A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era

Plant genome sequencing has dramatically increased,and some species even have multiple high-quality reference versions.Demands for clade-specific homology inference and analysis have increased in the pangenomic era.Here we present a novel method,GeneTribe(https://chenym1.github.io/genetribe/),for homology inference among genetically similar genomes that incorporates gene collinearity and shows bet-ter performance than traditional sequence-similarity-based methods in terms of accuracy and scalability.The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops,such as wheat,barley,and rye.We built Triticeae-GeneTribe(http://wheat.cau.edu.cn/TGT/),a homology database,by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions.With macrocollinearity analysis,we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events.With collinearity analysis at both the macro-and microscale,we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vm2,which evolved as a combined result of genome translocation,duplication,and polyploidization and gene loss events.Our work provides a useful practice for connecting emerging genome assemblies,with awareness of the extensive polyploidy in plants,and will help researchers efficiently exploit genome sequence re-sources.

Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae

Triticeae species,including wheat,barley,and rye,are critical for global food security.Mapping agronomically important genes is crucial for elucidating molecular mechanisms and improving crops.However,Triticeae includes many wild relatives with desirable agronomic traits,and frequent introgressions occurred during Triticeae evolution and domestication.Thus,Triticeae genomes are generally large and complex,making the localization of genes or functional elements that control agronomic traits challenging.Here,we developed Triti-Map,which contains a suite of user-friendly computational packages specifically designed and optimized to overcome the obstacles of gene mapping in Triticeae,as well as a web interface integrating multi-omics data from Triticeae for the efficient mining of genes or functional elements that control particular traits.The Triti-Map pipeline accepts bothDNA and RNAbulk-segregated sequencing data as well as traditional QTL data as inputs for locating genes and elucidating their functions.We illustrate the usage of Triti-Map with a combination of bulk-segregated ChIP-seq data to detect a wheat disease-resistance gene with its promoter sequence that is absent from the reference genome and clarify its evolutionary process.We hope that Triti-Map will facilitate gene isolation and accelerate Triticeae breeding.

Triticeae Genomics and Genetics (TGG)

Triticeae Genomics and Genetics(ISSN 1925-203X)is committed to publishing and disseminating significant original achievements in the related research fields of Triticeae genomics and Triticeae genetics.All papers chosen for publication should be innovative research work in the field of Triticeae genomics and Triticeae genetics,including classical genetics analysis,structural and functional analysis of Triticeae genome,isolation

Triticeae Genomics and Genetics(TGG)

Triticeae Genomics and Genetics(ISSN 1925-203X)is committed to publishing and disseminating significant original achievements in the related research fields of Triticeae genomics and Triticeae genetics.All papers chosen for publication should be innovative research work in the field of Triticeae genomics and Triticeae genetics,including classical genetics analysis,structural and functional analysis of Triticeae genome,isolation

Triticeae Genomics and Genetics(TGG)

Triticeae Genomics and Genetics(ISSN 1925-203X)is committed to publishing and disseminating significant original achievements in the related research fields of Triticeae genomics and Triticeae genetics.All papers chosen for publication should be innovative research work in the field of Triticeae genomics and Triticeae genetics,including

Triticeae Genomics and Genetics(TGG)

Triticeae Genomics and Genetics (ISSN 1925-203X)is committed'to publishing and disseminating significant original achievements in the related research,fields of Triticeae genomics and Triticeae genetics.All papers chosen for publication should be innovative research work in the field ofTriticeae genomics and Triticeae genetics,including classical genetics analysis,structural and functional analysis of Triticeae genome,isolation and identification of growth/development trait-controlling genes in Triticeae at the genome- wide,Triticeae gene expression regulation and its functional analysis,the development of transgenic Triticeae,as well as Triticeae varietal improvement and its application in Triticeae production.

