Providing genomic resources for important forage grasses

Response Doctoral Programme

Forage grasses are the primary source of roughage for ruminant livestock and substantially contribute to sustainable milk and meat production. Cultivars adapted to specific environments and management conditions are needed to produce the required amounts of high-quality roughage. Moreover, there is a need to efficiently breed for novel forage grass cultivars to mitigate challenges emerging through climate change and to facilitate sustainable and productive agriculture. 

Relevance of deciphering plant genetic information for plant breeding

Traditional plant breeding is usually based on crossing parental plants with distinct traits to produce offspring with the desired combination of traits. Selecting the expected plants among thousands of offspring is a numbers game, and it can be time-consuming. For example, in the context of climate change and sustainable agriculture, high yield, drought tolerance and pest resistance will need to be combined in a new cultivar to produce food and feed using less inputs. To select such plants with the expected combination of traits, numerous plants need to be tested for yield, drought tolerance and pest resistance, which is a huge effort. In today’s genomics-assisted plant breeding, in contrast to laboriously measuring the traits of many offspring to select the desired plants, genetic markers linked to genes that are contributing to the traits, are used to guide selection. Directly selecting plants with genes contributing to high yield, strong drought tolerance and effective pest resistance makes the selection much more accurate, faster and less laborious. However, to enable genomics-assisted breeding, detailed knowledge of a species’ genome is indispensable.

A plant genome contains a set of chromosomes with the genetic information of an organism. The genetic information is stored as the DNA sequences of the chromosomes, encoded with four letters A, T, C and G. Genes are essentially short stretches of the DNA sequences controlling the traits of an organism. Modern sequencing technologies and bioinformatics tools enable decoding the genome and storing it as a digital sequence, comparable to an eBook where each chromosome is a chapter, and the individual genes represent sentences.

Given the genetic information can now be stored in an eBook, selecting the desirable plants based on genes for breeding is no different than looking up the expected sentences (genes) in the eBooks (genomes). However, for many important forage grass species, these eBooks are still rare and often incomplete. This lack of genomic resources hinders the application of genomic-assisted breeding in today’s plant breeding.

Constructing the most complete reference eBook for perennial ryegrass

Yutang Chen, a doctoral student of the Molecular Plant Breeding group at ETH Zurich and RESPONSE fellow, has been working on providing such an eBook for an important forage crop, perennial ryegrass (Lolium perenne L.). In his work, Yutang found that in the previously established eBook (genome) of a perennial ryegrass plant (Kyuss), some sentences (genes) were assigned to wrong chapters (chromosomes), and some sentences were incorrectly ordered and oriented within the chapter. These mistakes may lead to misunderstandings and wrong conclusions for researchers and breeders, who use this eBook (genome) as reference for their work.

With this in mind, in collaboration with IPK Gatersleben (Germany), Yutang generated new data for Kyuss, the perennial ryegrass plant originally derived from germplasm provided by the project collaborator DLF Seeds A/S (Denmark). The newly generated data provided bookmark information, such as the page number, the line number and the direction of the sentences, which helped Yutang to accurately locate, order and orient the sentences when constructing the eBook. As a result, Yutang successfully constructed a new eBook for Kyuss, Kyuss v2.0, which completely and accurately represents the genetic information of the Kyuss genome.

Benefits for policymakers, researchers, breeders and civil society

This new reference eBook (Kyuss v2.0) will serve as an invaluable genomic resource for the forage and turf grass community, including private and public institutes, to advance forage and turf research and breeding. This eBook is now publicly available via the open access GenBank sequence database, a library of such eBooks maintained by the National Center for Biotechnology Information (NCBI). Yutang believes that this eBook will facilitate genomics-assisted breeding, which will accelerate the development of new grass cultivars better adapted to current and future needs and conditions. Besides agriculture, Yutang added, this eBook could also be used in genetics or ecology to enable new methods of measuring biodiversity of grasses which may lead to better policies on biodiversity conservation.

The Spring 2024 edition of the PSC newsletter provides further detailed information on the novel approaches for assembling Kyuss v2.0 developed by Yutang and the team in the Molecular Plant Breeding group at ETH Zurich.

More information on the new chromosome-level assembly Kyuss v2.0 can be accessed through Yutang’s latest publication.

Yutang Chen is a fellow of the RESPONSE Doctoral Programme (DP) «RESPONSE – to society and policy needs through plant, food and energy sciences» funded by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No 847585.

This article is co-authored by Yutang Chen, Roland Kölliker, Bruno Studer and Mary Ann George (University of Zurich, RESPONSE Program office assistant).

The featured image is generated by AI (Copilot, Designer) on 6 May 2024 at 12:03 pm using the prompt: “Wide landscape of forage grass with a DNA molecule illustration superimposing the image to the right side”.

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