博文
小麦 PAG 2018 摘要 （一）
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1 The Reference Sequence for the Bread Wheat Genome
INRA GDEC
The generation of a high-quality reference genome sequence for bread wheat, linked to genetic and genomic resources, has been the goal of the International Wheat Genome Sequencing Consortium (IWGSC) since its foundation in 2005. Here, we report on the assembly and deep analysis of the 21 chromosomes of the allohexaploid bread wheat cv. Chinese Spring: IWGSC RefSeq v1.0. We used an Illumina-based whole genome shotgun approach integrated with a wealth of community resources and were able to assemble 21 high-quality pseudomolecules representing 94% of the predicted wheat genome size, with a scaffold N50 of 23 Mb. We predicted 107,886 high confidence gene models and ~4 million transposable elements accounting for 85% of the genome.
Comparative analyses of the A-B-D sub-genomes revealed no subgenome dominance, and a highly conserved gene set although only 55% of the homeologous groups correspond to 1:1:1 triplets, meaning that A-B-D have been strongly impacted by lineage-specific gene duplications. Insights into gene expression have been described through 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, the community now has a key resource in place for future research and breeding.
2、Characterisation of the Pentatricopeptide Repeat Protein Family in the Wheat IWGSC Refseq v1.0 Reference Genome
The University of Western Australia
The family of pentatricopeptide repeat (PPR) proteins is one of the largest gene families in flowering plants and has agronomical importance as a source of restorer of fertility (Rf) genes used to suppress cytoplasmic male sterility during the development of F1 hybrids. Typically, flowering plant genomes contain 550-700 PPR genes, in the wheat IWGSC RefSeq v1.0 reference genome we found 1686 PPRs. The large number of PPR genes is primarily due to polyploidy and it’s actually lower than expected from simply adding genes present in the progenitor diploid genomes. This implies PPR gene inactivation and loss during polyploidization, for which we found evidence in the form of truncated or frame-shifted gene fragments. 207 PPRs were identified as restorer of fertility-like (RFL) genes in the wheat reference genome, far more than in any other plant genome analysed to date. We show that locations of some of the previously mapped restorer genes overlap with the genomic locations of RFL clusters identified in our study. This is the first comprehensive analysis of the PPR and RFL families in wheat. The sequence knowledge gained from this project has the potential to accelerate hybrid wheat breeding programs by facilitating the identification of active restorer genes in potential restorer lines. Hybrid wheat varieties are expected to have higher and more consistent yields by better adaptation to increasingly unpredictable weather conditions in the era of global climate change.
3、Map-Based Cloning of Powdery Mildew Resistance QTL Introgressed to Bread Wheat from the Timopheevi Group Reveals a Highly Divergent Region with Suppressed Recombination containing a Cluster of NLR Gene Homologues
Institute of Experimental Botany
Introgression of QPm.tut-4A locus from Triticum militinae into the distal end of bread wheat chromosome 4AL confers improved resistance against powdery mildew. The locus was high-density mapped and delimited to 0.024 cM using 8327 individuals and 75 markers. Using additional 2052 ph1 *lines seven new recombinations were identified. After chromosome walking, final flanking markers *owm169 *and *owm228 were mapped and the region was found 640.8 kbp and 480.2 kbp long in cv. Chinese Spring (CS) and *T. militinae *(TM), respectively. The cM/Mb ratio is much smaller compared to these commonly found at the end of wheat chromosomes. The sequenced region was annotated and 16 and 12 protein coding genes were identified in CS and TM, respectively. Out of them, seven CS and six TM genes were not syntenic. Furthermore, intergenic regions do not show a significant similarity between CS and TM. The TM region containing the remaining six genes has a syntenic counterpart in CS, but that region was duplicated and one of the duplications was inverted. The duplication and inversion were accompanied by gene loss and four of the TM genes have their counterparts in both duplicated regions in CS. Finally, three genes from the CS region do not have their homologs in the TM region. These structural and sequence differences are major reasons for the discrepancy between the expected and observed cM/Mb ratio. This work was supported by award LO1204 from the National Program of Sustainability I and by the Estonian Ministry of Agriculture.
4、Hunting Yellow Rust Resistance Genes in Bread Wheat
John Innes Centre
Achieving wheat yields to meet current and future demands is crucial. This, however, remains challenging in part due to the numerous pathogens threatening wheat production, including yellow (stripe) rust (Puccinia striiformis fsp tritici; Pst). Despite over 70 designated yellow rust resistance genes (Yr) in wheat, few have been cloned. This lack of knowledge hinders efficient marker assisted breeding and exploitation of novel allelic variation. We recently exome sequenced a mutant population of UK cultivar Cadenza which carries the major gene Yr7. Screening 1,000 mutagenized individuals with Pst identified seven susceptible lines presumed to carry mutations in Yr7. To test this, mutational resistance gene enrichment sequencing (MutRenSeq) was conducted on the susceptible lines and a candidate for Yr7 was identified. Taking advantage of the IWGSC RefSeqv1.0 assembly, we quickly determined the physical position of the closest Chinese Spring homolog within the Yr7 region and confirmed this linkage in an F2 population. Previously, Yr5 was proposed to be allelic to Yr7. Therefore, a similar approach was carried out on Yr5 susceptible mutants and a single candidate gene, different from Yr7, was identified. The Yr5homolog is located in close physical proximity to Yr7 on IWGSC RefSeqv1.0. This suggests that Yr5 and Yr7 are very closely linked genes rather than true alleles. The closest homologs to both Yr7 and Yr5 reside in a complex disease resistance cluster in RefSeqv1.0. We will present a phylogenetic analysis of this resistance gene cluster in Chinese Spring and additional commercial varieties and discuss the implications for breeding.
