CultiBeet: Molecular analysis of beet crop diversification

Domestication and diversification are the driving forces to generate the wide variety of currently available crop plants. Diversification of cultivated beets (Beta vulgaris ssp. vulgaris) has resulted in four cultivar groups of very different phenotypes, i. e. leaf beets (chard), fodder beet, table beet, and sugar beet. The proposed research will address the question if domestication of beet crops occurred only once or multiple times. It will be investigated how the genomes of the different beet crops are related to each other. We will aim for the identification of diversification genes in order to understand the molecular basis of the phenotypic difference of the cultivar groups. To address theses goals, genome sequencing will be performed, followed by an analysis of the data using reference genomes and statistical interpretation of population differentiation. CultiBeet will create important knowledge on the domestication history of beets. The experimental setup and computational analyses may serve as a general paradigm for crop diversification studies. Primary researchers involved: The project will be jointly led by Ass. Prof. Dr. Juliane Dohm and Prof. Dr. Heinz Himmelbauer.

Beets (Beta vulgaris) are important crop plants. Today, four distinct cultivar groups can be distinguished: Chard, fodder beet, sugar beet, and red beet. Sugar beet holds great value as the second most important industrial source of sugar, while red beet and chard are essential vegetable crops. Only the fodder beet has lost importance, with its cultivation steadily declining over the past decades. The wild species from which all cultivated beets are derived is the sea beet (Beta vulgaris ssp. maritima), which is widespread in coastal habitats along the European Atlantic coasts and in the Mediterranean region. Research conducted here demonstrated that the domestication of beets took place in the eastern Mediterranean region and that the wild beets most closely related to cultivated beets originated from Greece. An initial domestication is typically followed by diversification. This means that a domesticated species is adapted through breeding to meet various human needs. In the case of beets, diversification can be clearly illustrated by the aforementioned four cultivar groups. In this project, hundreds of varieties of chard, fodder beet, and red beet were selected from a public seed bank. The varieties were grown in a greenhouse, leaves were harvested, and DNA was extracted. Subsequently, the genomes were sequenced and analyzed alongside comparable data from sugar beets and wild beets. To identify sequence differences between wild beets and cultivars, all sequencing data were compared to the reference sequence of the sugar beet genome. This resulted in a catalog of sequence differences, documenting the position of the variation in the genome as well as the type of variation. These data were used to group the sequenced plants using a statistical method known as Principal Component Analysis (PCA). The analysis revealed that the groups fodder beet, sugar beet, and red beet can be clearly distinguished from one another as well as from their wild ancestors. Additionally, it was found that chard is sometimes difficult to separate from wild beets and represents a heterogeneous group. Of particular interest is the identification of variants that are characteristic of specific groups. For this purpose, machine learning methods were applied and optimized. The known groups were compared, and subgroups were formed when necessary. In this way, genes were identified that had been altered through targeted breeding. For example, in sugar beet, genes involved in sugar transport were identified. Other findings suggest how modern varieties differ from older ones. Taken together, this project generated valuable knowledge about beet domestication and their subsequent diversification into different cultivar groups. The experimental approach and computational methods developed herein can be applied to other crop plants. Primary researchers involved: The project was jointly led by Assoc. Prof. Dr. Juliane Dohm and Prof. Dr. Heinz Himmelbauer.