Biology subjects

Marelli, J.-P.

Publications and source records attributed to Marelli, J.-P..

6 recordsLinked to original sources

bioRxiv2026

Evaluating cacao pod resistance to black pod disease caused by three Phytophthora species

Black pod disease is a major threat to global cacao (Theobroma cacao L.) production. It is caused by multiple Phytophthora species with geographic ranges from regionally restricted to pantropical, and developing resistant cultivars requires screening against the diversity of these pathogens. This study evaluated the response of 25 cacao clones to 13 isolates of P. palmivora (eight), P. megakarya (two), and P. theobromicola (three) by nonwounding inoculation of detached pods. Lesion size and lesion expansion status were evaluated 4 days after inoculation. The linear mixed model included 178 combinations among 17 clones and 12 isolates, each represented by at least two biological replicate pods. Lesion size differed among clones (F(16, 449.2) = 25.16) and among isolates (F(11, 416.0) = 32.90), and the clone by isolate interaction was significant (F(150, 465.4) = 1.72; all P < 0.001). PENTAGONA-17 had the smallest estimated marginal lesion size (9.3 mm) and fitted values of 3.8 to 16.9 mm across 11 isolates representing all three species. ARF-31, ICS-47, POUND-7, and PMCT-73 had the next four smallest estimates, whereas NA-246 had the largest (36.7 mm). Isolate estimates varied more than fourfold, from 9.6 to 42.0 mm. Despite a marginal estimate of 12.9 mm, POUND-7 had a fitted estimate of 49.2 mm with P. megakarya GH34. The probability of lesion expansion also differed among clones and isolates (both P < 0.001). Together, these findings identify candidates for further resistance evaluation and show that multi-isolate screening provides a stronger basis for selecting materials for black pod resistance breeding.

plant biology↗

bioRxiv2025

Stable Inheritance of Transgene and Yellow Fluorescent Protein Gene Expression in Progeny of Transgenic Cacao (Theobroma cacao) Plants

Genetic engineering tools have the potential to rapidly and precisely improve the genome of slow-to-breed cacao. We previously developed an efficient protocol for transforming cacao using cotyledonary explants derived from secondary somatic embryos via Agrobacterium tumefaciens. In this study, we demonstrate that our transformation protocol is successful in elite cultivars, INIAPG-038 and Matina 1-6, producing fertile seeds with stable visual marker inheritance regardless of whether the transgenic plants were used as the pollen or ovule donor. Three vectors were used in the transformations, each containing genes for enhanced yellow fluorescent protein (eyfp) and neomycin phosphotransferase II (nptII). Three transgenic INIAPG-038 events and one transgenic Matina 1-6 event were used to evaluate seed fertility and the stability of transgene inheritance in cacao seeds and plants. The T1 progeny of these four transgenic events were analyzed for YFP expression and transgene presence. YFP expression segregated at a 1:1 ratio in all events when the transgenic plants were crossed with non-transgenic plants, while a 3:1 segregation was observed when transgenic events were crossed with each other. The transgenic plants exhibited a normal phenotype compared to non-transgenic control plants, producing seeds with a 97% germination rate.

plant biology↗

bioRxiv2025

Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires

Phytophthora theobromicola is an emerging cacao pathogen recently identified in Brazil as an aggressive agent of black pod rot. We generated genome assemblies for two P. theobromicola isolates using long-read sequencing and five additional isolates using short reads. Comparative analysis revealed a genome size and predicted gene content comparable to P. citrophthora, a closely related species with a broad host range that includes both citrus and cacao. An intraspecies sequence-graph analysis revealed a highly dynamic genome structure with high proportion of variable effectors. Syntenic orthology analysis across 13 Phytophthora species identified orthologous gene groups conserved only in cacao pathogens and others specific to P. theobromicola. RxLR effectors and CAZymes were particularly enriched among lineage-specific syntenic groups, with RxLRs preferentially located near transposable elements and within gene-sparse, repeat-rich regions. Transcriptome analysis of infected cacao tissues showed that 88% of predicted effectors were expressed, with pods exhibiting the highest number of upregulated genes. Notably, several RxLRs classified as P. theobromicola-specific syntenic orthologs were highly expressed in infected tissues, suggesting that these lineage-specific effectors may play key roles in host-pathogen interactions unique to cacao. Together, our findings highlight the dynamic architecture and functional plasticity of the P. theobromicola genome, providing foundational insights into its virulence strategies and supporting future studies on host adaptation and effector evolution in emerging cacao pathogens.

genomics↗

bioRxiv2020

Screening of Cultivars for Tissue Culture Response and Establishment of Genetic Transformation in a High-yielding and Disease-resistant Cultivar of Theobroma cacao

