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

Barreto, Mariana Araújo; Rosa, João Ricardo Bachega Feijó; Holanda, Ioná Santos Araújo; Cardoso-Silva, Cláudio Benício; Vildoso, Carlos Ivan Aguilar; Ahnert, Dário; Souza, Margarete Magalhães; Corrêa, Ronan Xavier; Royaert, Stefan; Marelli, Jean-Philippe; Santos, Elisa Susilene Lisboa dos; Luz, Edna Dora Martins Newman; Garcia, Antônio Augusto Franco; Souza, Anete Pereira de

doi:10.1007/s10681-018-2273-5

Cited by 19 publications

(16 citation statements)

References 55 publications

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“…Progress in breeding of cacao has been hampered by long generation times, self-incompatibility, complex inheritance of oligogenic resistance, limited resources of breeding programs, and reliance on a relatively small proportion of available genetic diversity ( Lanaud et al, 2009 , 2017 ; Bekele and Phillips-Mora, 2019 ). Significant strides have been made in genetic mapping of resistance QTL associated with BPR and WBD resistance ( Lanaud et al, 2009 ; Akaza et al, 2016 ; Barreto et al, 2018 ). Application of microsatellite markers and genomic selection has shown promise for accelerating breeding of cacao ( Schnell et al, 2007 ; McElroy et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

“…Several studies have been undertaken to elucidate cacao defense mechanisms against BPR. Since the first genetic map of cacao in 1995 ( Lanaud et al, 1995 ), several quantitative trait loci (QTL) analyses have identified over 60 QTL associated with BPR resistance ( Lanaud et al, 2009 ; Akaza et al, 2016 ; Barreto et al, 2018 ), highlighting the oligogenic nature of BPR resistance and the challenge this presents to breeders. Functional characterization of genes and associated mechanisms underlying QTL has not been demonstrated.…”

Section: Introductionmentioning

confidence: 99%

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Clovamide, a Hydroxycinnamic Acid Amide, Is a Resistance Factor Against Phytophthora spp. in Theobroma cacao

Knollenberg

Lambert

et al. 2020

Front. Plant Sci.

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The hydroxycinnamic acid amides (HCAAs) are a diverse group of plant-specialized phenylpropanoid metabolites distributed widely in the plant kingdom and are known to be involved in tolerance to abiotic and biotic stress. The HCAA clovamide is reported in a small number of distantly related species. To explore the contribution of specialized metabolites to disease resistance in cacao (Theobroma cacao L., chocolate tree), we performed untargeted metabolomics using liquid chromatography – tandem mass spectrometry (LC-MS/MS) and compared the basal metabolite profiles in leaves of two cacao genotypes with contrasting levels of susceptibility to Phytophthora spp. Leaves of the tolerant genotype ‘Scavina 6’ (‘Sca6’) were found to accumulate dramatically higher levels of clovamide and several other HCAAs compared to the susceptible ‘Imperial College Selection 1’ (‘ICS1’). Clovamide was the most abundant metabolite in ‘Sca6’ leaf extracts based on MS signal, and was up to 58-fold higher in ‘Sca6’ than in ‘ICS1’. In vitro assays demonstrated that clovamide inhibits growth of three pathogens of cacao in the genus Phytophthora, is a substrate for cacao polyphenol oxidase, and is a contributor to enzymatic browning. Furthermore, clovamide inhibited proteinase and pectinase in vitro, activities associated with defense in plant-pathogen interactions. Fruit epidermal peels from both genotypes contained substantial amounts of clovamide, but two sulfated HCAAs were present at high abundance exclusively in ‘Sca6’ suggesting a potential functional role of these compounds. The potential to breed cacao with increased HCAAs for improved agricultural performance is discussed.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Clovamide, a Hydroxycinnamic Acid Amide, Is a Resistance Factor Against Phytophthora spp. in Theobroma cacao

Knollenberg

Lambert

et al. 2020

Front. Plant Sci.

