AgRenSeq
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB23912 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2219380_1.fastq.gz | Fastqsanger.gz | |||
| ERR2219380_2.fastq.gz | Fastqsanger.gz | |||
| ERR2219390_1.fastq.gz | Fastqsanger.gz | |||
| ERR2219390_2.fastq.gz | Fastqsanger.gz | |||
| ERR2219400_1.fastq.gz | Fastqsanger.gz |
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Project description:Take-all is a devastating soil-borne disease that affects wheat production. The continuous generation of disease-resistance germplasm is an important aspect of the management of this pathogen. In this study, we characterized the wheat-Psathyrostachys huashania Keng-derived progeny H139 that exhibits significantly improved resistance to wheat take-all disease compared with its susceptible parent 7182. GISH) and mc-FISH analyses revealed that H139 is a stable wheat-P. huashania disomic substitution line lacking wheat chromosome 2D.EST-STS marker and Wheat Axiom 660K Genotyping Array analysis further revealed that H139 was a novel wheat-P. huashania 2Ns/2D substitution line, and that the P. huashania 2Ns chromosome shares high sequence similarity to wheat chromosome 2D. These results indicate that H139, with its enhanced wheat take-all disease resistance and desirable agronomic traits, provides valuable genetic resources for wheat chromosome engineering breeding.
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Project description:<p>Although multi-agent combination chemotherapy is curative in a significant fraction of childhood acute lymphoblastic leukemia (ALL) patients, 20% of cases relapse and most die due to chemo-refractory disease. Here we used whole-exome and whole-genome sequencing to analyze the mutational landscape and pattern of clonal evolution at relapse in pediatric ALL cases. These analyses showed that ALL relapses originate from a common ancestral precursor clone of the diagnosis and relapsed populations and frequently harbor mutations implicated in chemotherapy resistance. RAS-MAPK pathway activating mutations in NRAS, KRAS and PTPN11 were present in 24/55 (44%) cases in our series. Notably, while some cases showed emergence of RAS mutant clones at relapse, in others, RAS mutant clones present at diagnosis were replaced by RAS wild type populations. Mechanistically, functional dissection of mouse and human wild type Kras and mutant Kras (Kras G12D) isogenic leukemia cells demonstrated induction of methotrexate resistance, but also improved response to vincristine, in mutant Kras- expressing lymphoblasts. These results identify chemotherapy driven selection as a central mechanism of leukemia clonal evolution and pave the road for the development of tailored personalized therapies for the treatment of relapsed ALL. </p>
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Project description:Introduction: Pre-harvest Sprouting (PHS) seriously affects wheat quality and yield. However, to date there have been limited reports. It is of great urgency to breed resistance varieties via quantitative trait nucleotides (QTNs) or genes for PHS resistance in white-grained wheat. Methods: 629 Chinese wheat varieties, including 373 local wheat varieties from 70 years ago and 256 improved wheat varieties were phenotyped for spike sprouting (SS) in two environments and genotyped by wheat 660K microarray. These phenotypes were used to associate with 314,548 SNP markers for identifying QTNs for PHS resistance using several multi-locus genome-wide association study (GWAS) methods. Their candidate genes were verified by RNA-seq, and the validated candidate genes were further exploited in wheat breeding. Results: As a result, variation coefficients of 50% and 47% for PHS in 629 wheat varieties, respectively, in 2020-2021 and 2021-2022 indicated large phenotypic variation, in particular, 38 white grain varieties appeared at least medium resistance, such as Baipimai, Fengchan 3, and Jimai 20. In GWAS, 22 significant QTNs, with the sizes of 0.06% ~ 38.11%, for PHS resistance were stably identified by multiple multi-locus methods in two environments, e.g., AX-95124645 (chr3D:571.35Mb), with the sizes of 36.390% and 45.850% in 2020-2021 and 2021-2022, respectively, was detected by several multi-locus methods in two environments. As compared with previous studies, the AX-95124645 was used to develop Kompetitive Allele-Specific PCR marker QSS.TAF9-3D (chr3D:569.17Mb~573.55Mb) for the first time, especially, it is available in white-grain wheat varieties. Around this locus, nine genes were significantly differentially expressed, and two of them (TraesCS3D01G466100 and TraesCS3D01G468500) were found by GO annotation to be related to PHS resistance and determined as candidate genes. Discussion: The QTN and two new candidate genes related to PHS resistance were identified in this study. The QTN can be used to effectively identify the PHS resistance materials, especially, all the white-grained varieties with QSS.TAF9-3D-TT haplotype are resistant to spike sprouting. Thus, this study provides candidate genes, materials, and methodological basis for breeding wheat PHS resistance in the future.
