Genetic basis of resistance against powdery mildew in the wheat cultivar "Tabasco".

European winter wheat cultivar "Tabasco" was reported to have resistance to powdery mildew disease caused by Blumeria graminis f. sp. tritici (Bgt) in China. In previous studies, Tabasco was reported to have the resistance gene designated as Pm48 on the short arm of chromosome 5D when a mapping population was phenotyped with pathogen isolate Bgt19 collected in China and was genotyped with simple sequence repeat (SSR) markers. In this study, single-nucleotide polymorphism (SNP) chips were used to rapidly determine the resistance gene by mapping a new F2 population that was developed from Tabasco and a susceptible cultivar "Ningmaizi119" and inoculated with pathogen isolate NCF-D-1-1 that was collected in the USA. The segregation of resistance in the population was found to link with Pm2 which was identified in Tabasco. Therefore, it was concluded that the previously reported Pm48 on chromosome arm 5DS in Tabasco should be the Pm2 gene on the same chromosome. The Pm2 was also found in European cultivars "Mattis" and "Claire" but not in any of the accessions from diploid wheat Aegilops tauschii or modern cultivars such as "Gallagher," "Smith's Gold," and "OK Corral" being used in the Great Plains in the USA. A KASP marker was developed to track the resistance allele Pm2 in wheat breeding. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01402-3.

Rapid identification and deployment of major genes for flowering time and awn traits in common wheat.

Molecular markers are developed to accelerate deployment of genes for desirable traits segregated in a bi-parental population of recombinant inbred lines (RILs) or doubled haplotype (DH) lines for mapping. However, it would be the most effective if such markers for multiple traits could be identified in an F2 population. In this study, single nucleotide polymorphisms (SNP) chips were used to identify major genes for heading date and awn in an F2 population without developing RILs or DH lines. The population was generated from a cross between a locally adapted spring wheat cultivar "Ningmaizi119" and a winter wheat cultivar "Tabasco" with a diverse genetic background. It was found that the dominant Vrn-D1 allele could make Ningmaizi119 flowered a few months earlier than Tabasco in the greenhouse and without vernalization. The observed effects of the allele were validated in F3 populations. It was also found that the dominant Ali-A1 allele for awnless trait in Tabasco or the recessive ali-A1 allele for awn trait in Ningmaizi119 was segregated in the F2 population. The allelic variation in the ALI-A1 gene relies not only on the DNA polymorphisms in the promoter but also on gene copy number, with one copy ali-A1 in Ningmaizi119 but two copies Ali-A1 in Tabasco based on RT-PCR results. According to wheat genome sequences, cultivar "Mattis" has two copies Ali-A1 and cultivar "Spelta" has four copies Ali-A in a chromosome that was uncharacterized (ChrUN), in addition to one copy on chromosome 5A. This study rapidly characterized the effects of the dominant Vrn-D1 allele and identified the haplotype of Ali-A1 in gene copy number in the F2 segregation population of common wheat will accelerate their deployment in cycling lines in breeding.

TaCol-B5 modifies spike architecture and enhances grain yield in wheat.

Spike architecture influences grain yield in wheat. We report the map-based cloning of a gene determining the number of spikelet nodes per spike in common wheat. The cloned gene is named TaCOL-B5 and encodes a CONSTANS-like protein that is orthologous to COL5 in plant species. Constitutive overexpression of the dominant TaCol-B5 allele but without the region encoding B-boxes in a common wheat cultivar increases the number of spikelet nodes per spike and produces more tillers and spikes, thereby enhancing grain yield in transgenic plants under field conditions. Allelic variation in TaCOL-B5 results in amino acid substitutions leading to differential protein phosphorylation by the protein kinase TaK4. The TaCol-B5 allele is present in emmer wheat but is rare in a global collection of modern wheat cultivars.

Development of the Wheat Practical Haplotype Graph database as a resource for genotyping data storage and genotype imputation.

