Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao.

Jaime A Osorio-Guarín,Omar E Cornejo,Corey R Quackenbush

doi:10.1371/journal.pone.0203973

Abstract

As the source of chocolate, cacao has become one of the most important crops in the world. The identification of molecular markers to understand the demographic history, genetic diversity and population structure plays a pivotal role in cacao breeding programs. Here, we report the use of a modified genotyping-by-sequencing (GBS) approach for large-scale single nucleotide polymorphism (SNP) discovery and allele ancestry mapping. We identified 12,357 bi-allelic SNPs after filtering, of which, 7,009 variants were ancestry informative. The GBS approach proved to be rapid, cost-effective, and highly informative for ancestry assignment in this species.

Highlights

Theobroma cacao L, the tree from which chocolate is confectioned, originated in the Amazonian basin [1] and has become a globally cultivated crop in recent times [2]
We further show that the data generated produced genetic diversity estimates consistent with what has been shown in previous work
Due to the lower cost of generating this type of data we propose that this strategy could be widely used to perform genetic diversity analysis on thousands of samples, facilitating association mapping studies aimed at identifying the genetic basis of important agronomic traits in cacao such as disease resistance and bean quality

Summary

Introduction

Theobroma cacao L, the tree from which chocolate is confectioned, originated in the Amazonian basin [1] and has become a globally cultivated crop in recent times [2]. T. cacao is the only species that is cultivated extensively because it can be manufactured into chocolate, liquors, confections, cosmetics, and animal feed [4,5]. The domestication of cacao has resulted in the development of an important crop that sustains the livelihood of communities throughout Central and South America, Asia, and Africa [1,9,10], and is the principal income for about six million smallholder farmers globally that produce up to 90% of the world’s cocoa [11]

Methods

Results

Discussion

Conclusion