23 research outputs found

    Additional file 33: of OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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    Notes S1. Natural population and linkage mapping (Additional file 2: Figure S2 and Additional file 11). Notes S2. Fine mapping of qGL3-3 (Additional file 10). Notes S3. Ho-LAMap – a potential method for validating association peak. Table S2. Summary of the taxa and source of 506 varieties of Oryza sativa L. Table S3. Environments used to evaluate association and linkage populations. Table S4. The heritability of grain traits in MCC1 Panel. Table S9. Summary of causal allele and type of variation about several grain size genes. Table S10. Grain phenotypes of six different parents. Table S11. Quantitative trait loci mapped in the four populations. Table S12. Simulation reveals the cross number need for several known genes (such as TGW6, GS3) about grain size when using Ho-LAMap. Table S13. OsLG3 polymorphisms associated with grain length in the MCC panel. Table S14. Comparison of polymorphisms between three large grain parents and three small grain parents. Table S16. Primers used for fine mapping and sequencing. Table S17. Primers used for DNA constructs and transcript analysis. (DOCX 73 kb

    Additional file 5: Figure S5. of OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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    Effect of Q structure (indica and japonica) for grain length. (a) Comparison of grain length between big-grain-haplotype and small-grain-haplotype when Q structure exists. (b) Comparison of grain length between big-grain-haplotype and small-grain-haplotype when the phenotype variation from Q structure was removed. Ind, indica; jap, japonica. Data are means ± SEM. Letters indicate a significant difference at P < 0.01 (n = 3) by the Student’s t-test. (PPTX 362 kb

    Additional file 15: Figure S15. of OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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    Identification of the causal SNPs of QTL qGL3-2 using Ho-LAMap. We also used Ho-LAMap to clone OsLG3b from qGL3-2, a new gene for grain length, which encodes a MADS-box transcription factor. The top is Manhattan plot for candidate region association mapping for QTL region of qGL3-2; the middle correspond to Ho index plots for QTL region of qGL3-2. The bottom correspond to candidate gene (OsLG3b), the green dashed lines label the region for significant signal. (PDF 82 kb

    Additional file 6: Figure S6. of OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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    Size of association regions about GS3, TGW6, GW8, and OsLG3. Manhattan plots in candidate region of three known genes and OsLG3 in different models. The red points indicate their SNPs within gene region, respectively. The horizontal full lines indicate the genome-wide significance threshold (0.05/n). (PDF 311 kb

    Additional file 30: Figure S30. of OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap

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    Proposed strategy of gene discovery by Ho-LAMap. The number 1 and 2 in the red cycle indicate two pathways for gene discovery by Ho-LAMap. At the first way, a lot of QTL had been co-localized in many crosses by predecessors. Therefore, we re-sequenced parents of those crosses and isolated gene from the target QTL via Ho-LAMap. For the second way, we obtained the QTL region by GWAS and selected extreme materials to construct several F2 or recombinant inbred line populations according to peak SNP and phenotypes. Then, we could ascertain several crosses that can map the same QTL by linkage mapping and rapidly isolated gene from QTL by Ho-LAMap directly. (PDF 19 kb
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