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1.
J Environ Sci (China) ; 147: 165-178, 2025 Jan.
Article in English | MEDLINE | ID: mdl-39003037

ABSTRACT

In this study, two wheat-derived cadmium (Cd)-immobilizing endophytic Pseudomonas paralactis M14 and Priestia megaterium R27 were evaluated for their effects on wheat tissue Cd uptake under hydroponic conditions. Then, the impacts of the biochar (BC), M14+R27 (MR), and BC+MR treatments on wheat Cd uptake and the mechanisms involved were investigated at the jointing, heading, and mature stages of wheat plants under field-plot conditions. A hydroponic experiment showed that the MR treatment significantly decreased the above-ground tissue Cd content compared with the M14 or R27 treatment. The BC+MR treatment reduced the grain Cd content by 51.5%-67.7% and Cd translocation factor at the mature stage of wheat plants and increased the organic matter-bound Cd content by 31%-75% in the rhizosphere soils compared with the BC or MR treatment. Compared with the BC or MR treatment, the relative abundances of the biomarkers associated with Gemmatimonas, Altererythrobacter, Gammaproteobacteria, Xanthomonadaceae, Phenylobacterium, and Nocardioides in the BC+MR-treated rhizosphere microbiome decreased and negatively correlated with the organic matter-bound Cd contents. In the BC+MR-treated root interior microbiome, the relative abundance of the biomarker belonging to Exiguobacterium increased and negatively correlated with the Cd translocation factor, while the relative abundance of the biomarker belonging to Pseudonocardiaceae decreased and positively correlated with the Cd translocation factor. Our findings suggested that the BC+MR treatment reduced Cd availability and Cd transfer through affecting the abundances of these specific biomarkers in the rhizosphere soil and root interior microbiomes, leading to decreased wheat grain Cd uptake in the contaminated soil.


Subject(s)
Cadmium , Charcoal , Soil Microbiology , Soil Pollutants , Triticum , Triticum/metabolism , Triticum/microbiology , Cadmium/metabolism , Soil Pollutants/metabolism , Endophytes/physiology , Rhizosphere , Soil/chemistry , Biodegradation, Environmental , Microbiota/drug effects
2.
Genome Biol ; 25(1): 171, 2024 07 01.
Article in English | MEDLINE | ID: mdl-38951917

ABSTRACT

BACKGROUND: The massive structural variations and frequent introgression highly contribute to the genetic diversity of wheat, while the huge and complex genome of polyploid wheat hinders efficient genotyping of abundant varieties towards accurate identification, management, and exploitation of germplasm resources. RESULTS: We develop a novel workflow that identifies 1240 high-quality large copy number variation blocks (CNVb) in wheat at the pan-genome level, demonstrating that CNVb can serve as an ideal DNA fingerprinting marker for discriminating massive varieties, with the accuracy validated by PCR assay. We then construct a digitalized genotyping CNVb map across 1599 global wheat accessions. Key CNVb markers are linked with trait-associated introgressions, such as the 1RS·1BL translocation and 2NvS translocation, and the beneficial alleles, such as the end-use quality allele Glu-D1d (Dx5 + Dy10) and the semi-dwarf r-e-z allele. Furthermore, we demonstrate that these tagged CNVb markers promote a stable and cost-effective strategy for evaluating wheat germplasm resources with ultra-low-coverage sequencing data, competing with SNP array for applications such as evaluating new varieties, efficient management of collections in gene banks, and describing wheat germplasm resources in a digitalized manner. We also develop a user-friendly interactive platform, WheatCNVb ( http://wheat.cau.edu.cn/WheatCNVb/ ), for exploring the CNVb profiles over ever-increasing wheat accessions, and also propose a QR-code-like representation of individual digital CNVb fingerprint. This platform also allows uploading new CNVb profiles for comparison with stored varieties. CONCLUSIONS: The CNVb-based approach provides a low-cost and high-throughput genotyping strategy for enabling digitalized wheat germplasm management and modern breeding with precise and practical decision-making.


