Several species of the ambrosia beetle Euwallacea (Coleoptera: Curculionidae: Scolytinae) cultiva... more Several species of the ambrosia beetle Euwallacea (Coleoptera: Curculionidae: Scolytinae) cultivate Ambrosia Fusarium Clade (AFC) species in their galleries as a source of food. Like all other scolytine beetles in the tribe Xyleborini, Euwallacea are thought to be obligate mutualists with their fungal symbionts. Published diversification-time estimates suggest that the Euwallacea-Fusarium symbiosis evolved once approximately 21 million years ago. Female Euwallacea possess paired oral mycangia Phytoparasitica
Frosty pod rot (FPR), caused by Moniliophthora roreri (MR), is one of the most important diseases... more Frosty pod rot (FPR), caused by Moniliophthora roreri (MR), is one of the most important diseases of cacao, causing losses of up to 90% in areas where it is present. A limited number of resistant clones have been identified, but additional sources of disease resistance are being sought by breeding programs. RNA-sequencing was used to identify differences in constitutive (mock-inoculated) and pathogen-induced gene expression in cacao pods from trees resistant and susceptible to MR. The greatest number of differentially expressed genes (DEGs) (n=2,039) was identified in susceptible material following inoculation with MR (7 days post inoculation), with the most common pathway categories being cell growth/death (n=102), signaling (n=308), and carbohydrate metabolism (n=141). Resistant material showed little overall change in gene expression (5 DEGs) following pathogen inoculation, suggesting that infection had not become established. For this reason, differences in constitutive gene exp...
Proceedings of The 1st International Electronic Conference on Entomology, 2021
Theobroma cacao is affected by viruses on every continent where the crop is cultivated, with the ... more Theobroma cacao is affected by viruses on every continent where the crop is cultivated, with the best-known ones belonging to the Badnavirus genus. Badnaviruses are transmitted by several species of Pseudococcidae, a large, taxonomically diverse group of insects collectively known as mealybugs. Effective management of mealybugs depends on accurate identification of species present, as even closely related species have distinct life cycles and are vulnerable to different biological control organisms. This study compares the usefulness of the COI, ITS2, and 28S markers using the primer pairs (MFCO1/MRCO1, ITS2-M-F/ITS2-M-R, D10F/D10R, and D2F/D2R) to identify mealybugs associated with cacao plants in North America. All markers were informative for Pseudococcus comstocki (n=4) and Maconellicoccus hirsutus (n=8), but only CO1 provided unambiguous identification for Pseudococcus jackbeardsleyi (n=11). Primer pair D2F/D2R is not recommended for mealybug identification, as it frequently yielded sequences of Anagyrus sp., an Encyrtid parasitoid wasp commonly used for biocontrol. This study describes molecular diagnostic protocols for identifying cacao-associated mealybugs and detecting the presence of certain parasitoids. This information is essential for selecting the most effective interventions as part of an integrated pest management program.
Perennial agroecosystems often seek to optimize productivity by breeding nutrient-efficient, dise... more Perennial agroecosystems often seek to optimize productivity by breeding nutrient-efficient, disease-resistant rootstocks. In cacao (Theobroma cacao L.), however, rootstock selection has traditionally relied on locally available open pollinated populations with limited data on performance. Furthermore, rootstock associations with the rhizobiome, or rhizosphere microbiome, have been neglected. Better understanding of rootstock and scion effects on cacao-specific traits, particularly those involved in root-microbe interactions and nutrient acquisition, could contribute to more efficient rootstock selection and breeding. A rootstock-scion interaction study was conducted using three scion genotypes and eight rootstock populations under greenhouse conditions to better understand the relationships among rootstock and scion identities, soil fertility, and rhizobiome composition and the impacts of these factors on plant uptake of macro- and micronutrients. We show that rootstock genotype ha...
