IC4R012-GWAS-2016-26552884 - Revision history

Guangyi: /* Research Findings */

2016-07-19T04:55:39Z

‎Research Findings

Guangyi: /* The Background of This Project */

2016-07-19T04:50:33Z

‎The Background of This Project

Guangyi: /* Research Findings */

2016-07-19T04:49:44Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T04:48:41Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T04:47:00Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T04:45:28Z

‎Research Findings

Guangyi: /* The Background of This Project */

2016-07-19T04:38:43Z

‎The Background of This Project

Guangyi: /* Research Findings */

2016-07-19T04:34:13Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T04:29:58Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-19T04:29:06Z

‎Research Findings

@@ Line 24: / Line 24: @@
 *There was a significant difference (P < 0.001) in gall number between rice subpopulations that explained 21% of the variation in relative gall number (Fig. 3). The temperate japonica had the highest number of galls, followed by tropical japonica, aromatic, indica, and aus. A Tukey’s test indicated that the number of galls in the temperate japonicas was significantly higher than in the other subpopulations.
 <br>
-[[File:IC4R012-GWAS-2016-26552884.png |center |thumb |10000px |''''''Fig. 3. Box plot of relative gall numbers in the different subgroups of rice.Temperate japonicas were significantly higher.'''''']]
+[[File:IC4R012-GWAS-2016-26552884-f3.png |center |thumb |10000px |''''''Fig. 3. Box plot of relative gall numbers in the different subgroups of rice.Temperate japonicas were significantly higher.'''''']]
 <br>
 *The number of galls observed in the 10 selected accessions of the RDP1 5 weeks after inoculation was highly significantly different between accessions (P < 0.001, R2 = 79%) and correlated very strongly (r = 0.970, P < 0.001) with the nematode gall numbers in the initial 2-week nematode screening of 332 diverse cultivars (Fig. 4).
 <br>
-[[File:IC4R012-GWAS-2016-26552884.png |center |thumb |10000px |''''''Fig. 4. Plot of mean and standard error of gall numbers in 10 RDP1 accessions inoculated for 5 weeks in large pots versus the relative gall numbers obtained after 2 weeks when RDP1 was screened. Note no galls were detected in Khao Pahk Maw and LD 24. Correlation r = 0.967.'''''']]
+[[File:IC4R012-GWAS-2016-26552884-f4.png |center |thumb |10000px |''''''Fig. 4. Plot of mean and standard error of gall numbers in 10 RDP1 accessions inoculated for 5 weeks in large pots versus the relative gall numbers obtained after 2 weeks when RDP1 was screened. Note no galls were detected in Khao Pahk Maw and LD 24. Correlation r = 0.967.'''''']]
 <br>

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 ==The Background of This Project==
 *The root-knot nematode Meloidogyne graminicola is one of the most serious nematode pests worldwide and represents a major constraint on rice production. While variation in the susceptibility of Asian rice (Oryza sativa) exists,so far no strong and reliable resistance has been reported. Quantitative trait loci for partial resistance have been reported but no underlying genes have been tagged or cloned. Here, 332 accessions of the Rice Diversity Panel 1 were assessed for gall formation, revealing large variation across all subpopulations of rice and higher susceptibility in temperate japonica accessions.
 ==Plant Culture & Treatment==

@@ Line 27: / Line 27: @@
 *The number of galls observed in the 10 selected accessions of the RDP1 5 weeks after inoculation was highly significantly different between accessions (P < 0.001, R2 = 79%) and correlated very strongly (r = 0.970, P < 0.001) with the nematode gall numbers in the initial 2-week nematode screening of 332 diverse cultivars (Fig. 4).
 <br>
-[[File:IC4R012-GWAS-2016-26552884.png |center |thumb |10000px |'''''']]
+[[File:IC4R012-GWAS-2016-26552884.png |center |thumb |10000px |''''''Fig. 4. Plot of mean and standard error of gall numbers in 10 RDP1 accessions inoculated for 5 weeks in large pots versus the relative gall numbers obtained after 2 weeks when RDP1 was screened. Note no galls were detected in Khao Pahk Maw and LD 24. Correlation r = 0.967.'''''']]
 <br>

