Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement

Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with compound genomes such as common wheat(Triticum aestivum).In this work,we constructed genome resources for the modern elite common wheat variety Aikang 58(AK58).Comparative genomics between AK58 and the landrace cultivar Chinese Spring(CS)shed light on genomic changes that occurred through recent varietal improvement.We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study(HGWAS)approach,which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci.A total of 123 major HGWAs loci were detected using a genetic population derived from AK58 and cs.Elite homoeologous haplotypes(HHs),formed by combinations of subgenomic homoeologs of the associated loci,were found in both parents and progeny,and many could substantially improve wheat yield and related traits.We built a website where users can download genome assembly sequence and annotation data for AK58,perform blast analysis,and run JBrowse.Our work enriches genome resources for wheat,provides new insights into genomic changes during modern wheat improve-.ment,and suggests that efficientmining of elite HHs can make a substantial contribuutionto genomics-assisted breeding in common wheat and other polyploid crops.

Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat

Wheat(Triticum aestivum,BBAADD)is an allohexaploid species that originated from two polyploidization events.The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii,respectively.Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome.However,whether Ae.speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae.speltoides and the B subgenome remain unclear.Here,we assembled a high-quality reference genome for Ae.speltoides,resequenced 53 accessions from seven species(Aegilops bicornis,Aegilops longissima,Aegilops searsii,Aegilops sharonensis,Ae.speltoides,Aegilops mutica[syn.Amblyopyrum muticum],and Triticumdicoccoides)and revealed their genomic contributions to the wheat B subgenome.Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae.speltoides and the B subgenome.We classified five groups of conserved and non-conserved genes between Aegilops and Triticum,revealing their biological characteristics,differentiation in gene expression patterns,and collinear relationships between Ae.speltoides and the wheat B subgenome.We also identified gene families that expanded in Ae.speltoides during its evolution and 789 genes specific to Ae.speltoides.These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress.The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.

GSK3 regulates VRN1 to control flowering time in wheat

The precise control of flowering time is important for the regional adaptability and productivity of many crops.Various categories of genes related to flowering have been isolated and characterized functionally in wheat(Triticum aestivum) in response to vernalization to adjust flowering initiation. Before vernalization, the inhibitory histone modification H3K27me3 is enriched in the promoter and the first intron of the vernalization gene VRN1.

WheatGmap:a comprehensive platform for wheat gene mapping and genomic studies

Bulked segregant analysis(BSA)is an efficient and low-cost strategy that is widely used to identify causal genes in segregating populations.BSA-based methods,such as BSA sequencing(Wenger et al.,2010),bulked segregant RNA sequencing(BSR-seq)(del Viso et al.,2012),and MutMap(Abe et al.,2012),are powerful tools that can be used for rapidly discovering genetic markers and gene mapping.Although BSA is increasingly being used in wheat(Triticum aestivum)gene mapping efforts,few user-friendly BSA tools have been developed for researchers lacking a strong bioinformatics background.Here,we developed the web-based BSA platform WheatGmap(https://www.wheatgmap.org),which integrates multiple BSA mapping models and large amounts of public data to accelerate gene cloning and functional research and facilitate resource sharing.

Gene expression profiling related to powdery mildew resistance in wheat with the method of suppression subtractive hybridization

'Bainong 3217 × Mardler' BC5F4 wheat line at the initial stage of inoculation with powdery mildew pathogen (Erysiphe graminis DC) was used to construct a suppression subtractive hybridization (SSH) cDNA library. Totally 760 ESTs were obtained through sequencing. Similarity analysis of ESTs based on BLASTn and BLASTx with the sequences in GenBank, in combination with macroarray differential screening, revealed that 199 ESTs of 65 kinds were known to be functionally disease resistance related. Based on the gene expression profiling in the present study, it is postulated that salicylic acid (SA) and MAP-related signal transduction pathways were involved in powdery mildew resistance in wheat. System acquired resistance genes were predominant in terms of kinds and quantity. With the initiation of cell defense reaction, the genes conferring anti-oxidation substances were largely expressed and thus cell protection mechanism was activated. Much evidence revealed that phenylpropanes metabolic pathway was

The wheat MYB-related transcription factor TaMYB72 promotes flowering in rice

Through large-scale transformation analyses, Ta MYB72 was identified as a flowering time regulator in wheat. Ta MYB72 is a MYB family transcription factor localized to the nucleus. Three Ta MYB72 homologs,Ta MYB72-A, Ta MYB72-B and Ta MYB72-D, cloned from hexaploid wheat were mapped to the short arm of the group 6 chromosomes. Under the long-day conditions,over-expression of the Ta MYB72 in rice shortened the flowering time by approximately 12 d. Expression analyses suggest that Ta MYB72 may function through upregulation of florigen genes Hd3 a and RFT1.

Cloning and characterization of a C genome-specific repetitive sequence in Aegilops caudata L.

pAeca212 is 204 bp in length, and the G + C content is 51%. It disperses on all seven chromosome pairs of Aegilops caudata except centromeres and secondary constrictions.Compared with the 316893 DNA sequences registered in Genbank/EMBL/DDJB/PDB, pAeca212 is a new C-genome specific repetitive sequence. The results of genomic specificity analysis of pAeca212 show that there are no hybridization signals detected in all donor Poaceae plants except in rye. pAeca212 is a very useful molecular marker in the study of the origin of Triticeace and the detection of C chromatin in wheat background.

Wheat male-sterile 2 reduces ROS levels to inhibit anther development by deactivating ROS modulator 1

Ms2 is an important dominant male-sterile gene in wheat,but the biochemical function of Ms2 and the mechanism by which it causes male sterility remain elusive.Here,we report the molecular basis underlying Ms2-induced male sterility in wheat.We found that activated Ms2 specifically reduces the reactive oxygen species(ROS)signals in anthers and thereby induces termination of wheat anther development at an early stage.Furthermore,our results indicate that Ms2 is localized in mitochondria,where it physically interacts with a wheat homolog of ROS modulator 1(TaRomo1).Romo1 positively regulates the ROS levels in humans but has never been studied in plants.We found that single amino acid substitutions in the Ms2 protein that rescue the ms2 male-sterile phenotype abolish the interaction between Ms2 and TaRomo1.Significantly,Ms2 promotes the transition of TaRomo1 proteins from active monomers to inactive oligomers.Taken together,our findings unravel the molecular basis of Ms2-induced male sterility and reveal a regulatory mechanism in which ROS act as essential signals guiding the anther development program in wheat.