The economic feasibility of producing biomass-based fuels requires high-yielding feedstocks to su... more The economic feasibility of producing biomass-based fuels requires high-yielding feedstocks to supply biomass to biorefineries. Populus trees are a potential biomass feedstock due to their high yield, but their high water requirement limits productivity under drought conditions. The number of genes controlling drought tolerance, and the long generation time for perennial species, slows cultivar development. Accelerated domestication proposes using the sequenced Populus genome to quickly incorporate target traits into productive clones by transgenesis. Six putative drought tolerance transcription factors: DREB2A, DREB2B, AtMYB, AREB1/ABF2, MYB, and NAC, had been previously identified and manipulated in eastern cottonwood (Populus deltoides). Three constructs of each gene were transformed into a P. deltoides background clone, including constitutive overexpression (OE), drought inducible OE, and knockdown. This greenhouse study examines the effect of these previously transformed constr...
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Neofusicoccum parvum is a recently reported pathogen affecting Theobroma cacao L., and has been i... more Neofusicoccum parvum is a recently reported pathogen affecting Theobroma cacao L., and has been isolated from symptomatic pods on Oahu and Hawaii Islands. Determining infection routes and virulence are essential for assessing the impact of N. parvum on cacao production and developing effective disease management strategies. Infection routes were determined by inoculating unwounded stems and pods with six isolates of N. parvum alongside Lasiodiplodia theobromae and Phytophthora palmivora. Fifty percent of unwounded stems inoculated with P. palmivora developed lesions, but only a single lesion developed following inoculation with N. parvum (isolate H44). L. theobromae and the remaining N. parvum isolates did not induce lesion development on unwounded stems. In contrast, all N. parvum and L. theobromae isolates produced lesions on 40–100% of unwounded pods of GNV 164 and GNV 360. Low incidences of infection were observed in unwounded pods of ICS 95 (0–66.7%), SHRS 21 (0–75%), and SHRS ...
Black pod disease, caused by Phytophthora species, is among the main limiting factors of cacao (T... more Black pod disease, caused by Phytophthora species, is among the main limiting factors of cacao (Theobroma cacao L.) production. High incidence levels of black pod disease have been reported in Brazil, being induced by Phytophthora capsici, Phytophthora citrophthora, Phytophthora heveae, and Phytophthora palmivora. To assess the diversity of Phytophthora species affecting cacao in Brazil, 40 new isolates were obtained from cacao pods exhibiting symptoms of black pod disease collected in different smallholder farms in 2017. Further, ten cacao-infecting isolates morphologically identified as P. citrophthora and P. palmivora were molecularly characterized. The genomic regions beta-tubulin, elongation factor 1 alpha, heat shock protein 90, and internal transcribed spacer, and the mitochondrially encoded cytochrome c oxidase I and II genes were PCR-amplified and Sanger-sequenced from the cacao-infecting Phytophthora isolates. The morphological characterization and evaluation of the myceli...
Lasiodiplodia theobromae (Pat.) Griffon & Maubl., a member of the family Botryosphaeriaceae, is b... more Lasiodiplodia theobromae (Pat.) Griffon & Maubl., a member of the family Botryosphaeriaceae, is becoming a significant threat to crops and woody plants in many parts of the world, including the major cacao growing areas. While attempting to isolate Ceratobasidium theobromae, a causal agent of vascular streak dieback (VSD), from symptomatic cacao stems, 74% of isolated fungi were Lasiodiplodia spp. Sequence-based identification of 52 putative isolates of L. theobromae indicated that diverse species of Lasiodiplodia were associated with cacao in the studied areas, and the isolates showed variation in aggressiveness when assayed using cacao leaf discs. The present study reports a 43.75 Mb de novo assembled genome of an isolate of L. theobromae from cacao. Ab initio gene prediction generated 13 061 protein-coding genes, of which 2862 are unique to L. theobromae, when compared with other closely related Botryosphaeriaceae. Transcriptome analysis revealed that 11 860 predicted genes were ...