Subject(s)
DNA Copy Number Variations , Triticum , Triticum/genetics , Genome, Plant , High-Throughput Nucleotide Sequencing , Genetic Markers , Alleles
3.
Skin Res Technol ; 30(7): e13829, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38951954

ABSTRACT

BACKGROUND: In the continuous endeavor to find safe and efficient treatments for Atopic Dermatitis (AD), there remains a considerable focus on dietary adjustments. Nevertheless, the limited availability of research and conflicting findings in the academic literature pose a hurdle in establishing conclusive recommendations. METHOD: Mendelian randomization (MR) was applied to the most comprehensive genome-wide association studies (GWAS) data on tea intake (447 485), green tea intake (n = 64 949), flavored milk intake (n = 64 941), never eat eggs, dairy, wheat, sugar: Wheat products(n = 461 046), never eat eggs, dairy, wheat, sugar: Sugar or foods/drinks containing sugar (n = 461 046), never eat eggs, dairy, wheat, sugar: I eat all of the above (n = 461 046) and atopic dermatitis (n = 218 467). We used the inverse-variance weighted method (IVW) as the primary method. RESULTS: The IVW analyses have demonstrated an increased tea intake was genetically associated with a reduced risk of AD (odds ratio [OR]: 0.646, 95% confidence interval [CI]: 0.430-0.968, p = 0.034). Furthermore, green tea intake was significantly negatively associated with AD (IVW OR: 0.986, 95% CI: 0.975-0.998; p = 0.024) in the IVW model. AD risk could be reduced by never eating wheat products (IVW OR: 8.243E-04, 95% CI: 7.223E-06-9.408E-02, p = 0.003). There was no association between never eating eggs, dairy, wheat, sugar: Sugar, or foods/drinks containing sugar, I eat all of the above and AD. CONCLUSIONS: Our MR study suggests a causal relationship between tea intake, green tea intake, and the avoidance of eating wheat products with atopic dermatitis. Our findings recommend that preventing and managing atopic dermatitis may be achieved by never eating wheat products while increasing tea and green tea intake.


Subject(s)
Dermatitis, Atopic , Diet , Genome-Wide Association Study , Mendelian Randomization Analysis , Dermatitis, Atopic/genetics , Humans , Diet/adverse effects , Tea , Eggs , Milk , Triticum/genetics , Dairy Products , Polymorphism, Single Nucleotide
4.
Mol Plant Pathol ; 25(7): e13490, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38952297

ABSTRACT

Employing race-specific resistance genes remains an effective strategy to protect wheat from leaf rust caused by Puccinia triticina (Pt) worldwide, while the newly emerged Pt races, owing to rapid genetic evolution, frequently overcome the immune response delivered by race-specific resistance genes. The molecular mechanisms underlying the newly evolved virulence Pt pathogen remain unknown. Here, we identified an avirulence protein AvrLr15 from Pt that induced Lr15-dependent immune responses. Heterologously produced AvrLr15 triggered pronounced cell death in Lr15-isogenic wheat leaves. AvrLr15 contains a functional signal peptide, localized to the plant nucleus and cytosol and can suppress BAX-induced cell death. Evasion of Lr15-mediated resistance in wheat was associated with a deletion and point mutations of amino acids in AvrLr15 rather than AvrLr15 gene loss in the Lr15-breaking Pt races, implying that AvrLr15 is required for the virulence function of Pt. Our findings identified the first molecular determinant of wheat race-specific immunity and facilitated the identification of the first AVR/R gene pair in the Pt-wheat pathosystem, which will provide a molecular marker to monitor natural Pt populations and guide the deployment of Lr15-resistant wheat cultivars in the field.


Subject(s)
Disease Resistance , Plant Diseases , Puccinia , Triticum , Triticum/microbiology , Triticum/genetics , Triticum/immunology , Plant Diseases/microbiology , Plant Diseases/genetics , Plant Diseases/immunology , Disease Resistance/genetics , Puccinia/pathogenicity , Fungal Proteins/genetics , Fungal Proteins/metabolism , Genes, Plant , Virulence/genetics , Mutation/genetics , Plant Proteins/genetics , Plant Proteins/metabolism , Basidiomycota/pathogenicity , Basidiomycota/genetics , Plant Leaves/microbiology , Plant Leaves/immunology , Cell Death , Sequence Deletion/genetics
5.
Sci Rep ; 14(1): 15114, 2024 07 02.
Article in English | MEDLINE | ID: mdl-38956155

