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Crop Genetic Improvement

Work Package 2.1 - Crop and grassland production and disease control

Research Deliverable 
2.1.2 Crop genetic improvement
Leading Ideas 
Agriculture
Climate and the Environment

Introduction

New genomic/genetic approaches: The overall aim of this research is to generate the information necessary to improve our translational pipelines that will enable the production of new crop plant varieties with improved performance in terms of yield, quality and resilience to pests, pathogens and climate change. New genomic/genetic approaches provide the capability to dissect key traits in crop plants and will be the most important vehicle for delivery of improved cultivars to cope with climate change and improve food security over the next 20-30 years. To achieve these goals, we will build on advances in crop genomics achieved in the last SG programme to investigate the genetic architecture of key traits and explore the genomic, transcriptomic, metabolomic and proteomic signatures that have been shaped by the natural processes of mutation, selection and adaptation.

Aim of Research

The main activities will focus on barley, wheat, potato and soft fruit, the crops of major importance to the Scottish economy. For each crop, the spectrum of capabilities is linked into translational crop genomics pipelines that ultimately deliver improved cultivars. Underpinning research in all projects will be the continued development of novel technologies and approaches including custom platforms for genomic and functional characterisation of important traits. Improvements in genome sequencing and annotation, high-throughput genetic analysis and trait analysis capabilities will allow identification of genes and gene variants which determine key traits. Data generation, analysis and hypothesis testing will require a significant input from genetic analysis, imaging and genome technology facilities, along with statistical and computational data analysis inputs. Together, these will allow us to explore new approaches to genomic and functional characterisation of individual genes and gene networks and consolidation of translational pipelines.

Specific targets will include: novel gene variants for adaptation in barley, genes controlling morphological and developmental variation, manipulation of the way in which barley exchanges genetic material in breeding crosses, tolerance to future climate and environmental change, product quality for consumers and producers and biotic stress resistance.

Progress

2020 / 2021
2020 / 2021

Genetic and genomic approaches have been developed and applied to key Scottish crops including potato, soft fruit and barley. The research has led to important new insights into key traits for these crops. Examples include the identification and characterisation of genes in the control of inflorescence development in barley, new insights into tuber development in potato and understanding of resilience (to both environment and disease) in soft fruit and potato.

Highlights:

Gene expression analysis of potatoes with different tuberisation characterisitics has been completed and the datasets analysed. These results have led to the development of a new model for tuberisation and have been published.   The results of this work were presented in a World Potato Congress webinar viewed by over 400 scientists and potato industry representatives, feedback has been positive and collaborative links have been established in a new EU-funded project called ADAPT.

The curation and development of novel barley germplasm resources, with extensive genomics data, have led to a BBSRC funded project examining embryo size changes during domestication and subsequent range expansion and breeding, in collaboration with NIAB (Developing nutrient-enriched cereal grains with large embryos” BBSRC Response Mode. [2019-2022]). The collections have also been an invaluable resource to identify novel variation in salt tolerance genes and important duplications and structural variants.

SEFARI scientists brought together stakeholders from across the barley value chain, including agronomy, breeding, crop protection, government, charitable trusts, environment and conservation, food and drink and growers for a two-day workshop in Dunkeld. The aim was to understand the issues facing stakeholders, particularly in terms of priorities for a sustainable future and to explore how barley research could address these needs. A summary and road-map outlining the findings and potential solutions is published on the SEFARI website (A sustainable future for Scottish barley | SEFARI)

Using a new genomics approach termed dRenSeq technology, we have assessed the top 50 potato cultivars currently being grown in the UK for deployed and effective disease resistance genes. Markers for selected late blight resistance genes have been developed and successfully utilised in pre-breeding programs.

The release of ‘Glen Mor’ the first commercial raspberry with resistance to Phytophthora root rot is the culmination of years of research and will enable the industry to reduce substrate use and chemical inputs. Further research from this work is developing sustainable media and additives (IUK 48163). Advances in understanding crumbly fruit and potential for marker assisted breeding have been achieved. Other markers are now routinely used in the breeding programme and new markers for crop sustainability and resilience are being developed assisted by imaging technologies.