Laurel wilt is a lethal disease of redbay (Persea borbonia (L.) Spreng.), swamp bay (Persea palus... more Laurel wilt is a lethal disease of redbay (Persea borbonia (L.) Spreng.), swamp bay (Persea palustris (Raf.) Sarg.
The fate of carbon below ground is likely to be a major factor determining the success of carbon ... more The fate of carbon below ground is likely to be a major factor determining the success of carbon sequestration strategies involving plants. Despite their importance, molecular processes controlling belowground C allocation and partitioning are poorly understood. This project is leveraging the Populus trichocarpa genome sequence to discover genes important to C sequestration in plants and soils. The focus is on the identification of genes that provide key control points for the flow and chemical transformations of carbon in roots, concentrating on genes that control the synthesis of chemical forms of carbon that result in slower turnover rates of soil organic matter (i.e., increased recalcitrance). We propose to enhance carbon allocation and partitioning to roots by 1) modifying the auxin signaling pathway, and the invertase family, which controls sucrose metabolism, and by 2) increasing root proliferation through transgenesis with genes known to control fine root proliferation (e.g....
The economic feasibility of producing biomass-based fuels requires high-yielding feedstocks to su... more The economic feasibility of producing biomass-based fuels requires high-yielding feedstocks to supply biomass to biorefineries. Populus trees are a potential biomass feedstock due to their high yield, but their high water requirement limits productivity under drought conditions. The number of genes controlling drought tolerance, and the long generation time for perennial species, slows cultivar development. Accelerated domestication proposes using the sequenced Populus genome to quickly incorporate target traits into productive clones by transgenesis. Six putative drought tolerance transcription factors: DREB2A, DREB2B, AtMYB, AREB1/ABF2, MYB, and NAC, had been previously identified and manipulated in eastern cottonwood (Populus deltoides). Three constructs of each gene were transformed into a P. deltoides background clone, including constitutive overexpression (OE), drought inducible OE, and knockdown. This greenhouse study examines the effect of these previously transformed constr...
Commercial production of cacao in Hawaii has doubled in the past 10 years, and farmers are receiv... more Commercial production of cacao in Hawaii has doubled in the past 10 years, and farmers are receiving premium prices for their beans from the expanding local confectionery industry. Black pod, caused by Phytophthora spp., is the only major cacao disease that has been reported in Hawaii but distribution and molecular identification are lacking. To determine the species of Phytophthora affecting Theobroma cacao, a sampling trip was conducted on Hawaii Island and Oahu. Ten isolates of Phytophthora palmivora were obtained from diseased cacao on Hawaii Island, but none from Oahu, despite the presence of symptomatic pods. No other Phytophthora species were found. Laboratory studies showed that all isolates produced lesions on unwounded cacao pods, but they differed in terms of their temperature–growth responses. Fungicide sensitives for a subset of isolates (n = 4) were determined using media amended with a range of fungicide concentrations. The Hawaiian isolates of P. palmivora were more ...
Economically, cacao (Theobroma cacao L.) is a major tropical commodity for the Americas; however,... more Economically, cacao (Theobroma cacao L.) is a major tropical commodity for the Americas; however, severe losses due to Moniliophthora roreri (Cif. and Par.), which causes frosty pod rot (FPR), and Phytophthora spp., which causes black pod rot (BPR), have reduced cacao production in the Americas. The objectives of this study are to (i) re-confirm the QTL using different marker set; (ii) discover new QTL associated with FPR and BPR resistance using SNP markers; and (iii) find genes in the candidate QTL regions. At CATIE in Turrialba, Costa Rica, an F1 mapping population of cacao was obtained by crossing “POUND 7,” a clone moderately susceptible to FPR and resistant to BPR, with “UF 273,” resistant to FPR and highly susceptible to BPR. A total of 179 F1 progeny were fingerprinted with 5149 SNP markers and a dense linkage map composed of 10 linkage groups was developed using 2910 polymorphic SNP markers. Also segregating F1 trees were screened for resistance to FPR and BPR diseases. Sev...