ABSTRACT

Wheat straw returning is a common agronomic measure in the farmland. Understanding organic carbon transformation is of great significance for carbon budget under the premise of widespread distribution of cadmium (Cd) contaminated soils. An incubation experiment was conducted to assess the influence of Cd contamination on the decomposition and accumulation of total organic carbon (TOC) as well as the composition and abundance of bacterial communities in eight soil types with wheat straw addition. The results showed that inhibition of Cd contamination on microbially mediated organic carbon decomposition was affected by soil types. The lower cumulative C mineralization and higher TOC content could be observed in the acidic soils relative to that in the alkaline soils. The content of Cd in soil exhibits different effects on the inhibition in decomposition of TOC. The high dosage level of Cd had stronger inhibitory impact due to its high toxicity. The decomposition of TOC was restricted by a reduction in soil bacterial abundance and weakening of bacterial activities. Redundancy analysis (RDA) indicated that Proteobacteria and Gemmatimonadetes were abundant in alkaline Cd-contaminated soils with wheat straw addition, while Bacteroidetes dominated cumulative C mineralization in acidic Cd-contamination soils. Moreover, the abundance of predicted functional bacteria indicated that high-dose Cd-contamination and acid environment all inhibited the decomposition of TOC. The present study suggested that pH played an important role on carbon dynamics in the Cd-contaminated soils with wheat straw addition.


Subject(s)
Cadmium , Carbon , Soil Microbiology , Soil Pollutants , Soil , Triticum , Cadmium/metabolism , Cadmium/analysis , Triticum/metabolism , Triticum/chemistry , Soil Pollutants/analysis , Soil Pollutants/metabolism , Carbon/metabolism , Carbon/analysis , Soil/chemistry , Bacteria/metabolism , Biodegradation, Environmental , Hydrogen-Ion Concentration
6.
BMC Genomics ; 25(1): 664, 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38961357

ABSTRACT

BACKGROUND: Wheat landraces are considered a valuable source of genetic diversity for breeding programs. It is useful to evaluate the genetic diversity in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. In addition, constructing a core germplasm set that represents the genetic diversity of the entire variety set is of great significance for the efficient conservation and utilization of wheat landrace germplasms. RESULTS: To understand the genetic diversity in wheat landrace, 2,023 accessions in the Jiangsu Provincial Crop Germplasm Resource Bank were used to explore the molecular diversity and population structure using the Illumina 15 K single nucleotide polymorphism (SNP) chip. These accessions were divided into five subpopulations based on population structure, principal coordinate and kinship analysis. A significant variation was found within and among the subpopulations based on the molecular variance analysis (AMOVA). Subpopulation 3 showed more genetic variability based on the different allelic patterns (Na, Ne and I). The M strategy as implemented in MStratv 4.1 software was used to construct the representative core collection. A core collection with a total of 311 accessions (15.37%) was selected from the entire landrace germplasm based on genotype and 12 different phenotypic traits. Compared to the initial landrace collections, the core collection displayed higher gene diversity (0.31) and polymorphism information content (PIC) (0.25), and represented almost all phenotypic variation. CONCLUSIONS: A core collection comprising 311 accessions containing 100% of the genetic variation in the initial population was developed. This collection provides a germplasm base for effective management, conservation, and utilization of the variation in the original set.


Subject(s)
Genetic Variation , Polymorphism, Single Nucleotide , Triticum , Triticum/genetics , China , Genetics, Population , Phenotype , Genotype
7.
Commun Biol ; 7(1): 812, 2024 Jul 04.
Article in English | MEDLINE | ID: mdl-38965407

ABSTRACT

Wheat blast caused by Pyricularia oryzae pathotype Triticum is now becoming a very serious threat to global food security. Here, we report an essential pathogenicity factor of the wheat blast fungus that is recognized and may be targeted by a rice resistance gene. Map-based cloning of Pwt2 showed that its functional allele is the ACE1 secondary metabolite gene cluster of the wheat blast fungus required for its efficient penetration of wheat cell walls. ACE1 is required for the strong aggressiveness of Triticum, Eleusine, and Lolium pathotypes on their respective hosts, but not for that of Oryza and Setaria pathotypes on rice and foxtail millet, respectively. All ACE1 alleles found in wheat blast population are recognized by a rice resistance gene, Pi33, when introduced into rice blast isolates. ACE1 mutations for evading the recognition by Pi33 do not affect the aggressiveness of the rice blast fungus on rice but inevitably impair the aggressiveness of the wheat blast fungus on wheat. These results suggest that a blast resistance gene already defeated in rice may be revived as a durable resistance gene in wheat by targeting an Achilles heel of the wheat blast fungus.