2019 / 2020
2019 / 2020

New genetic and genomic tools have been developed and are being applied to study biological processes in crop plants that help us to understand key developmental and quality traits and how plants respond to threats from environmental conditions and pathogen attack. This knowledge provides the underpinning information that is feeding through to plant breeders to enable the development of crops with improved resilience and quality for the future. A significant example is the development of reference transcript databases which in barley has allowed unprecedented detail of responses to environmental stress. Similar technology is in development for potato.

Highlights:

Barley accessions varying in key traits, such as flowering time have been identified and used to generate populations for genetic analysis. This work led to funding for a project titled ‘BARISTA: Advanced tools for breeding barley for intensive and sustainable agriculture under climate change scenarios’ (SusCrop ERA-NET) that commenced April 2019. 

Using a new gene expression analysis pipeline (3D-RNAseq) gene expression networks in barley developmental mutants has been analysed to improve our understanding of these complex processes.

An analysis of the recently discovered gene (StCEN) provided new insights into how the potato tuber life-cycle is regulated. Natural variants in the StCEN gene underpin variation in important aspects of the tuber life-cycle such as tuber dormancy and tuber initiation, factors that are critical for crop yield.

Tuber greening during storage remains a major source of waste in the potato supply chain and in the home. New understanding of tuber greening provides a molecular framework for developing new approaches to reducing waste due to potato greening and is being taken forward with Industry.

Accessions from The Commonwealth Potato Collection have been selected and screened for susceptibility/resistance to potato late blight. New variations in resistance genes have been identified in accessions of a wild potato species and could lead to the deployment of novel resistances. This work has led to BBSRC Industrial Partner Award funding valued at £633,267.

2018 / 2019
2018 / 2019

Cutting edge genetic and genomic approaches have been used to identify genetic variation associated with adaptation to different environments, important developmental processes in crop plants and resilience to disease and environmental stresses. The work has leveraged external funding from  research councils, levy boards and industry. A knowledge exchange programme has ensured the outcomes of the research are visible to academics, industry, policy makers and the general public..

Highlights:

  • The work has progressed to examining how several important genes involved in barley row type determination interact to exert control over important aspects of barley development, revealing novel routes to improved grain quality.
  • A barley reference transcript dataset has been assembled called BaRTv1.0. A database of the BaRT transcripts has been established. This resource will enable rapid quantification of gene expression datasets and has been used to identify changes in gene expression associated with cold stress. These experiments identify key circadian clock genes induced within two hours of cold application that may have a role in winter hardiness.
  • A gene that has a major effect on important aspects of potato tuber development including tuberisation time and rate of sprouting has been identified. Naturally occurring variants of this gene are under test and may be useful in breeding improved potato varieties. Aspects of the work have been presented to scientific and industrial audiences.
  • Measurements of effects of heat stress on fertility in barley have been initiated and new genetic factors involved in cell division processes have been identified..  Some landrace barleys that have resistance to the effect of heat stress on seed fertility have been identified which will give a means of improving this trait in adapted varieties and crosses have been set up with this material to do this. 
  • Understanding causes of ear sterility in wheat: SEFARI research has contributed to reporting of physiological and genetic influences on seed set in wheat. This research is helping an ongoing study into causes and control of environmentally induced ear sterility which can result in significant yield loss in Scottish wheat crops. The AHDB Report considers risk factors contributing to poor seed set, including wheat breeding material that could be used in future crop improvement.
  • A novel source of resistance to potato late blight disease has been identified and characterised genetically using a new approach to identify resistance genes in potato cultivars termed dRenSeq.
  • Genomic sequences associated with resistance to raspberry root rot disease have been identified. A range of genes differentially expressed between Glen Moy (susceptible) and Latham (resistant) raspberry varieties have been identified and potential novel control mechanisms have been suggested. These data are included in new tools for visualising genome sequences (genome browsers) available for Rubus and Ribes species.
2017 / 2018
2017 / 2018

Further progress in understanding key traits related to crop productivity has been made using approaches informed by genetics and genomics. Tools developed in this respect include high density gene marker (Single Nucleotide Polymorphisms (SNP)),  approaches for identifying important gene variants and gene editing in barley and potato.

