Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases
Chocolate is a highly valued and palatable confectionery product. Chocolate is primarily made from the processed seeds of the tree species Theobroma cacao. Cacao cultivation is highly relevant for small-holder farmers throughout the tropics, yet its productivity remains limited by low yields and wid...
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doaj-cc9317a2e6af437c83fc61316ea016702020-11-24T23:21:58ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2017-11-01810.3389/fpls.2017.01905295133Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod DiseasesJ. Alberto Romero Navarro0Wilbert Phillips-Mora1Adriana Arciniegas-Leal2Allan Mata-Quirós3Niina Haiminen4Guiliana Mustiga5Donald Livingstone III6Harm van Bakel7David N. Kuhn8Laxmi Parida9Andrew Kasarskis10Juan C. Motamayor11Mars Incorporated, Miami, FL, United StatesTropical Agricultural Research and Higher Education Center, Turrialba, Costa RicaTropical Agricultural Research and Higher Education Center, Turrialba, Costa RicaTropical Agricultural Research and Higher Education Center, Turrialba, Costa RicaIBM Thomas J. Watson Research Center, New York, NY, United StatesMars Incorporated, Miami, FL, United StatesMars Incorporated, Miami, FL, United StatesIcahn School of Medicine at Mount Sinai, Icahn Institute of Genomics and Multiscale Biology, New York, NY, United StatesSubtropical Horticulture Research Station, United States Department of Agriculture-Agricultural Research Service, Miami, FL, United StatesIBM Thomas J. Watson Research Center, New York, NY, United StatesIcahn School of Medicine at Mount Sinai, Icahn Institute of Genomics and Multiscale Biology, New York, NY, United StatesMars Incorporated, Miami, FL, United StatesChocolate is a highly valued and palatable confectionery product. Chocolate is primarily made from the processed seeds of the tree species Theobroma cacao. Cacao cultivation is highly relevant for small-holder farmers throughout the tropics, yet its productivity remains limited by low yields and widespread pathogens. A panel of 148 improved cacao clones was assembled based on productivity and disease resistance, and phenotypic single-tree replicated clonal evaluation was performed for 8 years. Using high-density markers, the diversity of clones was expressed relative to 10 known ancestral cacao populations, and significant effects of ancestry were observed in productivity and disease resistance. Genome-wide association (GWA) was performed, and six markers were significantly associated with frosty pod disease resistance. In addition, genomic selection was performed, and consistent with the observed extensive linkage disequilibrium, high predictive ability was observed at low marker densities for all traits. Finally, quantitative trait locus mapping and differential expression analysis of two cultivars with contrasting disease phenotypes were performed to identify genes underlying frosty pod disease resistance, identifying a significant quantitative trait locus and 35 differentially expressed genes using two independent differential expression analyses. These results indicate that in breeding populations of heterozygous and recently admixed individuals, mapping approaches can be used for low complexity traits like pod color cacao, or in other species single gene disease resistance, however genomic selection for quantitative traits remains highly effective relative to mapping. Our results can help guide the breeding process for sustainable improved cacao productivity.http://journal.frontiersin.org/article/10.3389/fpls.2017.01905/fullTheobroma cacaotree cropsbreedingdisease resistancegenomic selectionlinkage disequilibrium |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
J. Alberto Romero Navarro Wilbert Phillips-Mora Adriana Arciniegas-Leal Allan Mata-Quirós Niina Haiminen Guiliana Mustiga Donald Livingstone III Harm van Bakel David N. Kuhn Laxmi Parida Andrew Kasarskis Juan C. Motamayor |
spellingShingle |
J. Alberto Romero Navarro Wilbert Phillips-Mora Adriana Arciniegas-Leal Allan Mata-Quirós Niina Haiminen Guiliana Mustiga Donald Livingstone III Harm van Bakel David N. Kuhn Laxmi Parida Andrew Kasarskis Juan C. Motamayor Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases Frontiers in Plant Science Theobroma cacao tree crops breeding disease resistance genomic selection linkage disequilibrium |
author_facet |
J. Alberto Romero Navarro Wilbert Phillips-Mora Adriana Arciniegas-Leal Allan Mata-Quirós Niina Haiminen Guiliana Mustiga Donald Livingstone III Harm van Bakel David N. Kuhn Laxmi Parida Andrew Kasarskis Juan C. Motamayor |
author_sort |
J. Alberto Romero Navarro |
title |
Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases |
title_short |
Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases |
title_full |
Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases |
title_fullStr |
Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases |
title_full_unstemmed |
Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases |
title_sort |
application of genome wide association and genomic prediction for improvement of cacao productivity and resistance to black and frosty pod diseases |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Plant Science |
issn |
1664-462X |
publishDate |
2017-11-01 |
description |
Chocolate is a highly valued and palatable confectionery product. Chocolate is primarily made from the processed seeds of the tree species Theobroma cacao. Cacao cultivation is highly relevant for small-holder farmers throughout the tropics, yet its productivity remains limited by low yields and widespread pathogens. A panel of 148 improved cacao clones was assembled based on productivity and disease resistance, and phenotypic single-tree replicated clonal evaluation was performed for 8 years. Using high-density markers, the diversity of clones was expressed relative to 10 known ancestral cacao populations, and significant effects of ancestry were observed in productivity and disease resistance. Genome-wide association (GWA) was performed, and six markers were significantly associated with frosty pod disease resistance. In addition, genomic selection was performed, and consistent with the observed extensive linkage disequilibrium, high predictive ability was observed at low marker densities for all traits. Finally, quantitative trait locus mapping and differential expression analysis of two cultivars with contrasting disease phenotypes were performed to identify genes underlying frosty pod disease resistance, identifying a significant quantitative trait locus and 35 differentially expressed genes using two independent differential expression analyses. These results indicate that in breeding populations of heterozygous and recently admixed individuals, mapping approaches can be used for low complexity traits like pod color cacao, or in other species single gene disease resistance, however genomic selection for quantitative traits remains highly effective relative to mapping. Our results can help guide the breeding process for sustainable improved cacao productivity. |
topic |
Theobroma cacao tree crops breeding disease resistance genomic selection linkage disequilibrium |
url |
http://journal.frontiersin.org/article/10.3389/fpls.2017.01905/full |
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