Subject(s)
Multigene Family , Oryza , Plant Diseases , Triticum , Triticum/microbiology , Plant Diseases/microbiology , Oryza/microbiology , Ascomycota/genetics , Ascomycota/pathogenicity , Fungal Proteins/genetics , Fungal Proteins/metabolism , Disease Resistance/genetics , Virulence Factors/genetics , Virulence Factors/metabolism , Secondary Metabolism/genetics
8.
PeerJ ; 12: e17633, 2024.
Article in English | MEDLINE | ID: mdl-38948208

ABSTRACT

Wheat stem rust, which is caused by Puccinia graminis f. sp. tritici (Pgt), is a highly destructive disease that affects wheat crops on a global scale. In this study, the reactions of 150 bread wheat varieties were evaluated for natural Pgt infection at the adult-plant stage in the 2019-2020 and 2020-2021 growing seasons, and they were analyzed using specific molecular markers to detect stem rust resistance genes (Sr22, Sr24, Sr25, Sr26, Sr31, Sr38, Sr50, and Sr57). Based on phenotypic data, the majority of the varieties (62%) were resistant or moderately resistant to natural Pgt infection. According to molecular results, it was identified that Sr57 was present in 103 varieties, Sr50 in nine varieties, Sr25 in six varieties, and Sr22, Sr31, and Sr38 in one variety each. Additionally, their combinations Sr25 + Sr50, Sr31 + Sr57, Sr38 + Sr50, and Sr38 + Sr57 were detected in these varieties. On the other hand, Sr24 and Sr26 were not identified. In addition, many varieties had low stem rust scores, including a large minority that lacked Sr57. These varieties must have useful resistance to stem rust and could be the basis for selecting greater, possibly durable resistance.


Subject(s)
Disease Resistance , Genetic Variation , Plant Diseases , Puccinia , Triticum , Triticum/microbiology , Triticum/genetics , Triticum/immunology , Plant Diseases/microbiology , Plant Diseases/genetics , Plant Diseases/immunology , Disease Resistance/genetics , Puccinia/pathogenicity , Genetic Variation/genetics , Plant Stems/microbiology , Plant Stems/immunology , Plant Stems/genetics , Genes, Plant , Basidiomycota/pathogenicity
9.
PeerJ ; 12: e17618, 2024.
Article in English | MEDLINE | ID: mdl-38948218

ABSTRACT

Leaf inclination angle (LIA) and tillering impact the winter wheat (Triticum aestivum L.) population canopy structure. Understanding their effects on water use (WU) parameters and yield can guide water-saving strategies through population control. In this study, six near-isogenic lines (NILs) and their parents were selected as materials. These special materials were characterized by varying tillering at the current sowing density, a similar genetic background, and, particularly, a gradient in mean flag leaf LIA. The investigation focused on the jointing to early grain-filling stage, the peak water requirement period of wheat crops. Population-scale transpiration (PT) and evaporation from the soil surface (E) were partitioned from total evapotranspiration (ET) by the means of micro-lysimeters. The results showed decreased PT, E, and ET with increased population density (PD) within a narrow density range derived from varying tillering across genotypes. Significant correlations existed between PD and ET, E, and PT, especially in the wettest 2017-2018 growing season. Within such narrow PD range, all the correlations between WU parameters and PD were negative, although some correlations were not statistically significant, thereby suggesting the population structure's predominant impact. No significant correlation existed between LIA and both ET and PT within the LIA range of 35°-65°. However, significant correlations occurred between LIA and E in two growing seasons. Genotypes with similar LIA but different PD produced varied ET; while with similar PD, the four pairs of genotypes with different LIA each consumed similar ET, thus highlighting PD's more crucial role in regulating ET. The yield increased with higher LIA, and showed a significant correlation, emphasizing the LIA's significant effect on yield. However, no correlation was observed with PD, indicating the minor effect of tillering at the current sowing density. Therefore these results might offer valuable insights for breeding water-saving cultivars and optimizing population structures for effective field water conservation.


