131 Genetic Analysis of Grain Shape, Grain Weight, Test Weight, Milling Yield, and Plant Height in a Spring Wheat Cross

Curt McCartney

Agriculture and Agri-Food Canada

Wheat grain shape affects traits under selection by breeders (e.g. grain weight, test weight, and milling yield). A doubled haploid (DH) population of the cross RL4452/‘AC Domain’ was used to study the genetic basis of seed shape. Quantitative trait loci (QTL) analyses were conducted on a total of 18 traits: 14 grain shape traits, plant height, 1000-grain weight, test weight, and milling yield. Grain samples were harvested from trials grown at Glenlea, Brandon and Morden in Manitoba, Canada, between 1999 and 2004. Kernel shape was studied through digital image analysis with an Acurum® grain analyzer. Plant height, grain weight, test weight, flour yield, and grain shape were correlated with each other and QTL analysis revealed that QTL for these traits often mapped to the same genetic locations. The most significant QTL for grain shape traits were located on chromosomes 4B and 4D coincident with QTL for plant height. The most significant QTL for plant height, grain weight, and test weight mapped to the Rht-D1 locus on chromosome 4D. Rht-D1b *decreased plant height, grain weight, test weight, and kernel width relative to the *Rht-D1a allele. A narrow genetic interval on chromosome 4B contained significant QTL for grain shape, grain weight, and plant height. The ‘AC Domain’ allele reduced plant height, grain weight, kernel length and width traits, but had no detectable effect on test weight. The cumulative data indicated that this variation was inconsistent with segregation at Rht-B1. Numerous additional QTL were also identified that control these traits in this population.

132 Genome-Wide Association Study of Winter Bread Wheat (Triticum aestivum L.) in Response to Drought in a Multi-Environment European Network.

Gaëtan Touzy

ARVALIS Institut du Végétal

Drought is one of the main abiotic stresses limiting wheat (Triticum aestivum L.) growth and productivity around the world. Many climate-based simulations have predicted an increase in the frequency and intensity of this abiotic stress. The delivery of new high yielding and stress-tolerant cultivars is now necessary and requires an improved understanding of the basis of the physiological and genetic response to drought.

A panel of 220 European elite cultivars was evaluated in 32 field experiments. Grain yield and yield components were scored for each trial. A crop model was run with detailed climatic data and soil water status, to identify the timing, intensity and history of stress for each combination of genotype/trial. Cultivars were genotyped with the TaBW420K chip. This dataset gives us the opportunity for a detailed study of genetic by environmental interactions.

Three scenarios of water deficit have been identified in this trial network. The grain yield loss in the two stressed scenarios was between 7 to 12% when compared to the non-stressed scenarios. A large genetic variability of grain yield was identified, with a genotypic variation affecting the mean by ± 15%. In the same way, GxE interactions affected the grain yield mean by 12.5%. GWAS were performed using multi-environment mixed models. Several QTLs were identified in the different stress scenarios, the allelic effects of these QTLs have been related to the environmental co-variables. Methods and results will be discussed especially those regarding the impacts of QTLxE interactions on grain yield and components and grain yield.

133 Getting to the Finishing Line: Integrating Optical and Physical Mapping for Megabase-Scale Resolution and Correct Annotation of Wheat Chromosome 7A

Rudi Appels

Murdoch University

Recent advances in whole-genome sequence assembly algorithms and chromosome conformation capture (Hi-C) have enabled the production of the first full-scale pseudomolecules in hexaploid wheat (IWGSC RefSeq v1.0). Resources developed by the IWGSC over the last decade, including BAC libraries and physical maps were critical in validating the sequence and extending scaffolds into super-scaffolds, tripling the assembly N50 from 7Mb to 21Mb in IWGSC RefSeq v1.0.

