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

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 highyielding cacao varieties through marker-assisted selection in our existing cacao-breeding experiments.

The spatial distribution and height of associated crops influence cocoa tree productivity in complex agroforestry systems

“…Finally, neither the agronomic and morphological characteristics nor the competition or facilitation of plant communities in the neighborhood of the cocoa tree are enough to explain all the variations in cocoa production. These variations are also linked to genetic factors, with certain genes involved in the formation of cocoa production (Fernandes et al 2020), that are more or less active depending on soil and climate conditions. Indeed, within the same plot, we observed significant differences in productivity between cocoa trees of the same origin, whether directly sown using beans from own pods or cocoa clones produced in the nursery.…”

Geographic distribution, conservation, and genomic resources of cacao Theobroma cacao L

“…Cacao candidate genes determining seed and yield traits were identified on chromosome IV via QTL mapping (Fernandes et al., 2020). Nine out of 13 candidate genes were involved in specialized functions such as sugar transport; other genes were involved in carbohydrate, lipid, and glucose metabolism (Fernandes et al., 2020).…”

“…Cacao candidate genes determining seed and yield traits were identified on chromosome IV via QTL mapping (Fernandes et al., 2020). Nine out of 13 candidate genes were involved in specialized functions such as sugar transport; other genes were involved in carbohydrate, lipid, and glucose metabolism (Fernandes et al., 2020). For each agronomic trait, such as number of pods (fruits) harvested per tree, dry seed weight, average yield per tree (kg of dry seeds/year), and pod index, it was possible to link at least one significant SNP contributing to the phenotypic variation of these traits, respectively (Fernandes et al., 2020).…”

“…Nine out of 13 candidate genes were involved in specialized functions such as sugar transport; other genes were involved in carbohydrate, lipid, and glucose metabolism (Fernandes et al., 2020). For each agronomic trait, such as number of pods (fruits) harvested per tree, dry seed weight, average yield per tree (kg of dry seeds/year), and pod index, it was possible to link at least one significant SNP contributing to the phenotypic variation of these traits, respectively (Fernandes et al., 2020). Pod index refers to the number of fruits needed to produce 1 kg of dry seeds; a low pod index (e.g., 21–25) is preferred because it helps to select trees that yield heavier and larger seeds (Bekele et al., 2020; Goenaga et al., 2009).…”

Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars

“…SSRs have been the most used molecular marker type in DNA fingerprinting technology, for their convenience of usage and the high polymorphic information content (PIC) per marker (Gramazio et al, 2017). However, even though SNPs usually have lower polymorphic information content (PIC) per marker than SSRs, the usage of SNPs has been increasing dramatically in recent years due to several advantages (Fernandes et al, 2020;Hadizadeh et al, 2020;Wu and Alexander, 2020;Xin et al, 2020). SNPs are generally more abundant and more stable than SSRs, which are located at simple repeat regions and had mutation rates several orders of magnitude higher than SNPs (Fischer et al, 2017).…”