Os03g0597200 - Revision history

Xysj2017: /* Phenotypic analysis */

2017-02-13T14:37:24Z

‎Phenotypic analysis

Xysj2017: /* Phenotypic analysis */

2017-02-13T14:37:13Z

‎Phenotypic analysis

Xysj2017 at 14:36, 13 February 2017

2017-02-13T14:36:01Z

Xysj2017: /* References */

2017-02-13T03:16:04Z

‎References

Xysj2017 at 02:55, 13 February 2017

2017-02-13T02:55:36Z

192.168.72.52: /* Structured Information */

2015-06-12T05:55:36Z

‎Structured Information

Gylu: /* Annotated Information */

2014-06-08T14:31:30Z

‎Annotated Information

Yilutongxing: /* Expression */

2014-06-07T09:07:21Z

‎Expression

Sancunriguang: /* Expression */

2014-06-07T03:47:05Z

‎Expression

Sancunriguang: /* Expression */

2014-06-04T04:21:27Z

‎Expression

@@ Line 10: / Line 10: @@
 ===Phenotypic analysis===
 <br>
 [[File:Os03g0597200-1.png|center|thumb|727px|'''Figure 1.''' ''Phenotypic analysis of the ysa mutant plants. A to C, Phenotypes of Pei’ai64S (left) and ysa mutant (right) seedlings at 1 (A), 2 (B), and 3 (C) weeks after sowing.<ref name="ref1" />.'']]

@@ Line 10: / Line 10: @@
 ===Phenotypic analysis===
 * The researchers showed that the '''''YSA''''' mutation has no apparent negative effects on several important agronomic traits, such as fertility, stigma extrusion rate, selfed seed-setting rate, hybrid seed-setting rate, and yield heterosis under normal growth conditions.
-[[File:Os03g0597200-1.png|center|thumb|800px|'''Figure 1.''' ''Phenotypic analysis of the ysa mutant plants. A to C, Phenotypes of Pei’ai64S (left) and ysa mutant (right) seedlings at 1 (A), 2 (B), and 3 (C) weeks after sowing.<ref name="ref1" />.'']]
+[[File:Os03g0597200-1.png|center|thumb|727px|'''Figure 1.''' ''Phenotypic analysis of the ysa mutant plants. A to C, Phenotypes of Pei’ai64S (left) and ysa mutant (right) seedlings at 1 (A), 2 (B), and 3 (C) weeks after sowing.<ref name="ref1" />.'']]
 ==Labs working on this gene==

@@ Line 11: / Line 11: @@
 ===Phenotypic analysis===
 * The researchers showed that the '''''YSA''''' mutation has no apparent negative effects on several important agronomic traits, such as fertility, stigma extrusion rate, selfed seed-setting rate, hybrid seed-setting rate, and yield heterosis under normal growth conditions.
+[[File:Os03g0597200-1.png|center|thumb|800px|'''Figure 1.''' ''Phenotypic analysis of the ysa mutant plants. A to C, Phenotypes of Pei’ai64S (left) and ysa mutant (right) seedlings at 1 (A), 2 (B), and 3 (C) weeks after sowing.<ref name="ref1" />.'']]
 ==Labs working on this gene==

@@ Line 20: / Line 20: @@
 ==References==
+<references>
-[1] Bentolila S, Alfonso AA, Hanson MR (2002) A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. Proc Natl Acad Sci USA 99: 10887–10892
+* <ref name="ref1">
+Su, Ning, et al. "Disruption of a rice pentatricopeptide repeat protein causes a seedling-specific albino phenotype and its utilization to enhance seed purity in hybrid rice production." Plant physiology 159.1 (2012): 227-238.
-[2] Brown GG, Formanová N, Jin H, Wargachuk R, Dendy C, Patil P, Laforest M, Zhang J, Cheung WY, Landry BS (2003) The radish Rfo restorer gene of Ogura cytoplasmic male sterility encodes a protein with multiple pentatricopeptide repeats. Plant J 35: 262–272
+</ref>
+</references>
 ==Structured Information==