Highlights:

  • Delivering fundamental biological knowledge for Scottish crops: An international consortium of scientists, including a SEFARI group, has published a high-resolution draft of the barley genetic code. The breakthrough is a critical step towards breeding barley varieties able to cope with the demands of climate change. It will also help in the fight against cereal crop diseases. (Mascher et al., 2017).
  • A database of co-ordinated barley yield trial results (FACCE-JPI ClimBar project) ranging from Scandinavia to North Africa was assembled and tied to meteorological data that is being used to predict the best barley varieties for future climate change scenarios. In addition, research on the use of temperature stress to affect patterns of barley cell division was extended in the EU ITN COMREC project.
  • Barley grain row-type is an important agronomic trait impacting on grain yield and uniformity. SEFARI researchers have identified and characterised an important gene that controls row-type in barley. The mechanism of how this gene functions has been determined and could find application in breeding barley with improved yield and quality.
  • The trend towards warmer winters has resulted in the exposure of several blackcurrant varieties to insufficient winter chilling, leading to reduced yield and uniformity of maturity. In response,  research is developing and testing winter chill models on grower farms, which, in combination with a greater understanding of varietal response to future winter scenarios will enable breeding for appropriate varieties in collaboration with industry (Lucozade Ribena Suntory Ltd). The output from this  is a set of dormancy-related genes in blackcurrant that can be analysed further in conjunction with the enhanced blackcurrant genetic map and genetic code.  This will enable differences in climate response between blackcurrant cultivars to be examined in terms of these key genes, but further work will also focus on generic genes/mechanisms with other woody species.
2016 / 2017
2016 / 2017

Genetic and genomic approaches are being used to understand key traits in barley, wheat, soft fruit and potatoes. Progress has been reported in several high impact publications and presentations to industry and science audiences. Funding has been leveraged from a wide range of funding bodies including industry, research councils and levy boards emphasising the relevance of this research.

Highlights:

  • Data has been collected from 300 landraces and 116 wild geo-referenced barley accessions, with over one million SNPs (genetic differences) identified, enabling variation associated with adaptation to different environments to be analysed. The data has formed the basis of a high impact publication in Nature Genetics.
  • An important gene involved in barley row type determination has been identified and its precise function is being analysed. This work will underpin efforts to develop barley varieties with improved yield and quality.
  • Resistance genes effective against important diseases of potato and soft fruit species are being identified and characterised using a range of cutting edge genetic and genomic approaches.
  • Barley accessions have been selected with variable response to low temperature. High resolution gene expression analysis (HR RT-PCR) has identified unique responses between temperature sensitive and temperature resistant accessions. These findings could lead to novel strategies for forms of marker selection for breeding tolerant barley varieties

Future Activities

We shall continue the development of tools that will underpin the breeding of improved varieties. Examples include the use of a barley reference transcript dataset that will give unprecedented insights into adaptation of barley to different environmental conditions. Important crop developmental processes such as barley grain development and the potato tuber life cycle will be the focus of further work that has the potential to lead to new markers for breeding improved varieties. Tools such as gene editing in potato will enable the role of specific mutations to be identified. Genomic approaches such as dRenSeq will be employed to further characterise novel resistance genes in potato and routes to application are being taken forward with industry support. New genetic and trait analysis methodologies will be further developed for soft fruit species and will underpin the development of varieties resilient to challenges from climatic conditions and plant diseases.

Selected Outputs

Calixto, C.P., Simpson, C.G., Waugh, R. and Brown, J.W., 2016. Alternative splicing of barley clock genes in response to low temperature. PloS one, 11(12), p.e0168028.

Giolai, M., Paajanen, P., Verweij, W., Percival-Alwyn, L., Baker, D., Witek, K., Jupe, F., Bryan, G., Hein, I., Jones, J.D. and Clark, M.D., 2016. Targeted capture and sequencing of gene-sized DNA molecules. Biotechniques, 61(6), pp.315-322.