A highly efficient transformation protocol is a prerequisite to developing genetically modified and genome-edited crops. A tissue culture system spanning the initiation of floral material to the regeneration of plantlets into soil has been tested and improved in cacao. Fourteen cultivars were screened for their tissue culture response and transfer DNA (T-DNA) delivery efficiency via Agrobacterium. These key factors were used to determine the genetic transformability of various cultivars. The high-yielding, disease-resistant cultivar INIAPG-038 was selected for stable transformation and the method was further optimized. Multiple transgenic events were produced using two vectors containing both yellow fluorescent protein and neomycin phosphotransferase II genes. A two-fold strategy to improve both T-DNA delivery and secondary somatic embryogenesis rates was conducted to improve overall transformation frequency. The use of Agrobacterium strain AGL1 and cotyledon tissue derived from immature somatic embryos ranging in size between 4-10 mm resulted in the highest T-DNA delivery efficiency. Furthermore, the use of higher concentrations of basal salts and cupric sulfate in secondary callus growth medium increased the percentage of explants producing greater than ten embryos by 504% and 443%, respectively. Consequently, an optimal combination of all these components resulted in a successful transformation of INIAPG-038 with 3.7% frequency at the T0 plant level. Grafting transgenic scions with undeveloped roots to wild-type seedlings with strong, healthy roots helped make plantlets survive and facilitated quick transplantation to the soil. The present methods can be applied to improve tissue culture response and transformation frequency in other cacao cultivars. Key messageTissue culture and genetic transformation methods for a high-yielding, disease-resistant cultivar of Theobroma cacao were established while factors affecting T-DNA delivery and somatic embryogenesis were identified.

plant biology↗

bioRxiv2019

The unique genome architecture of the devastating West African cacao black pod pathogen Phytophthora megakarya

Phytophthora megakarya (Pmeg) and P. palmivora (Ppal) are oomycete pathogens that cause black pod rot of cacao (Theobroma cacao), the most economically important disease on cacao globally. While Ppal is a cosmopolitan pathogen, Pmeg, which is more aggressive on cacao than Ppal, has been reported only in West and Central Africa where it has been spreading and devastating cacao farms since the 1950s. In this study, we reconstructed the complete diploid genomes of multiple isolates of both species using single-molecule sequencing. Thirty-one additional genotypes were sequenced to analyze inter- and intra-species genomic diversity. These resources make it possible to better understand the molecular basis of virulence differences in closely related and consequential pathogens and study their evolutionary history. The Pmeg genome is exceptionally large (222 Mbp) and nearly twice the size Ppal (135 Mbp) and most known Phytophthora species ([~]100 Mbp on average). We show that the genomes of both species recently expanded by independent whole-genome duplications (WGD). WGD and the dramatic transposable element associated expansion of a few gene families led to the exceptionally large genome and transcriptome of Pmeg and the diversification of virulence-related genes including secreted RxLR effectors. Finally, this study provides evidence of adaptive evolution among well-known effectors and discusses the implications of effector expansion and diversification.

genomics↗

bioRxiv2018

QTL mapping and identification of corresponding genomic regions for black pod disease resistance to three Phytophthora species in Theobroma cacao L.

The cacao tree (Theobroma cacao L.) is a species of great importance because cacao beans are the raw material used in the production of chocolate. However, the economic success of cacao is largely limited by important diseases such as black pod, which is responsible for losses of up to 30-40% of the global cacao harvest. The discovery of resistance genes could extensively reduce these losses. Therefore, the aims of this study were to construct an integrated multipoint genetic map, align polymorphisms against the available cacao genome, and identify quantitative trait loci (QTLs) associated with resistance to black pod disease in cacao. The genetic map had a total length of 956.41 cM and included 186 simple sequence repeat (SSR) markers distributed among 10 linkage groups. The physical \"in silico\" map covered more than 200 Mb of the cacao genome. Based on the mixed model predicted means of Phytophthora evaluation, a total of 6 QTLs were detected for Phytophthora palmivora (1 QTL), Phytophthora citrophthora (1 QTL), and Phytophthora capsici (4 QTLs). Approximately 1.77% to 3.29% of the phenotypic variation could be explained by the mapped QTLs. Several SSR marker-flanking regions containing mapped QTLs were located in proximity to disease regions. The greatest number of resistance genes was detected in linkage group 6, which provides strong evidence for a QTL. This joint analysis involving multipoint and mixed-model approaches may provide a potentially promising technique for detecting genes resistant to black pod and could be very useful for future studies in cacao breeding.

plant biology↗