Making a Chocolate Chip: Development and Evaluation of a 6K SNP Array for Theobroma Cacao

Overview

Journal DNA Res

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2015 Jun 14

PMID 26070980

Citations 14

Authors

Donald Livingstone

Stefan Royaert

Conrad Stack

Keithanne Mockaitis

Greg May

Andrew Farmer

Christopher Saski

Ray Schnell

David Kuhn

Juan Carlos Motamayor

Affiliations

Soon will be listed here.

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.

Citing Articles

Comparing the performances of SSR and SNP markers for population analysis in Theobroma cacao L., as alternative approach to validate a new ddRADseq protocol for cacao genotyping.

Ramirez-Ramirez A, Bidot-Martinez I, Mirzaei K, Rasoamanalina Rivo O, Menendez-Grenot M, Clape-Borges P PLoS One. 2024; 19(5):e0304753.

PMID: 38820504 PMC: 11142705. DOI: 10.1371/journal.pone.0304753.

Genome-wide SNP genotyping as a simple and practical tool to accelerate the development of inbred lines in outbred tree species: An example in cacao (Theobroma cacao L.).

Lopes U, Pires J, Gramacho K, Grattapaglia D PLoS One. 2022; 17(10):e0270437.

PMID: 36288356 PMC: 9604995. DOI: 10.1371/journal.pone.0270437.

Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing.

Ahmar S, Ballesta P, Ali M, Mora-Poblete F Int J Mol Sci. 2021; 22(19).

PMID: 34638922 PMC: 8508745. DOI: 10.3390/ijms221910583.

QTL mapping and identification of SNP-haplotypes affecting yield components of L.

Fernandes L, Correa F, Ingram K, de Almeida A, Royaert S Hortic Res. 2020; 7:26.

PMID: 32140235 PMC: 7049306. DOI: 10.1038/s41438-020-0250-3.

Identification of Climate and Genetic Factors That Control Fat Content and Fatty Acid Composition of L. Beans.

Mustiga G, Morrissey J, Stack J, DuVal A, Royaert S, Jansen J Front Plant Sci. 2019; 10:1159.

PMID: 31681345 PMC: 6802002. DOI: 10.3389/fpls.2019.01159.

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