Russell, J., Mascher, M., Dawson, I.K., Kyriakidis, S., Calixto, C., Freund, F., Bayer, M., Milne, I., Marshall-Griffiths, T., Heinen, S. and Hofstad, A., 2016. Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nature Genetics, 48(9), p.1024.

Van Weymers, P.S., Baker, K., Chen, X., Harrower, B., Cooke, D.E., Gilroy, E.M., Birch, P.R., Thilliez, G.J., Lees, A.K., Lynott, J.S. and Armstrong, M.R., 2016. Utilizing “Omic” technologies to identify and prioritize novel sources of resistance to the oomycete pathogen Phytophthora infestans in potato germplasm collections. Frontiers in plant science, 7, p.672.

Bull, H., Casao, M.C., Zwirek, M., Flavell, A.J., Thomas, W.T., Guo, W., Zhang, R., Rapazote-Flores, P., Kyriakidis, S., Russell, J. and Druka, A., 2017. Barley SIX-ROWED SPIKE3 encodes a putative Jumonji C-type H3K9me2/me3 demethylase that represses lateral spikelet fertility. Nature communications, 8(1), p.936.

Mascher, M., Gundlach, H., Himmelbach, A., Beier, S., Twardziok, S.O., Wicker, T., Radchuk, V., Dockter, C., Hedley, P.E., Russell, J. and Bayer, M., 2017. A chromosome conformation capture ordered sequence of the barley genome. Nature, 544(7651), p.427.

Zhang, R., Calixto, C.P., Marquez, Y., Venhuizen, P., Tzioutziou, N.A., Guo, W., Spensley, M., Entizne, J.C., Lewandowska, D., Ten Have, S. and Frei dit Frey, N., 2017. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic acids research, 45(9), pp.5061-5073.

Calixto, C.P., Guo, W., James, A.B., Tzioutziou, N.A., Entizne, J.C., Panter, P.E., Knight, H., Nimmo, H.G., Zhang, R. and Brown, J.W., 2018. Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome. The Plant Cell, 30(7), pp.1424-1444.

Chen, X., Lewandowska, D., Armstrong, M.R., Baker, K., Lim, T.Y., Bayer, M., Harrower, B., McLean, K., Jupe, F., Witek, K. and Lees, A.K., 2018. Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies. Theoretical and applied genetics, 131(6), pp.1287-1297.

Colas, I., Barakate, A., Macaulay, M., Schreiber, M., Stephens, J., Vivera, S., Halpin, C., Waugh, R. and Ramsay, L., 2019. desynaptic5 carries a spontaneous semi-dominant mutation affecting Disrupted Meiotic cDNA 1 in barley. Journal of experimental botany, 70(10), pp.2683-2698.

Hackett, C.A., Milne, L., Smith, K., Hedley, P., Morris, J., Simpson, C.G., Preedy, K. and Graham, J., 2018. Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening. BMC genetics, 19(1), p.59.

Hoad S. et al., AHDB "Project Report No. PR599. Wheat Ear Sterility Project (WESP)".

Morris, W.L., Alamar, M.C., Lopez-Cobollo, R.M., Castillo Cañete, J., Bennett, M., Van der Kaay, J., Stevens, J., Kumar Sharma, S., McLean, K., Thompson, A.J. and Terry, L.A., 2018. A member of the TERMINAL FLOWER 1/CENTRORADIALIS gene family controls sprout growth in potato tubers. Journal of experimental botany, 70(3), pp.835-843.

Strachan, S.M., Armstrong, M.R., Kaur, A., Wright, K.M., Lim, T.Y., Baker, K., Jones, J., Bryan, G., Blok, V. and Hein, I., 2019. Mapping the H2 resistance effective against Globodera pallida pathotype Pa1 in tetraploid potato. Theoretical and Applied Genetics, pp.1-12.

Zwirek, M., Waugh, R. and McKim, S.M., 2019. Interaction between row‐type genes in barley controls meristem determinacy and reveals novel routes to improved grain. New Phytologist, 221(4),

Armstrong, M.R., Vossen, J., Lim, T.Y., Hutten, R.C., Xu, J., Strachan, S.M., Harrower, B., Champouret, N., Gilroy, E.M. and Hein, I., 2019. Tracking disease resistance deployment in potato breeding by enrichment sequencing. Plant Biotechnology Journal, 17(2), pp.540-549.