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Project description:Hybrid chlorosis, one of the hybrid incompatibilities, has frequently been reported in inter- and intraspecific crosses of allopolyploid wheat. In our previous study, hybrid chlorosis was observed in the wheat triploids between a tetraploid wheat cultivar Langdon and four Ae. tauschii accessions and in their derived synthetic hexaploids. However, the molecular mechanisms underlying hybrid chlorosis are not well understood. Here, we performed cytological and comparative gene expression analyses in leaves to characterize the abnormal growth in wheat synthetics showing mild and severe chlorosis symptom. In addition, disease resistance was comparatively assessed. A number of carbohydrate metabolism- and defense-related genes were markedly up-regulated in the hybrid chlorosis lines, and abnormal chloroplasts were formed in the mesophyll cells before the leaves turned to be yellowish. The mild chlorosis plants showed increased resistance to a wheat blast fungus, although little significant differences of agricultural traits were found between the wild-type and mild chlorosis-showing plants. These observations suggest that the senescence processes might be accelerated in the hybrid chlorosis lines of wheat synthetics. Moreover, the negative effects on biomass can be minimized and the substantial fitness may be obtained under pathogen-polluted conditions in the mild chlorosis-showing wheat synthetics.
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Project description:To reveal the differences between soft wheat and hard wheat proteomes, three hard wheat varieties (MY26, GX3, and ZM1) with different puroindoline-encoding genes were compared with a soft wheat variety (CM605) with the wild-type puroindoline genotype. Specifically, proteomic methods (TMT) were used to screen for differentially abundant proteins (DAPs).
2023-10-24 | PXD041989 | Pride
Project description:Hybrid chlorosis, one of the hybrid incompatibilities, has frequently been reported in inter- and intraspecific crosses of allopolyploid wheat. In our previous study, hybrid chlorosis was observed in the wheat triploids between a tetraploid wheat cultivar Langdon and four Ae. tauschii accessions and in their derived synthetic hexaploids. However, the molecular mechanisms underlying hybrid chlorosis are not well understood. Here, we performed cytological and comparative gene expression analyses in leaves to characterize the abnormal growth in wheat synthetics showing mild and severe chlorosis symptom. In addition, disease resistance was comparatively assessed. A number of carbohydrate metabolism- and defense-related genes were markedly up-regulated in the hybrid chlorosis lines, and abnormal chloroplasts were formed in the mesophyll cells before the leaves turned to be yellowish. The mild chlorosis plants showed increased resistance to a wheat blast fungus, although little significant differences of agricultural traits were found between the wild-type and mild chlorosis-showing plants. These observations suggest that the senescence processes might be accelerated in the hybrid chlorosis lines of wheat synthetics. Moreover, the negative effects on biomass can be minimized and the substantial fitness may be obtained under pathogen-polluted conditions in the mild chlorosis-showing wheat synthetics. Expression patterns were compared between a wild-type synthetic wheat line (as a reference) and two hybrid chlorosis-showing hybrid chlorosis lines. Total RNA samples were isolated from the 3-week-old leaf tissues. Two independent experiments were conducted in each line.
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Project description:These data are from two wild-type RPE1 clones (WT11, WT20), a RAB18-null clone, a TBC1D20-null clone, a RAB3GAP1-null clone and a RAB3GAP2-null clone, each analysed in triplicate.
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