植物和动物基因组XXVI大会（PAG）于2018年1月13 - 17日举行。目前官网已发布相关的摘要集，大家可以关注以下。小编把摘要也下载了下来，回复PAG即可获取。

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以下摘录的部分麦类相关的摘要，其中有大家比较关注的有小麦基因组联盟公布了小麦的参考基因组

P0995:  The Reference Sequence for the Bread Wheat Genome 

The International Wheat Genome Sequencing Consortium, IWGSC, Lee's Summit, MO and Rudi Appels, Murdoch University, Perth, Australia 

The goal of the IWGSC since its inception in 2005 has been the generation of a high quality reference genome sequence for bread wheat that integrates genetic and genomic resources and supports the acceleration of wheat production and improvement to keep pace with projected rises in human population. The IWGSC RefSeq v1.0 has been assembled from a whole genome shotgun assembly of allohexaploid bread wheat cv. Chinese Spring and integrated with a wealth of community resources including: chromosome survey sequences (IWGSC CSS), chromosome-specific BAC-based physical maps, WGPTM tag sequences and optical maps, POPSEQ genetic maps, Hi-C and radiation hybrid maps. The assembly represents ~94% of the predicted wheat genome size in large scaffolds (N50 22.8Mb) that are assigned and ordered along the 21 wheat chromosomes. 107,886 high confidence gene models have been annotated and further sets of incompletely supported sets of gene models and pseudogenes identified. The annotated genes have been used to analyze the distribution of homoeologous genes across A,B,D genomes, together with gene duplications and losses that play important roles in wheat evolution. Insights into gene expression and its regulation have been revealed using a transcriptome atlas developed from 850 RNASeq datasets representing all stages of wheat phenological development. With a sequence assembly that now supports the resolution of complex gene families associated with important traits such as yield, grain quality or disease resistance, wheat now has a key resource in place to anchor all QTL knowledge to the reference sequence and stimulate new molecular approaches for the future

P1093: Comparison of Durum Landraces with Northern Great Plains Adapted Cultivars and Identification of Selection Sweeps 

Jason Fiedler1 , Justin Hegstad1 , Elias Elias1 , Stephen Xu2 , Shiaoman Chao2 and Xuehui Li1 , (1)North Dakota State University, Fargo, ND, (2)USDA-ARS, Fargo, ND 

Durum wheat (T. turgidum ssp. Durum, AABB) is a key crop for high-value food production. Modern breeding programs over the last century have developed a number of elite cultivars that are adapted for growth in the Northern Great Plains. To investigate the genomics underlying this adaptation, we compare 449 global durum lines from the Wheat Coordinated Agricultural Project with 34 advanced lines from the North Dakota State University (NDSU) Durum Breeding Program. We used genotype-by-sequencing (GBS) to identify 21,030 single nucleotide polymorphisms (SNP)s in the populations and measured genetic diversity on several scales. We find that population sub-structure designations largely agree with regional adaptation, and lines adapted to the Northern Great Plains show relatively low genetic diversity and high allelic fixation. We identified 23 genetic intervals that display differential allelic fixation between un-adapted and improved lines, suggesting that these linkage blocks are important for durum improvement. Screening potential lines for these linkage blocks could accelerate breeding efforts, and understanding the genes in these regions could shed light on the molecular characteristics of "elite" lines. 

