Hutton Highlights, February 2021

Developing new breeding strategies for resilient and highly nutritious berries Fulfilling increased demand across Europe for berries is hampered by the challenges of climate change, environmental conservation and the need for new cultivation systems and high-quality produce. BreedingValue, an 8-country, 20-partner European research collaboration will explore the most promising berry genetic resources to address these challenges. Receiving just short of EUR 7 million from EU Horizon 2020, the Italian-led 4-year project features the Institute, commercial subsidiary James Hutton Limited and Biomathematics and Statistics Scotland (BioSS) as research partners.  Berry production is widely established throughout Europe. Strawberries (Fragaria) are the most important crop with a harvest area of 105,798 ha and total production of 1,275,946 tonnes compared to raspberries (Rubus) with 41,436 ha and 219,112 tonnes and blueberries (Vaccinium spp.) with 15,395 ha and 95,674 tonnes. Thanks to their high value in both fresh and processed market segments, these berries offer valuable prospects for the development and economy of rural areas with gross margins also far higher than crops such as wheat or corn. In response to increasing market demand fed by consumer preference and awareness of nutritional qualities, cultivation has enjoyed sustained expansion. Growing berries requires specialist knowledge and current cultivation systems are very resource-intensive. Current berry cultivars have a limited environmental tolerance which is determined by the plant’s germplasm and reduces resilience to different environmental factors. At the same time, quality determines the success in the market and failure to produce high-quality berries that consumers want reduces profitability and sustainability not just for individual farmers but also the market as a whole due to high wastage. This is where BreedingValue intends to make an impact. The project will bring together public and private actors, scientists, genetic resource managers and SMEs with substantial experience in managing and characterising berry genetic resources. Consumers will also be involved. The aim is to use and develop germplasm and new genetic and phenotyping tools to study current biodiversity in these crops and identify new pre-breeding materials to be used to create new resilient cultivars with high-quality fruit. BreedingValue will also expand communication between breeders and consumers both nationally and EU-wide, to the benefit of all parts of the sector and market. To build links between public and private institutions, berry breeders will be invited to participate in open calls for proposals to collaborate on specific activities such as marker-assisted selection, genomic selection, genome-wide association studies and the development of methodological tool kits for sensorial quality assessment of berry genetic resources. “Central to the success of BreedingValue is the establishment of a large network of experts in conservation, genetics, genomics, breeding, biotechnology, biochemistry, phytopathology, bioinformatics, statistics and the production of berries. This unprecedented multidisciplinary structure will help us gain and develop new insights, information and concepts benefitting the berry GenRes community and reinforcing the connection between EU producers and consumers,” says consortium coordinator Bruno Mezzetti, Professor in Fruit Crop Breeding and Biotechnology at the Università Politecnica Delle Marche. Soft fruit breeding has been a staple output of the science at the James Hutton Institute and its forebears since the 1930s. Today, raspberry, blackberry, blackcurrant, blueberry and redcurrant all have their own industry-funded breeding programmes in place at the Institute, managed by James Hutton Limited. Recent success from the raspberry programme includes the first-ever root rot-resistant variety Glen Mor. “Consumer tastes are changing and production costs are increasing so growers need varieties that are productive, have low picking and management costs, good pest and disease tolerance and require reduced inputs. But they must also satisfy retailer and processor requirements like large fruit, good flavour, extended shelf life and season,” notes Dr Susan McCallum, blueberry breeder and Hutton lead on the project. The Institute is contributing to the project alongside colleagues at Biomathematics and Statistics Scotland. Hutton bioinformaticians will develop and deliver solutions to store and visualize phenotype, genotype and passport data for the project building on the Institute’s established Germinate platform . An international research team including scientists from the James Hutton Institute and the University of Dundee has reached a milestone on the way to unravelling the species- wide genetic diversity of domesticated barley. By sequencing the complete genomes of 20 diverse genotypes, the researchers have taken the first step in decoding the genetic information of the entire species - the barley pan-genome. Scientists and breeders will greatly benefit from these new findings, recently published in Nature. Dundee scientists and international partners already succeeded in decoding the genome of one specific variety three years ago but to understand the genetic information of the entire species, much more is required. Individual genomes sometimes differ considerably in their number of genes and the arrangement and orientation of large parts of individual chromosomes. These “structural” changes in the barley genome can present an insurmountable barrier for manipulating important plant characteristics in breeding. The team used species-wide genetic diversity data to identify and select twenty highly diverse genotypes for complete sequencing. “Criteria for the selection included the greatest possible differences in their genetic diversity, geographical origin and biological traits such as winter or spring type, grain hull, row-type,” says Prof Dr Nils Stein, head of the Genomics of Genetic Resources research group at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) which led the study. Besides observing that two barley varieties can differ substantially in their total gene content, the scientists found amazing differences in the linear order of the genetic information in the chromosomes that are termed structural variants. Two of these attracted particular interest from the scientists. In the first, a link was established to ‘mutation breeding’ in the 1960s that has since spread unnoticed through breeding to present-day varieties. In the second, the observed variation possibly occurred and was selected during environmental adaptation as barley production spread from its origins in the Fertile Crescent. One of the genes encompassed by this region had previously been identified by the Hutton group as being critical for adaptation to northern European environments. “We never knew that this gene was part of a much bigger chromosomal rearrangement,” says Prof Robbie Waugh, of the Institute and the University of Dundee. “This new observation confirms that major structural variants can play a decisive role in both crop evolution and breeding. The only way these could have been discovered is through the complete genome sequencing of diverse individuals. Naturally occurring or artificially induced inversions are evidence of considerable dynamics in the genome organisation of the species.”  The new findings will have significant scientific and practical impact. “We now know for sure that in the future, structural variation will need to be accounted for in barley research and breeding,” Prof Waugh adds. Despite current progress, major challenges remain. “The pan-genome study is largely restricted to cultivated barleys that have gone through the massive genetic bottleneck resulting from domestication” he notes. “We still need to explore the direct ancestors of today’s cultivated crop.” Faced with growing climate and other environmental concerns, the consortium is convinced that the solutions to many of our future agricultural challenges will lie in the genomes of diverse relatives of our currently cultivated crop varieties. The project involved scientists from Germany, Australia, Canada, USA, China and Japan. Read the full Nature paper . Barley pan-genome: scientists unravel diversity of domesticated barley 20 Hutton Highlights February 2021 21 Comments?