Subject(s)
Plant Leaves , Plant Transpiration , Soil , Triticum , Triticum/genetics , Triticum/physiology , Triticum/growth & development , Plant Leaves/physiology , Soil/chemistry , Seasons , Water/metabolism , Genotype
10.
PeerJ ; 12: e17656, 2024.
Article in English | MEDLINE | ID: mdl-38948216

ABSTRACT

Fusarium crown rot (FCR), caused by Fusarium spp., is a devastating disease in wheat growing areas. Previous studies have shown that FCR is caused by co-infection of F. graminearum, F. pseudograminearum, F. proliferatum and F. verticillioides in Hubei Province, China. In this study, a method was developed to simultaneously detected DNAs of F. graminearum, F. pseudograminearum, F. proliferatum and F. verticillioides that can efficiently differentiate them. Whole genome sequence comparison of these four Fusarium spp. was performed and a 20 bp sequence was designed as an universal upstream primer. Specific downstream primers of each pathogen was also designed, which resulted in a 206, 482, 680, and 963 bp amplicon for each pathogen, respectively. Multiplex PCR specifically identified F. graminearum, F. pseudograminearum, F. proliferatum and F. verticillioides but not from other 46 pathogens, and the detection limit of target pathogens is about 100 pg/µl. Moreover, we accurately determined the FCR pathogen species in wheat samples using the optimized multiplex PCR method. These results demonstrate that the multiplex PCR method established in this study can efficiently and rapidly identify F. graminearum, F. pseudograminearum, F. proliferatum, and F. verticillioides, which should provide technical support for timely and targeted prevention and control of FCR.


Subject(s)
Fusarium , Multiplex Polymerase Chain Reaction , Plant Diseases , Triticum , Fusarium/genetics , Fusarium/isolation & purification , Triticum/microbiology , Plant Diseases/microbiology , Multiplex Polymerase Chain Reaction/methods , China , DNA, Fungal/genetics
11.
PeerJ ; 12: e17587, 2024.
Article in English | MEDLINE | ID: mdl-38952963

ABSTRACT

Watermelon is commonly affected by Fusarium wilt in a monoculture cropping system. Wheat intercropping alleviates the affection of Fusarium wilt of watermelon. The objective of this study was to determine the effects of wheat and watermelon intercropping on watermelon growth and Fusarium wilt. Our results showed that wheat and watermelon intercropping promoted growth, increased chlorophyll content, and photosynthesis of watermelon. Meanwhile, wheat and watermelon intercropping inhibited watermelon Fusarium wilt occurrence, decreased spore numbers, increased root vigor, increased antioxidant enzyme activities, and decreased malondialdehyde (MDA) content in watermelon roots. Additionally, wheat and watermelon intercropping enhanced the bacterial colonies and total microbes growth in soil, decreased fungi and Fusarium oxysporum f. sp. niveum (FON) colonies, and increased soil enzyme activities in watermelon rhizosphere soil. Our results indicated that wheat and watermelon intercropping enhanced watermelon growth and decreased the incidence of Fusarium wilt in watermelon. These effects could be due to intercropping inducing physiological changes, regulating soil enzyme activities, and/or modulating soil microbial communities.


Subject(s)
Citrullus , Fusarium , Plant Diseases , Soil Microbiology , Triticum , Citrullus/microbiology , Citrullus/growth & development , Triticum/microbiology , Triticum/growth & development , Fusarium/growth & development , Plant Diseases/microbiology , Plant Diseases/prevention & control , Plant Roots/microbiology , Plant Roots/growth & development
12.
Theor Appl Genet ; 137(8): 177, 2024 Jul 07.
Article in English | MEDLINE | ID: mdl-38972024