P1094:Unique Sources of Resistance to Fusarium Head Blight for Durum Wheat 

George Fedak1 , Danielle Wolfe1 , Dawn Chi1 , Sylvie Cloutier1 , Allen Xue1 and Lianquan Zhang2 , (1)Agriculture and Agri-Food Canada, Ottawa, ON, Canada, (2)Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China There was a major epidemic of FHB in the durum wheat crop in Canada in 2016. There is not as much variability for FHB resistance in the primary gene pool of T. durum as there is in bread wheat. In a recent screening of synthetic hexaploids and their parents for FHB resistance by point inoculation, a number of T. dicoccon accessions appeared to have enhanced levels of FHB resistance. The floret infection frequencies ranged from 10-12% while the values for Langdon durum were 73%. These inoculations were repeated for a second time with similar results. The T. dicoccon accessions were accessed from various gene banks. Records indicate that some of these accessions were collected in Russia and Georgia in the 1930s by N. I. Vavilov and deposited in the genebanks. As would be expected from T. dicoccon accessions collected in the wild, some are deficient in useful agronomic traits. For example some are very tall and others have smaller spikes. However such traits could easily be removed by a few backcrosses so as to minimize any linked drag. On the other hand other accessions had very large seeds, a trait that could be an asset to a breeding program. Another potential source of FHB resistance for durum wheat is that found in the amphiploid Triticum durum x Hordeum chilense with the genomes AABBHH. This source of resistance will be more difficult to integrate into durum wheat. 

P1095: Population Structure of Aegilops tauschii 

Le Wang1 , Naxin Huo1,2, Karin R. Deal1 , Meiling Zou1 , Jirui Wang3 , Yong Q. Gu2 , Jan Dvorak1 and Ming-Cheng Luo1 , (1)Department of Plant Sciences, University of California, Davis, Davis, CA, (2)USDA ARS, Western Regional Research Center, Albany, CA, (3)Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China Aegilops tauschii, the donor of the hexaploid wheat D genome, is distributed widely and is genetically diverse. The availability of a highquality genomic sequence of Ae. tauschii enables us to analyze its population structure using whole genome resequencing strategy. Due to Ae. tauschii’s large genome size and abundance of repetitive sequences, whole genome exome capture was chosen to analyze the population structure of Ae. tauschii collections. In this study, a core collection of 63 accessions representing diversity panel of Ae. tauschii was subjected to capturing and sequencing with Illumina’s HiSeq platform. There were 60 to 161 million high-quality reads per accession generated; of these reads, 99.4% were mapped to the Ae. tauschii reference genome. A total of 1,355,118 SNPs and 119,319 Indels were obtained among the 63 accessions using BWA-MEM and SAMtools. Structural analysis revealed two distinct lineages, which is in agreement with our previous observations based on the 10K Infinium assay (Wang et al. 2013), and shows that there is little gene flow between these two lineages. This work is a part of the NSF-funded Project IOS-1238231 to generate a reference genome for the genome of Ae. tauschii(http://aegilops.wheat.ucdavis.edu/ATGSP/).

 P1096: Structural Organization and Gene Duplication in the Chromosomal Region Harboring the Alpha-Gliadin Gene Family in Aegilops tauschii 

Yong Q. Gu1 , Naxin Huo1 , Lingli Dong2 , Shengli Zhang3 , Tingting Zhu4 , Toni Mohr1 , Susan B. Altenbach1 , Daowen Wang2 , Zhiyong Liu2 , Ming-Cheng Luo4 and Jan Dvorak4 , (1)USDA ARS, Western Regional Research Center, Albany, CA, (2)Institute of Genetics and Developmental Biology, CAS, Beijing, China, (3)Henan Institute of Science and Technology, China, (4)Department of Plant Sciences, University of California, Davis, Davis, CA 

Among the wheat prolamins important for its end-use traits, α-gliadins are the most abundant and also a major cause of food-related allergies and intolerances. Previous studies of various wheat species estimated between 25 to 150 α-gliadin genes reside in the Gli-2 locus regions. To better understand the evolution of this complex gene family, the DNA sequence of a 1.75-Mb genomic region spanning the Gli-2 locus was analyzed in the diploid grass, Aegilops tauschii, the ancestral source of D genome in hexaploid bread wheat. Comparison with orthologous regions from rice, sorghum, and Brachypodium revealed rapid and dynamic changes only occurring to the Ae. tauschii Gli-2 region, including insertions of high numbers of non-syntenic genes and a high rate of tandem gene duplications, the latter of which have given rise to 12 copies of α-gliadin genes clustered within a 550-kb region. Among them, five copies have undergone pseudogenization by various mutation events. Insights into the evolutionary relationship of the duplicated α-gliadin genes were obtained from their genomic organization, transcription patterns, transposable element insertions, and phylogenetic analyses. An ancestral GLR gene encoding putative amino acid sensor in all four grass species has duplicated only in Ae. tauschii and generated three more copies that are interspersed with the α-gliadin genes. Phylogenetic inference and different gene expression patterns support functional divergence of the Ae. tauschii GLR copies after duplication. Our results suggest that the duplicates of α-gliadin and GLR genes have likely taken different evolutionary paths; conservation for the former and neofunctionalization for the latter.

