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Article|01 Mar 2020|OPEN
QTL mapping and identification of SNP-haplotypes affecting yield components of Theobroma cacao L.
Luciel dos Santos Fernandes1, Fábio M. Correa2, Keith T. Ingram3, Alex-Alan Furtado de Almeida2 & Stefan Royaert3,
1Mars Center for Cocoa Science, CP 55, Itajuípe, BA CEP 45.630-000, Brazil
2Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, Km 16, Bairro Salobrinho, Ilhéus, BA CEP 45.662-900, Brazil
3Mars, Incorporated, 13601 Old Cutler Road, Miami, FL 33158, USA

Horticulture Research 7,
Article number: 20026 (2020)
doi: 10.1038/hortres.2020.26
Views: 380

Received: 25 Sep 2019
Revised: 15 Jan 2020
Accepted: 16 Jan 2020
Published online: 01 Mar 2020

Abstract

Cacao is a crop of global relevance that faces constant demands for improved bean yield. However, little is known about the genomic regions controlling the crop yield and genes involved in cacao bean filling. Hence, to identify the quantitative trait loci (QTL) associated with cacao yield and bean filling, we performed a QTL mapping in a segregating mapping population comprising 459 trees of a cross between ‘TSH 1188’ and ‘CCN 51’. All variables showed considerable phenotypic variation and had moderate to high heritability values. We identified 24 QTLs using a genetic linkage map that contains 3526 single nucleotide polymorphism (SNP) markers. Haplotype analysis at the significant QTL region on chromosome IV pointed to the alleles from the maternal parent, ‘TSH 1188’, as the ones that affect the cacao yield components the most. The recombination events identified within these QTL regions allowed us to identify candidate genes that may take part in the different steps of pod growth and bean filling. Such candidate genes seem to play a significant role in the source-to-sink transport of sugars and amino acids, and lipid metabolism, such as fatty acid production. The SNP markers mapped in our study are now being used to select potential high-yielding cacao varieties through marker-assisted selection in our existing cacao-breeding experiments.