5、Reconstructing Wheat Evolutioanry History
INRA
Polyploidization have been reported as a major evolutionary force during plant paleohistory. Following the triplication reported in *Brassiceae *~10 million years ago, and at the basis of rosids ~100 million years ago, bias in organisation and regulation, known as subgenome dominance, has been reported between the three post-polyploidy compartments referenced to as less fractionated (LF), medium fractionated (MF1) and more fractionated (MF2), that have been proposed to derive from an hexaploidization event involving ancestor intermediate of 7-14-21 chromosomes. Modern bread wheat experienced similar paleohistory during the last half million year of evolution opening a new hypothesis where the wheat genome is at the earliest stages on the road of diploidization through subgenome dominance driving asymmetry in gene content, gene expression abundance, transposable element content as dynamics and epigenetic regulation between the A, B and D subgenomes.
6、Tetraploid Wheat Germplasm Diversity SCAN Based on the Durum Wheat Genome Assembly
DipSA, Department of Agricultural Science, University of Bologna
The genome of modern durum wheat (DW) cultivar Svevo has been assembled based on a combination of whole genome shotgun sequencing (270X), NRGene deNovoMagic assembler, high-resolution genetic mapping obtained from the cross between Svevo DW and Zavitan wild emmer wheat (WEW) and scaffold ordering based on chromosome conformation capture sequencing (Hi-C). The assembly consisted of 9.96 Gb of ordered sequences with 66,559 high-confidence (HC) genes. We used this resource to investigate the genetic diversity and ancestry of tetraploid wheat germplasm. iSelect 90K SNP array was used to genotype a global collection of 1,858 non-redundant accessions covering the whole range of tetraploid genetic resources from WEW, cultivated emmer (CEW), durum landraces (DWL) and modern durum cultivars (DWC). We performed a whole-genome scan for population genetic structure, selective sweeps together with the tetraploid QTLome projection. Average whole-genome genetic diversity were pWEW= 0.285, pCEW = 0.254, pDWL = 0.201, pDWC = 0.192, with an overall WEW-DWC decrease in diversity equal to 32.6%. Diversity depletions were more relevant in peri-centromeric regions (pWEW_C = 0.269, pDWC_C = 0.151) as compared to the highly-recombinogenic distal regions (pWEW_R = 0.287, pDWC_R = 0.250). From WEW to DWC, 68 chromosome regions were subjected to diversity depletion, affecting up to 38% of the genome in total: 19 of these were associated to WEW-CEW transition, 41 to CEW-DWL and 8 to DWL-DWC. The gene content of these regions is being explored in relation to known QTL content and haplotype analysis. Overall, the analysis pointed out the chromosome regions subjected to strong selective sweeps during the domestication and breeding selection, on one side, and those regions that would benefit from targeted genetic diversity restoration on the other side.
7、Exploring Epigenomic Diversity in Polyploid Wheat
Earlham Institute
Wheat has been domesticated into a large number of agricultural environments, a key question is what drives the ability for crops to rapidly adapt. To address this question, we survey genotype and DNA methylation across the core Watkins bread wheat landrace collection that is representative of global wheat genetic diversity. We identify independent variation in methylation, genotype and transposon copy number. These three sources of variation are likely to be driving phenotypic differences across this diverse wheat collection. Methylation and transposon diversity could therefore be used alongside single nucleotide polymorphism (SNP) based markers for breeding.
8、Mutations in the Branched Head Homoeo-Allele Bht-B1 Modify Inflorescence Architecture in Tetraploid Wheat
Leib-Inst Plant Gen & Crop Plant Res
Inflorescence morphology directly affects the reproductive success and yield of crops. The wheat inflorescence, also known as spike, forms an unbranched inflorescence where individual spikelets are arranged distichously on the central axis of the spike, the rachis. Previously, we reported the causative mutation in the branched headt (bht) gene of tetraploid wheat (TtBH-A1) being responsible for the loss of spikelet meristem identity, converting the non-branching wheat spike into a branched spike. Since spike-branching in wheat is a quantitatively inherited trait, we further performed whole-genome quantitative trait loci (QTL) analysis and Genome Wide Association Scans (GWAS) based on 146 recombinant inbred lines (RILs) and a collection of 302 tetraploid wheat accessions, respectively. Results showed that besides the previously found gene at the bht-A1 locus on the short arm of chromosome 2A, mutations in the homoeologous gene, TtBH-B1, was linked to the increased penetrance and expressivity of the supernumerary spikelet (SS) and /or mini-spike formation during spike-branching thereby increasing spikelet and grain number per plant. Furthermore, we developed bht-A1 *Near Isogenic Lines (bht-A1-*NILs) using an elite durum wheat cultivar, Floradur, for the molecular genetic dissection of the wheat spike morphogenesis and the agronomic implications of the homoeo-allele(s) for increasing grain yield production in wheat.