 P1097: 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, Tbilisi, Georgia and Tengiz Beridze, Agricultural University of Georgia, Tbilisi, 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.

 P1098: Molecular Genetic Characterisation of Triple Rust Resistance in Aegilops tauschii 

Naveenkumar Athiyannan1,2, Robert A. McIntosh3 , Peng Zhang3 , Timothy Hewitt2,3, Sutha Chandramohan2 , Sami Hoxha3 , Kerrie Forrest4 , Pippa Kay4 , Narayana Upadhyaya2 , Burkhard Steuernagel5 , Brande Wulff5 , Terese Richardson2 , Smitha Louis2 , Dhara Bhatt2 , Michael Ayliffe2 , Matthew Hayden4 , Lee Hickey1 , Yuming Long6 , Steven S. Xu7 , Evans Lagudah2 and Sambasivam Periyannan1,2, (1)Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia, (2)Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia, (3)Plant Breeding Institute, University of Sydney, Cobbitty, Australia, (4)School of Applied Systems Biology, AgriBio, La Trobe University, Melbourne, Australia, (5)John Innes Centre, Norwich, United Kingdom, (6)North Dakota State University, Fargo, ND, (7)USDAARS, Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND 

Bread wheat (Triticum aestivum) is the third most cultivated crop worldwide, and a major caloric source for the human population. Global wheat production is under constant threat due to the constant evolution of highly virulent fungal pathogens such as Puccinia sp that cause rust disease. Losses due to rust disease are routinely minimised through the deployment of host plant-mediated genetic resistance in commercial cultivars. However, pathogens evolve virulence to overcome this resistance. Therefore continuous supply of new sources of resistance is essential for sustainable rust management. Resistance from the wild relatives of hexaploid wheat is a valuable resource as they broaden the gene pool of available resistance genes. In this study, CPI110672, an accession of the D genome progenitor Aegilops tauschii, was chosen for in-depth analysis as it resists the three wheat rust diseases namely leaf, stem and stripe rust. To characterise this triple rust resistance, we conducted genetic analysis using a mapping population derived from the cross between CPI110672 and a susceptible accession CPI110717. Through rust infection screening and 90K SNP marker analysis, the chromosome position and closely linked markers were identified. Physical maps for the chromosome region carrying these rust resistance genes were generated using the new reference genome sequences of hexaploid wheat Chinese Spring IWGSC Ref Seq v1.01 and the diploid Ae. tauschii accession, AL8/782,3. Comparative genomics of these reference sequences together with contigs assembled from the sequenced genome of CPI110672 facilitated the identification of candidate genes. Functional analysis will be conducted through transformation into the rust-susceptible wheat cultivar fielder. 

 P1101: Developing Bioinformatics Resources to Study Meiosis in the Barley Cultivar Golden Promise 

Miriam Schreiber1 , Abdellah Barakate1 , Nicola Uzrek1 , Isabelle Colas1 , Dominika Lewandowska1 , Malcolm Macaulay1 , Sybille Mittmann2 , Mikel Arrieta2 , Jonathan M Wright3 , Bernardo J. Clavijo3 , Luke Ramsay1 and Robbie Waugh1,2, (1)The James Hutton Institute, Invergowrie, Dundee, United Kingdom, (2)The University of Dundee at JHI, Invergowrie, Dundee, United Kingdom, (3)Earlham Institute, Norwich, United Kingdom

