Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process

Genetic analyses and dispersal patterns unveil the Amazonian origin of guava domestication

Guava (Psidium guajava L.) is a semi-domesticated fruit tree of moderate importance in the Neotropics, utilized for millennia due to its nutritional and medicinal benefits, but its origin of domestication remains unknown. In this study, we examine genetic diversity and population structure in 215 plants from 11 countries in Mesoamerica, the Andes, and Amazonia using 25 nuclear microsatellite loci to propose an origin of domestication. Genetic analyses reveal one gene pool in Mesoamerica (Mexico) and four in South America (Brazilian Amazonia, Peruvian Amazonia and Andes, and Colombia), indicating greater differentiation among localities, possibly due to isolation between guava populations, particularly in the Amazonian and Andean regions. Moreover, Mesoamerican populations show high genetic diversity, with moderate genetic structure due to gene flow from northern South American populations. Dispersal scenarios suggest that Brazilian Amazonia is the probable origin of guava domestication, spreading from there to the Peruvian Andes, northern South America, Central America, and Mexico. These findings present the first evidence of guava domestication in the Americas, contributing to a deeper understanding of its evolutionary history.

Occurrence of heavy metals coupled with elevated levels of essential elements in chocolates: Health risk assessment

The presence of contaminants in cacao-derived products, especially in chocolates, has raised concerns regarding food safety and human health. The study assessed the concentration variation of 16 elements in 155 chocolate samples from the US market by cacao content and country of geographic origin. The study further examined the potential health risks posed by toxic metals and determined the contribution of essential elements to the Daily Recommended Intake (DRI), estimated based on an ounce (∼28.4 g) of daily chocolate consumption. Dark chocolates with ≥50 % cacao exhibited consecutively increasing mean levels from 1.2 to 391 µg/kg for U, Tl, Th, As, Pb, Se, Cd, and Co. Similarly, Ni, Sr, Cu, Mn, Zn, Fe, Ca, and Mg had mean concentrations from 4.0 to 1890 mg/kg. Dark chocolates sourced from Central and South America exhibited the highest mean levels of Cd, and South America samples also contained elevated Pb, whereas those from West Africa and Asia had low Cd and Pb, respectively. Cacao contents showed increasingly strong association with Cd, Co, Mn, Sr, Ni, Cu, Zn, and Mg (r = 0.60-0.84), and moderately with Se, Fe, As, and Tl (r = 0.35-0.49), indicating these elements are primarily derived from cacao beans. Weak association of cacao contents with Pb, Th, and U levels (r < 0.25), indicates post-harvest contaminations. Hazard Quotient (HQ) > 1 was found only for Cd in 4 dark chocolates, and Hazard Index (HI) > 1 for cumulative risk of Cd, Pb, Ni, As, and U was found in 33 dark chocolates, indicating potential non-carcinogenic risks for 15 kg children but none for 70 kg adults. Dark chocolate also substantially contributed to 47-95 % of the DRI of Cu for children and 50 % for adults. Dark chocolates also provided notable Fe, Mn, Mg, and Zn contributions to the DRI. These essential elements are recognized to reduce the bioavailability of toxic metals such as Cd, Pb, or Ni, thereby potentially lowering associated health risks. This study informs consumers, food industries, and regulatory agencies to target cacao origins or chocolate brands with lower toxic metal contents for food safety and minimizing adverse health effects.

The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L

BACKGROUND

Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate industry. However, the long generation time and difficulties associated with breeding a tropical tree crop have limited the progress of breeders to develop high-yielding disease-resistant varieties. Development of marker-assisted breeding methods for cacao requires discovery of genomic regions and specific alleles of genes encoding important traits of interest. To accelerate gene discovery, we developed a gene atlas composed of a large dataset of replicated transcriptomes with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao.

RESULTS

We describe the creation of the Cacao Transcriptome Atlas, its global characterization and define sets of genes co-regulated in highly organ- and temporally-specific manners. RNAs were extracted and transcriptomes sequenced from 123 different tissues and stages of development representing major organs and developmental stages of the cacao lifecycle. In addition, several experimental treatments and time courses were performed to measure gene expression in tissues responding to biotic and abiotic stressors. Samples were collected in replicates (3-5) to enable statistical analysis of gene expression levels for a total of 390 transcriptomes. To promote wide use of these data, all raw sequencing data, expression read mapping matrices, scripts, and other information used to create the resource are freely available online. We verified our atlas by analyzing the expression of genes with known functions and expression patterns in Arabidopsis (ACT7, LEA19, AGL16, TIP13, LHY, MYB2) and found their expression profiles to be generally similar between both species. We also successfully identified tissue-specific genes at two thresholds in many tissue types represented and a set of genes highly conserved across all tissues.

CONCLUSION

The Cacao Gene Atlas consists of a gene expression browser with graphical user interface and open access to raw sequencing data files as well as the unnormalized and CPM normalized read count data mapped to several cacao genomes. The gene atlas is a publicly available resource to allow rapid mining of cacao gene expression profiles. We hope this resource will be used to help accelerate the discovery of important genes for key cacao traits such as disease resistance and contribute to the breeding of elite varieties to help farmers increase yields.