@@ Line 23: / Line 23: @@
 *There was a significant difference (P < 0.001) in gall number between rice subpopulations that explained 21% of the variation in relative gall number (Fig. 3). The temperate japonica had the highest number of galls, followed by tropical japonica, aromatic, indica, and aus. A Tukey’s test indicated that the number of galls in the temperate japonicas was significantly higher than in the other subpopulations.
 <br>
-[[File:IC4R012-GWAS-2016-26552884.png |center |thumb |10000px |'''''']]
+[[File:IC4R012-GWAS-2016-26552884.png |center |thumb |10000px |''''''Fig. 3. Box plot of relative gall numbers in the different subgroups of rice.Temperate japonicas were significantly higher.'''''']]
 <br>
 *The number of galls observed in the 10 selected accessions of the RDP1 5 weeks after inoculation was highly significantly different between accessions (P < 0.001, R2 = 79%) and correlated very strongly (r = 0.970, P < 0.001) with the nematode gall numbers in the initial 2-week nematode screening of 332 diverse cultivars (Fig. 4).

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 *As an example, the results for some accessions of the RDP1 in one run that show low, medium, and high galls numbers are presented in Fig. 2. Within most runs there was highly significant variation due to genotype (significant in 9 out of 10 runs), indicating genetic variation for gall numbers is readily detectable. The result of the repeat run with the 30 randomly selected rice accessions revealed a strong correlation with the initial assessment (r = 0.730, P < 0.001) (data not shown),indicating the method is highly repeatable.
 <br>
-[[File:IC4R012-GWAS-2016-26552884.png |center |thumb |10000px |'''''']]
+[[File:IC4R012-GWAS-2016-26552884-f2.png |center |thumb |10000px |''''''Fig. 2. Plot of example accessions in one run, including reference cultivars Azucena and Bala and 12 RDP1 accessions grouped as four low, four medium, and four high. Bar is standard error.'''''']]
 <br>
 *There was a significant difference (P < 0.001) in gall number between rice subpopulations that explained 21% of the variation in relative gall number (Fig. 3). The temperate japonica had the highest number of galls, followed by tropical japonica, aromatic, indica, and aus. A Tukey’s test indicated that the number of galls in the temperate japonicas was significantly higher than in the other subpopulations.

@@ Line 13: / Line 13: @@
 *Figure 1 shows the frequency distribution of the relative gall numbers, while all values are given in Supplementary Table 1.
 <br>
-[[File:IC4R012-GWAS-2016-26552884.png |center |thumb |10000px |'''''']]
+[[File:IC4R012-GWAS-2016-26552884-f1.png |center |thumb |10000px |''''''Fig. 1. Frequency distribution of gall numbers in 332 RDP1 accessions relative to the check genotypes Azucena and Bala.'''''' ]]
 <br>
-[[File:IC4R012-GWAS-2016-26552884.png |center |thumb |10000px |'''''']]
+[[File:IC4R012-GWAS-2016-26552884-sf1.png |center |thumb |10000px |''''''Supplemrnt Fig.1. qq plots for all data with navie and mixed modle results'''''']]
 <br>
 *As an example, the results for some accessions of the RDP1 in one run that show low, medium, and high galls numbers are presented in Fig. 2. Within most runs there was highly significant variation due to genotype (significant in 9 out of 10 runs), indicating genetic variation for gall numbers is readily detectable. The result of the repeat run with the 30 randomly selected rice accessions revealed a strong correlation with the initial assessment (r = 0.730, P < 0.001) (data not shown),indicating the method is highly repeatable.

@@ Line 20: / Line 20: @@
 *There was a significant difference (P < 0.001) in gall number between rice subpopulations that explained 21% of the variation in relative gall number (Fig. 3). The temperate japonica had the highest number of galls, followed by tropical japonica, aromatic, indica, and aus. A Tukey’s test indicated that the number of galls in the temperate japonicas was significantly higher than in the other subpopulations.
 <br>
 ==Labs working on this Project==