9、Wheat Leaf Rust Resistance Gene from Marquis Wheat
Agriculture and Agri-Food Canada
Marquis wheat, released in 1911, was one of the most widely grown cultivars in Canada and the north-central USA. It was susceptible to all leaf rust (Puccinia triticina) isolates tested, up to the emergence of a group of races in the early 2000s, predominantly TDBG. Marquis had an unusual mesothetic resistance phenotype when inoculated with TDBG. To characterize this resistance the Marquis backcross line RL6071was crossed with a leaf rust resistant accession from the Kyoto University wheat germplasm collection KU168-2 to create a doubled haploid population. Seedling resistance from RL6071 was inherited as a single resistance gene that mapped to chromosome 7BL. Tightly linked molecular markers, along with seedling leaf rust testing and pedigree analysis revealed that this gene, temporarily named LrMar, was present in Marquis, Red Fife and a number of cultivars derived from Red Fife, such as White Fife, Percy and Renfrew. The same group of races that were avirulent to LrMarwere also avirulent to LrCen, previously mapped to 7AL, with a similar mesothetic infection type. Both genes are only effective against this small group of P. triticina isolates, are ineffective in conditioning field resistance against the broader Canadian population, and neither were detected prior to the emergence of these races. These could be homeologous resistance genes based on their respective positions on chromosomes 7BL and 7AL, and phenotypic similarities.
10、The Genome of Triticum urartu, a Progenitor of Wheat a Genome
Institute of Genetics and Developmental Biology, CAS
Triticum urartu, a wild diploid wheat, is the progenitor of the A subgenome of tetraploid and hexaploid wheat. Ample genetic studies have shown the value of T. urartu for investigating the structure, function, and evolution of polyploid wheat genomes. Here, we report the generation of a high-quality genome sequence of T. urartu by combining BAC-by-BAC sequencing, single molecule real-time (SMRT) sequencing, and next-generation mapping (BioNano genome map and 10x Genomics linked reads) technologies. We produced seven chromosome-scale pseudomolecules that spanned 4,666 Mb and annotated 37,516 high confidence and 3,991 low confidence protein-coding genes. By comparing collinear segments between T. urartu and its grass relatives rice, sorghum, and Brachypodium, we propose an evolution model of T. urartu chromosomes, and found that T. urartuand Brachypodium *were independently evolved from the grass ancestor with 12 chromosomes. Furthermore, the ancient genome duplications, which are well maintained in rice, sorghum, and *Brachypodium, were strongly corrupted in T. urartubecause of extensive amplifications of transposable elements and widespread gene loss. Overall, the T. urartugenome sequence described here provides a valuable reference for systematic studies of Triticeae genomes and for genetic improvement of wheat.
11、Identification of QTLs Associated with Kernel Texture Variation in a Soft-Kernel Durum Wheat (Triticum turgidum ssp. durum) Population
Washington State University
Kernel texture is one of the major determinants of wheat quality. This trait is primarily controlled by the Puroindoline genes, located at the Hardness (Ha) locus on the short arm of chromosome 5D. However additional factors contribute to minor variations in endosperm texture. Durum wheat (Triticum turgidum *sbsp. *durum) lacks the Ha *locus and, therefore, its kernels exhibit an extremely hard texture that limits its end-uses. Recently, the *Puroindoline *genes from the chromosome 5DS of common wheat (T. aestivum* L.) were introgressed into the durum wheat cultivar Langdon through the Ph1b-mediated homoelogous recombination, thus obtaining soft-textured kernel durum wheat lines. In the present study, soft durum wheat line Langdon 1-678 was crossed with the durum wheat variety Creso. The progeny were analyzed for kernel texture through the single kernel characterization system (SKCS) and only the lines exhibiting a hardness index (HI) < 40 were advanced, obtaining 590 soft-textured kernel F6 lines. These lines were phenotyped through SKCS and exhibited a wide variation of kernel hardness (HI ranging from -0.3 to 37). In order to identify the genetic factors associated with variation of this phenotype, the same lines were genotyped using a targeted amplicon sequencing (TAS) approach. The identification of QTLs significantly associated with kernel hardness is in progress. To date, this is the first study to investigate the genetic control at the basis of endosperm texture in durum wheat. These results will facilitate the selection of soft durum wheat lines with superior milling properties and novel end-use applications.