ABSTRACT

KEY MESSAGE: Underpinned natural variations and key genes associated with yield under different water regimes, and identified genomic signatures of genetic gain in the Indian wheat breeding program. A novel KASP marker for TKW under water stress was developed and validated. A comprehensive genome-wide association study was conducted on 300 spring wheat genotypes to elucidate the natural variations associated with grain yield and its eleven contributing traits under fully irrigated, restricted water, and simulated no water conditions. Utilizing the 35K Wheat Breeders' Array, we identified 1155 quantitative trait nucleotides (QTNs), with 207 QTNs exhibiting stability across diverse conditions. These QTNs were further delimited into 539 genomic regions using a genome-wide LD value of 3.0 Mbp, revealing pleiotropic control across traits and conditions. Sub-genome A was significantly associated with traits under irrigated conditions, while sub-genome B showed more QTNs under water stressed conditions. Favourable alleles with significantly associated QTNs were delineated, with a notable pyramiding effect for enhancing trait performance. Additionally, allele of only 921 QTNs significantly affected the population mean. Allele profiling highlighted C-306 as a most potential source of drought tolerance. Moreover, 762 genes overlapping significant QTNs were identified, narrowing down to 27 putative candidate genes overlapping 29 novel and functional SNPs expressing (≥ 0.5 tpm) relevance across various growth conditions. A new KASP assay was developed, targeting a gene TraesCS2A03G1123700 regulating thousand kernel weight under severe drought condition. Genomic selection models (GBLUP, BayesB, MxE, and R-Norm) demonstrated an average prediction accuracy of 0.06-0.58 across environments, indicating potential for trait selection. Retrospective analysis of the Indian wheat breeding program supported a genetic gain in GY at the rate of ca. 0.56% per breeding cycle, since 1960, supporting the identification of genomic signatures driving trait selection and genetic gain. These findings offer insight into improving the rate of genetic gain in wheat breeding programs globally.


Subject(s)
Edible Grain , Genotype , Phenotype , Plant Breeding , Polymorphism, Single Nucleotide , Quantitative Trait Loci , Triticum , Water , Triticum/genetics , Triticum/growth & development , Edible Grain/genetics , Edible Grain/growth & development , Genetic Association Studies , Droughts , Chromosome Mapping/methods , Linkage Disequilibrium , Alleles , Genome-Wide Association Study , India
13.
Sci Rep ; 14(1): 15546, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38969785

ABSTRACT

Plant growth-promoting rhizobacteria (PGPR) boost crop yields and reduce environmental pressures through biofilm formation in natural climates. Recently, biofilm-based root colonization by these microorganisms has emerged as a promising strategy for agricultural enhancement. The current work aims to characterize biofilm-forming rhizobacteria for wheat growth and yield enhancement. For this, native rhizobacteria were isolated from the wheat rhizosphere and ten isolates were characterized for plant growth promoting traits and biofilm production under axenic conditions. Among these ten isolates, five were identified as potential biofilm-producing PGPR based on in vitro assays for plant growth-promoting traits. These were further evaluated under controlled and field conditions for their impact on wheat growth and yield attributes. Surface-enhanced Raman spectroscopy analysis further indicated that the biochemical composition of the biofilm produced by the selected bacterial strains includes proteins, carbohydrates, lipids, amino acids, and nucleic acids (DNA/RNA). Inoculated plants in growth chamber resulted in larger roots, shoots, and increase in fresh biomass than controls. Similarly, significant increases in plant height (13.3, 16.7%), grain yield (29.6, 17.5%), number of tillers (18.7, 34.8%), nitrogen content (58.8, 48.1%), and phosphorus content (63.0, 51.0%) in grains were observed in both pot and field trials, respectively. The two most promising biofilm-producing isolates were identified through 16 s rRNA partial gene sequencing as Brucella sp. (BF10), Lysinibacillus macroides (BF15). Moreover, leaf pigmentation and relative water contents were significantly increased in all treated plants. Taken together, our results revealed that biofilm forming PGPR can boost crop productivity by enhancing growth and physiological responses and thus aid in sustainable agriculture.