An independent assembly of chromosome 7A based on integrating a variety of datasets, including a BAC-based physical map, mate-pair sequencing, and optical mapping, resulted in the chromosome being assembled into 129 scaffold islands covering 735.1Mb. This assembly combined with the IWGSC RefSeq v1.0 enabled extensive validation as well as the elevation of regions of the chromosome from its existing high-quality draft status to finished status (less than one error per 100,000 base pairs). Integrating all available assembly resources, provided a complete classification of the chromosome into 17 contiguous regions with an N50 of 120Mb, the linear order of which could be independently validated using an 8-way MAGIC molecular genetic map. The value of fully validated sequence at long- and short-range is demonstrated using a number of regions of agronomic importance, including manual curation of the gene space.

134 RNA-Seq Analysis Reveals Jasmonates Related Pathways Associate with Salinity Tolerance in Wheat

Qiaoling Luo

Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

To explore the salt tolerance mechanism of wheat, we carried out RNA sequencing with 12 samples from three seedling tissues of salt-tolerant variety Xiaoyan 60 and high-yielding variety Zhongmai 175 under the salt treatment and the control. After analysis of different expression, 703, 979, 1197 differentially expressed genes (DEGs) were found respectively in new leaves, old leaves and root in Xiaoyan 60 when compared the salt treatment and the control, while the corresponding DEGs number in Zhongmai 175 were 613, 1401 and 1301. Further analysis demonstrated many DEGs were related with salt tolerance. Gene Ontology (GO) analysis showed the term “fatty acid biosynthesis process” was significantly enriched in new and old leaves of Xiaoyan 60, concurrently, the KEGG pathways “linoleic acid metabolism” and “alpha-linolenic acid metabolism” were also enriched. And most DEGs in these processes were up regulated, which indicated the level of jasmonate could be improved because the synthesis of jasmonate (JA) was through “alpha-linolenic acid metabolism”. In root tissue of Xiaoyan 60, the most significantly enriched KEGG pathway was “glucosinolate biosynthesis”, which could be induced by JAs. Differently, the most significantly enriched GO terms in the new and old leaves of Zhongmai 175 were “response to red or far red light” and “cellular response to starvation”. And similarly, the KEGG pathway “photosynthesis – antenna proteins” was also significantly enriched. Further analysis demonstrated that almost all the DEGs in these terms or pathways in Zhongmai 175 were down regulated, which manifested that the photosynthesis system may be damaged in Zhongmai 175, especially in the old leaves.These results indicate the jasmonates (JAs) related signal pathways may play a vital role in the salt tolerance of Xiaoyan 60. Inversely, the effects of JAs related pathways may be weaker in Zhongmai 175, and the photosynthesis system is destroyed due to the salinity stress.

135 GrainGenes: New Content, New Tools, New Tutorials

Victoria Carollo Blake

USDA ARS WRRC

GrainGenes (https://graingenes.org; https://wheat.pw.usda.gov) is the USDA-ARS database for wheat, barley, oat, and rye genetics and genomics. The GrainGenes project is moving toward a genome-centric resource to accommodate the ‘big data’ now available for the Triticeae and Avena. In this demo, we will 1) demonstrate the use of the new genome browsers on GrainGenes; 2) describe the variety-specific BLAST databases; 3) review the wealth of new content; and 4) share the collection of recently created topic-specific tutorials. Collaborations with The Triticeae Toolbox (T3), WheatIS, and Agriculture and Agri-Food Canada (AAFC) will assure that GrainGenes remains an important resource for the small grains research community. Mutual projects with our collaborators and future directions for the GrainGenes project will be discussed.