12、Development and Validation of a Single Nucleotide Polymorphic Marker for the Yield Component Kernel Weight in Wheat
Agriculture and Agri-Food Canada
Canada is a major producer and exporter of hard red spring (HRS) wheat. The HRS wheat is well known for its excellent milling and baking quality. With high protein requirement in the HRS class of wheat, it lags in yield compared to other classes of wheat. Yield is of utmost importance to producers and is one of the primary focuses of wheat breeding programs. An important yield component is the thousand kernel weight (TKW) and is highly heritable. Selection for high TKW in early generations of wheat breeding is effective, but is difficult to access phenotypically due to limited seed availability. Marker-assisted selection (MAS) using single nucleotide polymorphisms (SNPs) and insertion-deletion (indels) mutations will allow selection in early generations breeding lines based on genotype. Kompetitive Allele Specific PCR (KASP) assays based on SNPs and indels are high-throughput, easy to use, and requiring limited amounts of DNA. Trehalose-6-phosphate (T6P) is a regulator of starch accumulation, the most important contributor of TKW. Trehalose 6-phosphate phosphatase (T6PP) activity can affect T6P levels, and a wheat T6PP gene has been cloned. This gene was found to be polymorphic in Chinese accessions of wheat using a cleaved amplified polymorphic sequence assay and linked to TKW. Here we developed a much simpler and high-throughput KASP assay and showed that this gene is polymorphic in Canadian wheat germplasm. This should allow selection for TKW in early generations of wheat breeding in Canada.
13、Genome-Wide Homology Analysis Reveals New Insights into the Origin of the Wheat B Genome
North Dakota State University
Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The ancestors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a candidate ancestor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure, which has puzzled the wheat research community for nearly a century. In the present study, we performed genome-wide homology analysis to assess the B-S relationship using an integrative molecular cytogenetics and comparative genomics approach. Noticeable homology was detected between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was identified on the long arm of chromosome 1B (1BL) in all wheat species containing the B genome. The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome in wheat species. Thereby, we conclude that Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive ancestor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These findings provide new insight into the origin and evolution of the wheat B genome, and will facilitate genome studies in wheat and its relatives.
14、Comparison of Durum Wheat and Wild Emmer Genomes Provides Insights into Genomic Diversity in Tetraploid Wheat
CREA - Research Centre for Genomics and Bioinformatics
The domestication of wild emmer wheat ~10,000 years ago by early agrarian societies led to the selection of modern durum wheat widely grown today, mainly for pasta. We report the fully-assembled genome of a modern durum wheat variety (cv. Svevo) and present, via comparison with the previously published genome of wild emmer accession Zavitan, a genome-wide account of the modifications imposed by 10,000 years of selection and breeding. The durum wheat genome was assembled with the NR-Gene DeNovoMAGICTM pipeline (N50 = 6 Mb) and ordered by chromosome conformation capture sequencing (Hi-C), resulting in 14 pseudomolecules plus one group of unassigned scaffolds. A total of 66,559 high-confidence (HC) genes have been identified on the durum wheat assembly. This first genome-wide comparison between a wild and cultivated form of tetraploid wheat revealed several thousand copy-number and presence-absence variations with significantly expanded gene families in durum wheat (e.g. for disease resistance), as well as of widespread polymorphism with putative impacts on gene function. While the gene sets of durum wheat and wild emmer are highly similar, the compositions of the pseudogene sets differ in both number and enrichment for particular GO categories. Inspection at the pseudogenes in syntenic regions of durum wheat and wild emmer indicates potentially distinct duplication and pseudogenization dynamics. The comparison of the two genomes offers an overall picture of the genomic diversity between the cultivated tetraploid wheat and its wild relative progenitor.
15、Genomic Dissection of Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon
University of Campinas
Wheat stem rust caused by the fungus Puccinia graminis f.sp. tritici (Pgt) is a devastating disease that has largely been controlled for decades by the deployment of resistance genes. However, new races of this pathogen have emerged that overcome many important wheat stem rust resistance genes used by breeding programs, and their spread toward major wheat production areas poses a threat to global wheat production. Nonhost resistance in plants, which provides durable and broad-spectrum resistance to non-adapted pathogens, holds great promise for helping to control wheat stem rust, but the genetic and molecular basis of nonhost resistance is poorly understood. This study employed the model plant Brachypodium distachyon(Brachypodium), a nonhost of Pgt, to genetically dissect nonhost resistance to wheat stem rust. Using bulked segregant analysis, next-generation sequencing, cumulative allele frequency differences and statistical analysis, seven quantitative trait loci (QTL) that contribute to stem rust resistance were identified in a recombinant inbred population derived from a cross between two Brachypodium genotypes with differing levels of resistance. The QTL effects vary in their magnitude, and act both additively and in some cases interact, indicating that the resistance is genetically complex. The delineation of regions of the Brachypodium genome that harbor these QTLs will guide future research aiming to identify genes essential to the nonhost resistance response and their mechanisms of action.
16、Development of a Complete Set of Wheat-Barley Group-7 Robertsonian Translocation Chromosomes Conferring an Increased Content of ß-Glucan
Kansas State University
Many valuable genes for agronomic performance, disease resistance and increased yield have been transferred from relative species to wheat (Triticum aestivum L.) through whole-arm Robertsonian translocations (RobT). Although of a great value, the sets of available translocations from barley (Hordeum vulgare L.) are limited. Here we present the production of a complete set of six compensating RobT chromosomes involving barley chromosome 7H and three group-7 chromosomes of wheat. The barley group-7 long arm RobTs had a higher grain ß-glucan content compared to the wheat control. The ß-glucan levels varied depending on the temperature and were higher under hot conditions. Implicated in this increase, the barley cellulose synthase-like F6 gene (CslF6) responsible for ß-glucan synthesis was physically mapped near the centromere in the long arm of barley chromosome 7H. Likewise, wheat *CslF6 *homoeologs were mapped near the centromere in the long arms of all group-7 wheat chromosomes. With the set of novel wheat-barley translocations, we demonstrate a valuable increase of ß-glucan, along with a resource of genetic stocks that are likely to carry many other important genes from barley into wheat.