Comparing the performances of SSR and SNP markers for population analysis in Theobroma cacao L., as alternative approach to validate a new ddRADseq protocol for cacao genotyping

Proper cacao (Theobroma cacao L.) plant genotyping is mandatory for the conservation and use of the species genetic resources. A set of 15 international standard SSR markers was assumed as universal cacao genotyping system. Recently, different SNPs and SNP genotyping techniques have been exploited in cacao. However, a consensus on which to use has not been reached yet, driving the search for new approaches. To validate a new ddRADseq protocol for cacao genotyping, we compared the performances for population analysis of a dataset with 7,880 SNPs obtained from ddRADseq and the genotypic data from the aforementioned SSR set, using 158 cacao plants from productive farms and gene bank. Four genetic groups were identified with STRUCTURE and ADMIXTURE softwares using SSR and SNP data, respectively. Similarities of cacao ancestries among these groups allowed the identification of analogous pairs of groups of individuals, referred to as: G1SSR/G1SNP, G2SSR/G2SNP, G3SSR/G3SNP, G4SSR/G4SNP, whether SSRs or SNPs were used. Both marker systems identified Amelonado and Criollo as the most abundant cacao ancestries among all samples. Genetic distance matrices from both data types were significantly similar to each other according to Mantel test (p < 0.0001). PCoA and UPGMA clustering mostly confirmed the identified genetic groups. AMOVA and FST pairwise comparison revealed a moderate to very large genetic differentiation among identified groups from SSR and SNP data. Genetic diversity parameters from SSR (Hobs = 0.616, Hexp = 0.524 and PIC = 0.544) were higher than that from SNP data (0.288, 0.264, 0.230). In both cases, genetic groups carrying the highest Amelonado proportion (G1SSR and G1SNP) had the lowest genetic diversity parameters among the identified groups. The high congruence among population analysis results using both systems validated the ddRADseq protocol employed for cacao SNP genotyping. These results could provide new ways for developing a universal SNP-based genotyping system very much needed for cacao genetic studies.

Three de novo assembled wild cacao genomes from the Upper Amazon

Theobroma cacao, the chocolate tree, is indigenous to the Amazon basin, the greatest biodiversity hotspot on earth. Recent advancement in plant genomics highlights the importance of de novo sequencing of multiple reference genomes to capture the genome diversity present in different cacao populations. In this study, three high-quality chromosome-level genomes of wild cacao were constructed, de novo assembled with HiFi long reads sequencing, and scaffolded using a reference-free strategy. These genomes represent the three most important genetic clusters of cacao trees from the Upper Amazon region. The three wild cacao genomes were compared with two reference genomes of domesticated cacao. The five cacao genetic clusters were inferred to have diverged in the early and middle Pleistocene period, approximately 1.83-0.69 million years ago. The results shown here serve as an example of understanding how the Amazonian biodiversity was developed. The three wild cacao genomes provide valuable resources for studying genetic diversity and advancing genetic improvement of this species.

Using ddRADseq to assess the genetic diversity of in-farm and gene bank cacao resources in the Baracoa region, eastern Cuba, for use and conservation purposes

The Baracoa region, eastern Cuba, hosts around 80 % of the country cacao (Theobroma cacao L.) plantations. Cacao plants in farms are diverse in origin and propagation, with grafted and hybrid plants being the more common ones. Less frequent are plants from cuttings, TSH progeny, and traditional Cuban cacao. A national cacao gene bank is also present in Baracoa, with 282 accessions either prospected in Cuba or introduced from other countries. A breeding program associated with the gene bank started in the 1990s based on agro-morphological descriptors. The genetic diversity of cacao resources in Baracoa has been poorly described, except for traditional Cuban cacao, affecting the proper development of the breeding program and the cacao planting policies in the region. To assess the population structure and genetic diversity of cacao resources in Baracoa region, we genotyped plants from both cacao gene bank (CG) and cacao farms (CF) applying a new ddRADseq protocol for cacao. After data processing, two SNPs datasets containing 11,425 and 6,481 high-quality SNPs were generated with 238 CG and 135 CF plants, respectively. SNPs were unevenly distributed along the 10 cacao chromosomes and laid mainly in noncoding regions of the genome. Population structure analysis with these SNP datasets identified seven and four genetic groups in CG and CF samples, respectively. Clustering using UPGMA and principal component analysis mostly agree with population structure results. Amelonado was the predominant cacao ancestry, accounting for 49.22 % (CG) and 57.73 % (CF) of the total. Criollo, Contamana, Iquitos, and Nanay ancestries were detected in both CG and CF samples, while Nacional and Marañon backgrounds were only identified in CG. Genetic differentiation among CG (FST ranging from 0.071 to 0.407) was higher than among CF genetic groups (FST: 0.093-0.282). Genetic diversity parameters showed similar values for CG and CF samples. The CG and CF genetic groups with the lowest genetic diversity parameters had the highest proportion of Amelonado ancestry. These results should contribute to reinforcing the ongoing breeding program and updating the planting policies on cacao farms, with an impact on the social and economic life of the region.

A combination of conserved and diverged responses underlies Theobroma cacao's defense response to Phytophthora palmivora

BACKGROUND

Plants have complex and dynamic immune systems that have evolved to resist pathogens. Humans have worked to enhance these defenses in crops through breeding. However, many crops harbor only a fraction of the genetic diversity present in wild relatives. Increased utilization of diverse germplasm to search for desirable traits, such as disease resistance, is therefore a valuable step towards breeding crops that are adapted to both current and emerging threats. Here, we examine diversity of defense responses across four populations of the long-generation tree crop Theobroma cacao L., as well as four non-cacao Theobroma species, with the goal of identifying genetic elements essential for protection against the oomycete pathogen Phytophthora palmivora.

RESULTS

We began by creating a new, highly contiguous genome assembly for the P. palmivora-resistant genotype SCA 6 (Additional file 1: Tables S1-S5), deposited in GenBank under accessions CP139290-CP139299. We then used this high-quality assembly to combine RNA and whole-genome sequencing data to discover several genes and pathways associated with resistance. Many of these are unique, i.e., differentially regulated in only one of the four populations (diverged 40 k-900 k generations). Among the pathways shared across all populations is phenylpropanoid biosynthesis, a metabolic pathway with well-documented roles in plant defense. One gene in this pathway, caffeoyl shikimate esterase (CSE), was upregulated across all four populations following pathogen treatment, indicating its broad importance for cacao's defense response. Further experimental evidence suggests this gene hydrolyzes caffeoyl shikimate to create caffeic acid, an antimicrobial compound and known inhibitor of Phytophthora spp.

