Biocomputing – Group Stephan Reinert

Food security, consumer preferences, and the imminent threats of the global climate change represent a strong force for breeders to find fast and efficient ways to develop new crop varieties accordingly. Therefore, a precise and deep knowledge of abiotic stress resistance and the underlying genetic factors in plants is of utter most importance to find new targets for crop improvement. The aim of our research is the analysis of different crop plants to reveal candidate genes, allelic variation, and genetic markers associated with important agronomic traits. By identifying these we are able to improve crop productivity, quality, and sustainability. To achieve this we use state-of-the-art statistical and bioinformatic tools from the field of quantitative and population genetics to analyze and integrate diverse data sets such as genomics, transcriptomics, metabolomics, and phenomics. This helps us to disentangle gene regulatory networks and the genetic basis of complex traits and to find new targets for molecular breeding.

 

 

Area of research:

Currently, we are working on two main projects focusing on the improvement of important starchy root crops:

1) Improving the productivity of cassava (Manihot esculenta)

Cassava (Manihot esculenta) is a woody shrub that develops starchy underground storage roots and is one of the most important crops for food security, especially in the tropics and subtropics. Although it is the most important staple food for more than 800 million people in the Americas, Africa, and Asia, it is primarily grown by smallholder farmers. Because smallholders have only limited access to the tools of modern agriculture, like heavy farming machinery, pest control or fertilizer, yield increase must come from plants that are inherently more productive, even under conditions of low-input agriculture. Therefore, our research, as a part of the Cassava Source-Sink (CASS)-project, is dedicated in developing robust and yield-improved cassava varieties that will be provided to African smallholder farmers to improve food security in Sub-Saharan Africa.

Unfortunately, conventional cassava breeding is very time-consuming, and it often takes several years before an improved variety can be approved. For this reason, as one of the bioinformatics parts of the CASS project consortium, we are working to complement conventional breeding and use bioinformatics approaches to achieve accelerated research success. For that, we use a wide variety of state-of-the-art methods including RNA (RNAseq) and whole genome sequencing (WGS) data analysis; expression-based genome- and transciptome-wide association studies (GWAS, TWAS, eGWAS); comparative analysis using clustering, association, regression, and dimensionality reduction methods; as well as the integration of phenotypic, metabolomic, and proteomic data. We are especially interested in agronomic, agro-morphological, as well as biotic and abiotic stress traits such as storage root quality, cassava mosaic disease, and cassava green mite severity to name just a few.

As a part of the CASS project we have close collaborations with national and international research facilities:

  •   Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
  •   International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria.
  •   National Root Crops Research Institute (NRCRI), Umudike, Nigeria.
  •   Institute of Bio- and Geosciences at Forschungszentrum Jülich, Germany.
  •   Max-Planck-Institute of Molecular Plant Physiology, Golm, Germany.
  •   Technische Universität Kaiserslautern, Germany.
  •   University of Cambridge, UK.
  •   University of Helsinki, Finland.
  •   Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY, USA.

2) Heat tolerance in Potato (Solanum tuberosum)

Potato is one of the most important food crops globally and ranks third only behind the cereals rice and wheat. Due it’s steady increase in overall production it is considered an important staple food source. The modern cultivars originated from the Andes in South America between Bolivia and Peru. Domestication of wild potato dates back nearly 8,000 years. Cultivated potatoes were introduced into Europe in the 1570s and were distributed globally in the late 17th century. Today, potatoes are grown world-wide from latitudes of 65°N to 50°S and from altitudes of up to 4,000 m. This demonstrates the immense adaptability of potato to many different environmental conditions. Even though potato is well adapted to a variety of environmental conditions, it shows a high sensitivity to abiotic stress conditions such as heat and drought. Especially high temperature (temperatures above 20°C) impacts tuber production of potato negatively.

As a result, our research on potato focuses on the bioinformatic analysis of potatoes under controlled and heat stress conditions to identify genomic regions associated with heat resistance. For that, we analyze genotype and phenotype information of more than 250 potato varieties and correlate them using a method called genome-wide association study (GWAS). A GWAS enables the identification of genomic regions associated with a trait of interested and how specific genome differences among different potato varieties influence the trait of interest. In our potato heat tolerance project we are especially interested in the agronomic traits, tuber starch content and tuber yield under heat stress conditions. By performing GWAS on genotype and the agronomic trait data of all potato varieties we will be able to identify candidate genes which are important for heat tolerance. Using these candidate genes in subsequent transcriptome and gene structure analyses we will get a better understanding of the underlying genetic mechanisms and factors for heat tolerance in potato as well as present new targets for molecular breeding to potato breeders.

In our potato project we collaborate closely with several breeders, the industry, and research facilities:

  •   Bayerische Landesanstalt für Landwirtschaft, Freising, Germany.
  •   Bavaria Saat, Schrobenhausen, Germany.
  •   Saatzucht Firlbeck, Atting, Germany.
  •   Südstärke, Schrobenhausen, Germany.
  •   Vermarktungsgesellschaft Bio-Bauern mbH, Pöttmes, Germany.
  •   Landesverband der Saatkartoffel-Erzeugervereinigung in Bayern e.V, Freising, Germany.