IC4R005-Microarray-2012-22419825 - Revision history

Xysj1988: /* The Background of This Project */

2016-06-22T12:45:00Z

‎The Background of This Project

Xysj1988: /* The Background of This Project */

2016-06-22T12:44:53Z

‎The Background of This Project

Xysj1988: /* Plant Materials & Treatment */

2016-06-22T12:44:39Z

‎Plant Materials & Treatment

Xysj1988: /* Plant Materials & Treatment */

2016-06-22T12:43:23Z

‎Plant Materials & Treatment

Xysj1988: /* Plant Materials & Treatment */

2016-06-22T12:42:52Z

‎Plant Materials & Treatment

Xysj1988 at 12:41, 22 June 2016

2016-06-22T12:41:40Z

Xysj1988: /* The Background of This Project */

2016-06-22T12:39:39Z

‎The Background of This Project

Xysj1988: /* The Background of This Project */

2016-06-22T12:39:32Z

‎The Background of This Project

Xysj1988: /* The Background of This Project */

2016-06-22T12:39:23Z

‎The Background of This Project

Xysj1988: /* The Background of This Project */

2016-06-22T12:39:07Z

‎The Background of This Project

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 ==The Background of This Project==
 * Nowadays, and especially in the tropics, the rice cropping system is shifting from transplanting to direct sowing because it is less labor intensive (Erguiza et al. 1990). For the establishment of such a direct sowing system, strong seedling vigor is one of the most important agronomic traits. The level of seedling vigor is determined by many morphological and physiological traits, among which the germination rate and early seedling growth are the major targets in a breeding program (Williams and Peterson 1973, Sasahara et al. 1986). Moreover, several studies have suggested that phytohormones, such as gibberellin and auxin, are important for their control (Oikawa et al. 2004, Chhun et al. 2007, Lo et al. 2008).<br><br>
-  [[File:IC4R005-Microarray-2012-22419825-1.png|center|thumb|870px|'''Figure 1. Phenotype of Koshihikari, Habataki, SL qEPD1 and SL qEPD2 .''']]<br><br>
+  [[File:IC4R005-Microarray-2012-22419825-1.png|center|thumb|870px|'''Figure 1. Phenotype of Koshihikari, Habataki, SL qEPD1 and SL qEPD2 .''']]<br>
 * Microarray-based transcriptome profiling studies have been primarily used to address gene regulations related to morphological and physiological traits of animals and　plants. However, results from these studies tend to identify a large number of differentially expressed genes due to　the complex interactions between various signaling pathways.　Previously, a report　combining expression profiling using　microarrays with genetic mapping significantly contributed to　the isolation of genetic factors in animal research (Aitman　et al. 1999). However, the identification of QTL genes　using this approach has never been reported in plants.
 * '''This study is the first to use this new approach for the isolation of QTL genes in rice; we conducted combined QTL mapping and microarray profiling analyses to identify QTL genes for seedling vigor at the initial growth stage. Our QTL analysis identified two QTLs, early-stage plant develop- ment1/2 (qEPD1 and qEPD2) for increasing plant height and/ or leaf sheath length at the initial growth stage. By combining QTL mapping and microarray profiling, we predicted that qEPD1 or qEPD2 correspond to gibberellin 20 oxidase-1 or -2 genes (OsGA20ox1, 2), respectively, and confirmed this prediction by complementation analysis. Our study demonstrated that the integration of QTL mapping and expression profiling could be a powerful method to narrow down the number of candidate genes for QTL(s) of interest'''.

@@ Line 4: / Line 4: @@
 ==The Background of This Project==
 * Nowadays, and especially in the tropics, the rice cropping system is shifting from transplanting to direct sowing because it is less labor intensive (Erguiza et al. 1990). For the establishment of such a direct sowing system, strong seedling vigor is one of the most important agronomic traits. The level of seedling vigor is determined by many morphological and physiological traits, among which the germination rate and early seedling growth are the major targets in a breeding program (Williams and Peterson 1973, Sasahara et al. 1986). Moreover, several studies have suggested that phytohormones, such as gibberellin and auxin, are important for their control (Oikawa et al. 2004, Chhun et al. 2007, Lo et al. 2008).<br><br>
-  [[File:IC4R005-Microarray-2012-22419825-1.png|center|thumb|870px|'''Figure 1. Phenotype of Koshihikari, Habataki, SL qEPD1 and SL qEPD2 .''']]
+  [[File:IC4R005-Microarray-2012-22419825-1.png|center|thumb|870px|'''Figure 1. Phenotype of Koshihikari, Habataki, SL qEPD1 and SL qEPD2 .''']]<br><br>
 * Microarray-based transcriptome profiling studies have been primarily used to address gene regulations related to morphological and physiological traits of animals and　plants. However, results from these studies tend to identify a large number of differentially expressed genes due to　the complex interactions between various signaling pathways.　Previously, a report　combining expression profiling using　microarrays with genetic mapping significantly contributed to　the isolation of genetic factors in animal research (Aitman　et al. 1999). However, the identification of QTL genes　using this approach has never been reported in plants.
 * '''This study is the first to use this new approach for the isolation of QTL genes in rice; we conducted combined QTL mapping and microarray profiling analyses to identify QTL genes for seedling vigor at the initial growth stage. Our QTL analysis identified two QTLs, early-stage plant develop- ment1/2 (qEPD1 and qEPD2) for increasing plant height and/ or leaf sheath length at the initial growth stage. By combining QTL mapping and microarray profiling, we predicted that qEPD1 or qEPD2 correspond to gibberellin 20 oxidase-1 or -2 genes (OsGA20ox1, 2), respectively, and confirmed this prediction by complementation analysis. Our study demonstrated that the integration of QTL mapping and expression profiling could be a powerful method to narrow down the number of candidate genes for QTL(s) of interest'''.