CONCLUSIONS

Our results indicate most expression variation associated with resistance is unique to populations. Moreover, our findings demonstrate the value of using a broad sample of evolutionarily diverged populations for revealing the genetic bases of cacao resistance to P. palmivora. This approach has promise for further revealing and harnessing valuable genetic resources in this and other long-generation plants.

Molecular, biochemical, and sensorial characterization of cocoa (Theobroma cacao L.) beans: A methodological pathway for the identification of new regional materials with outstanding profiles

Cocoa is an economically important product in Colombia. On-farm germplasm evaluations enable the selection of superior genotypes for propagation and distribution across the country. This study examined 12 cocoa samples from Antioquia along with five reference materials, employing 96 single nucleotide polymorphism (SNP) markers. Furthermore, these genetic findings were correlated with physical, chemical, and sensory attributes. Primary coordinate analysis revealed that the majority of samples were hybrids derived from five original germplasm pools, including Criollo, Amelonado, and three Upper Amazon Forastero cocoas. The integral profile of the 12 selected materials was classified into Modern Criollo (Rodriguez-Medina et al., 2019) [3], Forasteros (Rodriguez-Medina et al., 2019) [3], and Trinitarios (Borja Fajardo et al., 2022) [6]. Three key factors were identified to best account for the sample classification: type of variety, functional properties, and quality.

3D pollination biology using micro-computed tomography and geometric morphometrics in Theobroma cacao

Premise

Imaging technologies that capture three-dimensional (3D) variation in floral morphology at micro- and nano-resolutions are increasingly accessible. In herkogamous flowers, such as those of Theobroma cacao, structural barriers between anthers and stigmas represent bottlenecks that restrict pollinator size and access to reproductive organs. To study the unresolved pollination biology of cacao, we present a novel application of micro-computed tomography (micro-CT) using floral dimensions to quantify pollinator functional size limits.

Methods

We generated micro-CT data sets from field-collected flowers and museum specimens of potential pollinators. To compare floral variation, we used 3D Slicer to place landmarks on the surface models and performed a geometric morphometric (GMM) analysis using geomorph R. We identified the petal side door (an opening between the petal hoods and filament) as the main bottleneck for pollinator access. We compared its mean dimensions with proposed pollinators to identify viable candidates.

Results

We identified three levels of likelihood for putative pollinators based on the number of morphological (body) dimensions that fit through the petal side door. We also found floral reward microstructures whose presence and location were previously unclear.

Discussion

Using micro-CT and GMM to study the 3D pollination biology of cacao provides new evidence for predicting unknown pollinators. Incorporating geometry and floral rewards will strengthen plant-pollinator trait matching models for cacao and other species.

Bioinformatic, genetic and molecular analysis of several badnavirus sequences integrated in the genomes of diverse cocoa (Theobroma cacao L.) germplasm

Endogenous viral elements (EVEs) are integrations of whole or partial viral genomes into the host genome, where they act as host alleles. They exist in a wide range of plant species including Theobroma cacao, the source of chocolate. Because of the international transfer of cacao germplasm, it is important to discriminate between the presence of these inserts and any episomal viruses that may be present in the material. This study was designed to survey a wide range of cacao germplasm, to assess the number, length, orientation, and precise location of the inserts and to identify any effect on the transcription of the gene into which they are inserted. Using a combination of bioinformatic, genetic and molecular approaches, we cloned and sequenced a series of different inserts, including one full-length virus sequence. We also identified, for the first time, an inhibitory effect of the insert on the expression of host genes. Such information is of practical importance in determining the regulation of germplasm transfer and of fundamental relevance to aiding an understanding of the role that such inserts may have on the performance of the host plant.

An investigation of zinc isotope fractionation in cacao (Theobroma cacao L.) and comparison of zinc and cadmium isotope compositions in hydroponic plant systems under high cadmium stress

This study aims to establish whether zinc (Zn) and cadmium (Cd) share similar physiological mechanisms for uptake and translocation in cacao plants (Theobroma cacao L.). Multiple-collector ICP-MS was used to determine the Zn stable isotope compositions in the roots, stems and leaves of 19 diverse cacao genotypes grown in hydroponics with 20 µmol L^-1 CdCl₂. Additional plants of one genotype were grown in hydroponic solutions containing lower Cd concentrations (0 and 5 µmol L^-1 added CdCl₂). Regardless of the Cd concentration used in the exposures, the Zn stable isotope compositions show the same systematic patterns in plant organs, with δ⁶⁶Zn_root > δ⁶⁶Zn_stem > δ⁶⁶Zn_leaf (δ⁶⁶Zn denotes relative differences in ⁶⁶Zn/⁶⁴Zn ratios in parts per thousand). The mean Zn stable isotope fractionation between the plants and the hydroponic solutions was ε⁶⁶Zn_uptake = -1.15 ± 0.36‰ (2SD), indicating preferential uptake of isotopically light Zn by plants from the hydroponic solution. The mean  stable isotope fractionation factor associated with translocation of Zn from roots to shoots, ε⁶⁶Zn_seq-mob =  + 0.52 ± 0.36‰ (2SD), shows that isotopically heavy Zn is preferentially sequestered in the cacao roots, whilst isotopically light Zn is mobilised to the leaves. A comparison with the Cd stable isotope compositions of the same plants shows that both isotopically light Zn and Cd are preferentially taken up by cacao plants. In contrast to Zn, however, the cacao roots retain isotopically light Cd and transfer isotopically heavy Cd to the leaves.

Genome-wide SNP genotyping as a simple and practical tool to accelerate the development of inbred lines in outbred tree species: An example in cacao (Theobroma cacao L.)