To improve the efficiency of high-density genotype data storage and imputation in bread wheat (Triticum aestivum L.), we applied the Practical Haplotype Graph (PHG) tool. The Wheat PHG database was built using whole-exome capture sequencing data from a diverse set of 65 wheat accessions. Population haplotypes were inferred for the reference genome intervals defined by the boundaries of the high-quality gene models. Missing genotypes in the inference panels, composed of wheat cultivars or recombinant inbred lines genotyped by exome capture, genotyping-by-sequencing (GBS), or whole-genome skim-seq sequencing approaches, were imputed using the Wheat PHG database. Though imputation accuracy varied depending on the method of sequencing and coverage depth, we found 92% imputation accuracy with 0.01× sequence coverage, which was slightly lower than the accuracy obtained using the 0.5× sequence coverage (96.6%). Compared to Beagle, on average, PHG imputation was ∼3.5% (P-value < 2 × 10-14) more accurate, and showed 27% higher accuracy at imputing a rare haplotype introgressed from a wild relative into wheat. We found reduced accuracy of imputation with independent 2× GBS data (88.6%), which increases to 89.2% with the inclusion of parental haplotypes in the database. The accuracy reduction with GBS is likely associated with the small overlap between GBS markers and the exome capture dataset, which was used for constructing PHG. The highest imputation accuracy was obtained with exome capture for the wheat D genome, which also showed the highest levels of linkage disequilibrium and proportion of identity-by-descent regions among accessions in the PHG database. We demonstrate that genetic mapping based on genotypes imputed using PHG identifies SNPs with a broader range of effect sizes that together explain a higher proportion of genetic variance for heading date and meiotic crossover rate compared to previous studies.

O-linked N-acetylglucosamine transferase is involved in fine regulation of flowering time in winter wheat.

Vernalization genes underlying dramatic differences in flowering time between spring wheat and winter wheat have been studied extensively, but little is known about genes that regulate subtler differences in flowering time among winter wheat cultivars, which account for approximately 75% of wheat grown worldwide. Here, we identify a gene encoding an O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) that differentiates heading date between winter wheat cultivars Duster and Billings. We clone this TaOGT1 gene from a quantitative trait locus (QTL) for heading date in a mapping population derived from these two bread wheat cultivars and analyzed in various environments. Transgenic complementation analysis shows that constitutive overexpression of TaOGT1b from Billings accelerates the heading of transgenic Duster plants. TaOGT1 is able to transfer an O-GlcNAc group to wheat protein TaGRP2. Our findings establish important roles for TaOGT1 in winter wheat in adaptation to global warming in the future climate scenarios.

A semi-dominant NLR allele causes whole-seedling necrosis in wheat.

Programmed cell death (PCD) and apoptosis have key functions in development and disease resistance in diverse organisms; however, the induction of necrosis remains poorly understood. Here, we identified a semi-dominant mutant allele that causes the necrotic death of the entire seedling (DES) of wheat (Triticum aestivum L.) in the absence of any pathogen or external stimulus. Positional cloning of the lethal allele mDES1 revealed that this premature death via necrosis was caused by a point mutation from Asp to Asn at amino acid 441 in a nucleotide-binding leucine-rich repeat protein containing nucleotide-binding domain and leucine-rich repeats. The overexpression of mDES1 triggered necrosis and PCD in transgenic plants. However, transgenic wheat harboring truncated wild-type DES1 proteins produced through gene editing that exhibited no significant developmental defects. The point mutation in mDES1 did not cause changes in this protein in the oligomeric state, but mDES1 failed to interact with replication protein A leading to abnormal mitotic cell division. DES1 is an ortholog of Sr35, which recognizes a Puccinia graminis f. sp. tritici stem rust disease effector in wheat, but mDES1 gained function as a direct inducer of plant death. These findings shed light on the intersection of necrosis, apoptosis, and autoimmunity in plants.

Genome-wide analysis of the HSP101/CLPB gene family for heat tolerance in hexaploid wheat.

Heat Shock Protein 101 (HSP101), the homolog of Caseinolytic Protease B (CLPB) proteins, has functional conservation across species to play roles in heat acclimation and plant development. In wheat, several TaHSP101/CLPB genes were identified, but have not been comprehensively characterized. Given the complexity of a polyploid genome with its phenomena of homoeologous expression bias, detailed analysis on the whole TaCLPB family members is important to understand the genetic basis of heat tolerance in hexaploid wheat. In this study, a genome-wide analysis revealed thirteen members of TaCLPB gene family and their expression patterns in various tissues, developmental stages, and stress conditions. Detailed characterization of TaCLPB gene and protein structures suggested potential variations of the sub-cellular localization and their functional regulations. We revealed homoeologous specific variations among TaCLPB gene copies that have not been reported earlier. A study of the Chromosome 1 TaCLPB in four wheat genotypes demonstrated unique patterns of the homoeologous gene expression under moderate and extreme heat treatments. The results give insight into the strategies to improve heat tolerance by targeting one or some of the TaCLPB genes in wheat.