136 Multiplex Restriction Amplicon Sequencing (MRASeq), a New Next Generation Sequencing-Based Marker Platform for Genotyping

Amy N. Bernardo

Kansas State University

Marker-assisted breeding enables the indirect selection of traits that are difficult and/or costly to phenotype thereby saving time and money, and increasing selection efficiency. To be useful in breeding programs, markers for genome-wide genotyping must be low cost, randomly distributed throughout the genome, high-throughput, and technically simple. We developed a PCR and NGS-based, low cost, high-throughput genotyping technology for genome-wide marker assays. This technology, designated as Multiplex Restriction Amplicon Sequencing (MRASeq), reduces genome complexity by PCR-amplification of selected portions of genomic regions flanked by restriction sites and is achieved using tailed and semi-degenerate PCR primers with restriction enzyme sequence at the 3’-end. MRASeq is flexible because the restriction enzyme sequence and the adjacent degenerate base sequence in the primers can be altered to suit the species of interest. MRASeq uses restriction sites as primer sites and does not make use of restriction enzymes. The incorporation of unique barcodes during a second PCR allows hundreds of samples to be multiplexed in one sequencing run. Linkage mapping of polymorphic MRASeq SNP markers in an allohexaploid wheat biparental population showed random distribution of SNPs across genomes. MRASeq on wheat and barley natural populations generated thousands of SNPs suitable for genomic selection. Therefore, this marker platform can be used for linkage mapping, background selection, or any other purpose in which large numbers of markers are needed. This simple, flexible and high-throughput genotyping method should be useful in genotyping laboratories, plant breeding programs, and genetic research.

137 Complete Chloroplast Genomes of *Aegilops tauschii *coss. and *Ae.Cylindrica *Host Sheds Light on Plasmon D Evolution

Mari Gogniashvili

Institute of Molecular Genetics, Agricultural University of Georgia

Hexaploid wheat (Triticum aestivum L., genomes AABBDD) originated in South Caucasus by allopolyploidization of the cultivated Emmer wheat T. dicoccum (genomes AABB) with the Caucasian Ae. tauschii ssp strangulata (genomes DD). Genetic variation of Ae. tauschii is an important natural resource, that is why it is of particular importance to investigate how this variation was formed during Ae. tauschii evolutionary history and how it is presented through the species area. The D genome is also found in tetraploid Ae. cylindrica Host (2n = 28, CCDD). The plasmon diversity that exists in Triticum and Aegilops species is of great significance for understanding the evolution of these genera. In the present investigation the complete nucleotide sequence of plasmon D (chloroplast DNA) of nine accessions of Ae. tauschii and two accessions of Ae. cylindrica are presented. Twenty-eight SNPs are characteristic for both TauL1 and TauL2 accessions of Ae. tauschii using TauL3 as a reference. Four SNPs are additionally observed for TauL2 lineage. The longest (27 bp) indel is located in the intergenic spacer Rps15-ndhF of SSC. This indel can be used for simple determination of TauL3 lineage among Ae. tauschii accessions. In the case of Ae. cylindrica additionally 7 SNPs were observed. The phylogeny tree shows that chloroplast DNA of TauL1 and TauL2 diverged from the TauL3 lineage. TauL1 lineage is relatively older then TauL2. The position of Ae. cylindrica accessions on Ae. tauschii phylogeny tree constructed on chloroplast DNA variation data is intermediate between TauL1 and TauL2. The complete nucleotide sequence of chloroplast DNA of Ae. tauschii and Ae. cylindrica allows to refine the origin and evolution of D plasmon of genus Aegilops.

