Prediction of Cacao (Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection
Cacao (Theobroma cacao) is a globally important crop, and its yield is severely restricted by disease. Two of the most damaging diseases, witches’ broom disease (WBD) and frosty pod rot disease (FPRD), are caused by a pair of related fungi: Moniliophthora perniciosa and Moniliophthora roreri, respec...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fpls.2018.00343/full |
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| author | Michel S. McElroy Alberto J. R. Navarro Guiliana Mustiga Conrad Stack Salvador Gezan Geover Peña Widem Sarabia Diego Saquicela Ignacio Sotomayor Gavin M. Douglas Zoë Migicovsky Freddy Amores Omar Tarqui Sean Myles Juan C. Motamayor |
| author_facet | Michel S. McElroy Alberto J. R. Navarro Guiliana Mustiga Conrad Stack Salvador Gezan Geover Peña Widem Sarabia Diego Saquicela Ignacio Sotomayor Gavin M. Douglas Zoë Migicovsky Freddy Amores Omar Tarqui Sean Myles Juan C. Motamayor |
| author_sort | Michel S. McElroy |
| collection | DOAJ |
| description | Cacao (Theobroma cacao) is a globally important crop, and its yield is severely restricted by disease. Two of the most damaging diseases, witches’ broom disease (WBD) and frosty pod rot disease (FPRD), are caused by a pair of related fungi: Moniliophthora perniciosa and Moniliophthora roreri, respectively. Resistant cultivars are the most effective long-term strategy to address Moniliophthora diseases, but efficiently generating resistant and productive new cultivars will require robust methods for screening germplasm before field testing. Marker-assisted selection (MAS) and genomic selection (GS) provide two potential avenues for predicting the performance of new genotypes, potentially increasing the selection gain per unit time. To test the effectiveness of these two approaches, we performed a genome-wide association study (GWAS) and GS on three related populations of cacao in Ecuador genotyped with a 15K single nucleotide polymorphism (SNP) microarray for three measures of WBD infection (vegetative broom, cushion broom, and chirimoya pod), one of FPRD (monilia pod) and two productivity traits (total fresh weight of pods and % healthy pods produced). GWAS yielded several SNPs associated with disease resistance in each population, but none were significantly correlated with the same trait in other populations. Genomic selection, using one population as a training set to estimate the phenotypes of the remaining two (composed of different families), varied among traits, from a mean prediction accuracy of 0.46 (vegetative broom) to 0.15 (monilia pod), and varied between training populations. Simulations demonstrated that selecting seedlings using GWAS markers alone generates no improvement over selecting at random, but that GS improves the selection process significantly. Our results suggest that the GWAS markers discovered here are not sufficiently predictive across diverse germplasm to be useful for MAS, but that using all markers in a GS framework holds substantial promise in accelerating disease-resistance in cacao. |
| first_indexed | 2024-12-11T11:32:51Z |
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| id | doaj.art-32b1e823e2464d8ba3a635d1018eb1d7 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-11T11:32:51Z |
| publishDate | 2018-03-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-32b1e823e2464d8ba3a635d1018eb1d72022-12-22T01:08:50ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-03-01910.3389/fpls.2018.00343325158Prediction of Cacao (Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic SelectionMichel S. McElroy0Alberto J. R. Navarro1Guiliana Mustiga2Conrad Stack3Salvador Gezan4Geover Peña5Widem Sarabia6Diego Saquicela7Ignacio Sotomayor8Gavin M. Douglas9Zoë Migicovsky10Freddy Amores11Omar Tarqui12Sean Myles13Juan C. Motamayor14Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, CanadaMARS, Incorporated c/o United States Department of Agriculture – Agricultural Research Service, Miami, FL, United StatesMARS, Incorporated c/o United States Department of Agriculture – Agricultural Research Service, Miami, FL, United StatesMARS, Incorporated c/o United States Department of Agriculture – Agricultural Research Service, Miami, FL, United StatesSchool of Forest Resources and Conservation, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, United StatesInstituto Nacional de Investigaciones Agropecuarias, Quito, EcuadorInstituto Nacional de Investigaciones Agropecuarias, Quito, EcuadorInstituto Nacional de Investigaciones Agropecuarias, Quito, EcuadorInstituto Nacional de Investigaciones Agropecuarias, Quito, EcuadorDepartment of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, CanadaDepartment of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, CanadaFacultad de Ciencias Agrarias, Universidad Técnica Estatal de Quevedo, Quevedo, EcuadorInstituto Nacional de Investigaciones Agropecuarias, Quito, EcuadorDepartment of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, CanadaMARS, Incorporated c/o United States Department of Agriculture – Agricultural Research Service, Miami, FL, United StatesCacao (Theobroma cacao) is a globally important crop, and its yield is severely restricted by disease. Two of the most damaging diseases, witches’ broom disease (WBD) and frosty pod rot disease (FPRD), are caused by a pair of related fungi: Moniliophthora perniciosa and Moniliophthora roreri, respectively. Resistant cultivars are the most effective long-term strategy to address Moniliophthora diseases, but efficiently generating resistant and productive new cultivars will require robust methods for screening germplasm before field testing. Marker-assisted selection (MAS) and genomic selection (GS) provide two potential avenues for predicting the performance of new genotypes, potentially increasing the selection gain per unit time. To test the effectiveness of these two approaches, we performed a genome-wide association study (GWAS) and GS on three related populations of cacao in Ecuador genotyped with a 15K single nucleotide polymorphism (SNP) microarray for three measures of WBD infection (vegetative broom, cushion broom, and chirimoya pod), one of FPRD (monilia pod) and two productivity traits (total fresh weight of pods and % healthy pods produced). GWAS yielded several SNPs associated with disease resistance in each population, but none were significantly correlated with the same trait in other populations. Genomic selection, using one population as a training set to estimate the phenotypes of the remaining two (composed of different families), varied among traits, from a mean prediction accuracy of 0.46 (vegetative broom) to 0.15 (monilia pod), and varied between training populations. Simulations demonstrated that selecting seedlings using GWAS markers alone generates no improvement over selecting at random, but that GS improves the selection process significantly. Our results suggest that the GWAS markers discovered here are not sufficiently predictive across diverse germplasm to be useful for MAS, but that using all markers in a GS framework holds substantial promise in accelerating disease-resistance in cacao.http://journal.frontiersin.org/article/10.3389/fpls.2018.00343/fullTheobroma cacaowitches’ broom diseasefrosty pod rotSNPsGWASgenomic selection |
| spellingShingle | Michel S. McElroy Alberto J. R. Navarro Guiliana Mustiga Conrad Stack Salvador Gezan Geover Peña Widem Sarabia Diego Saquicela Ignacio Sotomayor Gavin M. Douglas Zoë Migicovsky Freddy Amores Omar Tarqui Sean Myles Juan C. Motamayor Prediction of Cacao (Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection Frontiers in Plant Science Theobroma cacao witches’ broom disease frosty pod rot SNPs GWAS genomic selection |
| title | Prediction of Cacao (Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection |
| title_full | Prediction of Cacao (Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection |
| title_fullStr | Prediction of Cacao (Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection |
| title_full_unstemmed | Prediction of Cacao (Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection |
| title_short | Prediction of Cacao (Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection |
| title_sort | prediction of cacao theobroma cacao resistance to moniliophthora spp diseases via genome wide association analysis and genomic selection |
| topic | Theobroma cacao witches’ broom disease frosty pod rot SNPs GWAS genomic selection |
| url | http://journal.frontiersin.org/article/10.3389/fpls.2018.00343/full |
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