Across fields and grasslands, clovers often go unnoticed beneath our feet, but for PhD researcher Jhih-Sheng Liu, they provide a fascinating opportunity to understand how genomics can deliver tangible benefits for farmers and the environment.
A rich source of protein for livestock grazing, clover also plays a valuable role in naturally enriching our soils. Like other legumes, such as lentil, soybean and lupin, clover works with soil bacteria to capture nitrogen from the air and turn it into plant-available nutrients - reducing the need for additional chemical fertilisers.
These qualities have made clover an incredibly valuable crop for centuries. Used as green manure since ancient times it remains one of the most important forage legumes in Western Europe.
However, as climate change increases the frequency of extreme environmental conditions, persistence (the ability to keep growing) in clover becomes a challenge across the globe.
Improving its resilience to cold, drought and other stresses has become a major target for plant breeding companies, helping support climate-resilient agriculture and safeguard food production.
“Clover, despite being so valuable, is still a relatively understudied crop. Compared to many other major crops there are limited genetic resources available,” says Jhih-Sheng Liu, a second-year PhD researcher in the De Vega Group at Earlham Institute.
His NRPDTP PhD is in collaboration with the research and innovation expertise at Germinal Horizon, and the Institute of Biological, Environmental and Rural Sciences (IBERS) at Aberystwyth University.
NRPDTP PhD Researcher, Jhih-Sheng Liu
Together, the research team are looking to uncover the genomic basis of cold tolerance in white clover to breed improved varieties. Jhih-Sheng is looking at how genetic variation in clover drives the development of these required traits.
To do so, he’s using a diversity panel of around 200 white clover samples from IBERS seed bank and others from across Europe, to explore their adaptations to different climates and build a pangenome reference for white clover.
Pangenomes are a powerful framework for crop breeding because plant genomes often contain substantial diversity from hybridisation, introgression and mixed ancestry. Clover is especially diverse, so a traditional single reference genome would fail to capture important variation that is absent from that single linear reference. Whereas pangenomes provide a much broader representation of genomic diversity, improving our ability to map sequencing reads, and identify genetic variants.
“We’re using publicly available reference genomes for white clover and its ancestral species, alongside new long-read sequencing data generated at the Earlham Institute. This will produce multiple high-quality genome assemblies to build the pangenome framework,” explains Jhih-Sheng.
The PhD project is allowing me to develop a unique combination of skills spanning evolutionary genomics, quantitative genetics, bioinformatics, data analysis, and practical plant breeding.
By combining this genomic information with environmental data from wild clovers from across Europe - including original locations, temperature, rainfall, and winter conditions - the team hopes to understand how some populations have adapted to colder conditions.
Understanding this complexity, and the potential for developing practical solutions, is exactly what attracted Jhih-Sheng to the Earlham Institute in the first place. Throughout his earlier studies and education, he’s always been drawn to the role of evolutionary genomics and its application to addressing sustainability challenges.
“By contributing to the development of climate-resilient clover varieties, I’m able to work at the interface between fundamental genomics and real-world agricultural impact. The PhD project is allowing me to develop a unique combination of skills spanning evolutionary genomics, quantitative genetics, bioinformatics, data analysis, and practical plant breeding,” says Jhih-Sheng.
This interdisciplinary skillset is increasingly important as breeding programmes become more data-driven: using genomics, high-throughput phenotyping, and advanced computational approaches to accelerate genetic gains and performance of crops.
Crop breeding is inherently practical, and our research needs to suit the requirements of the farmers and breeders that will be using these varieties.
As part of his PhD placement with Germinal Horizon, Jhih-Sheng has been able to learn first-hand how breeding trials are designed and how practical breeding is carried out. He’s sampled and propagated plants, handled genebank material, and learnt about the valuable role of different clover varieties used in his research.
“Crop breeding is inherently practical, and our research needs to suit the requirements of the farmers and breeders that will be using these varieties”, he says.
Working with Dr David Lloyd and Dr Christina Holland at Germinal, Jhih-Sheng’s work is helping develop cultivars that can withstand diverse environmental conditions, leading to reliable forage production, savings in seed costs, and economic stability in farming.
“Breeding clovers which can thrive in a changing climate is one of the greatest challenges we face. The collaboration between the Earlham Institute and Germinal Horizon has provided a unique opportunity to assess performance under environmental stresses across a European-wide gene pool, which in turn will facilitate the discovery of genetic markers to accelerate the development of elite commercial cultivars,” explains Dr Christina Holland, Forage Legume Breeder at Germinal Horizon.
“This knowledge will greatly benefit our long-term breeding efforts, providing farmers with resilient, protein-rich forage that supports sustainable livestock production in an increasingly unpredictable climate.”
This project builds on long-standing collaborations across Earlham Institute, Germinal, and IBERS.
In 2015 Earlham Institute sequenced and assembled the DNA of red clover to help improve genomic resources for this crop. And more recently, scientists working at Germinal and IBERS have developed the first hybrid variety from white and caucasian clover, creating a highly persistent clover.
The De Vega Group is also part of an international consortium - the Legume Generation project. Bringing together 16 partners across Europe, their aim is to bring together and improve genomic resources to boost breeding of food and feed legume crops in Europe.
“Working with our collaborators is a great opportunity to be exposed to different perspectives, helping me better understand the scientific, economic, and practical considerations that drive crop improvement programs and how genomics research can be of real value, says Jhih-Sheng.
Jhih-Sheng's PhD is part of the BBSRC Norwich Research Park Biosciences Doctoral Training Partnership (NRPDTP). To find out more information, visit their website.