 In barley (Hordeum vulgare) meiotic recombination shows a non-random pattern of recombination which is skewed towards the ends of the chromosomes. This results in around 30% of the genes in the centromeric region not recombining; a big restriction for geneticists and breeders alike. We are developing genetic resources, using different techniques and approaches to identify the roles of meiotic genes and their various natural and induced alleles in recombination in the barley cultivar Golden Promise (GP). First we developed a GP genome assembly by aligning scaffolds to the Morex reference and merging them together chromosome-wise. Second, we have established an EMS (ethyl methanesulfonate) TILLING (Targeting Induced Local Lesions in Genomes) population in GP. A first analysis of the M2 population showed a mutation frequency of approximately 10 mutations per Mb (per individual) and highlighted big differences between the individual plants. The population has and is currently being used to screen for mutations in meiotic genes. As GP is one of the few barley cultivars that can be used for genetic transformation we will be able to complement any identified mutant alleles and see if it rescues any observed phenotype. Third we’ve build an anther/meiocyte transcriptome covering four stages from premeiotic to pollen. This extensive transcriptome dataset will represent a reference for ongoing proteomics analyses and other comparative (e.g mutant vs. WT) experiments. It will be used to identify new genes involved in meiosis and to analyse the pattern of transcription during meiosis in genetically or environmentally perturbed plants. 

P1102: Multiparental Genomic Selection for Local Adaptation in Barley (Hordeum vulgare) 

Daniel W Sweeney, Cornell University, Ithaca, NY 

Genomic prediction accuracies are generally thought to be highest within biparental families. Related biparental families contain greater genetic diversity, create higher power for QTL detection, offer a larger set of segregating progeny that are useful for selection, and may enable higher prediction accuracies than single families. A training set of ~1430 two row spring barley breeding lines from seven biparental families with a common female parent were phenotyped for Fusarium head blight, Bipolaris spot blotch, leaf rust, pre-harvest sprouting, and grain protein in two locations. These traits are critical to the establishment of malting barley production in New York state. Cross-validation was used to assess prediction accuracy within full-sib families, across half-sib families, and across all families in all traits. Inclusion of significant markers from genome-wide association studies as fixed effects were tested. Prediction accuracies between spatially corrected and base models were also compared. A selection index will be used to make selections from the training population that will be used to initiate a multi-year genomic selection experiment. 

P1103: Environmental Driven Adaptation of Wild Barley in the Evolution Canyon Cong Tan1 , Fei Dai2 , Camilla Beate Hill1 , Penghao Wang3 , Brett S Chapman4 , Qisen Zhang5 , Yong Jia1 , Xiao-Qi Zhang1 , Roberto A. Barrero6 , Gaofeng Zhou1 , Yong Han1 , Wenying Zhang7 , Matthew I. Bellgard6 , Robbie Waugh8 , Dongfa Sun9 , Eviatar Nevo10, Guoping Zhang11 and Chengdao Li12, (1)Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia, (2)Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, Zhejiang University, Hangzhou, China, (3)School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia, (4)Centre for Comparative Genomics, Murdoch University, Murdoch, Australia, (5)Australian Export Grains Innovation Centre, Soth Perth, Australia, (6)Centre for Comparative Genomics, Murdoch University, Perth, Australia, (7)Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, China, (8)The James Hutton Institute, Invergowrie, Dundee, United Kingdom, (9)College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China, (10)Institute of Evolution, University of Haifa, Mount Carmel, Israel, (11)College of agriculture and biotechnology, HangZhou, China, (12)Western Barley Genetics Alliance, Murdoch University, Murdoch, Australia

 Background: Wild barley (Hordeum spontaneum L.) is the ancestor of cultivated barley (Hordeum vulgare L.) with a wide geographic distribution across highly diverse environments. The ‘Evolution Canyon’ I (EC) in Israel, consists of two abutting slopes, separated by only 250 m but with drastically different microclimates. It is an ideal microsite model to characterize incipient sympatric speciation of wild barleys and its adaptation to environmental stresses. Result: In this study, transcriptome sequencing was first performed with ten wild barley accessions collected from two opposing slopes of the ‘Evolution Canyon’. The wild barley accessions showed dramatic genomic diversity and were grouped into two apparent clusters based on population structure and principle component analysis as well as phylogenetic analysis. Then, whole genome sequencing with high-coverage was performed with another ten barley accessions including six wild barleys from two slops of the ‘Evolution Canyon’, two wild barley from Tibetan Plateau and two cultivars. It was further confirmed that the divergent distance between the wild barleys from the opposing slops is bigger than that between cultivar barley and Tibetan wild barley. Genomic regions with strong environmental selection were identified between two slops. Accessions from the two slopes showed dramatically response and differential gene expression genes to the drought treatment, which is the major environmental difference between the two slopes. Conclusion: Our results provided a comprehensive evidence indicating incipient sympatric speciation of wild barleys in the ‘Evolution Canyon’. Environmental divergence is a key driver for wild barley adaptation and genomic evolution between the two slopes. 

