IC4R011-GWAS-2016-26381647 - Revision history

Guangyi: /* Research Findings */

2016-07-19T07:10:09Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T07:07:10Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T07:03:26Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T07:00:20Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T06:48:14Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T06:46:31Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T06:36:44Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T06:33:17Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T06:31:27Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T06:29:50Z

‎Research Findings

@@ Line 36: / Line 36: @@
 *The researchers also checked the subpopulation and geographical distribution of all 412 accessions in relation to the four haplotypes of OsMYB2 (Fig. 4). It was noticed that 97.75% of the accessionsinHap1groupbelongto japonica,while89.03%oftheaccessions in Hap2 belong to indica. Meanwhile, 77.27% of the accessions in Hap3 group belong to aus subgroup, and 67.81% and 23.29% of the accessions in Hap4 group belong to indica and japonica, respectively (Fig. 4b), which may partially explain why Hap4 exhibits an intermediate type in terms of cold sensitivity. The researchers also found that accessions in Hap1 in red distributed widely no matter around the world or China(Fig. 4a,c). These results suggest that the rice accessions in different haplotypes of OsMYB2 had indica–japonica differentiation and differential latitudinal distribution tendency.
 <br>
-[[File:IC4R011-GWAS-2016-26381647-f4a.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f4a.png |center |thumb |10000px ]]
-[[File:IC4R011-GWAS-2016-26381647-f4b.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f4b.png |center |thumb |10000px |''''''Figure 4. Geographic and subpopulation distribution of accessions of the four OsMYB2 haplotypes. Geographic distribution of accessions in the four haplotypes on the world map (a) and map of China (c), the solid circles in different colours (red, light blue, dark blue and green) represent accession numbers of the four haplotypes (Hap1–4, respectively), except for five accessions in Hap1, 16 accessions in Hap2 and 14 accessions in Hap4
 ==Labs working on this Project==

@@ Line 30: / Line 30: @@
 *Further haplotype analysis was focused on the reported gene OsMYB2 because it was reported to participate in abiotic stress (including cold, salt and drought) response at the seedling stage(Yang et al. 2012), and the L33 containing OsMYB2 was overlapped with the known QTL qLVG3 (Han et al. 2006). The SNP data were referred to RiceVarMap including its intragenic region and 2 kb upstream (Zhao et al. 2014a). Four major haplotypes were observed, with low frequency haplotypes (less than five accessions) being omitted (Fig. 3a).The reserchers noticed that two non-synonymous SNPs led to changes in amino acids(one at 11325395 caused a C in Hap1 to a Y in the other three haplotypes, and the other at 11325747 caused a W in Hap1 to an R in the other three haplotypes), which suggests that these SNPs may be associated with the gene function to a certain degree. The researchers further checked the latitude distribution of the haplotypes by a scatter diagram of the latitude of origin of these accessions (Fig. 3b). The accessions in Hap1 were from higher latitude regions compared with the accessions in the other three haplotypes (P<0.05; (Fig. 3c).
 <br>
-[[File:IC4R011-GWAS-2016-26381647-f3a.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f3a.png |center |thumb |10000px ]]
-[[File:IC4R011-GWAS-2016-26381647-f3b.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f3b.png |center |thumb |10000px |''''''Figure 3. Haplotype analysis of OsMYB2. (a) Haplotypes in 412 accessions (haplotypes with less than five accessions were omitted) according to SNP data from RiceVarMap based on MSU6.1 annotation. The region contained coding region and 2 kb upstream of the gene. Letters on the right of the average are ranked by Duncan test at P < 0.05; different letters indicate significant difference. (b) Scatter diagram for the latitudes (ascending
 <br>
 *The researchers also checked the subpopulation and geographical distribution of all 412 accessions in relation to the four haplotypes of OsMYB2 (Fig. 4). It was noticed that 97.75% of the accessionsinHap1groupbelongto japonica,while89.03%oftheaccessions in Hap2 belong to indica. Meanwhile, 77.27% of the accessions in Hap3 group belong to aus subgroup, and 67.81% and 23.29% of the accessions in Hap4 group belong to indica and japonica, respectively (Fig. 4b), which may partially explain why Hap4 exhibits an intermediate type in terms of cold sensitivity. The researchers also found that accessions in Hap1 in red distributed widely no matter around the world or China(Fig. 4a,c). These results suggest that the rice accessions in different haplotypes of OsMYB2 had indica–japonica differentiation and differential latitudinal distribution tendency.