Triticeae Genomics and Genetics(TGG)

Triticeae Genomics and Genetics(ISSN 1925-203X)is committed to publishing and disseminating significant original achievements in the related research fields of Triticeae genomics and Triticeae genetics.All papers chosen for publication should be innovative research work in the field of Triticeae genomics and Triticeae genetics,including classical genetics analysis,structural and functional analysis of Triticeae genome,isolation

Triticeae Genomics and Genetics(TGG)

Triticeae Genomics and Genetics(ISSN 1925-203X)is committed to publishing and disseminating significant original achievements in the related research fields of Triticeae genomics and Triticeae genetics.All papers chosen for publication should be innovative research work in the field of Triticeae genomics and Triticeae genetics,including classical genetics analysis,structural and functional analysis of Triticeae genome,isolation

A recent burst of gene duplications in Triticeae

Gene duplication provides raw genetic materials for evolution and potentially novel genes for crop improvement.The two seminal genomic studies of Aegilops tauschii both mentioned the large number of genes independently duplicated in recent years,but the duplication mechanism and the evolutionary significance of these gene duplicates have not yet been investigated.Here,we found that a recent burst of gene duplications(hereafter abbreviated as the RBGD)has probably occurred in all sequenced Triticeae species.Further investigations of the characteristics of the gene duplicates and their flanking sequences suggested that transposable element(TE)activity may have been involved in generating the RBGD.We also characterized the duplication timing,retention pattern,diversification,and expression of the duplicates following the evolution of Triticeae.Multiple subgenome-specific comparisons of the duplicated gene pairs clearly supported extensive differential regulation and related functional diversity among such pairs in the three subgenomes of bread wheat.Moreover,several duplicated genes from the RBGD have evolved into key factors that influence important agronomic traits of wheat.Our results provide insights into a unique source of gene duplicates in Triticeae species,which has increased the gene dosage together with the two polyploidization events in the evolutionary history of wheat.

Triticeae Genomics and Genetics(TGG)

Triticeae Genomics and Genetics(ISSN 1925-203X)is committed to publishing and disseminating significant original achievements in the related research fields of Triticeae genomics and Triticeae genetics.All papers chosen for publication should be innovative research work in the field of Triticeae genomics and Triticeae genetics,

Triticeae Genomics and Genetics(TGG)

Triticeae Genomics and Genetics(ISSN 1925-203X)is committed to publishing and disseminating significant original achievements in the related research fields of Triticeae genomics and Triticeae genetics.All papers chosen for publication should be innovative research work in the field of Triticeae genomics and Triticeae genetics,including classical genetics analysis,structural and functional analysis of Triticeae genome,isolation

Triticeae Genomics and Genetics(TGG)

Triticeae Genomics and Genetics(ISSN 1925-203X)is committed to publishing and disseminating significant original achievements in the related research fields of Triticeae genomics and Triticeae genetics.All papers chosen for publication should be innovative research work in the field of Triticeae genomics and Triticeae genetics,including classical genetics analysis,structural and functional analysis of Triticeae genome,

4种禾本科小麦族植物微观形貌特征的比较(英文)

[Objective] This study was to investigate the difference in microscopic features of pollen grain and stoma of four triticeae species, as well as the relationship between the sizes of pollen grain and stoma, and the chromosome ploidy. [Method] Comparison of the micro-morphological characteristics of pollen grain and leaf epiderm among diaploid Thinopyrum elongatum, Elytrigia intermedia, hexaploid Triticum aestivum and octoploid Tritielytrigia types were carried out by observation under scanning electronic microscope(SEM). [Result] There were some differences among the four species in the micro-morphology, the size, the surface protuberance, the germ pore of pollen grain and the leaf epidermal stoma, in which diploid Thinopyrum elongatum was obviously different from the other three. Diploid, hexaploid and octoploid species of triticeae had remarkable differences in micro-morphological characteristics of pollen grain and stoma. However, some differences between hexaploid species and octoploid species were not significant. [Conclusion] Some microscopic characteristics of pollen grain and stoma could be used as the evidence to identify diaploid, hexaploid and octoploid spieces whose chromosome ploidy are hugely different.

Molecular genetic analysis of phosphomannomutase genes in Triticum monococcum

In higher plants, phosphomannomutase(PMM) is essential for synthesizing the antioxidant ascorbic acid through the Smirnoff–Wheeler pathway. Previously, we characterized six PMM genes(Ta PMM-A1, A2, B1, B2, D1 and D2) in common wheat(Triticum aestivum, AABBDD).Here, we report a molecular genetic analysis of PMM genes in Triticum monococcum(AmAm), a diploid wheat species whose Amgenome is closely related to the A genome of common wheat. Two distinct PMM genes, Tm PMM-1 and Tm PMM-2, were found in T. monococcum. The coding region of Tm PMM-1 was intact and highly conserved. In contrast, two main Tm PMM-2 alleles were identified, with Tm PMM-2a possessing an intact coding sequence and Tm PMM-2b being a pseudogene. The transcript level of Tm PMM-2a was much higher than that of Tm PMM-2b, and a bacterially expressed Tm PMM-2a recombinant protein displayed relatively high PMM activity. In general, the total transcript level of PMM was substantially higher in accessions carrying Tm PMM-1 and Tm PMM-2a than those harboring Tm PMM-1 and Tm PMM-2b. However, total PMM protein and activity levels did not differ drastically between the two genotypes. This work provides new information on PMM genes in T. monococcum and expands our understanding on Triticeae PMM genes, which may aid further functional and applied studies of PMM in crop plants.