Cacao is a globally important crop with a long history of domestication and selective breeding. Despite the increased use of elite clones by cacao farmers, worldwide plantations are established mainly using hybrid progeny material derived from heterozygous parents, therefore displaying high tree-to-tree variability. The deliberate development of hybrids from advanced inbred lines produced by successive generations of self-pollination has not yet been fully considered in cacao breeding. This is largely due to the self-incompatibility of the species, the long generation cycles (3–5 years) and the extensive trial areas needed to accomplish the endeavor. We propose a simple and accessible approach to develop inbred lines based on accelerating the buildup of homozygosity based on regular selfing assisted by genome-wide SNP genotyping. In this study we genotyped 90 clones from the Brazilian CEPEC´s germplasm collection and 49 inbred offspring of six S₁ or S₂ cacao families derived from self-pollinating clones CCN-51, PS-13.19, TSH-1188 and SIAL-169. A set of 3,380 SNPs distributed across the cacao genome were interrogated on the EMBRAPA multi-species 65k Infinium chip. The 90 cacao clones showed considerable variation in genome-wide SNP homozygosity (mean 0.727± 0.182) and 19 of them with homozygosity ≥90%. By assessing the increase in homozygosity across two generations of self-pollinations, SNP data revealed the wide variability in homozygosity within and between S₁ and S₂ families. Even in small families (<10 sibs), individuals were identified with up to ~1.5 standard deviations above the family mean homozygosity. From baseline homozygosities of 0.476 and 0.454, offspring with homozygosities of 0.862 and 0.879 were recovered for clones TSH-1188 and CCN-51 respectively, in only two generations of selfing (81–93% increase). SNP marker assisted monitoring and selection of inbred individuals can be a practical tool to optimize and accelerate the development of inbred lines of outbred tree species. This approach will allow a faster and more accurate exploitation of hybrid breeding strategies in cacao improvement programs and potentially in other perennial fruit and forest trees.

Microbes associated with spontaneous cacao fermentations - A systematic review and meta-analysis

Chocolate is a product of the fermentation of cacao beans. Performed on-farm or at local cooperatives, these are spontaneous cacao fermentations (SCFs). To better understand SCFs, this study sought to identify SCF microbes, their interrelationships, and other key parameters that influence fermentation. This is important because differences in fermentation can have an impact on final product quality. In this study, a systematic data extraction was performed, searching for literature that identified microbes from SCFs. Each unique microbe, whether by location or by fermentation material, was extracted from the articles, along with parameters associated with fermentation. Data were collected and analyzed for three interactions: microbe-to-geography, microbe-to-fermentation method, and microbe-to-microbe. The goal was to attribute microbes to geographical locations, fermentation materials, or to other microbes. Statistically significant relationships will reveal target areas for future research. Over 1700 microbes (440 unique species) were identified across 60 articles. The top three countries represented are Brazil (22 articles, n = 612 microbes), the Ivory Coast (14 articles, n = 237), and Ghana (10 articles, n = 257). Several countries were far less, or never represented, and should be considered for future research. No specific relationship was identified with microbes to either geographical location or fermentation method. Using a Presence-Absence chart, 127 microbe-to-microbe interactions were identified as statistically significant. Data extraction into SCF research has revealed major gaps of knowledge for the cacao microbiome. By better understanding the cacao microbiome, researchers will be able to identify key microbes and fermentation parameters to better influence the fermentation.

Identification of Cacao Mild Mosaic Virus (CaMMV) and Cacao Yellow Vein-Banding Virus (CYVBV) in Cocoa (Theobroma cacao) Germplasm

Cocoa, Theobroma cacao, is an important tropical perennial crop grown widely in the humid tropics. The exchange of cocoa germplasm between germplasm collections and breeding centres is vital for varietal development. Intermediate quarantine facilities, such as the International Cocoa Quarantine Centre, Reading UK (ICQC-R) play a vital role in ensuring the transfer of germplasm whilst minimising the risk of spreading pests and diseases. Current screening procedures combine visual inspection and molecular techniques, which are effective in detecting Cocoa swollen shoot virus (CSSV), a badnavirus, which causes severe losses but are restricted to West Africa. However, the detection of latent or mild virus infections that produce no visual symptoms has been a challenge. Recently two badnavirus species of cocoa producing mild symptoms, cacao mild mosaic virus (CaMMV) and cacao yellow vein-banding virus (CYVBV), have been sequenced. Here, we report new assays for the detection of these two species, for the first time in non-symptomatic accessions. Evolutionary and bioinformatic analyses of the viruses suggest their most recent source was from Trinidad, though there is historic evidence that these viruses may have their origin in South America and then become widespread globally over the last century. We also report a novel colorimetric Loop-mediated isothermal amplification (LAMP) assay for the detection of CYVBV. This simple and accurate method could be employed in field virus testing.

Cacao (Theobroma cacao L.) Response to Water Stress: Physiological Characterization and Antioxidant Gene Expression Profiling in Commercial Clones

The increase in events associated with drought constraints plant growth and crop performance. Cacao (Theobroma cacao L.) is sensitive to water deficit stress (DS), which limits productivity. The aim of this research was to characterise the response of seven (CCN51, FEAR5, ICS1, ICS60, ICS95, EET8, and TSH565) commercially important cacao clones to severe and temporal water deficit stress. Ten-month-old cacao trees were submitted to two treatments: well-watered and water-stressed until the leaf water potential (Ψ leaf) reached values between -3.0 and -3.5 MPa. The effects of hydric stress on water relations, gas exchange, photochemical activity, membrane integrity and oxidative stress-related gene expression were evaluated. All clones showed decreases in Ψ leaf, but TSH565 had a higher capacity to maintain water homeostasis in leaves. An initial response phase consisted of stomatal closure, a general mechanism to limit water loss: as a consequence, the photosynthetic rate dropped by approximately 98% on average. In some clones, the photosynthetic rate reached negative values at the maximum stress level, evidencing photorespiration and was confirmed by increased intracellular CO2. A second and photosynthetically limited phase was characterized by a drop in PSII quantum efficiency, which affected all clones. On average, all clones were able to recover after 4 days of rewatering. Water deficit triggered oxidative stress at the early phase, as evidenced by the upregulation of oxidative stress markers and genes encoding ROS scavenging enzymes. The effects of water deficit stress on energy metabolism were deduced given the upregulation of fermentative enzyme-coding genes. Altogether, our results suggest that the EET8 clone was the highest performing under water deficit while the ICS-60 clone was more susceptible to water stress. Importantly, the activation of the antioxidant system and PSII repair mechanism seem to play key roles in the observed differences in tolerance to water deficit stress among clones.

Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree

Genomic structural variants (SVs) can play important roles in adaptation and speciation. Yet the overall fitness effects of SVs are poorly understood, partly because accurate population-level identification of SVs requires multiple high-quality genome assemblies. Here, we use 31 chromosome-scale, haplotype-resolved genome assemblies of Theobroma cacao-an outcrossing, long-lived tree species that is the source of chocolate-to investigate the fitness consequences of SVs in natural populations. Among the 31 accessions, we find over 160,000 SVs, which together cover eight times more of the genome than single-nucleotide polymorphisms and short indels (125 versus 15 Mb). Our results indicate that a vast majority of these SVs are deleterious: they segregate at low frequencies and are depleted from functional regions of the genome. We show that SVs influence gene expression, which likely impairs gene function and contributes to the detrimental effects of SVs. We also provide empirical support for a theoretical prediction that SVs, particularly inversions, increase genetic load through the accumulation of deleterious nucleotide variants as a result of suppressed recombination. Despite the overall detrimental effects, we identify individual SVs bearing signatures of local adaptation, several of which are associated with genes differentially expressed between populations. Genes involved in pathogen resistance are strongly enriched among these candidates, highlighting the contribution of SVs to this important local adaptation trait. Beyond revealing empirical evidence for the evolutionary importance of SVs, these 31 de novo assemblies provide a valuable resource for genetic and breeding studies in T cacao.

Quality differentiation of cocoa beans: implications for geographical indications

Geographical indications may stimulate collective actions of governance for quality control, trade and marketing as well as innovation based on the use of local resources and regional biodiversity. Cocoa production, however, dominated by small family agriculture in tropical regions, has rarely made use of such strategies. This review is aimed at understanding major research interests and emerging technologies helpful for the origin differentiation of cocoa quality. Results from literature search and cited references of publications on cocoa research were imported into VOSviewer for data analysis, which aided in visualizing major research hotpots. Co-occurrence analysis yielded major research clusters which guided the discussion of this review. Observed was a consensus recognizing cocoa quality resulting from the interaction of genotype, fermentation variables and geographical origin. A classic view of cocoa genetics based on the dichotomy of 'fine versus bulk' has been reexamined by a broader perspective of human selection and cocoa genotype evolution. This new approach to cocoa genetic diversity, together with the understanding of complex microbiome interactions through fermentation, as well as quality reproducibility challenged by geographical conditions, have demonstrated the importance of terroir in the production of special attributes. Cocoa growing communities around the tropics have been clearly enabled by new omics and chemometrics to systematize producing conditions and practices in the designation of specifications for the differentiation of origin quality. © 2021 Society of Chemical Industry.

Repetitive genomic regions and the inference of demographic history

Inference of demographic histories using whole-genome datasets has provided insights into diversification, adaptation, hybridization, and plant-pathogen interactions, and stimulated debate on the impact of anthropogenic interventions and past climate on species demography. However, the impact of repetitive genomic regions on these inferences has mostly been ignored by masking of repeats. We use the Populus trichocarpa genome (Pop_tri_v3) to show that masking of repeat regions leads to lower estimates of effective population size (Ne) in the distant past in contrast to an increase in Ne estimates in recent times. However, in human datasets, masking of repeats resulted in lower estimates of Ne at all time points. We demonstrate that repeats affect demographic inferences using diverse methods like PSMC, MSMC, SMC++, and the Stairway plot. Our genomic analysis revealed that the biases in Ne estimates were dependent on the repeat class type and its abundance in each atomic interval. Notably, we observed a weak, yet consistently significant negative correlation between the repeat abundance of an atomic interval and the Ne estimates for that interval, which potentially reflects the recombination rate variation within the genome. The rationale for the masking of repeats has been that variants identified within these regions are erroneous. We find that polymorphisms in some repeat classes occur in callable regions and reflect reliable coalescence histories (e.g., LTR Gypsy, LTR Copia). The current demography inference methods do not handle repeats explicitly, and hence the effect of individual repeat classes needs careful consideration in comparative analysis. Deciphering the repeat demographic histories might provide a clear understanding of the processes involved in repeat accumulation.

Genome-wide SNP analysis to assess the genetic population structure and diversity of Acrocomia species

Acrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm (Elaeis guineenses) even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of Acrocomia genus, including 172 samples from seven species, with a focus on A. aculeata with 117 samples covering a wide geographical area of occurrence of the species, using Single Nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS).The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.