Molecular Characterization of Auxin Efflux Carrier- ABCB1 in hexaploid wheat.

Auxin is an important phytohormone that regulates response, differentiation, and development of plant cell, tissue, and organs. Along with its local production, long-distance transport coordinated by the efflux/influx membrane transporters is instrumental in plant development and architecture. In the present study, we cloned and characterized a wheat (Triticum aestivum) auxin efflux carrier ABCB1. The TaABCB1 was physically localized to the proximal 15% of the short arm of wheat homoeologous group 7 chromosomes. Size of the Chinese spring (CS) homoeologs genomic copies ranged from 5.3-6.2 kb with the 7A copy being the largest due to novel insertions in its third intron. The three homoeologous copies share 95-97% sequence similarity at the nucleotide, 98-99% amino acid, and overall Q-score of 0.98 at 3-D structure level. Though detected in all analyzed tissues, TaABCB1 predominantly expressed in the meristematic tissues likely due to the presence of meristem-specific activation regulatory element identified in the promoter region. RNAi plants of TaABCB1 gene resulted in reduced plant height and increased seed width. Promoter analysis revealed several responsive elements detected in the promoter region including that for different hormones as auxin, gibberellic acid, jasmonic acid and abscisic acid, light, and circadian regulated elements.

Evolution of Rubisco activase gene in plants.

KEY MESSAGE: Rubisco activase of plants evolved in a stepwise manner without losing its function to adapt to the major evolutionary events including endosymbiosis and land colonization. Rubisco activase is an essential enzyme for photosynthesis, which removes inhibitory sugar phosphates from the active sites of Rubisco, a process necessary for Rubisco activation and carbon fixation. The gene probably evolved in cyanobacteria as different species differ for its presence. However, the gene is present in all other plant species. At least a single gene copy was maintained throughout plant evolution; but various genome and gene duplication events, which occurred during plant evolution, increased its copy number in some species. The exons and exon-intron junctions of present day higher plant's Rca, which is conserved in most species seem to have evolved in charophytes. A unique tandem duplication of Rca gene occurred in a common grass ancestor, and the two genes evolved differently for gene structure, sequence, and expression pattern. At the protein level, starting with a primitive form in cyanobacteria, RCA of chlorophytes evolved by integrating chloroplast transit peptide (cTP), and N-terminal domains to the ATPase, Rubisco recognition and C-terminal domains. The redox regulated C-terminal extension (CTE) and the associated alternate splicing mechanism, which splices the RCA-α and RCA-ß isoforms were probably gained from another gene in charophytes, conserved in most species except the members of Solanaceae family.

Silencing of a metaphase I-specific gene results in a phenotype similar to that of the Pairing homeologous 1 (Ph1) gene mutations.

Although studied extensively since 1958, the molecular mode of action of the Pairing homeologous 1 (Ph1) gene is still unknown. In polyploid wheat, the diploid-like chromosome pairing is principally controlled by the Ph1 gene via preventing homeologous chromosome pairing (HECP). Here, we report a candidate Ph1 gene (C-Ph1) present in the Ph1 locus, transient as well as stable silencing of which resulted in a phenotype characteristic of the Ph1 gene mutants, including HECP, multivalent formation, and disrupted chromosome alignment on the metaphase I (MI) plate. Despite a highly conserved DNA sequence, the C-Ph1 gene homeologues showed a dramatically different structure and expression pattern, with only the 5B copy showing MI-specific expression, further supporting our claim for the Ph1 gene. In agreement with the previous reports about the Ph1 gene, the predicted protein of the 5A copy of the C-Ph1 gene is truncated, and thus perhaps less effective. The 5D copy is expressed around the onset of meiosis; thus, it may function during the earlier stages of chromosome pairing. Along with alternate splicing, the predicted protein of the 5B copy is different from the protein of the other two copies because of an insertion. These structural and expression differences among the homeologues concurred with the previous observations about Ph1 gene function. Stable RNAi silencing of the wheat gene in Arabidopsis showed multivalents and centromere clustering during meiosis I.