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“…It has been shown that molecular approaches, associated with morphological data, are required to resolve plant pathogen species complex, and they have revealed previously uncharacterized species affecting different crops ( Cooke et al, 2000 ; Blair et al, 2008 ; Bezuidenhout et al, 2010 ; Martin et al, 2014 ; Jung et al, 2017 ; Yang et al, 2017 ; Ruano-Rosa et al, 2018 ; Yang and Hong, 2018 ; Alves et al, 2019 ). Interestingly, several studies have shown that the genetic resistance to black pod rot in cacao is associated with different QTLs depending on the species of Phytophthora ( Risterucci et al, 2003 ; Barreto et al, 2018 ). Therefore, it is particularly important for cacao breeding studies to correctly identify the Phytophthora species that are used during phenotype screenings.…”

Section: Introductionmentioning

confidence: 99%

Phytophthora theobromicola sp. nov.: A New Species Causing Black Pod Disease on Cacao in Brazil

et al. 2021

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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 mycelial growth rates for the Phytophthora isolates were performed in vitro. Based on the molecular analysis and morphological comparisons, 19 isolates were identified as P. palmivora (clade 4). Interestingly, 31 isolates grouped together in the phylogenetic tree and were placed apart from previously known species in Phytophthora clade 2. Therefore, these isolates are considered as a new species herein referred to as Phytophthora theobromicola sp. nov., which produced papillate, semipapillate, and persistent sporangia on simple sporangiophores. The P. palmivora isolates were identified as A1 mating type by pairing each isolate with known A1 and A2 tester strains of P. capsici, but no oogonia/antheridia were observed when P. theobromicola was paired with the different tester strains. The P. theobromicola and P. citrophthora isolates showed higher mycelial growth rates, when compared to P. palmivora, on different media at 10, 15, and 20°C, but similar values were observed when grown on clarified CA media at 25 and 30°C. The pathogenicity tests carried out on pods of four cacao clones (CCN51, PS1319, Cepec2004, and CP49) showed significant variability among the isolates of both Phytophthora species, with P. theobromicola inducing higher rates of necrotic lesion expansion, when compared to P. palmivora. Here, two Phytophthora species were found associated with black pod disease in the state of Bahia, Brazil, and the previously undescribed P. theobromicola seems to be prevalent in field conditions. This is the first report of P. theobromicola on T. cacao. Also, these findings are crucial to improve the disease control strategies, and for the development of cacao materials genetically resistant to Phytophthora.

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“…It implements the model proposed by Gazaffi et al (2014), allowing to estimate the number of QTLs, their position, effects, segregation patterns, and linkage phases with flanking markers. This methodology has been successfully applied in different studies (Souza et al, 2013;Margarido et al, 2015;Costa et al, 2016;Balsalobre et al, 2017;da Silva Pereira et al, 2017;Barreto et al, 2018;Conson et al, 2018;Curtolo et al, 2020;Soratto et al, 2020), but currently there is no competing software with such features.…”

mentioning

confidence: 99%

fullsibQTL: an R package for QTL mapping in biparental populations of outcrossing species

Gazaffi

Amadeu

Mollinari

et al. 2020

Preprint

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Accurate QTL mapping in outcrossing species requires software programs which consider genetic features of these populations, such as markers with different segregation patterns and different level of information. Although the available mapping procedures to date allow inferring QTL position and effects, they are mostly not based on multilocus genetic maps. Having a QTL analysis based in such maps is crucial since they allow informative markers to propagate their information to less informative intervals of the map. We developed fullsibQTL, a novel and freely available R package to perform composite interval QTL mapping considering outcrossing populations and markers with different segregation patterns. It allows to estimate QTL position, effects, segregation patterns, and linkage phase with flanking markers. Additionally, several statistical and graphical tools are implemented, for straightforward analysis and interpretations. fullsibQTL is an R open source package with C and R source code (GPLv3). It is multiplatform and can be installed from https://github.com/augusto-garcia/fullsibQTL.

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

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

Cited by 19 publications

References 55 publications

Clovamide, a Hydroxycinnamic Acid Amide, Is a Resistance Factor Against Phytophthora spp. in Theobroma cacao

Clovamide, a Hydroxycinnamic Acid Amide, Is a Resistance Factor Against Phytophthora spp. in Theobroma cacao

Phytophthora theobromicola sp. nov.: A New Species Causing Black Pod Disease on Cacao in Brazil

fullsibQTL: an R package for QTL mapping in biparental populations of outcrossing species

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