Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases

@article{RomeroNavarro2017ApplicationOG,
  title={Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases},
  author={J. Alberto Romero Navarro and Wilbert Phillips-Mora and Adriana Arciniegas-Leal and Allan Mata-Quir{\'o}s and Niina Haiminen and Guiliana M. Mustiga and Donald Livingstone III and Harm van Bakel and David N. Kuhn and Laxmi Parida and Andrew Kasarskis and Juan Motamayor},
  journal={Frontiers in Plant Science},
  year={2017},
  volume={8}
}
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… 

Figures and Tables from this paper

Genome wide association study reveals novel candidate genes associated with productivity and disease resistance to Moniliophthora spp. in cacao (Theobroma cacao L.)
TLDR
The work presented herein provides the first association mapping study in cacao using SNP markers based on GBS data, which identified two genes associated to productivity and seven to disease resistance.
Genome-Wide Association Study Reveals Novel Candidate Genes Associated with Productivity and Disease Resistance to Moniliophthora spp. in Cacao (Theobroma cacao L.)
TLDR
A genome-wide association study was performed on 102 accessions, discovering two genes associated with productivity and seven to disease resistance in cacao, enriched the knowledge of the genetic regions associated with important cacao traits that can have significant implications for conservation and breeding strategies like marker-assisted selection.
SNP markers associated with resistance to frosty pod and black pod rot diseases in an F1 population of Theobroma cacao L.
TLDR
The objectives of this study are to re-confirm the QTL using different marker set, discover new QTL associated with FPR and BPR resistance using SNP markers, and find genes in the candidate QTL regions.
Prediction of Cacao (Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection
TLDR
The 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.
Mapping of a Major QTL for Ceratocystis Wilt Disease in an F1 Population of Theobroma cacao
TLDR
The identification of a major QTL associated with CWC in an F1 mapping population from a cross between a resistant, “TSH 1188,” and a susceptible genotype, and the haplotype combination T1C2 on chromosome VI was the most significant for resistance.
Widely distributed variation in tolerance to Phytophthora palmivora in four genetic groups of cacao
TLDR
The results indicate that each of the four included genetic groups show variability for quantitative resistance to P. palmivora, a major cacao pathogen with global importance, which provides a foundation for future genomic and transcriptomic analysis of disease tolerance and susceptibility in the field at CATIE.
Association mapping reveals genomic regions associated with bienniality and resistance to biotic stresses in arabica coffee
TLDR
The genomic regions identified in this study can be incorporated into the coffee breeding program, through assisted selection, leading to more efficient breeding strategies in coffee.
Phenotypic Description of Theobroma cacao L. for Yield and Vigor Traits From 34 Hybrid Families in Costa Rica Based on the Genetic Basis of the Parental Population
TLDR
Preliminary comparison of clonal parents vs. seedlings yield in the family with the highest SCA suggest for the first time presence of heterobeltiosis in cacao.
Candidate SSR tags for fruit and seed traits of Theobroma cacao L . in the International Cocoa Genebank
Increasing yield is a prominent feature of crop breeding programmes including the economically important cacao (Theobroma cacao L.). As a tropical tree crop, the time and acreage needed for selection
Genome-wide association studies and genomic selection assays made in a large sample of cacao (Theobroma cacao L.) germplasm reveal significant marker-trait associations and good predictive value for improving yield potential
TLDR
The findings of this study could facilitate genomic selection and marker-assisted breeding of cacao thereby expediting improvement in the yield potential of cacoa planting material.
...
...

References

SHOWING 1-10 OF 59 REFERENCES
A meta–QTL analysis of disease resistance traits of Theobroma cacao L.
TLDR
This alternative approach confirms the existence of several sources of resistance to different diseases of cocoa which could be cumulated in new varieties to increase the sustainability of cocoa resistance using MAS strategies.
Mapping QTLs for Resistance to Frosty Pod and Black Pod Diseases and Horticultural Traits in Theobroma cacao L.
TLDR
A heterozygous F 1 mapping population of cacao was created and evaluated for resistance to frosty pod, black pod, and Phytophthora palmivora diseases and for horticultural traits at CATIE in Turrialba, Costa Rica.
A genomewide admixture mapping study for yield factors and morphological traits in a cultivated cocoa (Theobroma cacao L.) population
TLDR
C cultivated populations of Modern Criollo or Trinitario varieties may be suitable for admixture mapping analysis, as large blocks of alleles derived from two identified divergent ancestors are still preserved, after a few generations of recombination, similar to experimental mapping progenies.
Genome-wide association mapping of sexual incompatibility genes in cacao (Theobroma cacao L.)
TLDR
This study aimed to identify SNP markers associated with sexual compatibility in cacao, by utilizing genome-wide association (GWAS) mapping and found significant markers associated to incompatibility within a region of 196 kb, in the proximal end of chromosome 4, suggesting the existence of a major gene in that region.
Adding value to cocoa (Theobroma cacao L.) germplasm information with domestication history and admixture mapping
TLDR
This work confirmed that linkage disequilibrium extended over long genetic distances along chromosome regions, as expected in populations derived from recent admixture in cacao trees derived from three centuries of admixture between Meso-American Criollo and South American Forastero genomes.
Sources of Resistance to Phytophthora Pod Rot at the International CocoaGenebank, Trinidad
TLDR
One hundred and five promising resistant genotypes were identified among the 816 cacao accessions evaluated for resistance to Phytophthora pod rot, reinforcing the idea of a pre-breeding programme (germplasm enhancement) to accumulate resistance genes over several populations as a strategy for improving the genetic base of resistance in national cacao breeding programmes.
Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L. and its impact on association mapping
TLDR
This work uses microsatellite marker data collected from a uniquely diverse sample of individuals broadly covering both wild and cultivated varieties to gauge the LD present in the different cacao diversity groups and populations and finds that genome-wide LD decays far more rapidly in the wild and primitive diversity groups of cacao as compared to those representing cultivated varieties.
The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color
TLDR
It is demonstrated that green/red pod color in cacao is likely regulated by the R2R3 MYB transcription factor TcMYB113, homologs of which determine pigmentation in Rosaceae, Solanaceae, and Brassicaceae.
OVERCOMING THE MAIN LIMITING FACTORS OF CACAO PRODUCTION IN CENTRAL AMERICA THROUGH THE USE OF IMPROVED CLONES DEVELOPED AT CATIE
Cacao cultivation has been an important component of Central American culture and commerce since pre-Columbian times. However, during the last decades of the 20 th century, cacao production declined
Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao
TLDR
This study enhances and expands the genetic resources available to the cacao research community, and provides the genome-scale set of tools that are critical for advancing breeding with molecular markers in an agricultural species with high genetic diversity.
...
...