Geographic Patterns of Genetic Variation among Cacao (Theobroma cacao L.) Populations Based on Chloroplast Markers

The cacao tree (Theobroma cacao L.) is native to the Amazon basin and widely cultivated in the tropics to produce seeds, the valuable raw material for the chocolate industry. Conservation of cacao genetic resources and their availability for breeding and production programs are vital for securing cacao supply. However, relatively little is still known about the phylogeographic structure of natural cacao populations. We studied the geographic distribution of cpDNA variation in different populations representing natural cacao stands, cacao farms in Ecuador, and breeding populations. We used six earlier published cacao chloroplast microsatellite markers to genotype 233 cacao samples. In total, 23 chloroplast haplotypes were identified. The highest variation of haplotypes was observed in western Amazonia including geographically restricted haplotypes. Two observed haplotypes were widespread across the Amazon basin suggesting long distance seed dispersal from west to east in Amazonia. Most cacao genetic groups identified earlier using nuclear SSRs are associated with specific chloroplast haplotypes. A single haplotype was common in selections representing cacao plantations in west Ecuador and reference Trinitario accessions. Our results can be used to determine the chloroplast diversity of accessions and in combination with phenotypic assessments can help to select geographically distinctive varieties for cacao breeding programs.

Identification and distribution of novel badnaviral sequences integrated in the genome of cacao (Theobroma cacao)

Theobroma cacao is one of the most economically important tropical trees, being the source of chocolate. As part of an ongoing study to understand the diversity of the badnavirus complex, responsible for the cacao swollen shoot virus disease in West Africa, evidence was found recently of virus-like sequences in asymptomatic cacao plants. The present study exploited the wealth of genomic resources in this crop, and combined bioinformatic, molecular, and genetic approaches to report for the first time the presence of integrated badnaviral sequences in most of the cacao genetic groups. These sequences, which we propose to name eTcBV for endogenous T. cacao bacilliform virus, varied in type with each predominating in a specific genetic group. A diagnostic multiplex PCR method was developed to identify the homozygous or hemizygous condition of one specific insert, which was inherited as a single Mendelian trait. These data suggest that these integration events occurred before or during the species diversification in Central and South America, and prior to its cultivation in other regions. Such evidence of integrated sequences is relevant to the management of cacao quarantine facilities and may also aid novel methods to reduce the impact of such viruses in this crop.

Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data

Demographic inference using the site frequency spectrum (SFS) is a common way to understand historical events affecting genetic variation. However, most methods for estimating demography from the SFS assume random mating within populations, precluding these types of analyses in inbred populations. To address this issue, we developed a model for the expected SFS that includes inbreeding by parameterizing individual genotypes using beta-binomial distributions. We then take the convolution of these genotype probabilities to calculate the expected frequency of biallelic variants in the population. Using simulations, we evaluated the model's ability to coestimate demography and inbreeding using one- and two-population models across a range of inbreeding levels. We also applied our method to two empirical examples, American pumas (Puma concolor) and domesticated cabbage (Brassica oleracea var. capitata), inferring models both with and without inbreeding to compare parameter estimates and model fit. Our simulations showed that we are able to accurately coestimate demographic parameters and inbreeding even for highly inbred populations (F = 0.9). In contrast, failing to include inbreeding generally resulted in inaccurate parameter estimates in simulated data and led to poor model fit in our empirical analyses. These results show that inbreeding can have a strong effect on demographic inference, a pattern that was especially noticeable for parameters involving changes in population size. Given the importance of these estimates for informing practices in conservation, agriculture, and elsewhere, our method provides an important advancement for accurately estimating the demographic histories of these species.

Environment and pathogens shape local and regional adaptations to climate change in the chocolate tree, Theobroma cacao L

Predicting the potential fate of a species in the face of climate change requires knowing the distribution of molecular adaptations across the geographic range of the species. In this work, we analysed 79 genomes of Theobroma cacao, an Amazonian tree known for the fruit from which chocolate is produced, to evaluate how local and regional molecular signatures of adaptation are distributed across the natural range of the species. We implemented novel techniques that incorporate summary statistics from multiple selection scans to infer selective sweeps. The majority of the molecular adaptations in the genome are not shared among populations. We show that ~71.5% of genes under selection also show significant associations with changes in environmental variables. Our results support the interpretation that these genes contribute to local adaptation of the populations in response to abiotic factors. We also found strong patterns of molecular adaptation in a diverse array of disease resistance genes (6.5% of selective sweeps), suggesting that differential adaptation to pathogens also contributes significantly to local adaptations. Our results are consistent with the interpretation that local selective pressures are more important than regional selective pressures in explaining adaptation across the range of a species.

Moniliophthora perniciosa, the mushroom causing witches' broom disease of cacao: Insights into its taxonomy, ecology and host range in Brazil

Witches' broom caused by Moniliophthora perniciosa is the main disease of cacao (Theobroma cacao) in Brazil. The fungus is known to occur on other host families and these populations have been addressed in the literature as biotypes: C (Malvaceae); H (Malpighiaceae); L (Bignoniaceae) and S (Solanaceae). No complete elucidation of the phylogenetic relationships of isolates obtained from this disparate host range appears in the literature. One member of H (ex Heteropterys acutifolia) has been described as a distinct species. But should other biotypes be also recognized as distinct taxa? In the present study, a survey yielding 24 isolates of M. perniciosa from ten hosts and covering a wide range of geographic regions in Brazil was undertaken. These isolates were compared with those from T. cacao using three DNA regions for the phylogenetic analyses: ITS, LSU and RPB1. Morphology was also examined. All isolates in this study were found to belong to M. perniciosa, including the population from H. acutifolia, formerly treated as Moniliophthora brasiliensis but reduced here to a synonym of M. perniciosa. This species ranged from pathogenic to a previously unreported occurrence as a non-pathogenic endophyte in the Atlantic rainforest tree Allophylus edulis (Sapindaceae). M. perniciosa was recorded on a range of solanaceous hosts (16 species) over a wide variety of ecosystems. The ecological and evolutionary significance of these novel findings are discussed.

