming at higher altitudes and novel agroforestry systems may assist in achieving lower night time temperatures. Importantly, data reveal that careful analysis of various cropping systems, particularly at lower altitudes, is critical for providing suitable microenvironments for the crop.XL201

The Interactions of Root-Knot Nematodes and Coffee

Coffee is a major crop that supports the economy of over 60 countries, many of which are developing nations. A major detriment to coffee production is damage caused by plant parasitic nematodes. The most damaging species is the root-knot nematode, Meloidogyne spp. Many conventional methods to control plant parasitic nematodes can be inefficient and costly. This study aimed to characterise the molecular mechanisms that drive interactions of plant parasitic nematodes and Robusta coffee (Coffea canephora), including immune and defence responses of coffee to root-knot nematodes, and behavioural response of the nematode to root exudate of coffee, with a view to the longer-term development of improved nematode control strategies and technologies. The Robusta coffee varieties tested showed a differential physiological response to the infection of root-knot nematodes, as well as showing subtle differences in susceptibility to attack by nematodes. Contrasting varieties in susceptibility and tolerance to nematode attack were then used to compare the transcriptomic changes induced in root and leaf tissue following infection by root-knot nematodes. Genes involved in pathogen recognition, general defence and hypersensitive responses were revealed as key mediators of the Robusta immune response to plant parasitic nematodes. Cell-wall-regulation in coffee was identified as a mechanism that could provide protection against root knot nematode infection. Genes and gene pathways that have been identified could be utilised to develop coffee varieties that have improved protection against plant parasitic nematodes. They may also be used as molecular identifiers of innate tolerance against plant parasitic nematodes. An alternative to identifying and manipulating genetic components of coffee for nematode control would be to disrupt parasitic behaviours of root-knot nematodes to inhibit invasion and reproduction within the crop. Serotonin was immunolocalised within infective stages of root-knot nematodes and established as a key neurotransmitter mediating behaviours essential for root-knot nematode pathogenicity, including chemosensation and stylet function for invasion and feeding. Disrupting serotonin biosynthesis, using established serotonergic chemical inhibitors, also decreased the infective capability of root-knot nematodes. Serotonergic molecular components are suggested that could be targets for root-knot nematode control. Integrating novel genomic controls discussed in this project would provide crop protection against plant parasitic nematodes in coffee and reduce yield losses caused by the pathogen

Shade and Altitude Implications on the Physical and Chemical Attributes of Green Coffee Beans from Gorongosa Mountain, Mozambique

Coffea arabica L. is as a tropical crop that can be grown under monocrop or agroforestry (AFS) systems, usually at altitudes greater than 600 m, with suitable environmental conditions to bean quality. This study aimed to assess the effect of altitude (650, 825, and 935 m) and light conditions (deep shade—DS, and moderate shade—MS provided by native trees, and full Sun—FS) on the physical and chemical attributes of green coffee beans produced in the Gorongosa Mountain. Regardless of altitude, light conditions (mainly MS and FS) scarcely affected most of the studied physical and chemical attributes. Among the few exceptions in physical attributes, bean mass tended to lower values under FS in all three altitudes, whereas bean density increased under FS at 650 m. As regards the chemical compound contents, sporadic changes were found. The rises in trigonelline (MS and FS at 935 m), soluble sugars (FS at 935 m), and the decline in p-coumaric acid (MS and FS at 825 m), may indicate an improved sensory profile, but the rise in FQAs (FS at 825 m) could have a negative impact. These results highlight a relevant uncertainty of the quality changes of the obtained bean. Altitude (from 650 to 935 m) extended the fruit maturation period by four weeks, and altered a larger number of bean attributes. Among physical traits, the average sieve (consistent tendency), bean commercial homogeneity, mass, and density increased at 935 m, whereas the bean became less yellowish and brighter at 825 and 935 m (b*, C* colour attributes), pointing to good bean trade quality, usually as compared with beans from 650 m. Furthermore, at 935 m trigonelline and 5-CQA (MS and FS) increased, whereas FQAs and diCQAs isomers declined (in all light conditions). Altogether, these changes likely contributed to improve the sensory cup quality. Caffeine and p-coumaric acid showed mostly inconsistent variations. Overall, light conditions (FS, MS, or DS) did not greatly and consistently altered bean physical and chemical attributes, whereas altitude (likely associated with lower temperature, greater water availability (rainfall/fog), and extended maturation period) was a major driver for bean changes and improved qualityinfo:eu-repo/semantics/publishedVersio

Precision Techniques and Agriculture 4.0 Technologies to Promote Sustainability in the Coffee Sector: State of the Art, Challenges and Future Trends

Precision Agriculture (PA) and Agriculture 4.0 (A4.0) have been widely discussed as a medium to address the challenges related to agricultural production. In this research, we present a Systematic Literature Review (SLR) supported by a Bibliometric Performance and Network Analysis (BPNA) of the use of A4.0 technologies and PA techniques in the coffee sector. To perform the SLR, 87 documents published since 2011 were extracted from the Scopus and Web of Science databases and processed through the Preferred Reporting Items for Systematic reviews and Meta-Analyzes (PRISMA) protocol. The BPNA was carried out to identify the strategic themes in the field of study. The results present 23 clusters with different levels of development and maturity. We also discovered and presented the thematic network structure of the most used A4.0 technologies in the coffee sector. Our findings shows that Internet of Things, Machine Learning and geostatistics are the most used technologies in the coffee sector, we also present the main challenges and trends related to technological adoption in coffee systems. We believe that the demonstrated results have the potential to be considered by researchers in future works and decision making related to the field of study