Several species of the ambrosia beetle Euwallacea (Coleoptera: Curculionidae: Scolytinae) cultiva... more Several species of the ambrosia beetle Euwallacea (Coleoptera: Curculionidae: Scolytinae) cultivate Ambrosia Fusarium Clade (AFC) species in their galleries as a source of food. Like all other scolytine beetles in the tribe Xyleborini, Euwallacea are thought to be obligate mutualists with their fungal symbionts. Published diversification-time estimates suggest that the Euwallacea-Fusarium symbiosis evolved once approximately 21 million years ago. Female Euwallacea possess paired oral mycangia Phytoparasitica
Frosty pod rot (FPR), caused by Moniliophthora roreri (MR), is one of the most important diseases... more Frosty pod rot (FPR), caused by Moniliophthora roreri (MR), is one of the most important diseases of cacao, causing losses of up to 90% in areas where it is present. A limited number of resistant clones have been identified, but additional sources of disease resistance are being sought by breeding programs. RNA-sequencing was used to identify differences in constitutive (mock-inoculated) and pathogen-induced gene expression in cacao pods from trees resistant and susceptible to MR. The greatest number of differentially expressed genes (DEGs) (n=2,039) was identified in susceptible material following inoculation with MR (7 days post inoculation), with the most common pathway categories being cell growth/death (n=102), signaling (n=308), and carbohydrate metabolism (n=141). Resistant material showed little overall change in gene expression (5 DEGs) following pathogen inoculation, suggesting that infection had not become established. For this reason, differences in constitutive gene exp...
Proceedings of The 1st International Electronic Conference on Entomology, 2021
Theobroma cacao is affected by viruses on every continent where the crop is cultivated, with the ... more Theobroma cacao is affected by viruses on every continent where the crop is cultivated, with the best-known ones belonging to the Badnavirus genus. Badnaviruses are transmitted by several species of Pseudococcidae, a large, taxonomically diverse group of insects collectively known as mealybugs. Effective management of mealybugs depends on accurate identification of species present, as even closely related species have distinct life cycles and are vulnerable to different biological control organisms. This study compares the usefulness of the COI, ITS2, and 28S markers using the primer pairs (MFCO1/MRCO1, ITS2-M-F/ITS2-M-R, D10F/D10R, and D2F/D2R) to identify mealybugs associated with cacao plants in North America. All markers were informative for Pseudococcus comstocki (n=4) and Maconellicoccus hirsutus (n=8), but only CO1 provided unambiguous identification for Pseudococcus jackbeardsleyi (n=11). Primer pair D2F/D2R is not recommended for mealybug identification, as it frequently yielded sequences of Anagyrus sp., an Encyrtid parasitoid wasp commonly used for biocontrol. This study describes molecular diagnostic protocols for identifying cacao-associated mealybugs and detecting the presence of certain parasitoids. This information is essential for selecting the most effective interventions as part of an integrated pest management program.
Perennial agroecosystems often seek to optimize productivity by breeding nutrient-efficient, dise... more Perennial agroecosystems often seek to optimize productivity by breeding nutrient-efficient, disease-resistant rootstocks. In cacao (Theobroma cacao L.), however, rootstock selection has traditionally relied on locally available open pollinated populations with limited data on performance. Furthermore, rootstock associations with the rhizobiome, or rhizosphere microbiome, have been neglected. Better understanding of rootstock and scion effects on cacao-specific traits, particularly those involved in root-microbe interactions and nutrient acquisition, could contribute to more efficient rootstock selection and breeding. A rootstock-scion interaction study was conducted using three scion genotypes and eight rootstock populations under greenhouse conditions to better understand the relationships among rootstock and scion identities, soil fertility, and rhizobiome composition and the impacts of these factors on plant uptake of macro- and micronutrients. We show that rootstock genotype ha...