@@ Line 15: / Line 15: @@
 *The results of seven electrolyte leakage indices (ELN,ELC1,ELC2, ELR, ELSN, ELSC1 andELSC2)indicatedthat with the prolonged time duration of stress treatment, large variation was observed for EL and the relevant ratio traits including ELR1, ELR2, ELR3, ELSR1 and ELSR2 (Table 1). The range of ELN and ELSN was not exactly the same, which may be due to the slight differences of seedling growth state inthetwoexperiments.Among thesetraits,thevariationrange of ELC1 is similar to ELN, but the variations of ELC2 and ELR were clearly increased, suggesting slight cell membrane damage at the early stage of natural chilling stress treatment but that the damage became serious and irreversible at the later stage of the stress treatment. The situation was different in the cold shock stress treatment, in which ELSN, ELSC1 and ELSC2 were increased since the onset of the stress treatment (Table 1), indicating that the cell membrane damage was faster and more significant.
 <br>
-[[File:IC4R011-GWAS-2016-26381647-t1.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-t1.png |center |thumb |10000px ]]
 <br>
 *A quantile–quantile plotof all 16 traits isprovided in Supporting Information FigsS3,S4andS5.Manhattan plots for the association analysis of these traits are displayed in Fig. 1.
@@ Line 25: / Line 25: @@
 *For a better view of the comprehensive association results,all of the detected association loci in the whole panel were marked on the 12 chromosomes according to their physical distance on the rice genome (Fig. 2), and the loci for natural chilling stress (57 loci) and cold shock stress (63 loci) are shown in blueand green, respectively.
 <br>
-[[File:IC4R011-GWAS-2016-26381647-f2a.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f2a.png |center |thumb |10000px ]]
-[[File:IC4R011-GWAS-2016-26381647-f2b.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f2b.png |center |thumb |10000px |''''''Figure 2. Distribution of 132 loci on 12 chromosomes according to physical distance. The loci and their associated traits were marked on the right of chromosomes with the relative position of each locus (200 kb) shown by its own front physical position; the overlapping known QTL are shown in grey column on the left, while the markers of QTL are shown on the right. The 57 loci in blue were identified under natural chilling stress condition, the 63 loci in green were identified under cold shock stress condition and the 12 loci in red were detected under both stress conditions.'''''']]
 <br>
 *Further haplotype analysis was focused on the reported gene OsMYB2 because it was reported to participate in abiotic stress (including cold, salt and drought) response at the seedling stage(Yang et al. 2012), and the L33 containing OsMYB2 was overlapped with the known QTL qLVG3 (Han et al. 2006). The SNP data were referred to RiceVarMap including its intragenic region and 2 kb upstream (Zhao et al. 2014a). Four major haplotypes were observed, with low frequency haplotypes (less than five accessions) being omitted (Fig. 3a).The reserchers noticed that two non-synonymous SNPs led to changes in amino acids(one at 11325395 caused a C in Hap1 to a Y in the other three haplotypes, and the other at 11325747 caused a W in Hap1 to an R in the other three haplotypes), which suggests that these SNPs may be associated with the gene function to a certain degree. The researchers further checked the latitude distribution of the haplotypes by a scatter diagram of the latitude of origin of these accessions (Fig. 3b). The accessions in Hap1 were from higher latitude regions compared with the accessions in the other three haplotypes (P<0.05; (Fig. 3c).

@@ Line 19: / Line 19: @@
 *A quantile–quantile plotof all 16 traits isprovided in Supporting Information FigsS3,S4andS5.Manhattan plots for the association analysis of these traits are displayed in Fig. 1.
 <br>
-[[File:IC4R011-GWAS-2016-26381647-f1a.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f1a.png |center |thumb |10000px ]]
-[[File:IC4R011-GWAS-2016-26381647-f1b.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f1b.png |center |thumb |10000px ]]
-[[File:IC4R011-GWAS-2016-26381647-f1c.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f1c.png |center |thumb |10000px |''''''Figure 1. Manhattan plots for six traits: (a) ELR2, (b) ELC2, (c) RLC, (d) ELSR2, (e) ELSC1 and (f) SRC. The negative log10 transformed P-values of genome-wide scan are plotted against the marker position in the genome. Dotted line: P = 1E�06. The positions of five reported genes are indicated with black arrow. Examples of some loci are indicated; L27, L104 and L63 in red were detected by EL-related traits under the two cold stress conditions, while locus L18 and L79 in blue were identified by two traits under natural chilling stress condition. L is short for locus.'''''']]
 <br>
 *For a better view of the comprehensive association results,all of the detected association loci in the whole panel were marked on the 12 chromosomes according to their physical distance on the rice genome (Fig. 2), and the loci for natural chilling stress (57 loci) and cold shock stress (63 loci) are shown in blueand green, respectively.