138 Can We Apply Lessons Learned from Manual Gene Annotation in Human and Mouse to Wheat?

Jane Loveland

EMBL-EBI

The Ensembl-HAVANA team have significant expertise in manual genome annotation and over the last 15 years have been providing reference gene annotation for whole genomes (human, mouse and zebrafish), individual chromosomes (Pig chr X and Y), genes (Rat, Pig) and regions (MHC of Gorilla, Pig, Dog, Wallaby, Tasmanian devil) of community interest. Comprehensive manual annotation of high quality genomes is labour intensive and as such is not practical for very many genomes, however, automated gene annotation methods such as the Ensembl genebuild pipeline, can do a good job of a capturing the geneset, particularly protein coding genes. It is clear that experts in individual communities will want to improve the baseline automated annotation, for example to adequately capture their knowledge of functionally important genes or resolve annotation errors in complex regions such as gene clusters that present particular challenges for automated pipelines. We have a history of successful annotation workshops that have been co-ordinated by our team, namely for cow, pig and rat, where we provided training and annotation expertise to particular communities. As individual groups and communities create their own gene annotation, there is a danger that any divergence in their approach could hinder accurate downstream analysis both within and between species. For example, the CCDS collaboration between ourselves and RefSeq was established to agree common annotation for at least one CDS in every protein-coding gene in the already well annotated human and mouse genomes. Despite the technical expertise in both groups and the wealth of available experimental data in these species, small differences in starting annotation guidelines led to significant differences in the annotated genes, requiring the resolution of many hundreds of annotation differences. We will present our guidelines and practices for annotation, based on our accumulated knowledge from producing reference gene annotation as framework that could be used to inform the approach of a community towards manual annotation, for example, by providing guidelines that can be used in a platform agnostic way to help inform decisions on annotating structural and functional information for genes and transcripts.

139 The Hexaploid Oat Genome

Nick Sirijovski

Lund University

Relative to other cereals such as rice, barley and wheat, very little is know about the genetics of oat. Cultivated oat (Avena sativa) is a hexaploid comprised of three diploid genomes (AACCDD). It has a 1C genome of 21 chromosomes with a total size estimated to 13Gb. The large genome size and polyploidy has meant that deciphering the genetics of cultivated oat has lagged behind other cereals. Recently, oat has received much attention due to well documented health benefits of consuming this ‘super food’, which in turn has lead to increased production of oat-based novel foods and ingredients e.g. dairy alternatives, beta-glucan extracts, and even meat substitutes. With the fast paced development of next generation sequencing technologies, it has now become possible and affordable to undertake genome sequencing of hexaploid oat using short read technology. Herein we report on the status of the Swedish oat genome sequencing project, which is part of the newly inaugurated ScanOats research center in Lund, Sweden.

140 Cloning of the Zero-Rowed Spike 1 in Barley

Shun Sakuma

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

Inflorescence architecture is a major determinant of the components of final grain yield in the cereals. The inflorescence can take the form of a panicle (rice, sorghum, and maize) or a spike (wheat, barley and rye). Barley’s spike is composed of three spikelets (one central spikelet and two lateral spikelets) per rachis node that is a unique character of Hordeum species among Triticeae. Cultivated barley (Hordeum vulgare ssp. vulgare L.) produces either two-rowed (central spikelet fertile; lateral spikelets sterile) or six-rowed (complete fertility of the three spikelets) spikes. The six-rowed spike or lateral spikelet fertility is under the control of Six-rowed spike 1 (vrs1), vrs2, vrs3, vrs4 and Intermedium spike-c (int-c). However, the genetic basis of three-spikelet structure in a distichous manner was not fully elucidated yet. To address this, we identified the zero-rowed spike 1 (zrs1) mutant derived from mutagenesis of wild barley (Hordeum vulgare ssp. spontaneum L.). The zrs1 mutant shows severe spikelet initiation defects and its distichous pattern is lost. At the vegetative growth the phylotaxis is normal as wildtype, however, after reproductive stage some tillers show onion-like leaf structure. We conducted genetic analysis using whole genome sequencing and RNA sequencing approach to reveal the genetic basis of the zrs1 mutant.