The economic feasibility of producing biomass-based fuels requires high-yielding feedstocks to su... more The economic feasibility of producing biomass-based fuels requires high-yielding feedstocks to supply biomass to biorefineries. Populus trees are a potential biomass feedstock due to their high yield, but their high water requirement limits productivity under drought conditions. The number of genes controlling drought tolerance, and the long generation time for perennial species, slows cultivar development. Accelerated domestication proposes using the sequenced Populus genome to quickly incorporate target traits into productive clones by transgenesis. Six putative drought tolerance transcription factors: DREB2A, DREB2B, AtMYB, AREB1/ABF2, MYB, and NAC, had been previously identified and manipulated in eastern cottonwood (Populus deltoides). Three constructs of each gene were transformed into a P. deltoides background clone, including constitutive overexpression (OE), drought inducible OE, and knockdown. This greenhouse study examines the effect of these previously transformed constr...
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Neofusicoccum parvum is a recently reported pathogen affecting Theobroma cacao L., and has been i... more Neofusicoccum parvum is a recently reported pathogen affecting Theobroma cacao L., and has been isolated from symptomatic pods on Oahu and Hawaii Islands. Determining infection routes and virulence are essential for assessing the impact of N. parvum on cacao production and developing effective disease management strategies. Infection routes were determined by inoculating unwounded stems and pods with six isolates of N. parvum alongside Lasiodiplodia theobromae and Phytophthora palmivora. Fifty percent of unwounded stems inoculated with P. palmivora developed lesions, but only a single lesion developed following inoculation with N. parvum (isolate H44). L. theobromae and the remaining N. parvum isolates did not induce lesion development on unwounded stems. In contrast, all N. parvum and L. theobromae isolates produced lesions on 40–100% of unwounded pods of GNV 164 and GNV 360. Low incidences of infection were observed in unwounded pods of ICS 95 (0–66.7%), SHRS 21 (0–75%), and SHRS ...
Black pod disease, caused by Phytophthora species, is among the main limiting factors of cacao (T... more Black pod disease, caused by Phytophthora species, is among the main limiting factors of cacao (Theobroma cacao L.) production. High incidence levels of black pod disease have been reported in Brazil, being induced by Phytophthora capsici, Phytophthora citrophthora, Phytophthora heveae, and Phytophthora palmivora. To assess the diversity of Phytophthora species affecting cacao in Brazil, 40 new isolates were obtained from cacao pods exhibiting symptoms of black pod disease collected in different smallholder farms in 2017. Further, ten cacao-infecting isolates morphologically identified as P. citrophthora and P. palmivora were molecularly characterized. The genomic regions beta-tubulin, elongation factor 1 alpha, heat shock protein 90, and internal transcribed spacer, and the mitochondrially encoded cytochrome c oxidase I and II genes were PCR-amplified and Sanger-sequenced from the cacao-infecting Phytophthora isolates. The morphological characterization and evaluation of the myceli...
Lasiodiplodia theobromae (Pat.) Griffon & Maubl., a member of the family Botryosphaeriaceae, is b... more Lasiodiplodia theobromae (Pat.) Griffon & Maubl., a member of the family Botryosphaeriaceae, is becoming a significant threat to crops and woody plants in many parts of the world, including the major cacao growing areas. While attempting to isolate Ceratobasidium theobromae, a causal agent of vascular streak dieback (VSD), from symptomatic cacao stems, 74% of isolated fungi were Lasiodiplodia spp. Sequence-based identification of 52 putative isolates of L. theobromae indicated that diverse species of Lasiodiplodia were associated with cacao in the studied areas, and the isolates showed variation in aggressiveness when assayed using cacao leaf discs. The present study reports a 43.75 Mb de novo assembled genome of an isolate of L. theobromae from cacao. Ab initio gene prediction generated 13 061 protein-coding genes, of which 2862 are unique to L. theobromae, when compared with other closely related Botryosphaeriaceae. Transcriptome analysis revealed that 11 860 predicted genes were ...