Bustos‐Korts, D., Dawson, I.K., Russell, J., Tondelli, A., Guerra, D., Ferrandi, C., Strozzi, F., Nicolazzi, E.L., Molnar‐Lang, M., Ozkan, H. and Megyeri, M., 2019. Exome sequences and multi‐environment field trials elucidate the genetic basis of adaptation in barley. The Plant Journal, 99(6), pp.1172-1191.

Darrier, B., Russell, J., Milner, S.G., Hedley, P.E., Shaw, P.D., Macaulay, M., Ramsay, L.D., Halpin, C., Mascher, M., Fleury, D.L. and Langridge, P., 2019. A comparison of mainstream genotyping platforms for the evaluation and use of barley genetic resources. Frontiers in plant science, 10, p.544

Demirel, U., Morris, W.L., Ducreux, L.J., Yavuz, C., Asim, A., Tindas, I., Campbell, R., Morris, J.A., Verrall, S.R., Hedley, P.E. and Gokce, Z.N.,  Caliskan, S., Aksoy E., Mehmet, E., Caliskan, M.E., Taylor M.A. and and Hancock, R.D. 2020. Physiological, Biochemical, and Transcriptional Responses to Single and Combined Abiotic Stress in Stress-Tolerant and Stress-Sensitive Potato Genotypes. Frontiers in Plant Science, 11, p.169.

Foster, T.M., Bassil, N.V., Dossett, M., Worthington, M.L. and Graham, J., 2019. Genetic and genomic resources for Rubus breeding: A roadmap for the future. Horticulture Research, 6(1), pp.1-9.

Houston, K., Qiu, J., Wege, S., Hrmova, M., Oakey, H., Qu, Y., Smith, P., Situmorang, A., Macaulay, M., Flis, P. and Bayer, M., 2020. Barley sodium content is regulated by natural variants of the Na+ transporter HvHKT1; 5. Communications biology, 3(1), pp.1-9.

Morris, W.L., Ducreux, L.J., Morris, J., Campbell, R., Usman, M., Hedley, P.E., Prat, S. and Taylor, M.A., 2019. Identification of TIMING OF CAB EXPRESSION 1 as a temperature-sensitive negative regulator of tuberization in potato. Journal of experimental botany, 70(20), pp.5703-5714.

Okamoto, H., Ducreux, L.J., Allwood, J.W., Hedley, P., Gururajan, V., Wright, A., Terry, M.J. and Taylor, M.A., 2020. Light regulation of chlorophyll and glycoalkaloid biosynthesis during tuber greening of potato S. tuberosum. Frontiers in Plant Science, 11, p.753. 3

Owen, H., Pearson, K., Roberts, A.M., Reid, A. and Russell, J., 2019. Single nucleotide polymorphism assay to distinguish barley (Hordeum vulgare L.) varieties in support of seed certification. Genetic Resources and Crop Evolution, 66(6), pp.1243-1256.

Patil, V., McDermott, H.I., McAllister, T., Cummins, M., Silva, J.C., Mollison, E., Meikle, R., Morris, J., Hedley, P.E., Waugh, R. and Dockter, C., 2019. APETALA2 control of barley internode elongation. Development, 146(11).

Schreiber, M., Mascher, M., Wright, J., Padmarasu, S., Himmelbach, A., Heavens, D., Milne, L., Clavijo, B.J., Stein, N. and Waugh, R., 2020. A genome assembly of the barley ‘transformation reference’cultivar Golden Promise. G3: Genes, Genomes, Genetics, 10(6), pp.1823-1827

Zhang X, Campbell R, Ducreux LJM, Morris J, Hedley PE, Mellado-Ortega E, Roberts AG, Stephens J, Bryan GJ, Torrance L, Chapman SN, Prat S and Taylor MA (2020) TERMINAL FLOWER-1/CENTRORADIALIS inhibits tuberization via protein interaction with the tuberigen activation complex. The Plant Journal in press

Zheng, J., Duan, S., Armstrong, M., Duan, Y., Xu, J., Chen, X., Hein, I., Jin, L. and Li, G., 2020. New Findings on the Resistance Mechanism of an Elite Diploid Wild Potato Species JAM1-4 in Response to a Super Race Strain of Phytophthora infestans. Phytopathology, (ja).