141  Gene Flow between Rye and its Wild Relatives

Mona Schreiber

IPK Gatersleben

Rye (Secale cereale L.) is a cereal grass that is an important food crop in Central and Eastern Europe. In contrast to its close relatives wheat and barley, it was not a founder crop of Neolithic agriculture, but is considered a secondary domesticate that may have become a crop plant only after a transitory phase as a weed. As a minor crop of only local importance, genomic resources in rye are underdeveloped, and few population genetic studies using genome-wide markers have been published to date. We collected genotyping-by-sequencing data for 603 individuals from 101 genebank accessions of domesticated rye and its wild progenitor S. cereale *subsp. vavilovii* and related species in the genus Secale. Variant detection in the context of a recently published draft sequence assembly of cultivated rye yielded 55,744 single-nucleotide polymorphisms with present genotype calls in 90 % of samples. Analysis of population structure recapitulated the taxonomy of the genus Secale. We found only weak genetic differentiation between wild and domesticated rye with likely gene flow between the two groups. Moreover, incomplete lineage sorting was frequent between Secale *species either because of on-going gene flow or recent speciation. Our study highlights the necessity of gauging the representativeness of *ex situ germplasm collections for domestication studies and motivates a more in-depth analysis of the interplay between sequence divergence and reproductive isolation in the genus Secale.

142 Challenges and Opportunities of Connecting Phenotype with Genotype; Perspectives from Seeds of Discovery and Excellence in Breeding.

Sarah Hearne

CIMMYT International Maize and Wheat Improvement Center

Management of data along complex and logistically challenged crop research and breeding processes is often the last thing to be considered in planning processes and is consequently an Achilles heel, limiting the impact of many projects and initiatives. Here we present a review of some of the challenges, interventions and opportunities in data management from the perspectives of an established initiative and a new cross commodity platform.

The Seeds of Discovery initiative (SeeD) aims to explore and leverage high value novel diversity for maize and wheat breeding application. In the 6.5 years since inception, SeeD has generated vast quantities of genotypic and phenotypic data from extensive evaluation of germplasm bank accessions. The effective management of this data along the collection, curation, analysis and dissemination continuum has evolved, resulting in multidisciplinary and multi-institutional development of systems, standard operating procedures and business rules. We present some of the experiences of SeeD in developing effective practices to connect genotype with phenotype.

The CGIAR Excellence in Breeding Platform (EiB), established in 2017, is developing a resource and support structure to modernize breeding programs targeting the developing world. EiB draws from innovations in the public and private sector to provide access to cutting-edge tools, services and best practices, training and practical advice for breeding programs. Data accuracy, integrity and interconnectivity are fundamental to breeding gain and EiB is placing strong emphasis on the sharing of best practices and resources in this area. Current plans and initial platform activities in this area will be presented.

143 Advanced Genomics Tools for Deep Insights into Complex Genome Systems

Jayson Talag

Arizona Genomics Institute

The Arizona Genomics Institute (AGI) has played significant roles in numerous genome projects over the past 15 years, including Asian and African rice and its 20 wild relatives, maize, wheat, Brachypodium, date palm, sugarcane, citrus, cacao, soybean and its wild relatives, brassicas, tomato, tree nuts, etc. AGI’s expertise is not limited to plants, and includes model species like Drosophila (19 genomes), zebra finch, Biomphalaria and nurse shark, dingo, as examples. AGI’s philosophy is that the first genome sequence of any species should be as high a quality as possible. To achieve this standard, AGI is currently employing long-read sequencing platform – e.g. PacBio’s SEQUEL. Using this instrument, our read lengths Sub read N50 average 20KB, with 23KB on some projects. The average output is ~5Gb/cell, with some over 9Gb/cell. Using this technology to sequence BAC-pool we published two of the highest quality indica rice genomes August of 2016. Theses genome have now been upgraded with the addition of whole genome shotgun PacBio data resulting in near gap free assemblies with less than 20 gaps/genome.

A critical key to our success lies in our ability to isolate high-quality high-molecular weight DNA as initial substrates for library construction. We have found that specific considerations must be addressed to achieve access to genomic substrates (HMW DNA and RNA) for downstream high quality performance. These include defined tissue types and collection protocols, careful extraction procedures and chemistry modifications, advanced purification steps using both chemical and electrophoretic methods, and very stringent quality control measures to assure substrate performance. Our methods have been used to produce high quality substrates for a variety of different applications such as Pacbio, Illumina, RNAseq, 10x Genomics, Dovetail, BAC library construction, etc.