Subject(s)
Biofilms , Plant Roots , Rhizosphere , Soil Microbiology , Triticum , Triticum/microbiology , Triticum/growth & development , Biofilms/growth & development , Plant Roots/microbiology , Plant Roots/growth & development , Bacteria/classification , Bacteria/genetics , Bacteria/metabolism , Bacteria/growth & development , Bacteria/isolation & purification , Plant Development , Biomass
14.
Methods Mol Biol ; 2830: 35-49, 2024.
Article in English | MEDLINE | ID: mdl-38977566

ABSTRACT

Seed dormancy is an important trait in cereal breeding, as it prevents preharvest sprouting (PHS). Although seed dormancy is a multifactorial trait, seed color has been demonstrated to be a major dormancy-related factor controlled by few genes. The R-1 gene is a seed color regulator that encodes a MYB-type transcription factor in wheat. A set of genetic markers designed against R-1 can provide a powerful tool for swift wheat breeding. Depth of seed dormancy varies not only among lines but also during seed development in each line. In this chapter, we describe how developmental seeds can be collected to perform germination tests, how seed color can be observed after NaOH staining, and how to genotype wheat R-1 genes using multiplex PCR.


Subject(s)
Germination , Multiplex Polymerase Chain Reaction , Plant Dormancy , Seeds , Triticum , Triticum/genetics , Triticum/growth & development , Seeds/genetics , Seeds/growth & development , Plant Dormancy/genetics , Germination/genetics , Multiplex Polymerase Chain Reaction/methods , Genotype , Color , Plant Breeding/methods , Genetic Markers/genetics , Plant Proteins/genetics , Plant Proteins/metabolism
15.
Methods Mol Biol ; 2830: 131-136, 2024.
Article in English | MEDLINE | ID: mdl-38977574

ABSTRACT

Seed dormancy genes typically suppress germination and cell division. Therefore, overexpressing these genes can negatively affect tissue culture, interfering with the generation of transgenic plants and thus hampering the analysis of gene function. Transient expression in target cells is a useful approach for studying the function of seed dormancy genes. Here, we describe a protocol for transiently expressing genes related to seed dormancy in the scutellum of immature wheat (Triticum aestivum) embryos to analyze their effects on germination.


Subject(s)
Gene Expression Regulation, Plant , Germination , Plant Dormancy , Seeds , Triticum , Triticum/genetics , Triticum/growth & development , Plant Dormancy/genetics , Seeds/genetics , Seeds/growth & development , Germination/genetics , Biolistics/methods , Plants, Genetically Modified/genetics , Genes, Plant , Gene Expression/genetics
16.
Methods Mol Biol ; 2830: 121-129, 2024.
Article in English | MEDLINE | ID: mdl-38977573

ABSTRACT

Genome-wide association study (GWAS) is widely used to characterize genes or quantitative trait loci (QTLs) associated with preharvest sprouting and seed dormancy. GWAS can identify both previously discovered and novel QTLs across diverse genetic panels. The high-throughput SNP arrays or next-generation sequencing technologies have facilitated the identification of numerous genetic markers, thereby significantly enhancing the resolution of GWAS. Although various methods have been developed, the fundamental principles underlying these techniques remain constant. Here, we provide a basic technological flow to perform seed dormancy assay, followed by GWAS using population structure control, and compared it with previous identified QTLs and genes.


Subject(s)
Genome-Wide Association Study , Germination , Plant Dormancy , Polymorphism, Single Nucleotide , Quantitative Trait Loci , Triticum , Genome-Wide Association Study/methods , Triticum/genetics , Triticum/growth & development , Germination/genetics , Plant Dormancy/genetics , Seeds/genetics , Seeds/growth & development , Phenotype
17.
Methods Mol Biol ; 2830: 163-171, 2024.
Article in English | MEDLINE | ID: mdl-38977577

ABSTRACT

Dependency on in vitro culture and regeneration limits the ability to use genome editing on elite wheat (Triticum aestivum L.) varieties. We recently developed an in planta particle bombardment (iPB) technique for gene editing in wheat that utilizes shoot apical meristems (SAMs) as a target tissue. Since the method does not require in vitro culture, it can therefore be used on recalcitrant varieties. In this chapter, we describe in detail the steps used in the iPB method. With this protocol, 3% to 5% of T0 plants grown from bombarded SAMs typically carry mutant alleles and approximately 1% to 2% of the T0 plants inherit mutant alleles in the next generation.


