A Larger Chocolate Chip—Development of a 15K Theobroma cacao L. SNP Array to Create High-Density Linkage Maps

Abstract

Cacao (Theobroma cacao L.) is an important cash crop in tropical regions around the world and has a rich agronomic history in South America. As a key component in the cosmetic and confectionary industries, millions of people worldwide use products made from cacao, ranging from shampoo to chocolate. An Illumina Infinity II array was created using 13,530 SNPs identified within a small diversity panel of cacao. Of these SNPs, 12,643 derive from variation within annotated cacao genes. The genotypes of 3,072 trees were obtained, including two mapping populations from Ecuador. High-density linkage maps for these two populations were generated and compared to the cacao genome assembly. Phenotypic data from these populations were combined with the linkage maps to identify the QTLs for yield and disease resistance.

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

“…In addition, the regions we mapped on chromosome II at 41.2 and 57.9 cM for DBW and PI are most likely the same regions mapped for bean traits (length, width, and thickness) and the number of ovules 3 . A significant region at the top of chromosome IV was also reported by Livingstone et al 24 for cherelle wilt, the total number of pods, and fresh bean weight. This QTL falls within one of the regions mapped for self-incompatibility 26 , which is a crucial yield factor 27 .…”

“…In our study, the region is associated with yield components. In other studies, the region from 1414 bp to 1,686,245 bp on chromosome IV is associated with other traits that may directly affect the cacao production, such as cherelle wilt ratio, fresh bean weight, fresh weight/pod, total number of pods, and disease resistance 24 , fatty acid composition 25 and sexualcompatibility 26 . Another QTL associated with fat content in the MP01 population was also found on chromosome IV from 19,637,361 bp to 26,233,319 bp 25 .…”

“…MP01 comprises 459 trees from a cross between 'TSH 1188', used as the female parent, and 'CCN 51', used as the male parent. The female parent is related to Iquitos and Nanay genetic groups 13,24 , and the male parent has predominant ancestries from Iquitos, Criollo, and Amelonado 13,14,24 . Those parents contrast for many important traits, and the MP01 progenies segregate for disease resistance 11,29,51 , pod color 5 , fat content and fat composition 25 .…”

Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process

“…We tested the hypothesis that the accumulation of deleterious mutations due to domestication would decrease fitness by examining the relationship between Criollo ancestry and a measure of performance in cacao using an independent dataset. Individuals were genotyped with a SNP array that was developed using a subset of genotypes inferred as part of this work and published elsewhere 61 . We measured bean (seed) productivity (yield in kilograms of bean per hectare per year for each plant) as a measure of fitness.…”

“…Finally, we genotyped an additional set of 151 accessions using a customized chip of 15 K SNPs specific for cacao that was developed in parallel to this work using the novel variants identified in a subset of the accessions 61 . We intersected the genotyped set with the 79 accessions from this work that clearly belong to each one of the putative genetically differentiated populations and performed a supervised ancestry analysis in ADMIXTURE with conditions similar to those explained previously.…”