P1108: Identifying Useful Alleles for Crop Improvement: Applying State of the Art Genomic Tools, Methods and Approaches to Characterise the WHEALBI Barley Genetic Resource 

Daniela Bustos-Korts1 , Alessandro Tondelli2 , Joanne Russell3 , Ian Dawson3 , Noemi Trabanco4 , Davide Guerra2 , Stefano Delbono2 , Stylianos Kyriakidis3 , Allan Booth3 , Chiara Ferrandi4 , Francesco Strozzi4 , Ezequiel L. Nicolazzi4 , Hakan Ozkan5 , Marta Molnar-Lang6 , Mária Megyeri6 , Mikó Péter6 , Benjamin Kilian7 , Nils Stein8 , Laura Rossini4 , Robbie Waugh3 , Luigi Cattivelli2 and Fred A. van Eeuwijk1 , (1)Wageningen University & Research - Biometris, Wageningen, Netherlands, (2)CREA - Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy, (3)The James Hutton Institute, Invergowrie, Dundee, United Kingdom, (4)Parco Tecnologico Padano, Lodi, Italy, (5)University of Cukurova, Adana, Turkey, (6)Agricultural Institute, MTA ATK, Martonvásár, Hungary, (7)The Global Crop Diversity Trust (GDCT), Bonn, Germany, (8)Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany 

The EU-funded WHEALBI project (Wheat and barley Legacy for Breeding Improvement; http://www.whealbi.eu) is taking a multidisciplinary approach to identify, understand and utilise the genetic diversity available in wheat and barley cultivars, landraces and wild relatives. This is strategic to meet the challenge of increasing crop yields while reducing environmental impact. Here we focus on a carefully selected set of 400 barley accessions from extensive ex situ collections which cover the geographical and agro-ecological adaptive range of barley. Agronomic and life history traits, collected from multi-environment common gardens experiments across Europe, provide a unique dataset to decipher the genetic basis of adaptation to environmental conditions. A comprehensive molecular variant analysis by exome sequencing identified 1.75 million SNPs that have been used to investigate allelic variation at candidate genes driving phenotypic differences for heading date, plant height, grain weight, and awn length. We were able to relate geographical origins using site information to genotypic diversity, providing valuable information to identify novel ‘adapted’ alleles for future breeding under a changing climate. 

P1109: Evaluation of (1,3;1,4)-β-D-Glucan in Barley (Hordeum vulgare) 

Endosperm. Ivonne Benitez1 , Jamie Sherman2 and Christopher Botanga1 , (1)Chicago State University, Chicago, IL, (2)Montana State University, Bozeman, MT 

Barley is an important cereal crop with global significance, and has recently attracted several areas of research interests. Worldwide usage of barley is concentrated in the alcoholic beverage industry followed by livestock feed, and only a small amount is used for human consumption. However, because barley has a high content of the polysaccharide beta glucan it is increasingly sought after for the numerous health benefits that may result from its consumption. In contrast, barley with high beta glucan content is undesirable by the malt and alcohol industries due to its negative impact on viscosity during the brewing process. Previous studies have identified QTL loci that are associated with the biosynthesis of beta glucan located on chromosomes 1H, 2H, 5H, and 7H. In this study, we are evaluating some genotypes of barley in order to characterize them as high or low in endosperm beta glucan content, and further carry out sequence homology analysis in order to determine if there are any differences in the sequences of the beta glucan genes. We are particularly interested in identifying polymorphisms arising from SNPs and INDELS that may serve as valuable markers for use in breeding programs aimed at altering the content of beta glucan. Funding: Funding support: USDA-NIFA Award No. 2016-70003-24775, USDA-NIFA Triticeae Coordinated Agricultural Project (T-CAP) and also by the U.S. Department of Education Award Number P382A110049. 

