Project description:A CNV map in pigs could facilitate the identification of chromosomal regions that segregate for important economic and disease phenotypes. The goal of this study was to identify CNV regions (CNVRs) in pigs based on a custom array comparative genome hybridization (aCGH). We carried out a custom-made array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the pig genome analysing animals of diverse pig breeds (White Duroc, Yangxin, Erhualian, Tongcheng, Large White, Pietrain, Landrace and Chinese new pig line DIV ) using a tiling oligonucleotide array with ~720,000 probes designed on the pig genome (Sus scrofa genome version 9.0). In this study, a custom-made tiling oligo-nucleotide 720k array was used with a median probe spacing of 2506 bp for screening 12 pigs with a female Duroc as the reference. WD: White Duroc (♀); YX: Yangxin (♂); EH: Erhualian (♀); TC: Tongcheng (♀); LW: Large White (♀); PT: Pietrain (♂); LD1: Landrace × DIV pig 1 (♂); LD2: Landrace × DIV pig 2 (♀); DIV1: Chinese new pig line DIV 1 (♀); DIV2: Chinese new pig line DIV 2 (♀); L1: Landrace 1 (♂); L2: Landrace 2 (♂).
Project description:Transcription profiling by high throughput sequencing of wheat cultivar Chinese Spring seedlings maintained without phosphate for 10 days
Project description:A comparison of Chinese Spring wheat to infection by the pathogenic fungi Gaeumannomyces tritici and G. hyphopodioides (not known as a wheat pathogen) at three time points
Project description:We performed ChIP-seq for the meiotic strand exchange protein DMC1, which marks an early stage in the meiotic recombination pathway, and the chromosome axis protein ASY1, which promotes interhomolog synapsis and recombination in plants, using tissue collected from immature pre-emergence spikes from wild type bread wheat cultivar Chinese Spring plants. To investigate connections between meiotic recombination and chromatin states in wheat, we also performed ChIP-seq for euchromatic (H3K4me3) and constitutive heterochromatic (H3K9me2 and H3K27me1) marks, and mapped genome-wide nucleosome occupancy via micrococcal nuclease sequencing (MNase-seq) using leaf tissue from Chinese Spring.
Project description:One day cold treatment of wheat (Triticum aestivum L.) lines Chinese Spring, Cheyenne and two 5A chromosome substitution lines of Chinese Spring, Chinese Spring(Cheyenne 5A) and Chinese Spring(Spelta 5A)
Project description:To reveal the origin of the wheat B sub-genome, we performed the whole genome sequencing of sitopsis species. Besides, we also conducted the RNA seq of Ae.speltoides and hexaploid wheat Chinese Spring.
Project description:To reveal the origin of the wheat B sub-genome, we performed the whole genome sequencing of sitopsis species. Besides, we also conducted the RNA seq of Ae.speltoides and hexaploid wheat Chinese Spring.
Project description:One day cold (14 and 19 °C) and hydrogen peroxide (H2O2) treatment of wheat (Triticum aestivum ssp. aestivum L.) variety Chinese Spring and two chromosome 5A substitution lines of Chinese Spring, Chinese Spring(T. ae. ssp. aestivum L. Cheyenne 5A) and Chinese Spring(T. ae. ssp. spelta L. 5A).
Project description:Fusarium graminearum (F.g) is responsible for Fusarium head blight (FHB), which is a destructive disease of wheat that accumulates mycotoxin such as deoxynivalenol (DON) and makes its quality unsuitable for end use. Several FHB resistant varieties development is going on world-wide. However the complete understanding of wheat defence response, pathogen (Fusarium graminearum) disease development mechanism and the gene crosstalk between organisms is still unclear. In our study focused to analyse pathogen (F. graminearum) molecular action in different Fusarium head blight resistance cultivars during the disease development. To understand the Fusarium graminearum pathogen molecular reaction, microarray gene expression analysis was carried out by using Fusarium graminearum (8 x 15k) Agilent arrays at two time points (3 & 7 days after infection) on three wheat genotypes (Japanese landrace cv. Nobeokabouzu-komugi - highly resistant, Chinese cv. Sumai 3 - resistant and Australian cv. Gamenya - susceptible), which spikes infected by Fusarium graminearum ‘H-3’strain. During the disease development the pathogen biomass as well as the expression of Trichothecene biosynthesis involved genes (Tri genes) in three wheat cultivars was determined. In our material no relation between fungus biomass and the disease symptoms were observed, however, it showed relation with fungus virulence factors expression (Tri genes). For the first time, we report the nature of Fusarium graminearum gene expression in the FHB-highly resistant cv. Nobeokabouzu-komugi during the disease development stage and the possible underlying molecular response.
Project description:Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), significantly affects wheat production worldwide. The most economical and effective way to control this disease is breeding resistant cultivars. Wheat cultivar Zhongmai 895 was earlier found to carry YR86 in an 11.6 Mb recombination-suppressed region in chromosome 2AL when crossed with Yangmai 16. To fine-map the YR86 locus, we developed two large F2 populations from crosses Emai 580/Zhongmai 895 and Avocet S/Zhongmai 895. Remarkably, both populations exhibited suppressed recombination in the same 2AL region. Collinearity analysis across Chinese Spring, Aikang 58, and 10+ wheat genomes revealed a 4.1 Mb chromosomal inversion spanning 708.5–712.6 Mb in the Chinese Spring reference genome. Molecular markers were developed in the breakpoint and used to assess a wheat cultivar panel, revealing that Chinese Spring, Zhongmai 895, and Jimai 22 shared a common sequence named InvCS, whereas Aikang 58, Yangmai 16, Emai 580, and Avocet S shared the sequence named InvAK58. The inverted configuration explained the suppressed recombination observed in all three bi-parental populations. Normal recombination was observed in a Jimai 22/Zhongmai 895 F2 population, facilitating mapping of YR86 to a genetic interval of 0.15 cM corresponding to 710.27–712.56 Mb falling within the inverted region. Thirty-three high-confidence genes were annotated in the interval using the Chinese Spring reference genome, with six identified as potential candidates for YR86 based on genome and transcriptome analyses. These results will accelerate map-based cloning of YR86 and its deployment in wheat breeding.