Dr. Helmuth E. Nieves-Orduña

Research interests
I focus on applied genomics of tropical trees and crops, with an emphasis on germplasm, population genetics, agronomic traits, climate adaptation, and breeding.

Education
2023 Doctor of Philosophy (magna cum laude). Georg-August-Universität Göttingen, Germany. Dissertation: Genetic diversity of cacao (Theobroma cacao L.) populations and agronomic traits for breeding.

2012 M.Sc. Forest Sciences, Tropical and International Forestry. Georg-August-Universität Göttingen. Germany.

Publications
ORCID https://orcid.org/0000-0002-9588-072X
Email: hnieves@gwdg.de
Project: Genetic diversity of cacao (Theobroma cacao L.) populations and agronomic traits for breeding (10/2018-11/2023).
The Amazonian cacao tree or the chocolate tree (Theobroma cacao L.) is cultivated to produce seeds, the valuable raw material for the global chocolate industry. Thus, the conservation and use of cacao genetic resources are vital for providing cacao farmers with optimal planting material to sustain the world cacao economy.
The research goal is to understand patterns of geographic genetic diversity of cacao populations and genetic control of agronomic traits in cacao populations (wild, cultivated and breeding populations) to provide novel genetic information and uncover valuable cacao genotypes for cacao breeding programs. We used two approaches: i) genotyping cacao chloroplast microsatellite (simple sequence repeat - SSR) markers, and ii) analysis of published SNP (single-nucleotide polymorphism) markers associated with agronomic traits such as disease resistance and yield. In addition, we analyzed the geographic distribution of wild cacao, reviewed the genetic basis of agronomic traits and available genomic resources for cacao breeding.
This research project is divided into three main parts:
The first part is presented in the scientific paper “Geographic distribution, conservation, and genomic resources of cacao Theobroma cacao L.” published in Crop Science analyses the geographic distribution of cacao and pinpoints new areas for germplasm collection. It discusses the conservation of cacao genetic resources, the genetic basis of agronomic traits, and genomic resources for cacao genetic improvement. It proposes research areas on germplasm management and agronomic traits for breeding new cacao varieties.
The second part is presented in the research paper “Geographic patterns of genetic variation among cacao (Theobroma cacao L.) populations based on chloroplast markers” published in Diversity and focused on the phylogeographic structure of natural and cultivated cacao populations using chloroplast DNA (cpDNA) polymorphisms. It showed how chloroplast genetic diversity is geographically distributed in Amazonia, and how it is represented in common cacao genotypes of farms and breeding populations.
The third part is presented in the research paper “Genotyping of cacao (Theobroma cacao L.) germplasm resources with SNP markers linked to agronomic traits”, published in Tree Genetics & Genomes describes the study of candidate genes whose variation is associated with important agronomic traits and could be under selection. It provides also information on population structure of wild and cultivated cacao, identifies agronomic traits under selection, and uncovers valuable cacao genotypes not observed yet in cultivated and breeding populations.
Samples and an external collaboration
To obtain cacao samples for genetic analysis we collaborated with the University of Reading (UK), the International Cocoa Quarantine Centre (ICQC, Reading, UK), and the Tropical Agricultural Research and Higher Education Center (CATIE, Turrialba, Costa Rica). The 346 analyzed samples represent wild populations with a wide geographic distribution in Amazonia, as well as cultivars and breeding populations. Phenotypic and passport information about the samples analyzed were obtained from published data and the International Cocoa Germplasm Database (ICGD).
Financing
The German Academic Exchange Service (DAAD). The Graduate School Forest and Agricultural Sciences (GFA), and the Department of Forest Genetics and Tree Breeding at the University of Göttingen.
Thesis committee
Prof. Dr. Oliver Gailing (First Supervisor)
Prof. Dr. Konstantin Krutovsky (Second Supervisor)
Prof. Dr. Ralph Mitlöhner (Second Supervisor)
Publications
Nieves-Orduña HE, Müller M, Krutovsky K, Gailing O. (2024). Genotyping of cacao (Theobroma cacao L.) germplasm resources with SNP markers linked to agronomic traits reveals signs of selection. Tree Genetics & Genomes 20, 13 (2024).
https://doi.org/10.1007/s11295-024-01646-w

Nieves‐Orduña HE, Krutovsky KV, Gailing O. (2023). Geographic distribution, conservation, and genomic resources of cacao Theobroma cacao L. Crop Sci. 63:1750–1778. https://doi.org/10.1002/csc2.20959

Nieves-Orduña HE, Müller M, Krutovsky KV, Gailing O. (2021). Geographic patterns of genetic variation among cacao (Theobroma cacao L.) populations based on chloroplast markers. Diversity 13:249. https://doi.org/10.3390/d13060249

Nieves-Orduña HE, Müller M, Krutovsky KV, Gailing O. (2021). High Chloroplast Diversity of Cacao (Theobroma Cacao L.) in Western Amazonia. Poster presented at the Tropentag 2021: Towards shifting paradigms in agriculture for a healthy and sustainable future, University of Hohenheim, Germany, September 15 - 17, 2021.
https://www.tropentag.de/2021/abstracts/links/Gailing_U6vQM79y.pdf
https://www.tropentag.de/2021/abstracts/posters/27.pdf