P1110: Wheat, Barley, Oat, and related Impact of Colchicine Treatment on Genetic and Epigenetic Variation in Barley Regenerants. 

Katarzyna Makowska, Plant Breeding and Acclimatization Institute - National Research Institute, Błonie, Poland and Joanna Machczyńska, Janusz Zimny, Piotr Bednarek, Renata Orłowska

 Androgenesis is a process of induced unusual microspore development - into embryos that can grow into plants. Along the way, spontaneous doubling of the chromosome (SCD) number may occur leading to doubled haploids (DHs). Homozygosity makes DHs interesting objects for genetic and genomic research, as well as valuable material in plant breeding. In barley, SCD may range from 55% to 90% depending on genotypes. Variable levels of SCD combined with low effectiveness of androgenesis dictate an antimitotic agents application to produce DHs. Colchicine is commonly used to induce chromosome doubling (ICD) but it has negative effects such as mixoploidy, abnormal morphology and changes in gene expression that may be due to DNA methylation changes. Here we address the effect of colchicine on DNA sequence changes and alteration of the DNA methylation patterns among androgenic regenerants. Haploid (H) green androgenic regenerants verified by flow cytometry were treated with colchicine in two concentrations (0.06% and 0.14%). The seed set of ICD plants ranged from sterile to full fertile. Control plants (without colchicine treatment), SCD regenerants and two groups of treated plants were studied using metAFLP and HPLC-RP. The global cytosine methylation was at the same level in the control and the colchicine treated samples, being at the same time higher than SCD plants. MetAFLP was performed to assess the level of sequence variation, de novo methylation and demethylation using two pairs of restriction enzymes (Acc65I/MseI, KpnI/MseI). The MetAFLP results showed differences between SCD and ICD plant what would be discussed. 

P1111:  Differential Expression Profiling of Barley Microspores during the Early Stages of Isolated Microspore Culture and Embryogenesis 

Sébastien Bélanger, Laval University, Québec, QC, Canada, Suzanne Marchand, Université Laval, Québec, QC, Canada, Pierre- Étienne Jacques, Sherbrooke University, Sherbrooke, QC, Canada, Blake Meyers, Donald Danforth Plant Science Center, St. Louis, MO and Francois Belzile, Laval University, Quebec, QC, Canada 

In barley, it is possible to induce embryogenesis in the immature microspore (male gametophyte) to obtain a diploid plant that is perfectly homozygous (doubled haploid or DH). To change developmental fates in this fashion, microspores need to engage in cellular de-differentiation, interrupting the transcriptional and translational activities leading to pollen formation, and restore totipotency prior to engaging in embryogenesis. In this work, our objective was to characterize the transcriptome of immature barley microspores prior to (day 0) and immediately after (days 2 and 5) the application of a stress pretreatment that induces embryogenesis. A deep RNA-seq analysis revealed that microspores at these three time points exhibit a transcriptome of ~14k transcripts, ~90% of which were shared. Despite this extensive overlap, the three transcriptomes proved highly reproducible and distinct, and these differences were due to differential expression of a small set of genes (<500). The microspore response to the pretreatment applied was marked by an increased expression level of numerous Glutathione Stransferase (GST) and Heat shock protein (HSP) genes known to be involved in protection against stresses. The transition from microspore to developing embryo was marked by the induction of transcription factor genes known to play important roles in early embryogenesis and many genes involved in the synthesis and response to growth regulators. This work sheds light on the transcriptional changes that accompany an important developmental shift and provides candidate biomarkers for embryogenesis in barley. 