@@ Line 15: / Line 15: @@
 *The results of seven electrolyte leakage indices (ELN,ELC1,ELC2, ELR, ELSN, ELSC1 andELSC2)indicatedthat with the prolonged time duration of stress treatment, large variation was observed for EL and the relevant ratio traits including ELR1, ELR2, ELR3, ELSR1 and ELSR2 (Table 1). The range of ELN and ELSN was not exactly the same, which may be due to the slight differences of seedling growth state inthetwoexperiments.Among thesetraits,thevariationrange of ELC1 is similar to ELN, but the variations of ELC2 and ELR were clearly increased, suggesting slight cell membrane damage at the early stage of natural chilling stress treatment but that the damage became serious and irreversible at the later stage of the stress treatment. The situation was different in the cold shock stress treatment, in which ELSN, ELSC1 and ELSC2 were increased since the onset of the stress treatment (Table 1), indicating that the cell membrane damage was faster and more significant.
 <br>
-[[File:IC4R011-GWAS-2016-26381647.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-t1.png |center |thumb |10000px |'''''']]
 <br>
-*A quantile–quantile plotof all 16 traits isprovided inSupportingInformationFigsS3,S4andS5.Manhattan plots for the association analysis of these traits are displayed in Fig. 1.
+*A quantile–quantile plotof all 16 traits isprovided in Supporting Information FigsS3,S4andS5.Manhattan plots for the association analysis of these traits are displayed in Fig. 1.
 <br>
-[[File:IC4R011-GWAS-2016-26381647.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f1a.png |center |thumb |10000px |'''''']]
-[[File:IC4R011-GWAS-2016-26381647.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f1b.png |center |thumb |10000px |'''''']]
-[[File:IC4R011-GWAS-2016-26381647.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f1c.png |center |thumb |10000px |'''''']]
 <br>
 *For a better view of the comprehensive association results,all of the detected association loci in the whole panel were marked on the 12 chromosomes according to their physical distance on the rice genome (Fig. 2), and the loci for natural chilling stress (57 loci) and cold shock stress (63 loci) are shown in blueand green, respectively.
 <br>
-[[File:IC4R011-GWAS-2016-26381647.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f2a.png |center |thumb |10000px |'''''']]
-[[File:IC4R011-GWAS-2016-26381647.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f2b.png |center |thumb |10000px |'''''']]
 <br>
 *Further haplotype analysis was focused on the reported gene OsMYB2 because it was reported to participate in abiotic stress (including cold, salt and drought) response at the seedling stage(Yang et al. 2012), and the L33 containing OsMYB2 was overlapped with the known QTL qLVG3 (Han et al. 2006). The SNP data were referred to RiceVarMap including its intragenic region and 2 kb upstream (Zhao et al. 2014a). Four major haplotypes were observed, with low frequency haplotypes (less than five accessions) being omitted (Fig. 3a).The reserchers noticed that two non-synonymous SNPs led to changes in amino acids(one at 11325395 caused a C in Hap1 to a Y in the other three haplotypes, and the other at 11325747 caused a W in Hap1 to an R in the other three haplotypes), which suggests that these SNPs may be associated with the gene function to a certain degree. The researchers further checked the latitude distribution of the haplotypes by a scatter diagram of the latitude of origin of these accessions (Fig. 3b). The accessions in Hap1 were from higher latitude regions compared with the accessions in the other three haplotypes (P<0.05; (Fig. 3c).
 <br>
-[[File:IC4R011-GWAS-2016-26381647.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f3a.png |center |thumb |10000px |'''''']]
-[[File:IC4R011-GWAS-2016-26381647.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f3b.png |center |thumb |10000px |'''''']]
 <br>
 *The researchers also checked the subpopulation and geographical distribution of all 412 accessions in relation to the four haplotypes of OsMYB2 (Fig. 4). It was noticed that 97.75% of the accessionsinHap1groupbelongto japonica,while89.03%oftheaccessions in Hap2 belong to indica. Meanwhile, 77.27% of the accessions in Hap3 group belong to aus subgroup, and 67.81% and 23.29% of the accessions in Hap4 group belong to indica and japonica, respectively (Fig. 4b), which may partially explain why Hap4 exhibits an intermediate type in terms of cold sensitivity. The researchers also found that accessions in Hap1 in red distributed widely no matter around the world or China(Fig. 4a,c). These results suggest that the rice accessions in different haplotypes of OsMYB2 had indica–japonica differentiation and differential latitudinal distribution tendency.
 <br>
-[[File:IC4R011-GWAS-2016-26381647.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f4a.png |center |thumb |10000px |'''''']]
-[[File:IC4R011-GWAS-2016-26381647.png |center |thumb |10000px |'''''']]
+[[File:IC4R011-GWAS-2016-26381647-f4b.png |center |thumb |10000px |'''''']]
 ==Labs working on this Project==