Improving Pathogen Resistance by Exploiting Plant Susceptibility Genes in Coffee (Coffea spp.)

Abstract

Coffee (Coffea spp.) is an economically important crop widely cultivated in (sub) tropical countries worldwide. Commercial coffee production relies mainly on two related species, namely C. arabica and C. canephora. Due to their perennial growth habit, cultivation practices, and narrow genetic diversity, coffees are constantly exposed to many diseases and pests. Coffee leaf rust (Hemileia vastatrix Berk. et Br.), coffee berry disease (Colletotrichum kahawae Bridge and Waller), and coffee wilt disease (Gibberella xylarioides Heim and Saccas/Fusarium xylarioides) are the top fungal diseases affecting C. arabica and C. canephora production areas worldwide. In many regions, chemical-based control measures are widely used and are the only way to control the diseases. Developing resistant cultivars is one of the prerequisites for increasing sustainable market demand and agriculture. However, desired and required resistance traits are not always available in the gene pool. Furthermore, from other crops it is clear that dominant resistance genes introduced into varieties are not durable because of pathogen variability and the emergence of new races of the different pathogens. Utilization of altered susceptibility genes (S genes) offers a novel and alternative strategy for the breeding of durable and broad-spectrum resistance. The S gene encodes a host factor that facilitates a compatible interaction with the pathogen, and impairment of S genes leads to loss-of-susceptibility. In this review, guidelines for effective identification, characterization, and utilization of dysfunctional S genes are proposed to aid breeding activities in order to introduce durable resistance in Coffea spp. Several candidate S genes likely contributing to the susceptibility of Colletotrichum spp., Fusarium spp., and Meloidogyne spp. are discussed. With the rapid development of genetic engineering techniques, including CRISPR-associated systems, we now have the potential to accelerate the application of S genes to achieve durable resistance in coffee.

An Overview of the Mechanisms Involved in Coffee-Hemileia vastatrix Interactions: Plant and Pathogen Perspectives

“…These genetic resources opened new possibilities for MAS-driven resistance breeding in coffee, prompting the first reports of successful marker validation and selection of coffee cultivars harboring distinct loci for resistance, not only to CLR, but also to coffee berry disease (CBD) [92,93]. Other promising genomic-driven approaches to improve coffee breeding for durable and broad-spectrum resistance have been studied, such as genomic selection [94], and genomics-assisted exploitation of mutant or impaired susceptibility (S)-genes in the host plant that will lead to ''loss of susceptibility" [95].…”

Alternative plant protection strategies for tomorrow's coffee

“…Plant biotechnology is continuously expanding its highly sophisticated molecular toolbox to develop new approaches to stop pests and pathogens in their tracks. Breeding efforts by “pyramiding” (or stacking) resistance ( R ) genes within the plant host genome allows for a multifaceted defence response, inhibiting establishment and/or persistence of the threatening organism (Collinge, 2016; Collinge & Sarrocco, 2022; Cui et al, 2020; van Schie & Takken, 2014). Proof of concept for host‐induced gene silencing in an invading fungus (Nowara et al, 2010) has given rise to yet another elegant tool.…”

“…Both transgenic pyramiding R genes and HIGS are referred to as NGT and promise to offer more durable resistance as well as broad‐spectrum plant resistance compared to past breeding strategies (Barbadikar et al, 2019; Collinge & Sarrocco, 2022; Cui et al, 2020; van Schie & Takken, 2014). However, these strategies require the frequent generation of new cultivars (as is the case for wheat, barley and rice) and have yet to be implemented in commercial varieties.…”

Screening for resistance and susceptibility in some beetroot cultivars to root-knot nematode, Meloidogyne javanica

“…Natural resistance is frequently attributable to specific genes that might segregate within the host species. On the other hand, the nematode is unable to reproduce on non-host species or resistant cultivars due to lack of host traits essential for parasitism (Cui et al, 2020;Alekcevetch et al, 2021). Therefore, this research will help to identify the resistant cultivar and reduce the nematode population below the economic threshold; both are sustainable and environmentally compatible.…”