@@ Line 10: / Line 10: @@
 == Plant Materials & Treatment==
 * The researchers used a population of 82 BILs (BC 1 F 12 ) derived from a cross between Koshihikari (japonica) and Habataki (indica) to identify QTLs for seedling traits at the initial growth stage and CL at the heading stage. Seeds of all the lines were immersed in water for 2 d and then sown into the cell plug tray (cell count,　14 × 32; tray size, 540 × 280 mm; depth of cell, 30 mm). These　lines were first grown under greenhouse conditions (15 h of　daylight, 25 × C) until 30 d after the germination to evaluate　seedling traits; then, they were transplanted to the paddy　field to measure CL at the heading stage. The phenotypic evaluation in BILs was conducted in three or four replicates. SLs were　selected from the BC4F2　generation.
   [[File:IC4R005-Microarray-2012-22419825-2.png|center|thumb|870px|'''Figure 2. QTL analyses for plant height (PH) and leaf sheath length (LSL) at 30 d after germination, and culm length (CL) at the heading stage. (A–C) Frequency distributions of PH (A), LSL (B) and CL (C) in 82 BILs of Koshihikari and Habataki. 'Koshihikari' and 'Habataki' indicate the mean scores obtained from two parent cultivars (three biological duplicates).''']]
+<br>
 * We used the Habataki (indica) and Koshihikari (japonica) cultivars as the respective low and high seedling growth cultivars at the initial growth stage (Fig. 1A). After 30 d of germination, the average plant height of Koshihikari was 13.81 cm, whereas that of Habataki was 12.35 cm (Fig. 1A, B). Since the plant height (PH) of rice seedling depends on the total of leaf sheath length (LSL) and leaf blade length (LBL), we measured the LBL and LSL (Fig. 1C, D). The average LSL of Koshihikari and Habataki was 6.91 and 4.88 cm, respectively (Fig. 1C), but there was no significant difference in the LBL (Fig. 1D). These results demonstrate that the initial growth vigor of Koshihikari is mainly due to its longer leaf sheath.
   [[File:IC4R005-Microarray-2012-22419825-3.png|right|thumb|527px|'''Figure 3. (D) Location of three QTLs for PH, LSL and CL on the linkage map. The names of the DNA markers are represented on the right of the corresponding chromosome. The Koshihikari allele of all identified QTLs promotes the values of these traits. S, short arm; L, long arm.''']]
+<br>
 * To identify genes for increasing PH and LSL at the initial growth stage, we conducted QTL analysis by using 82 backcross inbred lines (BILs) derived from these two parents. The PH of 82 BILs varied from 9.73 to 25.48 cm, whereas the LSL varied from 4.08 to 10.88 cm at 30 d after germination (Fig. 2A, B). The frequency of PH and LSL showed an almost normal distribution with a transgressive segregation (Fig. 2A, B). We also conducted QTL analysis of the total culm length (CL) at the heading stage, because we were interested in the difference in PH between the initial growth and the heading stages. CL also showed a continuous frequency distribution with a transgressive segregation (Fig. 2C).