Application of virus-induced gene silencing for identification of FHB resistant genes

Virus-induced gene silencing (VIGS) showed several advantages to identify gene functions such as short experimental cycle, more broad hosts, etc. In this study, the feasibility and efficiency of employing Barley stripe mosaic virus (BSMV)- based VIGS system to evaluate Fusarium head blight (FHB) resistance were explored in wheat. With variable conditions tested, it showed that the maximal silencing efficiency 78% on spike was obtained when the recombinant BSMV was inoculated on flag leaf at flagging stage. However, the plant may reduce its own immunity to FHB when inoculated with BSMV. To induce this impact, different Fusarium graminearum strains were tested and SF06-1 strain was selected for FHB resistance evaluation. Using this system, TaAOC, TaAOS, and TaOPR3 involved in jasmonic acid (JA) signaling pathway were identified to positively regulate FHB resistance, which was underpinned by the results when silencing TaAOS in wheat by stable transgenic plants.

Integrating the physical and genetic map of bread wheat facilitates the detection of chromosomal rearrangements

The bread wheat genome harbors a high content of repetitive DNA,which is amenable to detection and characterization using fluorescence in situ hybridization(FISH)karyotyping.An integrated genetic map was derived from a recombinant inbred population bred from a cross between a synthetic hexaploid wheat and a commercial Chinese bread wheat cultivar,based on 28 variable FISH sites and>150000 single nucleotide polymorphism(SNP)loci.The majority(20/28)of the variable FISH sites were physically located within a chromosomal region consistent with the genetic location inferred from that of their co-segregating SNP loci.The eight exceptions reflected the presence of either a translocation(1 R/1 B,1 A/7 A)or a presumptive intra-chromosomal inversion(4 A).For eight out of the nine FISH sites detected on the Chinese Spring(CS)karyotype,there was a good match with the reference genome sequence,indicating that the most recent assembly has dealt well with the problem of placing tandem repeats.The integrated genetic map produced for wheat is informative as to the location of blocks of tandemly repeated DNA and can aid in improving the quality of the genome sequence assembly in regions surrounding these blocks.

CRISPR/Cas9-based Editing of Acetyl-CoA Carboxylase (ACC1) Gene in Barley

Plastid localized acetyl-CoA carboxylase(ACCase;EC 6.4.1.2)is a target for aryloxyphenoxypropionates(APPs)and cyclohexanediones(CHDs),two groups of selective herbicides used in controlling grassy weeds.Wheat and barley are important cereal crops in the grass(Poaceae or Gramineae)family,and thus sensitive for those herbicides.Characterization of this form of ACCase(or ACC1)in wheat and barley is essential if these agents are used in the sustainable agriculture.In this study,it was confirmed that a single ACC1 gene presented on the second chromosome per homologous group in common wheat,wild emmer wheat,goat grass and barley.Using CRISPR/Cas9,the barley ACC1 gene was edited,specifically in the carboxyl transferase(CT)domain that was critical for herbicide responses in grass species.Two new alleles were generated,one with a 3-bp deletion leading to ACC1:p.Ile1878del and one with a 26-bp deletion causing ACC1:p.Ser2099_Lys2311del.Both were recovered as heterozygotes in the T0 generation.All the seven T0 plants harboring the 3-bp deletion grew normally,but the only T0 plant with 26-bp deletion died at the extension stage(Zadoks 32),probably because there was inadequate ACC1 activity when the plant was big.In the T1 generation,the 3-bp deletion(or Ile1878del)did not impact the edited plants in tiller numbers,tiller height,spike length and spikelet numbers,when compared to the wild-type allele in the non-edited segregants.This study demonstrated that CRISPR/Cas9 was practical to generate single amino acid deletions in the ACC1 protein and the Ile1878 deletion did not compromise plant growth.Unfortunately,the ACC1:p.Ile1878del protein did not confer resistance to the currently tested APP herbicides,including clethodim,haloxyfop,quizalofop-Pethyl and sethoxydim.