The History of Cacao and Its Diseases in the Americas

Cacao is a commodity crop from the tropics cultivated by about 6 million smallholder farmers. The tree, Theobroma cacao, originated in the Upper Amazon where it was domesticated ca. 5450 to 5300 B.P. From this center of origin, cacao was dispersed and cultivated in Mesoamerica as early as 3800 to 3000 B.P. After the European conquest of the Americas (the 1500s), cacao cultivation intensified in several loci, primarily Mesoamerica, Trinidad, Venezuela, and Ecuador. It was during the colonial period that cacao diseases began emerging as threats to production. One early example is the collapse of the cacao industry in Trinidad in the 1720s, attributed to an unknown disease referred to as the "blast". Trinidad would resurface as a production center due to the discovery of the Trinitario genetic group, which is still widely used in breeding programs around the world. However, a resurgence of diseases like frosty pod rot during the republican period (the late 1800s and early 1900s) had profound impacts on other centers of Latin American production, especially in Venezuela and Ecuador, shifting the focus of cacao production southward, to Bahia, Brazil. Production in Bahia was, in turn, dramatically curtailed by the introduction of witches' broom disease in the late 1980s. Today, most of the world's cacao production occurs in West Africa and parts of Asia, where the primary Latin American diseases have not yet spread. In this review, we discuss the history of cacao cultivation in the Americas and how that history has been shaped by the emergence of diseases.

Genome-Wide Association Study Reveals Novel Candidate Genes Associated with Productivity and Disease Resistance to Moniliophthora spp. in Cacao (Theobroma cacao L.)

Cacao (Theobroma cacao L.), the source of chocolate, is one of the most important commodity products worldwide that helps improve the economic livelihood of farmers. Diseases like frosty pod rot caused by Moniliophthora roreri and witches’ broom caused by Moniliophthora perniciosa limit the cacao productivity, this can be solved by using resistant varieties. In the current study, we sequenced 229 cacao accessions using genotyping-by-sequencing to examine the genetic diversity and population structure employing 9,003 and 8,131 single nucleotide polymorphisms recovered by mapping against two cacao genomes (Criollo B97-61/B2 v2 and Matina 1-6 v1.1). In the phenotypic evaluation, three promising accessions for productivity and 10 with good tolerance to the frosty pod rot and witches’ broom diseases were found. A genome-wide association study was performed on 102 accessions, discovering two genes associated with productivity and seven to disease resistance. The results enriched the knowledge of the genetic regions associated with important cacao traits that can have significant implications for conservation and breeding strategies like marker-assisted selection.

Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations

Background

Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation. This process impacts the ability of selection to eliminate deleterious mutations or increase the frequency of beneficial mutations in a population. To understand the role of recombination generating and maintaining haplotypic variation in a population, we can construct fine-scale recombination maps. Such maps have been used to study a variety of model organisms and proven to be informative of how selection and demographics shape species-wide variation. Here we present a fine-scale recombination map for ten populations of Theobroma cacao – a non-model, long-lived, woody crop. We use this map to elucidate the dynamics of recombination rates in distinct populations of the same species, one of which is domesticated.

Results

Mean recombination rates in range between 2.5 and 8.6 cM/Mb for most populations of T. cacao with the exception of the domesticated Criollo (525 cM/Mb) and Guianna, a more recently established population (46.5 cM/Mb). We found little overlap in the location of hotspots of recombination across populations. We also found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. We find mutations in FIGL-1, a protein shown to downregulate cross-over frequency in Arabidopsis, statistically associated to higher recombination rates in domesticated Criollo.

Conclusions

We generated fine-scale recombination maps for ten populations of Theobroma cacao and used them to understand what processes are associated with population-level variation in this species. Our results provide support to the hypothesis of increased recombination rates in domesticated plants (Criollo population). We propose a testable mechanistic hypothesis for the change in recombination rate in domesticated populations in the form of mutations to a previously identified recombination-suppressing protein. Finally, we establish a number of possible correlates of recombination hotspots that help explain general patterns of recombination in this species.

Tropical Trees as Time Capsules of Anthropogenic Activity

After the ice caps, tropical forests are globally the most threatened terrestrial environments. Modern trees are not just witnesses to growing contemporary threats but also legacies of past human activity. Here, we review the use of dendrochronology, radiocarbon analysis, stable isotope analysis, and DNA analysis to examine ancient tree management. These methods exploit the fact that living trees record information on environmental and anthropogenic selective forces during their own and past generations of growth, making trees living archaeological 'sites'. The applicability of these methods across prehistoric, historic, and industrial periods means they have the potential to detect evolving anthropogenic threats and can be used to set conservation priorities in rapidly vanishing environments.

Simulation-Based Evaluation of Three Methods for Local Ancestry Deconvolution of Non-model Crop Species Genomes

Hybridizations between species and subspecies represented major steps in the history of many crop species. Such events generally lead to genomes with mosaic patterns of chromosomal segments of various origins that may be assessed by local ancestry inference methods. However, these methods have mainly been developed in the context of human population genetics with implicit assumptions that may not always fit plant models. The purpose of this study was to evaluate the suitability of three state-of-the-art inference methods (SABER, ELAI and WINPOP) for local ancestry inference under scenarios that can be encountered in plant species. For this, we developed an R package to simulate genotyping data under such scenarios. The tested inference methods performed similarly well as far as representatives of source populations were available. As expected, the higher the level of differentiation between ancestral source populations and the lower the number of generations since admixture, the more accurate were the results. Interestingly, the accuracy of the methods was only marginally affected by i) the number of ancestries (up to six tested); ii) the sample design (i.e., unbalanced representation of source populations); and iii) the reproduction mode (e.g., selfing, vegetative propagation). If a source population was not represented in the data set, no bias was observed in inference accuracy for regions originating from represented sources and regions from the missing source were assigned differently depending on the methods. Overall, the selected ancestry inference methods may be used for crop plant analysis if all ancestral sources are known.