Duan, Y., Duan, S., Armstrong, M.R., Xu, J., Zheng, J., Hu, J., Chen, X., Hein, I., Li, G. and Jin, L., 2020. Comparative transcriptome profiling reveals compatible and incompatible patterns of potato toward Phytophthora infestans. G3: Genes, Genomes, Genetics10(2), pp.623-634.

Ducreux, L.J., Pont, S.D., Verrall, S.R., McManus, W., Hancock, R.D. and Taylor, M.A., 2021. The impact of home storage conditions on the accumulation of acrylamide precursors in potato tubers. Annals of Applied Biology178(2), pp.304-314.  

Gartner, U., Hein, I., Brown, L.H., Chen, X., Mantelin, S., Sharma, S.K., Dandurand, L.M., Kuhl, J.C., Jones, J.T., Bryan, G.J. and Blok, V.C., 2021. Resisting Potato Cyst Nematodes With Resistance. Frontiers in Plant Science12, p.483.

Graham, J., Jennings N., 2020 Rubus spp. Cane fruit. In Biotechnology of fruit and nut crops. Ed Litz, Pliego-Alfara and Hormaza. CAB International. 19.10 p606-620.

Guo, W., Tzioutziou, N.A., Stephen, G., Milne, I., Calixto, C.P., Waugh, R., Brown, J.W. and Zhang, R., 2020. 3D RNA-seq: A powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. RNA biology, pp.1-14.

Harb, A., Simpson, C., Guo, W., Govindan, G., Kakani, V.G. and Sunkar, R., 2020. The Effect of Drought on Transcriptome and Hormonal Profiles in Barley Genotypes With Contrasting Drought Tolerance. Frontiers in plant science11.

Looseley, M.E., Ramsay, L., Bull, H., Swanston, J.S., Shaw, P.D., Macaulay, M., Booth, A., Russell, J.R., Waugh, R. and Thomas, W.T., 2020. Association mapping of malting quality traits in UK spring and winter barley cultivar collections. Theoretical and Applied Genetics133(9), pp.2567-2582.  

Raxwal, V.K., Simpson, C.G., Gloggnitzer, J., Entinze, J.C., Guo, W., Zhang, R., Brown, J.W. and Riha, K., 2020. Nonsense-mediated RNA decay factor UPF1 is critical for Posttranscriptional and translational gene regulation in Arabidopsis. Plant Cell32(9), pp.2725-2741.

Saade, S., Brien, C., Pailles, Y., Berger, B., Shahid, M., Russell, J., Waugh, R., Negrão, S. and Tester, M., 2020. Dissecting new genetic components of salinity tolerance in two-row spring barley at the vegetative and reproductive stages. Plos one15(7), p.e0236037.
Scolari, L., Hancokc, R., Hedley, P.E., Morris, J., Smith, K., Graham, J. 2021. Combining QTL mapping and gene expression analysis to elucidate the genetic control of crumbly fruit in red raspberry (Rubus idaeus L.) Agronomy, 11:794.

Torrance, L., Cowan, G.H., McLean, K., MacFarlane, S., Al-Abedy, A.N., Armstrong, M., Lim, T.Y., Hein, I. and Bryan, G.J., 2020. Natural resistance to Potato virus Y in Solanum tuberosum Group Phureja. Theoretical and Applied Genetics133(3), pp.967-980.

Varypatakis, K., Véronneau, P.Y., Thorpe, P., Cock, P.J., Lim, J.T.Y., Armstrong, M.R., Janakowski, S., Sobczak, M., Hein, I., Mimee, B. and Jones, J.T., 2020. The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode, Globodera pallida. Genes11(12), p.1429. ; 

Yang, C.J., Russell, J., Ramsay, L., Thomas, W., Powell, W. and Mackay, I., 2021. Overcoming barriers to the registration of new plant varieties under the DUS system. Communications biology4(1), pp.1-10.