P1112: Cloning of the Zero-Rowed Spike 1 in Barley 

Shun Sakuma, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany, Martin Mascher, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany, Takao Komatsuda, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan and Thorsten Schnurbusch, LeibnizInstitute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, Germany 

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. P1113: Wheat, Barley, Oat, and related Genome-Wide Association Study for Seven Traits in Spring Barley from Eastern Canada Amina Abed, Laval University, Québec, QC, Canada and Francois Belzile, Laval University, Quebec, QC, Canada Genome-wide association studies (GWAS) are a powerful tool to identify quantitative trait loci (QTL) determining complex agronomic traits by relating genotypes at large numbers of markers to observed phenotypes. The detection of a credible genotype-phenotype association requires accurate genotypic data but also equally reliable phenotypic information. For many complex traits subject to environmental influences, extensive data obtained in registration trials (RTs) can help meet this goal. In this study, we explored the genetic basis of seven important traits in spring barley: deoxynivalenol (DON) content in kernels, heading time (HTM), days to maturity (MAT), thousand-kernel weight (TKW), specific weight (SPW), grain yield (GYD) and plant height (PHT). A population of 200 advanced lines representing the genetic diversity of an Eastern Canadian barley breeding program were used. Phenotypic data were recovered from RTs carried out in 14 different locations from 2004 to 2014, for a total of ~20 environments (location x year). Genotypic characterization was carried out using a genotyping-by-sequencing (GBS) approach, resulting in ~40.000 polymorphic and high-quality SNP markers adequately covering all chromosomes. Population structure was examined by various methods (P matrix, K matrix and Q matrix) and different statistical models were tested to control it and to calculate P-values for marker-trait associations. We report some significant marker-trait associations obtained with the best approach. Our results demonstrated that such historical phenotypic data could be extremely valuable for performing GWAS for various quantitative traits. The significant associations obtained should provide information on trait architecture and tools for designing the next breeding program. 

 P1115:  Regulation of Barley and Powdery Mildew Interaction by Small RNAs 

Qian-Hua Shen, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China 

During plant-pathogen interactions, some plant and pathogen derived small RNAs have also shown to participate in trans-kingdom targeting and gene silencing. Here, we aim to identify and characterize sRNAs that may fulfill trans-kingdom functions in barley (Hv) and barley powdery mildew (Bgh) interactions. We have performed deep sRNA sequencing of 14 libraries during barley-powdery mildew interactions and identified 516 Huv-miRNAs (85 novel, 431 conserved) from barley and 84 Bgh-milRNAs (83 novel, 1 conserved) from Bgh. On the basis of the microRNA’s cross kingdom targets we screened 25 Huv-miRNAs (10 novel) and 9 Bgh-milRNAs (8 novel) as candidate trans-kingdom miRNAs. The differential expression study on the candidate trans-kingdom miRNAs classified miRNAs in two groups; miRNAs from first group have higher expression in healthy epidermis (EPH) but expression level reached to zero in infected epidermis (EPI1) then increases with the disease progression till conidia formation. miRNAs from second group showed opposite tendency and the expression was almost zero in EPH and have higher expression in EPI1 then decreased with disease progression and reached to zero in conidia. We performed Agrobacterium-mediated transient co-expression assays in Nicotiana benthamiana to verify miRNA-target relations. Western blot analysis showed that Hvu-miR07, Hvu-miR535 and Hvu-miR6180 can reduce the protein level of Bgh-BUB3 (CCU74706), Bghhypothetical protein (CCU75788) and Bgh-DIL protein (CCU75480) respectively. Bgh-milRNA38 target one barley receptor-like kinase gene (HORVU2Hr1G087540). Further experiments will be performed to test the function of candidate trans-kingdom miRNAs and their targets in barley-powdery mildew interactions. 