Gene Expression Modularity Reveals Footprints of Polygenic Adaptation in Theobroma cacao

Separating footprints of adaptation from demography is challenging. When selection has acted on a single locus with major effect, this issue can be alleviated through signatures left by selective sweeps. However, as adaptation is often driven by small allele frequency shifts at many loci, studies focusing on single genes are able to identify only a small portion of genomic variants responsible for adaptation. In face of this challenge, we utilize coexpression information to search for signals of polygenetic adaptation in Theobroma cacao, a tropical tree species that is the source of chocolate. Using transcriptomics and a weighted correlation network analysis, we group genes with similar expression patterns into functional modules. We then ask whether modules enriched for specific biological processes exhibit cumulative effects of differential selection in the form of high FST and dXY between populations. Indeed, modules putatively involved in protein modification, flowering, and water transport show signs of polygenic adaptation even though individual genes that are members of those groups do not bear strong signatures of selection. Modeling of demography, background selection, and the effects of genomic features reveal that these patterns are unlikely to arise by chance. We also find that specific modules are enriched for signals of strong or relaxed purifying selection, with one module bearing signs of adaptive differentiation and an excess of deleterious mutations. Our results provide insight into polygenic adaptation and contribute to understanding of population structure, demographic history, and genome evolution in T. cacao.

Development of a core SNP panel for cacao (Theobroma cacao L.) identity analysis

Single nucleotide polymorphisms (SNPs) are preferred markers for DNA fingerprinting and diversity studies in cacao (Theobroma cacao L.). Yet, a consensus SNP panel with a minimum number of SNPs for optimal identity analysis is unavailable for cacao. An initial set of 146 SNP panels of varying sizes were assembled based on heterozygosity, linkage disequilibrium (LD), linkage group (LG) distribution, major allele frequency, minor allele frequency (M_iAF), polymorphism information content (PIC), and random distribution. These panels were assessed to determine their ability to distinguish among a training set of 155 accessions. The panels with the best separation ability were supplemented with additional SNPs to create 16 designer panels, which separated all 155 accessions. The 16 designer SNP panels were then assessed on a dataset of 1220 accessions coming from 10 ancestral groups. Increasing the number of SNPs generally yielded improved resolution of genetic identities with concomitant reduction of synonymous groups. The number and choice of SNPs were critical factors with LD, M_iAF, and PIC being important selection attributes but an even LG distribution was unnecessary. A robust set of 96 SNPs is recommended as a minimal core SNP panel for cacao DNA fingerprinting to the international cacao community.

Identification of Climate and Genetic Factors That Control Fat Content and Fatty Acid Composition of Theobroma cacao L. Beans

The main ingredients of chocolate are usually cocoa powder, cocoa butter, and sugar. Both the powder and the butter are extracted from the beans of the cacao tree (Theobroma cacao L.). The cocoa butter represents the fat in the beans and possesses a unique fatty acid profile that results in chocolate's characteristic texture and mouthfeel. Here, we used a linkage mapping population and phenotypic data of 3,292 samples from 420 progeny which led to the identification of 27 quantitative trait loci (QTLs) for fatty acid composition and six QTLs for fat content. Progeny showed extensive variation in fat levels and composition, with the level of palmitic acid negatively correlated to the sum of stearic acid, oleic acid, and linoleic acid. A major QTL explaining 24% of the relative level of palmitic acid was mapped to the distal end of chromosome 4, and those higher levels of palmitic acid were associated with the presence of a haplotype from the "TSH 1188" parent in the progeny. Within this region of chromosome 4 is the Thecc1EG017405 gene, an orthologue and isoform of the stearoyl-acyl carrier protein (ACP) desaturase (SAD) gene in plants, which is involved in fatty acid biosynthesis. Besides allelic differences, we also show that climate factors can change the fatty acid composition in the beans, including a significant positive correlation between higher temperatures and the higher level of palmitic acid. Moreover, we found a significant pollen donor effect from the variety "SIAL 70" which was associated with decreased palmitic acid levels.

Cocoa Bean Proteins-Characterization, Changes and Modifications due to Ripening and Post-Harvest Processing

The protein fractions of cocoa have been implicated influencing both the bioactive potential and sensory properties of cocoa and cocoa products. The objective of the present review is to show the impact of different stages of cultivation and processing with regard to the changes induced in the protein fractions. Special focus has been laid on the major seed storage proteins throughout the different stages of processing. The study starts with classical introduction of the extraction and the characterization methods used, while addressing classification approaches of cocoa proteins evolved during the timeline. The changes in protein composition during ripening and maturation of cocoa seeds, together with the possible modifications during the post-harvest processing (fermentation, drying, and roasting), have been documented. Finally, the bioactive potential arising directly or indirectly from cocoa proteins has been elucidated. The “state of the art” suggests that exploration of other potentially bioactive components in cocoa needs to be undertaken, while considering the complexity of reaction products occurring during the roasting phase of the post-harvest processing. Finally, the utilization of partially processed cocoa beans (e.g., fermented, conciliatory thermal treatment) can be recommended, providing a large reservoir of bioactive potentials arising from the protein components that could be instrumented in functionalizing foods.

Meiosis Research in Orphan and Non-orphan Tropical Crops

Plant breeding is directly linked to the development of crops that can effectively adapt to challenging conditions such as soil nutrient depletion, water pollution, drought, and anthropogenic climate change. These conditions are extremely relevant in developing countries already burdened with population growth and unchecked urban expansion, especially in the tropical global southern hemisphere. Engineering new crops thus has potential to enhance food security, prevent hunger, and spur sustainable agricultural growth. A major tool for the improvement of plant varieties in this context could be the manipulation of homologous recombination and genome haploidization during meiosis. The isolation or the design of mutations in key meiotic genes may facilitate DNA recombination and transmission of important genes quickly and efficiently. Genome haploidization through centromeric histone mutants could be an option to create new crosses rapidly. This review covers technical approaches to engineer key meiotic genes in tropical crops as a blueprint for future work and examples of tropical crops in which such strategies could be applied are given.