17、Nitrogen Use Efficiency Is Regulated By Interacting Proteins Relevant to Development in Wheat
Oklahoma State University
Nitrogen (N) is the most important nutrient for plant development and growth, and soil is often supplemented with N fertilizer to ensure successful seed production and high grain yield for non-N-fixing food crops such as wheat (Triticum aestivum L.). Only 30–35% of added N fertilizers are taken up and used by wheat plants in the year of application, and the remaining 65–70% (assuming fertilizer–soil equilibrium) is lost. Developing varieties of wheat that require less N input yet maintain the same or higher grain yield is an economically and environmentally sustainable goal in international agriculture. In this study, a major quantitative trait locus (QTL) for N-related agronomic traits was cloned from wheat. The vernalization gene TaVRN-A1 was tightly linked with the gene at the QTL. Due to the Ala180/Val180 substitution, TaVRN-A1a and TaVRN-A1b proteins had differential interactions with TaANR1 protein, which is encoded by a wheat orthologue of Arabidopsis nitrate regulated 1 (ANR1). A natural mutant of TaANR1 was found which is missing exon 6 in its mRNA, which had genetic effect on wheat development and growth. The transcripts of both TaVRN-A1 and TaANR1 were down-regulated by N. Genetically incorporating favorable alleles from TaVRN-A1, TaANR1, and TaHOX1 increased grain yield from 9.83% to 11.58% in a winter wheat population tested in the field.
18、Gene and Trait Discovery for Improvement of Processing and Nutrition Quality in Wheat
National Institute of Plant Genome Research (NIPGR)
Bread wheat (Triticum aestivum L.) is one of the most important food crops in the world, and its flour processed into various end-use food products such as bread, biscuits, and chapatti. The suitability of wheat grains for end-uses are largely affected by the biochemical composition of seeds including storage proteins, starch, and photochemical and hence, it indirectly affects the processing, cooking, and organoleptic qualities of wheat seed. Knowledge of genetics and molecular basis of processing quality related traits are important for their improvement. Thus, the present investigation was designed for the identification of candidate genes related to processing quality through genome-wide transcriptome analysis of wheat during seed development. The study also emphasizes the understanding of expression pattern of starch metabolic genes during seed development and the correlation of variation in physical and biochemical traits of seeds and the physicochemical properties of starches on large sets of Indian wheat varieties. Genome-wide transcriptome study using 61k wheat genome arrays in developing seeds of wheat genotypes identified 110 candidate probe sets for processing quality mainly chapatti. Further, quantitative expressions of the 25 starch metabolic genes, during seed development also identify the highly expressed key genes of starch metabolism, which are candidates for a development of markers for starch quality. Thus, these candidate genes would be useful for designing wheat improvement programs for processing quality or nutrition quality either by changing their expression (over-expression, silencing or genome editing) or development of bi-parental mapping populations for molecular breeding. Further, Physical (kernel length, kernel width and thousand kernel weights), Biochemical (total starch content, amylose content, total protein content and starch granules associated proteins) and Physico-chemical (starch granules size distribution, swelling power, starch solubility, Pasting, thermal, and gelatinization) traits of diverse sets of Indian wheat varieties and starch isolated from them showed strong correlation with each other. The detail analysis of these properties could lead to an appropriate selection of wheat cultivar, well-adapted to industrial end-uses, without encountering processing or end-products quality problems and with most cost-competitive production.
19、Wheat miR9678 Controls Seed Germination By Generating Phased ta-siRNAs and Modulating Abscisic Acid/Gibberellin Signaling
China Agricultural University
Seed germination is important for wheat yield and quality. However, our knowledge of mechanisms regulating seed germination in wheat remains limited. In this study, we found microRNA9678 (miR9678) is specifically expressed in the scutellum of developing and germinating wheat seeds. Overexpression of miR9678 delays germination and improves resistance to pre-harvest sprouting (PHS) in wheat; miR9678 silencing enhances germination rates. miR9678 triggers phased trans-acting small interfering RNAs (ta-siRNAs) by cleaving the long non-coding RNA, and ta-siRNAs also delay seed germination. In addition, miR9678 overexpression also reduces bioactive gibberellin (GA) levels through a ta-siRNAs independent mechanism. Finally, abscisic acid (ABA) signaling proteins bind the promoter of miR9678 precursor and activate its expression, indicating miR9678 regulates germination by modulating the GA/ABA signaling.