P1116: Zinc Oxide Nanoparticles Induce Transcriptional Reprogramming that Compromises Resistance to Pyrenophora teres f. teres in Barley Priyanka 

Deka1 , Roshan Sharma Poudel2 , Chrysafis Vogiatzis3 , Robert S. Brueggeman2 , Achintya Bezbaruah1 and NDSU Engineering and Plant Pathology, (1)North Dakota State University, Fargo, ND, (2)Department of Plant Pathology, North Dakota State University, Fargo, ND, (3)North Carolina A&T State University, Greensboro, NC 

Barley line CI5791 has effective and broad resistance to diverse isolates of the necrotrophic fungal pathogen Pyrenophora teres f. teres (Ptt), the causal agent of the disease net form net blotch (NFNB). We showed that ZnO engineered nanoparticle (NP) exposure compromises CI5791 NFNB resistance. Thus, this pathosystem can be used to characterize the effects of NPs on resistance mechanisms. A time course RNAseq analyses from leaf tissue at 0, 6, 24 and 48 hours post NP application (hpa) or pathogen inoculation (hpi) was conducted on CI5791 post ZnO NP exposure, post Ptt inoculation, and post dual application/inoculation with NPs + Ptt. The analyses identified differentially expressed genes (DEGs) in response to the treatments showing rapid responses to ZnO NPs (6 hpa) that quickly returned to basal levels (12 hpa). However, treatment with the pathogen alone and pathogen+ZnO NP, showed DEG profiles that persisted to 48hpi. The number of DEGs in the dual application/inoculation was the highest across all time-points compared to the pathogen and ZnO NPs alone. Gene ontology analysis of the DEGs revealed that the salicylic acid (SA)-signaling pathway persisted 48hpi in the dual application that resulted in compromised resistance. The SA and jasmonic acid (JA) responses returned to basal levels in the Ptt inoculated treatments (24hpi/hpa), which resulted in a resistance reaction. Thus, we hypothesize that the NP application resulted in extended SA responses when faced with the necrotrophic pathogen, which lead to the suppression of JA mediated necrotrophic pathogen resistance responses resulting in compromised immunity. 

P1118: A Reference Quality Assembly and Annotation of the Avena atlantica Genome 

Rebekah Lee1 , Peter J. Maughan1 , Tim Langdon2 , Jessica Schlueter3 and Rick Jellen1 , (1)Brigham Young University, Provo, UT, (2)IBERS, Aberystwyth University, Aberystwyth, United Kingdom, (3)University of North Carolina at Charlotte, Charlotte, NC 

Common oat (Avena) has held a significant place within the global crop community for centuries. Although its cultivation has decreased over the past century, its nutritional benefits has garnered renewed interest for human consumption. Until now there has not been a published reference genome for any of the three oat sub genomes. Here we report a quality sequence assembly, annotation and hybrid optical map assembly of the A-genome diploid Avena atlantica. The hybrid assembly is composed of 3417 scaffolds, spanning ~3.7 Gb, with an N50 of 11.86 Mb and a BUSCO estimated completeness of 97.6%. It is hoped that this genome sequence can escalate research within the oat community. P1119: Wheat, Barley, Oat, and related The Hexaploid Oat Genome Nick Sirijovski, Leif Bulow and Olof Olsson, Lund University, Lund, Sweden 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.

 P1120: Assembly and Annotation of the Hexaploid Oat Genome 

Rachel N. Walstead1 , Adam Whaley1 , Robert Reid1 , Veronica Vallejo2 , Cory Brouwer1 and Jessica Schlueter1 , (1)University of North Carolina at Charlotte, Charlotte, NC, (2)PepsiCo, Hawthorne, NY

 The hexaploid oat (Avena sativa L) is a staple cereal crop, used for both human consumption and animal feed. Genomic resources for oat, despite of the importance of cereals, are lagging behind many other crops. The estimated genome size of A. sativa is about 13GB. We aim to fully sequence, assemble, and annotate the hexaploid oat genome (2n = 6x = 42). To this aim, we have utilized PacBio RSII technologies and sequenced approximately 580 SMRT cells, achieving a coverage of approximately 40X. Continuing sequencing efforts utilizing PacBio Sequel technologies are underway, so far totaling 49 SMRT cells. We are currently assembling the genome using the Canu assembler. A draft assembly was completed with a size of ~7.5 Gb. Annotation efforts are underway on the draft assembly, utilizing RNAseq and Iso-Seq data. This data will be integrated with predictive gene models and comparative annotations from other grass genomes using the BRAKER1 annotation pipeline (http://exon.gatech.edu/braker1.html). The genomic information obtained by this project will be a valuable resource for crop scientists and breeders. 

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