144 Integrating and Displaying Plant Gene Expression in Expression Atlas

Laura Huerta

European Bioinformatics Institute (EMBL-EBI)

Expression Atlas (https://www.ebi.ac.uk/gxa) is a database and web-service at EMBL-EBI that selects, curates, re-analyses and displays gene expression data in a baseline context, e.g. to find genes expressed in different tissues in potato, and in a differential context, e.g. to find up-regulated genes in response to stripe rust and powdery mildew in wheat. Plant experiments from ArrayExpress, GEO and SRA/ENA/DDBJ are selected for curation and analysis. Data curation involves enriching sample annotation with additional metadata, annotating metadata with Experimental Factor Ontology (EFO) terms and deciding comparisons for differential expression analysis based on associated publications and correspondence with the original researchers. Data analysis is performed using open source tools for microarray data and our standardized pipeline iRAP (https://github.com/nunofonseca/irap) for RNA-seq data. Currently, we provide gene expression analysis results for more than 700 plant experiments across 20 different plant species. Expression Atlas can be searched by gene, gene set and biological condition queries. The use of EFO annotations allows efficient search via ontology-driven query expansion and facilitates data integration across multiple experiments. We offer downstream analysis and visualization such as gene co-expression, biological variation among replicates, transcript quantification, visualization of gene expression in Gramene genome browser and enrichment of Gene Ontology terms and Reactome pathways. Finally, we have developed an automatic pipeline that discovers new plant RNA-seq data at ENA for 45 different species, performs quality control, alignment to the genome reference in Ensembl plants and quantification of gene and exon expression. The analysis results are available via our RNASeq-er API (https://www.ebi.ac.uk/fg/rnaseq/api/).

145 Mining DNA Methylation Variations in Alleles and Homeologs using CGmapTools

Weilong Guo

China Agricultural University

DNA methylation is important for gene silencing and imprinting in both plants and animals. We developed software CGmapTools (freely available at https://cgmaptools.github.io/) as a toolset for mining DNA methylation information in BS-seq data, by integrating ~40 command-lines applications into one package. This package uses CGmap and ATCGmap as the format interfaces, and designed binary formats to reduce the file sizes and support fast data retrieval, and can be applied for context-wise, gene-wise, bin-wise, region-wise, and sample-wise analyses and visualizations. To accurately identifying heterozygous SNVs from partially C-to-T converted, we designed two methods, BayesWC and BinomWC, that substantially improved the precision of heterozygous SNV calls from ~80% to 99% while retaining comparable recalls. With these SNV calls, we provided functions for allele-specific DNA methylation (ASM) analysis and visualizing the methylation status on reads. Applying ASM analysis to a previous dataset, we found that an average of 1.5% of investigated regions showed allelic methylation, which were significantly enriched in transposon elements and likely to be shared by the same cell-type. A dynamic fragment strategy was utilized for DMR analysis in low-coverage data. Recently, we develop new method for mining differential DNA methylations among homeologs, suitable for allopolyploid genomes, such as bread wheat. The new method also support visualising DNA methylomes variations and genomic variations among homeologs.