20、A Genome Wide Association Study for Yield Traits in Soft Red Winter Wheat
University of Arkansas
Wheat (*Triticum aestivum *L.) is a widely produced grain crop, significantly contributing to global food security. As the global population continues to grow, so will the demand for food. In order to meet such demands, breeders must work to increase wheat yield potential. Wheat yield can be impacted by multiple quantitative traits which rely on several quantitative trait loci (QTL). A genome wide association study (GWAS) was conducted on 360 inbred soft red winter wheat genotypes adapted to the southern United States in an association mapping panel (AMP) in order to identify novel QTL associated with wheat yield traits, including yield, test weight, heading date, maturity date, and plant height. The AMP was grown over eight location-years between 2013 and 2017 in randomized complete block and augmented designs. Each location-year was evaluated for the five aforementioned traits impacting yield. Best linear unbiased estimates for the five traits were obtained from a spatial linear mixed model for each location-year and combined to obtain best linear unbiased predictions from SAS 9.4 software. Genotype-by-sequencing (GBS) identified 71,428 high quality single nucleotide polymorphisms (SNP) markers across all 21 wheat chromosomes. Marker-trait associations will be determined using the FarmCPU function in R software. Data analysis for the five phenotypic traits are still in progress. Marker-trait associations will also be performed in the near future, resulting in potential SNP that can be implemented by the University of Arkansas wheat breeding and genetics program through marker assisted selection or genomic selection in order to improve wheat yield.
21、Exploring Allelic Diversity Underlying Breeding Progress in European Wheat
The University of Queensland
Despite the remarkable successes that were achieved in the history of wheat breeding, future wheat production remains challenging. Climatic changes that lead to unprecedented extreme weather scenarios are accompanied by a rising disease pressure and a declining fertiliser availability. While the dramatic global population growth necessitates a significant further improvement of wheat productivity in the upcoming decades, a stagnation of wheat yield increases has recently been reported in all major production areas worldwide. This has mainly been attributed to a drastic loss of genetic diversity in elite breeding pools due to strong selective breeding and intensive germplasm exchange. At the same time there are public concerns that modern agriculture can only sustain productivity under extremely high resource inputs involving chemical fertilisers and plant protection, while the actual impact of genetic improvements remains elusive.
Here, we present the first large-scale investigation of the impact of wheat breeding on all major trait complexes in a historic panel of almost 200 registered European winter wheat varieties, including important representatives of the last five decades of winter wheat production. Presenting phenotype data from multiple locations and three different cropping systems that range from fully extensive to fully intensive, we are able to demonstrate the great impact of genetic improvement on performance increase under any environmental scenario. Linking this to genome-wide marker information we are able to track the influence of artificial selection on genetic parameters throughout the history of wheat breeding and to define target regions with the highest impacts on agronomically important traits. Our study gives first insights into the genetic basis of the improvement of high-yielding winter wheat and assesses the potential for further genetic gain in the European elite germplasm pool in the short- and mid-term
22、Development of Wheat-*Haynaldia villosa *Alien Chromosome Lines and their use in Gene Mining and Wheat Breeding
Nanjing Agricultural University
Wild relatives provide rich gene resources for wheat breeding.* Haynaldia villosa (2n=14, genome VV), is a diploid wild species and has proved to be resistant to several wheat diseases, such as powdery mildew, wheat yellow mosaic etc. The development of alien translocation lines conferring useful genes is the most effective way for the utilization of alien genes. In Cytogenetics Institute if Nanjing Agricultural University, a research platform for the induction of alien chromosome structural variation and for effective identification of alien chromatin has been established. A wheat-H. villosa* alien translocation pool was constructed and the their chromosome constitution was characterized. Genes conferring resistances to powdery mildew, wheat yellow mosaic virus, strip rust as well as loci controlling grain quality has been assigned specific regions of H. villosa chromosomes. The whole arm translocation lines carrying useful genes have been released and utilized in breeding programs. Using the T6VS/6AL translocation carrying the powdery mildew resistance gene Pm21 and the strip rust resistance gene Yr26, about 30 wheat varieties have been developed and commercially released in China.
23、Characterization, Validation, and Deployment of Chromosome 6BL and 7AL QTLs for Grain Yield Components in Hard Winter Wheat
Colorado State University
The United Nations has estimated that food production will need to double by 2050 to adequately feed a global population of 9 billion people. Improvements in wheat yields, which account for 30% of coarse grain production, will be essential to meet this goal. Yield is a complex trait due to a multitude of influential factors. To address this complexity we have identified individual yield components that are less complex and contribute to overall yield. A GWAS of a hard winter wheat association-mapping panel identified QTLs on the 7AL chromosome arm for spikelet number and the 6BL chromosome arm for kernel width. The Great Plains winter wheat cultivar Platte and experimental line CO940610 were identified as polymorphic in the 7AL and 6BL regions. A population of recombinant inbred lines was generated from the two parents and used to validate the 7AL and 6BL QTLs’ effects. Individual SNPs have been identified which will be used to introgress spikelet number and kernel width QTL into Colorado advanced lines and high biomass lines from the International Maize and Wheat Improvement Center (CIMMYT). Exome sequencing data generated from the parental lines will enable high-resolution mapping of the causative genetic variant underlying these QTL. The employment of novel genomic tools and resources enable unprecedented opportunities to identify allelic variation underlying individual yield components in wheat. This will ultimately aid in the development of higher yielding wheat varieties.
