Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback
Abstract Diseases of Theobroma cacao L. (Malvaceae) disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by Ceratobasidium theobromae, is a new encounter disease of cacao currently contained to southeast Asia and Melanesia. Resistance to VSD has been teste...
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| Format: | Article |
| Language: | English |
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Wiley
2024-12-01
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| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.20524 |
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| author | Peri A. Tobias Jacob Downs Peter Epaina Gurpreet Singh Robert F. Park Richard J. Edwards Eirene Brugman Andi Zulkifli Junaid Muhammad Agus Purwantara David I. Guest |
| author_facet | Peri A. Tobias Jacob Downs Peter Epaina Gurpreet Singh Robert F. Park Richard J. Edwards Eirene Brugman Andi Zulkifli Junaid Muhammad Agus Purwantara David I. Guest |
| author_sort | Peri A. Tobias |
| collection | DOAJ |
| description | Abstract Diseases of Theobroma cacao L. (Malvaceae) disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by Ceratobasidium theobromae, is a new encounter disease of cacao currently contained to southeast Asia and Melanesia. Resistance to VSD has been tested with large progeny trials in Sulawesi, Indonesia, and in Papua New Guinea with the identification of informative quantitative trait loci (QTLs). Using a VSD susceptible progeny tree (clone 26), derived from a resistant and susceptible parental cross, we assembled the genome to chromosome‐level and discriminated alleles inherited from either resistant or susceptible parents. The parentally phased genomes were annotated for all predicted genes and then specifically for resistance genes of the nucleotide‐binding site leucine‐rich repeat class (NLR). On investigation, we determined the presence of NLR clusters and other potential disease response gene candidates in proximity to informative QTLs. We identified structural variants within NLRs inherited from parentals. We present the first diploid, fully scaffolded, and parentally phased genome resource for T. cacao L. and provide insights into the genetics underlying resistance and susceptibility to VSD. |
| format | Article |
| id | doaj-art-026248aacb09436086732997fabd3cd7 |
| institution | Kabale University |
| issn | 1940-3372 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj-art-026248aacb09436086732997fabd3cd72024-12-10T06:52:55ZengWileyThe Plant Genome1940-33722024-12-01174n/an/a10.1002/tpg2.20524Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak diebackPeri A. Tobias0Jacob Downs1Peter Epaina2Gurpreet Singh3Robert F. Park4Richard J. Edwards5Eirene Brugman6Andi Zulkifli7Junaid Muhammad8Agus Purwantara9David I. Guest10School of Life and Environmental Sciences The University of Sydney Camperdown New South Wales AustraliaSchool of Life and Environmental Sciences The University of Sydney Camperdown New South Wales AustraliaSchool of Life and Environmental Sciences The University of Sydney Camperdown New South Wales AustraliaSchool of Life and Environmental Sciences The University of Sydney Camperdown New South Wales AustraliaSchool of Life and Environmental Sciences The University of Sydney Camperdown New South Wales AustraliaMinderoo OceanOmics Centre at UWA, Oceans Institute The University of Western Australia Perth Western Australia AustraliaCocoa Research Center Faculty of Agriculture Universitas Hasanuddin Makassar IndonesiaMegarezky University Makassar IndonesiaCocoa Research Center Faculty of Agriculture Universitas Hasanuddin Makassar IndonesiaMars Cocoa Research Station Pangkep IndonesiaSchool of Life and Environmental Sciences The University of Sydney Camperdown New South Wales AustraliaAbstract Diseases of Theobroma cacao L. (Malvaceae) disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by Ceratobasidium theobromae, is a new encounter disease of cacao currently contained to southeast Asia and Melanesia. Resistance to VSD has been tested with large progeny trials in Sulawesi, Indonesia, and in Papua New Guinea with the identification of informative quantitative trait loci (QTLs). Using a VSD susceptible progeny tree (clone 26), derived from a resistant and susceptible parental cross, we assembled the genome to chromosome‐level and discriminated alleles inherited from either resistant or susceptible parents. The parentally phased genomes were annotated for all predicted genes and then specifically for resistance genes of the nucleotide‐binding site leucine‐rich repeat class (NLR). On investigation, we determined the presence of NLR clusters and other potential disease response gene candidates in proximity to informative QTLs. We identified structural variants within NLRs inherited from parentals. We present the first diploid, fully scaffolded, and parentally phased genome resource for T. cacao L. and provide insights into the genetics underlying resistance and susceptibility to VSD.https://doi.org/10.1002/tpg2.20524 |
| spellingShingle | Peri A. Tobias Jacob Downs Peter Epaina Gurpreet Singh Robert F. Park Richard J. Edwards Eirene Brugman Andi Zulkifli Junaid Muhammad Agus Purwantara David I. Guest Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback The Plant Genome |
| title | Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback |
| title_full | Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback |
| title_fullStr | Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback |
| title_full_unstemmed | Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback |
| title_short | Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback |
| title_sort | parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback |
| url | https://doi.org/10.1002/tpg2.20524 |
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