Genomics
Intro
Crop Genomics
Our approach to maintaining and improving crop productivity under a changing climate is to identify relevant germplasm, determine the key traits that confer stable yield and quality for human, animal or industrial end uses, and understand and exploit their genomic regulation in response to current and predicted environments. Furthermore, crop systems must contribute to GHG reduction if we are to achieve and exceed Net Zero targets. A combination of trait biology, functional genomics and novel breeding methodologies are essential to develop and cultivate resilient and sustainable crops for the future. To deliver these improvements requires the development of new tools and resources to accelerate progress towards meeting the demands of a rapidly changing world.
The integration of existing and novel -omics data with the development of pangenomes for our crops provides a platform to understand the genomic variation within these species and how it is regulated under different environmental conditions and in hybrids.
This will provide insights into successful hybridisation, heterosis, and guide parental selections and provide a platform from which to launch new discovery science and translational projects, including how gene bank collections can be better utilised for future agricultural and environmental benefit and novel breeding strategies.
Approach & Aims
Approach and Aims
Genome references and high throughput sequencing are transforming our ability to dissect traits, detect diversity and predict phenotypes. The large initial investments are justified by subsequent gains in genotyping efficiency, ease of allele discovery and ability to dissect trait mechanisms. By combining resources and expertise across our crops we gain further economies of scale and accelerate use of genome data for application to trait biology in our crops: perennial ryegrass clover, and Miscanthus. We will build on the reference genomes that are now available for our crop species: perennial ryegrass, clover, oats and Miscanthus (refs below). These inform surveys of genomic diversity within each species and associate it with natural adaptations and breeders’ selection targets.
The aim now is to develop pangenomes for these species. Plant genomes can tolerate significant variation in gene content and chromosome organisation, so multiple genomes are needed to capture those haplotypes that represent the diversity in traits of interest and are most relevant for breeding programmes. The IBERS gene bank contains thousands of geolocated accessions of forage grasses, clover, Miscanthus and oats. Increased understanding of the genomic diversity within our crop species will provide the foundations for discoveries in terms of gene function, GxE, hybridisation/introgression potential and will ultimately inform the breeding programmes.
Kamal N, Renhuldt NT, Bentzer J, Gundlach H, Lang D, Gessel N Van, Reski R, Fu Y, Spégel P, & Ceplitis A (2022) The mosaic oat genome gives insights into a uniquely healthy cereal crop Nature 606 113–119, https://doi.org/10.1038/s41586-022-04732-y.
Byrne SL, Nagy I, Pfeifer M, Armstead I, Swain S, Studer B, Mayer K, Campbell JD, Czaban A, Hentrup S, Panitz F, Bendixen C, Hedegaard J, Caccamo M, & Asp T (2015) A synteny-based draft genome sequence of the forage grass Lolium perenne Plant J 84 816–826, https://doi.org/10.1111/tpj.13037.
De Vega J, Donnison I, Dyer S, & Farrar K (2021) Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus [ version 1 ; peer review : 2 approved ] F1000Research 10 29, https://doi.org/https://doi.org/10.12688/f1000research.44714.1.
Miao J, Feng Q, Li Y, Zhao Q, Zhou C, Lu H, Fan D, Yan J, Lu Y, Tian Q, Li W, Weng Q, Zhang L, Zhao Y, Huang T, Li L, Huang X, Sang T, & Han B (2021) Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome Nat Commun 12 2458, https://doi.org/10.1038/s41467-021-22738-4.
Mitros T, Session AM, James BT, Wu GA, Belaffif MB, Clark L V., Shu S, Dong H, Barling A, Holmes JR, Mattick JE, Bredeson J V., Liu S, Farrar K, Głowacka K, Jeżowski S, Barry K, Chae WB, Juvik JA, Gifford J, Oladeinde A, Yamada T, Grimwood J, Putnam NH, De Vega J, Barth S, Klaas M, Hodkinson T, Li L, Jin X, Peng J, Yu CY, Heo K, Yoo JH, Ghimire BK, Donnison IS, Schmutz J, Hudson ME, Sacks EJ, Moose SP, Swaminathan K, & Rokhsar DS (2020) Genome biology of the paleotetraploid perennial biomass crop Miscanthus Nat Commun 11 5442, https://doi.org/10.1038/s41467-020-18923-6.
De Vega JJ, Ayling S, Hegarty M, Kudrna D, Goicoechea JL, Ergon Å, Rognli OA, Jones C, Swain M, Geurts R, Lang C, Mayer KFX, Rössner S, Yates S, Webb KJ, Donnison IS, Oldroyd GED, Wing RA, Caccamo M, Powell W, Abberton MT, & Skøt L (2015) Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement Sci Rep 5 17394, https://doi.org/10.1038/srep17394.
Projects
Projects
ISPG Resilient Crops http://www.resilientcrops.org/
Miscanspeed Miscanthus breeding http://www.miscanthusbreeding.org/