24、Genetic Basis of the Short Life Cycle of ‘Apogee’ Wheat
Oklahoma State University
‘Apogee’ is a wheat cultivar that was developed for utilization of the NASA-ALSS food system and has the shortest life cycle in wheat in the world, with flowering only 25 days after planting under long day conditions and constant warm temperature without vernalization. This growth habit can be utilized to accelerate breeding cycles. It is intriguing to unravel the genetic mystery of this agronomic characteristic. In this study, Apogee was crossed with a strong winter wheat cultivar ‘Overland’, and over 800 F2 plants were generated and tested in a greenhouse under temperature and photoperiod controlled conditions. Apogee was found to have vrn-A1a and vrn-D3a that are the same alleles as observed in the winter wheat cultivar ‘Jagger’, Vrn-B1 that has a deletion in intron one, and PPD-D1b that is insensitive to photoperiod. The super-short life cycle of ‘Apogee’ wheat resulted from pyramiding of the early alleles for the four flowering time genes, whose effects are vrn-A1>VRN-B1>vrn-D3>PPD-D1. The dominant vrn-D3a alone was not sufficient to induce the transition from vegetative to reproductive development in winter plants without vernalization, but did accelerate heading in those plants that have been induced by vrn-A1a or Vrn-B1. This study greatly advanced the molecular understanding of the multiple flowering genes under different genetic backgrounds and provided useful molecular tools that can be used to accelerate winter wheat breeding schemes.
25、Hybrid Wheat from a Practical Breeder’s Perspective
Department of Agronomy and Horticulture, University of Nebraska-Lincoln
Hybrid wheat has proven to be elusive. From its previous highpoint in the 1980s, currently, only a few companies are producing hybrids in Europe, India, and South Africa. However, interest in hybrids has recently increased due to the need for greater and more efficient production to meet the projected future needs coupled with the availability of advanced breeding tools and insights. While most hybrid wheat discussions concentrate on the theoretical or genetic aspects, this talk will present how an applied wheat breeder is trying to make hybrid wheat a reality. Hybrid wheat requires: converting a self-pollinated crop into a cross-pollinated crop, the ability to make experimental hybrids, the use of genome-wide molecular markers and theory to develop genome-based high-yielding heterotic groups and patterns augmented by improved crossing block designs such as balanced incomplete factorial, and a path to commercial hybrid production. Preliminary results indicate that pollinator lines with good pollen shed can be readily found in existing breeding programs and anther extrusion genes can be mapped in doubled haploid populations from crosses that greatly differ in anther extrusion; identifying pollen receptive lines need more research perhaps through using genetic male sterility and random-mating populations; chemical hybridizing agents can be used to make experimental hybrids in sufficient seed quantity for multi-location trials; the genome-wide markers and algorithms are being developed to build heterotic groups which like maize will need to be bred, not discovered; and chemical hybridizing agents and cytoplasmic male sterility systems appear to be commercially viable.
26、The Interplay Among Subgenomes Shapes Genomic Variations and Transcriptomic Changes during Wheat Hexaploidization Events
CHINA AGRICULTURAL UNIVERSITY
Genomic variations and transcriptomic changes extensively occur in newly formed polyploids to reconcile immediate challenges caused by divergent subgenomes in one nucleus. To comprehensively investigate sequence elimination and expression alteration in wheat hexaploidization, here we performed whole exome capture experiments coupled with high throughput sequencing analysis by exploiting three sets of newly synthesized wheat species. We observed that the whole wheat chromosomes was subjected to extensive genomic elimination partially regulated by sequence homology in response to hexaploidization. But homeologous subgenomes exhibited distinct features that DNA sequences were preferentially eliminated on DD genome compared with AA and BB genome. In addition, a higher proportion of eliminated sequences occurred in exonic regions than in intergenic regions on DD genome, whereas a significant enrichment was observed in the repeat-rich intergenic regions for AA and BB genome, exhibiting a contrast distribution pattern compared to the gene density. Furthermore, we detected 488 overlapped genes with sequence elimination on DD genome but few on the other two genomes across three nascent hexaploid wheats. Interestingly, GO enrichment analysis showed genes with sequence elimination were enriched in distinct functional pathways between subgenomes. Transcriptome analysis indicates polyploidization enhanced gene expression differentiation between root and leaf and led to rapid and extensive gene expression changes in synthetic hexaploid wheat. AA and BB genome exhibited synergistic expression profiling which was distinct from DD genome, and interestingly, expression bias was observed for a proportion of homeologs in synthetic hexaploid wheat. Strikingly, only 3.3-23.6% genes with sequence elimination exhibited expression changes in synthetic hexaploid wheat compared with their respective progenitors, indicating genomic variation is not the major cause resulting in the transcirptomic changes during wheat polyploidization events, whereas epigenetic modifications might play an important role in regulating expression profiling alterations.