146 New Genotyping Technology, GRAS-Di, Using Next Generation Sequencer

Hiroyuki Enoki

Toyota Motor Corporation

We developed new genotyping technology, Genotyping by Random Amplicon Sequencing-Direct (GRAS-Di). This technology consisted of sample preparation using high concentration random primer, NGS and data analysis. The sample preparation was very simple. It was not necessary to do primer design, enzyme digestion, fragmentation, size selection, adaptor ligation, and sample normalization. It was only two steps PCR for NGS library without specialized equipment. Rice BIL population was used for evaluation of genotyping by GRAS-Di (96 samples / lane of HiSeq2500). The number of reads for each amplicon was highly reproducibility, r > 0.99, with repetition. Over ten thousand SNPs were detected among the BIL population and the SNPs were distributed uniformly rice genome. The ratio of missing value was very low, 1.5%. The reproducibility of SNP was 99.9% with repetition. If there was no reference sequence, genotype data could be detected by GRAS-Di using original algorism based on amplicon analysis. Theoretically, the technology is also applicable to other creatures, including highly polyploidy creatures. We performed the applicability test for several creatures. The result shown that the technology was applicable for over fifty creatures, including wheat, soybean, tomato, potato, sugarcane, cow, pig, chicken, tuna and human. The technology could be provided over 30,000 multiplex sequencing at once. We think that GRAS-Di would be very easy and very powerful technology for genome wide genotyping in many creatures. We signed licensing agreement with Kazusa DNA Research Institute, Eurofins Genomics, and GeneBay for GRAS-Di.

147、Stacking Multiple Stem Rust Resistance Genes at a Single Locus for Durable Resistance in Wheat

Ming Luo

Commonwealth Scientific and Industrial Research Organisation

Stem rust disease caused by the fungal pathogen Puccinia graminis f.sp tritici is a significant threat to global wheat production. The most cost effective way to control this disease is by genetic resistance. However major gene resistance is often readily overcome by pathogen evolution when resistance genes are deployed singularly. Combining major resistance genes is believed to extend their durability as multiple mutations are required in the pathogen to overcome this polygenic resistance. Major resistance genes can be combined by conventional breeding however this is a labour intensive process and resistance gene combinations are difficult to maintain in segregating families. In this study, we have used cloned stem rust resistance genes Sr22, Sr35, Sr45, Sr46 and Sr50 and the multi-pathogen adult plant rust resistance gene Sr55/Lr67/Yr46/Pm46/Ltn3 to produce binary vectors containing combinations of these genes. Constructs containing either 3, 4, 5 or 6 rust resistance genes were produced and transformed into bread wheat by Agrobacterium transformation. Molecular/genetic analysis demonstrated that some transgenic wheat lines contain all the resistance genes present in the binary vector used for transformation (ie. up to six) and these genes are inherited as a single locus in progeny plants. Transgenic plants are resistant to wheat stem rust disease with resistance co-segregating with the multigene transgenic locus.

148 MAGIC Yield: Using an Eight Founder Population for the Genetic Dissection of Yield and Yield Components in UK Winter Wheat

Benedetta Saccomanno

NIAB

Multiparent advanced generation inter-cross (MAGIC) populations are a powerful mapping resource in crop genetics for the dissection of complex traits, previously hindered by relatively low genetic recombination and allelic diversity of traditional bi-parental populations. Wheat (*Triticum aestivum *L.) is a major arable crop of global importance, covering 1.6 million hectares in the UK alone (AHDB survey, 2017). Breeders and farmers must continue to improve wheat grain yield and yield stability to help meet demand from an increasing population, and to ensure food security in the face of the effects of climate change. The Magic Yield project helps address these problems by using an eight-founder MAGIC population (Mackay *et al. *2014), consisting of 1,000 lines created by inter-crossing eight elite UK winter wheat varieties over three generations, to study the genetic basis of yield and yield components. With the participation of five wheat breeding companies, we conducted field trials at five UK sites for two consecutive years, phenotyping yield and a suite of pre- and post-harvest yield components. Phenotypic data coupled with Illumina iSelect 90k SNP genotype data (Gardner *et al. *2016) allowed the detection of a total of 76 quantitative trait loci (QTL) across all year, trait and site combinations. Flanking markers for selected QTL were converted to Kompetitive Allele Specific PCR (KASP) markers to aid fine-mapping and consequent characterization of genes controlling yield. Ultimately, the resources generated will aid the selection of wheat lines with improved performance within breeding programs, for the downstream benefit to growers and end-users.