Subject(s)
Gene Editing , Plant Dormancy , Triticum , Triticum/genetics , Triticum/growth & development , Gene Editing/methods , Plant Dormancy/genetics , Genome, Plant , Plants, Genetically Modified/genetics , Meristem/genetics , Seeds/genetics , Seeds/growth & development , CRISPR-Cas Systems
18.
Methods Mol Biol ; 2830: 175-193, 2024.
Article in English | MEDLINE | ID: mdl-38977578

ABSTRACT

Different methodologies have been applied for the selection of preharvest sprouting resistance in cereal breeding programs. We describe here a series of methods used in practical wheat breeding programs in Japan, including phenotyping based on germination score after artificial rain treatments and genotyping using DNA markers. These methods can be modified and applied to breeding programs in which preharvest sprouting is a problem during cereal cultivation.


Subject(s)
Germination , Phenotype , Plant Breeding , Triticum , Genetic Markers , Genotype , Germination/genetics , Japan , Plant Breeding/methods , Triticum/genetics , Triticum/growth & development
19.
Methods Mol Biol ; 2830: 137-148, 2024.
Article in English | MEDLINE | ID: mdl-38977575

ABSTRACT

Knockout mutants provide definitive information about the functions of genes related to agronomic traits, including seed dormancy. However, it takes many years to produce knockout mutants using conventional techniques in polyploid plants such as hexaploid wheat. Genome editing with sequence-specific nucleases is a promising approach for obtaining knockout mutations in all targeted homoeologs of wheat simultaneously. Here, we describe a procedure to produce a triple recessive mutant in wheat via genome editing. This protocol covers the evaluation of gRNA and Agrobacterium-mediated transformation to obtain edited wheat seedlings.


Subject(s)
CRISPR-Cas Systems , Gene Editing , Gene Knockout Techniques , Plant Dormancy , Triticum , Triticum/genetics , Gene Editing/methods , Plant Dormancy/genetics , Gene Knockout Techniques/methods , Mutation , Plants, Genetically Modified/genetics , Genome, Plant , RNA, Guide, CRISPR-Cas Systems/genetics , Seeds/genetics , Genes, Plant , Agrobacterium/genetics , Seedlings/genetics
20.
Int J Mol Sci ; 25(13)2024 Jul 03.
Article in English | MEDLINE | ID: mdl-39000431

ABSTRACT

Wheat allergy is a major type of food allergy with the potential for life-threatening anaphylactic reactions. Common wheat, Triticum aestivum (hexaploid, AABBDD genome), was developed using tetraploid wheat (AABB genome) and the ancient diploid wheat progenitor (DD genome)-Aegilops tauschii. The potential allergenicity of gluten from ancient diploid wheat is unknown. In this study, using a novel adjuvant-free gluten allergy mouse model, we tested the hypothesis that the glutenin extract from this ancient wheat progenitor will be intrinsically allergenic in this model. The ancient wheat was grown, and wheat berries were used to extract the glutenin for testing. A plant protein-free colony of Balb/c mice was established and used in this study. The intrinsic allergic sensitization potential of the glutenin was determined by measuring IgE response upon transdermal exposure without the use of an adjuvant. Clinical sensitization for eliciting systemic anaphylaxis (SA) was determined by quantifying the hypothermic shock response (HSR) and the mucosal mast cell response (MMCR) upon intraperitoneal injection. Glutenin extract elicited a robust and specific IgE response. Life-threatening SA associated and a significant MMCR were induced by the glutenin challenge. Furthermore, proteomic analysis of the spleen tissue revealed evidence of in vivo Th2 pathway activation. In addition, using a recently published fold-change analysis method, several immune markers positively and negatively associated with SA were identified. These results demonstrate for the first time that the glutenin from the ancient wheat progenitor is intrinsically allergenic, as it has the capacity to elicit clinical sensitization for anaphylaxis via activation of the Th2 pathway in vivo in mice.


Subject(s)
Allergens , Anaphylaxis , Glutens , Mice, Inbred BALB C , Th2 Cells , Triticum , Wheat Hypersensitivity , Animals , Anaphylaxis/immunology , Th2 Cells/immunology , Th2 Cells/metabolism , Mice , Triticum/immunology , Triticum/chemistry , Glutens/immunology , Wheat Hypersensitivity/immunology , Allergens/immunology , Immunoglobulin E/immunology , Immunoglobulin E/blood , Disease Models, Animal , Female , Mast Cells/immunology , Mast Cells/metabolism , Mast Cells/drug effects , Proteomics/methods
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