DataSheet_1_Mapping open chromatin by ATAC-seq in bread wheat.docx

Gene transcription is largely regulated by cis-regulatory elements. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is an emerging technology that can accurately map cis-regulatory elements in animals and plants. However, the presence of cell walls and chloroplasts in plants hinders the extraction of high-quality nuclei, thereby affects the quality of ATAC-seq data. Meanwhile, it is tricky to perform ATAC-seq with different tissue types, especially for those with limited size and amount. Moreover, with rapid growth of ATAC-seq datasets from plants, powerful and easy-to-use data analysis pipelines for ATAC-seq, especially for wheat is lacking. Here, we provided an all-in-one solution for mapping open chromatin in wheat including both experimental and data analysis procedure. We efficiently obtained nuclei with less cell debris from various wheat tissues. High-quality ATAC-seq data from young spike and ovary, which are hard to harvest were generated. We determined that the saturation sequencing depth of wheat ATAC-seq is about 16 Gb. Particularly, we developed a powerful and easy-to-use online pipeline to analyze the wheat ATAC-seq data and this pipeline can be easily extended to other plant species. The method developed here will facilitate plant regulatory genome study not only for wheat but also for other plant species.</p

Hydrothermal Synthesis of CaIn₂S₄‑Reduced Graphene Oxide Nanocomposites with Increased Photocatalytic Performance

A series of CaIn₂S₄-reduced graphene oxide (RGO) nanocomposites with different RGO contents were fabricated using a facile hydrothermal approach. During the hydrothermal process, the reduction of graphene oxide to RGO, in situ deposition of synthesized CaIn₂S₄ nanoparticles on RGO nanosheets and formation of chemical-bonding CaIn₂S₄-RGO nanocomposites were performed simultaneously. Under visible light irradiation, the as-prepared CaIn₂S₄-RGO nanocomposites showed enhanced photocatalytic performance for rhodamine B degradation and phenol oxidation. The sample with 5 wt % RGO hybridized CaIn₂S₄ exhibited the highest photocatalytic activity. The enhancement of photocatalytic performance may be related to the increased adsorption/reaction sites, positive shift of the valence band potential, and high separation efficiency of photogenerated charge carriers due to the electronic interaction between CaIn₂S₄ and RGO. We hope that this work can not only provide an in-depth study on the photocatalytic mechanism of RGO-enhanced activity, but also provide some insights for fabricating efficient and stable RGO-based photocatalysts in the potential applications of purifying polluted water resources

Results of GLM association of SNP traits.

<p>Result of structure-based association mapping (<i>P</i><0.05) of haplotypes H1–H5, by GLM analysis of TASSEL. <i>R²</i>, the total variation explained by the SNP.</p>a<p>7 SNPs in LD:S_194, S_278, S_968, S_1804, S_1808, S_3207, and S_3635. They were in complete linkage disequilibrium and gathered in haplotype H4.</p>b<p>10 SNP in LD:S_30, S_58, S_207, S_392, S_857, S_876, S_2652, S_3252, S_3346, and S_3815. They were in complete linkage disequilibrium and they were the introgressed SNPs transferred from <i>japonica</i> to <i>indica</i>.</p

Comparison of means between different haplotypes in the three traits.

<p>Hap, haplotype; SD, standard deviation; N, number of cultivars tested. Within an environment, means followed by different letters are significantly different at <i>P</i> = 0.05.</p

Haplotype analysis of the <i>Ghd7</i> gene region in the 104 cultivars.

<p>(a) The <i>Ghd7</i> containing two exons (indicated in gray) and the entire length of the 3923-bp genome is shown in graphics on the top. The position of every SNP is shown in the first row (SNP frequency>5%). Twelve haplotypes (H0–H11) were detected in the 104 cultivars of <i>O. sativa</i>, which can be divided into an <i>indica</i> group (<i>ind-G</i>) and a <i>japonica</i> group (<i>jap-G</i>) based on the population structure analysis. The number of cultivars (cvs) in every subpopulation is shown in the right columns: Q1 indicates the <i>indica</i> population and Q2 and Q3 indicate the <i>japonica</i> population. Yellow represents polymorphisms characteristic of the <i>indica</i> haplogroup, light blue shows the <i>japonica</i> haplogroup polymorphisms. Red indicates the new mutation. WR1–3 indicates the three wild rice varieties of <i>O.rufipogon.</i> (b) Phylogenetic tree of the twelve haplotypes (H0–H11).</p

Comparison of means of three traits among the major 4 protein types.

<p>The first line indicates the main 4 protein types. SD, standard deviation; N, number of cultivars tested. Means followed by different letters each row are significantly different at <i>P</i> = 0.05 within one environment. <i>F</i> ratio and probability based on one-way analysis of variance.</p

Comparison of expression levels in H1–H5.

<p>Hap, haplotype; SD, standard deviation; N, number of cultivars tested; characters not connected by the same letter are significantly different at <i>P</i> = 0.05.</p

Protein diversity of Ghd7.

<p>The two exons (indicated in black rectangle) and the 5′ and 3′ UTRs (indicated in white rectangle) of Ghd7 are shown in graphics on the top. The first row indicates the position of the SNPs, the last row reveals the amino acid change. Gray indicates synonymous SNP. Eight types of Ghd7 protein were identified. Ghd7-0 was a permutation type. Hap indicates the haplotypes that share the same protein type. The numbers in the right column are the numbers of cultivars (cvs) represented in every protein type.</p

Summary of DNA polymorphic sites of <i>Ghd7</i> genome.

<p>π, average number of nucleotide differences per site between two sequences; θ, Watterson estimator; Tajima’s <i>D</i>, test for neutral selection.</p>*<p>Significant at <i>P</i><0.05;</p>**<p>significant at <i>P</i><0.01.</p

CaIn₂O₄/Fe-TiO₂ Composite Photocatalysts with Enhanced Visible Light Performance for Hydrogen Production

A series of CaIn₂O₄/Fe-TiO₂ composite photocatalysts with tunable Fe-TiO₂ contents were prepared in which Fe-TiO₂ nanoparticles were uniformly deposited onto the surface of CaIn₂O₄ nanorods. The photocatalytic activities of Pt-loaded CaIn₂O₄/Fe-TiO₂ composites were evaluated for H₂ evolution from aqueous KI solution under visible light irradiation. It was found that the composites showed higher H₂ evolution rates in comparison with pure CaIn₂O₄ or Fe-TiO₂, which could be attributed to the increased surface area and enhanced visible light absorption. A high H₂ evolution rate of 280 μmol h^–1 g^–1 was achieved when the mass ratio of Fe-TiO₂ to CaIn₂O₄ was 0.5, which was 12.3 and 2.2 times higher than that of pure CaIn₂O₄ and Fe-TiO₂, respectively. Furthermore, the interfaces between CaIn₂O₄ nanorods and Fe-TiO₂ nanoparticles facilitated efficient charge separation that also led to the improved photocatalytic activity. This study may provide some inspiration for the fabrication of visible-light-driven photocatalysts with efficient and stable performance