27、Delimitation of Wheat ph1b Deletion and Development of the ph1b-Specific DNA Markers
North Dakota State University
The Ph1 (pairing homoeologous) locus has been considered a major genetic system responsible for the diploidized meiotic behavior of the allohexaploid genome in wheat. It functions as a defense system against homoeologous pairing in meiosis of polyploid wheat. A large deletion of the genomic region harboring the Ph1 locus on the long arm of chromosome 5B (5BL) led to the ph1b mutant in hexaploid wheat ‘Chinese Spring’ (CS), which has been widely used to induce meiotic homoeologous pairing/recombination for gene introgression from wild grasses into wheat. However, knowledge of the breakpoints and actual physical size for the ph1b deletion remains limited. In the present study, we first anchored the deletion region on 5BL by wheat 90K SNP assay, and then delimited the deletion to a genomic region of 60,014,523 bp by chromosome walking. The nucleotide positions of the distal and proximal breakpoints (DB and PB) were identified for the ph1b deletion. This will facilitate understanding of the genetic and molecular mechanism underlying the Ph1 activity in wheat. In addition, we developed user-friendly molecular markers specific for the ph1b deletion based on the DNA sequences immediately proximal to PB and distal to DB. These ph1b deletion-specific markers have dramatically improved the efficacy of the ph1b mutant in the meiotic recombination-based gene introgression and genome studies in wheat and its relatives. Also, these markers have been used to assist selection in the introgression of the ph1b deletion from CS into adapted wheat genotypes.
28、Efficient Wheat Transformation Can be Performed on Cold-Conserved Immature Hybrid Embryos
INRA UMR 1095 GDEC
Bread wheat is one of the three most cultivated crops in the world and a major economic challenge. However, since a few years, wheat production has reached a plateau. Despite the major role of conventional breeding programs in crop improvement, genetic engineering has become the fastest way to introduce new and well-characterized genes in plants leading researchers to elaborate each day new genetic transformation protocols. As wheat has become a new model plant for crop studying, especially in the word of genetic transformation, the need for an efficient protocol is without appeal. The present study aims to propose improvement of current immature embryo Biolistic® transformation protocols using cold conservation and hybrid immature embryos. We were able to show that using 4°C conservation for immature embryo storage do not affect regeneration and transformation efficiency. Moreover, using immature hybrid embryos can allow simultaneous transformation of two wheat genotypes, even if one of the genotypes is recalcitrant to genetic transformation. We think that those processes can be generalized to optimize wheat Biolistic® protocols.
29、Effect of Glutenin Genes and Glutenin Gene By Environmental Interaction on Quality in Spring Wheat
Department of Plant Pathology, Kansas State University
Wheat quality, comprised of milling yield, dough and baking quality, is a critical objective in the spring wheat breeding program at the International Maize and Wheat Improvement Center (CIMMYT). The glutenin genes encode the proteins that are part of the gluten matrix that gives rise to strength, extensibility and elasticity for which wheat dough is famous and are known to be an important determinate in processing and end-use quality. Previous studies have found significant genotype, environment and genotype by environment effects on grain quality traits. Recently, these same trends were also found in a population of 56 hard spring wheat lines grown in 6 environments representing 2 levels each of irrigation, drought or heat stress. It was hypothesized that glutenin genes were underlying the significant genotype effects and glutenin alleles may interact with environments. The effects of glutenin alleles as well as the environment by glutenin effects on quality were tested with a mixed linear model on this population. Glutenin loci were found to have a significant association with most grain quality phenotypes, with the high molecular weight glutenins (Glu-A1, Glu-B1, and Glu-D1) having larger effects. Additionally, the glutenin by environment interaction was significant for some of the glutenin loci. The results of this study confirm that glutenin alleles do underlie some of the genotype effect on quality traits in wheat and different glutenin alleles are performing different in contrasting environments. This information can help breeders at CIMMYT to target wheat quality profiles of lines to specific environments.
30、VERNALIZATION1* Modulates Root System Architecture in Wheat and Barley
Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland
As the primary interface for resource acquisition, plant roots play a key role in growth regulation. Evidence from rice, maize and sorghum demonstrates that the below-ground plant architecture significantly impacts plant performance under abiotic constraints. Roots assume critical functions in water uptake, nutrient acquisition and anchorage, an essential characteristic to maintain plant stability under increased grain load. Despite their fundamental importance, knowledge about genetic control of root growth in major grain crops is limited and very little is known about interactions between below-ground and above-ground plant development. Here we demonstrate that VERNALIZATION1 *(VRN1*), a key regulator of flowering behavior in cereals, also modulates root architecture in wheat and barley. Associations of *VRN1 *haplotypes to root growth habit were discovered in wheat by genome-wide association studies, and confirmed by allelic analyses in wheat and barley populations. Functional characterization in transgenic barley confirmed that *VRN1 *influences root growth angle directly, via gravitropism. These discoveries provide unexpected insight into underground functions of a major player in the well-characterized flowering pathway, revealing the intersection of above-ground gene regulation with the largely unexplored genetic architecture of plant root development. Understanding the pleiotropic involvement of this key developmental gene in overall plant architecture will help to breed cereal cultivars adapted to specific environmental scenarios.
https://blog.sciencenet.cn/blog-1094241-1094515.html
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