Laurel wilt is a lethal disease of redbay (Persea borbonia (L.) Spreng.), swamp bay (Persea palus... more Laurel wilt is a lethal disease of redbay (Persea borbonia (L.) Spreng.), swamp bay (Persea palustris (Raf.) Sarg.
The fate of carbon below ground is likely to be a major factor determining the success of carbon ... more The fate of carbon below ground is likely to be a major factor determining the success of carbon sequestration strategies involving plants. Despite their importance, molecular processes controlling belowground C allocation and partitioning are poorly understood. This project is leveraging the Populus trichocarpa genome sequence to discover genes important to C sequestration in plants and soils. The focus is on the identification of genes that provide key control points for the flow and chemical transformations of carbon in roots, concentrating on genes that control the synthesis of chemical forms of carbon that result in slower turnover rates of soil organic matter (i.e., increased recalcitrance). We propose to enhance carbon allocation and partitioning to roots by 1) modifying the auxin signaling pathway, and the invertase family, which controls sucrose metabolism, and by 2) increasing root proliferation through transgenesis with genes known to control fine root proliferation (e.g....
The economic feasibility of producing biomass-based fuels requires high-yielding feedstocks to su... more The economic feasibility of producing biomass-based fuels requires high-yielding feedstocks to supply biomass to biorefineries. Populus trees are a potential biomass feedstock due to their high yield, but their high water requirement limits productivity under drought conditions. The number of genes controlling drought tolerance, and the long generation time for perennial species, slows cultivar development. Accelerated domestication proposes using the sequenced Populus genome to quickly incorporate target traits into productive clones by transgenesis. Six putative drought tolerance transcription factors: DREB2A, DREB2B, AtMYB, AREB1/ABF2, MYB, and NAC, had been previously identified and manipulated in eastern cottonwood (Populus deltoides). Three constructs of each gene were transformed into a P. deltoides background clone, including constitutive overexpression (OE), drought inducible OE, and knockdown. This greenhouse study examines the effect of these previously transformed constr...
Commercial production of cacao in Hawaii has doubled in the past 10 years, and farmers are receiv... more Commercial production of cacao in Hawaii has doubled in the past 10 years, and farmers are receiving premium prices for their beans from the expanding local confectionery industry. Black pod, caused by Phytophthora spp., is the only major cacao disease that has been reported in Hawaii but distribution and molecular identification are lacking. To determine the species of Phytophthora affecting Theobroma cacao, a sampling trip was conducted on Hawaii Island and Oahu. Ten isolates of Phytophthora palmivora were obtained from diseased cacao on Hawaii Island, but none from Oahu, despite the presence of symptomatic pods. No other Phytophthora species were found. Laboratory studies showed that all isolates produced lesions on unwounded cacao pods, but they differed in terms of their temperature–growth responses. Fungicide sensitives for a subset of isolates (n = 4) were determined using media amended with a range of fungicide concentrations. The Hawaiian isolates of P. palmivora were more ...
Economically, cacao (Theobroma cacao L.) is a major tropical commodity for the Americas; however,... more Economically, cacao (Theobroma cacao L.) is a major tropical commodity for the Americas; however, severe losses due to Moniliophthora roreri (Cif. and Par.), which causes frosty pod rot (FPR), and Phytophthora spp., which causes black pod rot (BPR), have reduced cacao production in the Americas. The objectives of this study are to (i) re-confirm the QTL using different marker set; (ii) discover new QTL associated with FPR and BPR resistance using SNP markers; and (iii) find genes in the candidate QTL regions. At CATIE in Turrialba, Costa Rica, an F1 mapping population of cacao was obtained by crossing “POUND 7,” a clone moderately susceptible to FPR and resistant to BPR, with “UF 273,” resistant to FPR and highly susceptible to BPR. A total of 179 F1 progeny were fingerprinted with 5149 SNP markers and a dense linkage map composed of 10 linkage groups was developed using 2910 polymorphic SNP markers. Also segregating F1 trees were screened for resistance to FPR and BPR diseases. Sev...
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