@@ Line 13: / Line 13: @@
 * We used the Habataki (indica) and Koshihikari (japonica) cultivars as the respective low and high seedling growth cultivars at the initial growth stage (Fig. 1A). After 30 d of germination, the average plant height of Koshihikari was 13.81 cm, whereas that of Habataki was 12.35 cm (Fig. 1A, B). Since the plant height (PH) of rice seedling depends on the total of leaf sheath length (LSL) and leaf blade length (LBL), we measured the LBL and LSL (Fig. 1C, D). The average LSL of Koshihikari and Habataki was 6.91 and 4.88 cm, respectively (Fig. 1C), but there was no significant difference in the LBL (Fig. 1D). These results demonstrate that the initial growth vigor of Koshihikari is mainly due to its longer leaf sheath.
-  [[File:IC4R005-Microarray-2012-22419825-3.png|right|thumb|870px|'''Figure 3. Location of three QTLs for PH, LSL and CL on the linkage map. The names of the DNA markers are represented on the right of the corresponding chromosome. The Koshihikari allele of all identified QTLs promotes the values of these traits. S, short arm; L, long arm.''']]
+  [[File:IC4R005-Microarray-2012-22419825-3.png|right|thumb|527px|'''Figure 3. (D) Location of three QTLs for PH, LSL and CL on the linkage map. The names of the DNA markers are represented on the right of the corresponding chromosome. The Koshihikari allele of all identified QTLs promotes the values of these traits. S, short arm; L, long arm.''']]
 * To identify genes for increasing PH and LSL at the initial growth stage, we conducted QTL analysis by using 82 backcross inbred lines (BILs) derived from these two parents. The PH of 82 BILs varied from 9.73 to 25.48 cm, whereas the LSL varied from 4.08 to 10.88 cm at 30 d after germination (Fig. 2A, B). The frequency of PH and LSL showed an almost normal distribution with a transgressive segregation (Fig. 2A, B). We also conducted QTL analysis of the total culm length (CL) at the heading stage, because we were interested in the difference in PH between the initial growth and the heading stages. CL also showed a continuous frequency distribution with a transgressive segregation (Fig. 2C).

← Older revision		Revision as of 12:42, 22 June 2016
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	* We used the Habataki (indica) and Koshihikari (japonica) cultivars as the respective low and high seedling growth cultivars at the initial growth stage (Fig. 1A). After 30 d of germination, the average plant height of Koshihikari was 13.81 cm, whereas that of Habataki was 12.35 cm (Fig. 1A, B). Since the plant height (PH) of rice seedling depends on the total of leaf sheath length (LSL) and leaf blade length (LBL), we measured the LBL and LSL (Fig. 1C, D). The average LSL of Koshihikari and Habataki was 6.91 and 4.88 cm, respectively (Fig. 1C), but there was no significant difference in the LBL (Fig. 1D). These results demonstrate that the initial growth vigor of Koshihikari is mainly due to its longer leaf sheath.		* We used the Habataki (indica) and Koshihikari (japonica) cultivars as the respective low and high seedling growth cultivars at the initial growth stage (Fig. 1A). After 30 d of germination, the average plant height of Koshihikari was 13.81 cm, whereas that of Habataki was 12.35 cm (Fig. 1A, B). Since the plant height (PH) of rice seedling depends on the total of leaf sheath length (LSL) and leaf blade length (LBL), we measured the LBL and LSL (Fig. 1C, D). The average LSL of Koshihikari and Habataki was 6.91 and 4.88 cm, respectively (Fig. 1C), but there was no significant difference in the LBL (Fig. 1D). These results demonstrate that the initial growth vigor of Koshihikari is mainly due to its longer leaf sheath.
		+	[[File:IC4R005-Microarray-2012-22419825-3.png\|right\|thumb\|870px\|'''Figure 3. Location of three QTLs for PH, LSL and CL on the linkage map. The names of the DNA markers are represented on the right of the corresponding chromosome. The Koshihikari allele of all identified QTLs promotes the values of these traits. S, short arm; L, long arm.''']]
		+
	* To identify genes for increasing PH and LSL at the initial growth stage, we conducted QTL analysis by using 82 backcross inbred lines (BILs) derived from these two parents. The PH of 82 BILs varied from 9.73 to 25.48 cm, whereas the LSL varied from 4.08 to 10.88 cm at 30 d after germination (Fig. 2A, B). The frequency of PH and LSL showed an almost normal distribution with a transgressive segregation (Fig. 2A, B). We also conducted QTL analysis of the total culm length (CL) at the heading stage, because we were interested in the difference in PH between the initial growth and the heading stages. CL also showed a continuous frequency distribution with a transgressive segregation (Fig. 2C).		* To identify genes for increasing PH and LSL at the initial growth stage, we conducted QTL analysis by using 82 backcross inbred lines (BILs) derived from these two parents. The PH of 82 BILs varied from 9.73 to 25.48 cm, whereas the LSL varied from 4.08 to 10.88 cm at 30 d after germination (Fig. 2A, B). The frequency of PH and LSL showed an almost normal distribution with a transgressive segregation (Fig. 2A, B). We also conducted QTL analysis of the total culm length (CL) at the heading stage, because we were interested in the difference in PH between the initial growth and the heading stages. CL also showed a continuous frequency distribution with a transgressive segregation (Fig. 2C).