ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2015
Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Article
- Article
- Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing.International journal of molecular sciences · 2021Review
- QTL mapping and identification of SNP-haplotypes affecting yield components ofHorticulture research · 2020Article
- The development of a novel SNP genotyping assay to differentiate cacao clones.Scientific reports · 2019Article
- Low-cost assembly of a cacao crop genome is able to resolve complex heterozygous bubbles.Horticulture research · 2019Article
- Identification of Climate and Genetic Factors That Control Fat Content and Fatty Acid Composition ofFrontiers in plant science · 2019Article
- Cacao biotechnology: current status and future prospects.Plant biotechnology journal · 2018Review
- Mapping of a Major QTL forFrontiers in plant science · 2018Article
- Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao.PloS one · 2018Article
- A Larger Chocolate Chip-Development of a 15KFrontiers in plant science · 2017Article
- 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 · 2017Article
- Widespread natural variation of DNA methylation within angiosperms.Genome biology · 2016Article
- Identification of candidate genes involved in Witches' broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil.BMC genomics · 2016Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Theobroma cacao, the key ingredient in chocolate production, is one of the world's most important tree fruit crops, with ∼4,000,000 metric tons produced across 50 countries. To move towards gene discovery and marker-assisted breeding in cacao, a single-nucleotide polymorphism (SNP) identification project was undertaken using RNAseq data from 16 diverse cacao cultivars. RNA sequences were aligned to the assembled transcriptome of the cultivar Matina 1-6, and 330,000 SNPs within coding regions were identified. From these SNPs, a subset of 6,000 high-quality SNPs were selected for inclusion on an Illumina Infinium SNP array: the Cacao6kSNP array. Using Cacao6KSNP array data from over 1,000 cacao samples, we demonstrate that our custom array produces a saturated genetic map and can be used to distinguish among even closely related genotypes. Our 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.