@@ Line 1: / Line 1: @@
-Please input one-sentence summary here.
+The rice '''''Os03g0597200''''' was reported as '''''YSA''''' in 2012 <ref name="ref1" /> by researchers from China.
 ==Annotated Information==
-The pentatricopeptide repeat (PPR) gene family represents one of the largest gene families in higher plants. Accumulating data suggest that PPR proteins play a central and broad role in modulating the expression of organellar genes in plants. Here we report a rice mutant named ysa (young seedling albino) derived from the rice thermo/photoperiod sensitive genic male sterile (T/PGMS) line Pei'ai64S, which is a leading male-sterile line for commercial two-line hybrid rice production. The ysa mutant develops albino leaves before the three-leaf stage, but the mutant gradually turns green and recovers to normal green at the six-leaf stage. Further investigation showed that the change in leaf color in ysa mutant is associated with changes in chlorophyll content and chloroplast development. Map-based cloning revealed that YSA encodes a pentatricopeptide repeat protein with sixteen tandem PPR motifs. YSA is highly expressed in young leaves and stems, and its expression level is regulated by light. We showed that the ysa mutation has no apparent negative effects on several important agronomic traits, such as fertility, stigma extrusion rate, selfed seed-setting rate, hybrid seed-setting rate and yield heterosis under normal growth conditions. We further demonstrated that ysa can be used as an early marker for efficient identification and elimination of false hybrids in commercial hybrid rice production, resulting in yield increases by up to ~ 537 kg ha-1.
+*'''''Os03g0597200''''' '''''<=>''''' '''''YSA''''','''''OsYSA''''',
 ===Function===
-YSA is required for chloroplast development in early seedling leaves, and disruption of its function causes a seedling stage-specific albino phenotype, but the plant recovers and develops normal green leaves from the four-leaf stage onward.The ysa mutant develops albino leaves before the three-leaf stage, but the mutant gradually turns green and recovers to normal green at the six-leaf stage.(Su N, Hu ML, Wu DX, et al.2012)
+* Map-based cloning revealed that '''''YSA''''' encodes a PPR protein with 16 tandem PPR motifs.
-Functional studies of PPR proteins in higher plants remain very sparse. Accumulating data point to an involvement in posttranscriptional processes in organelles. Additional evidence for a role of PPR proteins in regulating organelle gene expression has also come from positional cloning of several cytoplasmic male sterility (CMS) restorer genes from petunia (Petunia hybrida; Bentolila et al., 2002) and radish (Raphanus sativus; Brown et al., 2003; Desloire et al., 2003; Koizuka et al., 2003). Genetic and biochemical data, and structural modeling of PPR tracts based on established tetratricopeptide repeat proteins together suggest that PPR proteins typically bind directly to specific organellar RNA sequences through a surface created by the stacked helical repeating units. However, still very little is known about the functions, substrates, and regulatory mechanisms for the vast majority of PPR proteins.The ysa mutant develops albino leaves before the three-leaf stage, but the mutant gradually turns green and recovers to normal green at the six-leaf stage. Further investigation showed that the change in leaf color in ysa mutant is associated with changes in chlorophyll content and chloroplast development. The albino phenotype of the young ysaseedlings is caused by a reduction in total chlorophyll content, rather than reduction of a particular pigment.
+* The researchers demonstrated that '''''YSA''''' can be used as an early marker for efficient identification and elimination of false hybrids in commercial hybrid rice production, resulting in yield increases by up to approximately 537 kg ha 21 .
 ===Expression===
-Tissue localization
+===Phenotypic analysis===
-Molecular analysis of an F2 population from the cross Taiziyuzhu3ysaplaced the YSAlocus between the markers RM411 and RM8208 on chromosome 3 .  The YSAlocus was further narrowed down to a 45-kb region, which includes 10 putative open reading frames(ORFs; Fig. 3, B–D). We sequenced all ORFs and found a 5-bp deletion in Os03g40020, causing a premature stop codon. that the 5-bp deletion in Os03g40020 is responsible for the albino phenotype of ysa mutant. light plays a major role in regulatingYSAexpression.YSA is highly expressed in young leaves and stems, but not in the roots (Fig. 1, A–D). Quantitative real-time reverse transcription (RT)-PCR analysis revealed that the expression of YSA peaked in the fourth leaf (Fig. 2E). Thus, the expression pattern of YSA is consistent with the seedling-stage-specific albino phenotype of ysa mutant and further supports the notion that YSA plays an important role in chloroplast development in the first few leaves of rice seedlings, but plays more minor roles in later stages.
+* The researchers showed that the '''''YSA''''' mutation has no apparent negative effects on several important agronomic traits, such as fertility, stigma extrusion rate, selfed seed-setting rate, hybrid seed-setting rate, and yield heterosis under normal growth conditions.
 ==Labs working on this gene==

@@ Line 77: / Line 77: @@
 ==Structured Information==
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

← Older revision		Revision as of 09:07, 7 June 2014
Line 26:		Line 26:
	5'-ctggatccttatatgtaattgtacttcgaggacaacc-3'.		5'-ctggatccttatatgtaattgtacttcgaggacaacc-3'.
	The resulting fragments were inserted into the binary vector pCUbi1390 in which the YSA gene was under the control of the constitutive maize ubiquitin promoter. The constructs were introduced into ysa mutant by A.tumefaciens-mediated transformation as described previously		The resulting fragments were inserted into the binary vector pCUbi1390 in which the YSA gene was under the control of the constitutive maize ubiquitin promoter. The constructs were introduced into ysa mutant by A.tumefaciens-mediated transformation as described previously
		+
		+	Subcellular Localization of GFP Proteins
		+	To investigate the subcellular localization of YSA, a gene fragment encoding the N-terminal region (amino acids 1–200) of the YSA protein was amplified by PCR and ligated into the PA7-GFP vector (kindly provided by Dr. Hongquan Yang), in-frame with GFP, resulting in pA7-YSA-GFP. The primer pair used for YSA was:
		+	5'-ggaccatggacatgccccgcgtttgcgccgcccctcg-3' and 5'-catcactagtttgctcccctccacaagaacattgag-3'.
		+	The vectors for the nuclear localization signal of the fibrillarin protein and the transit peptide of the small subunit of ribulose bisphosphate carboxylase of Arabidopsis were kindly provided by Dr. W Chi. The constructs were introduced into Arabidopsis protoplasts according to the protocols described previously. The transfected protoplast suspensions were incubated overnight on 12-well plates in the dark.To investigate the subcellular localization of YSA in rice protoplasts, the pA7-YSA-GFP vector was transformed into rice protoplasts according to the protocols described previously(Chen et al., 2006). GFP fluorescence in the transformed protoplasts was imaged using a confocal laser-scanning microscope.

← Older revision		Revision as of 03:47, 7 June 2014
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	Cloning of YSA		Cloning of YSA
	For genetic analysis, F2 populations were generated from crosses between the ysa mutant and three wild-type varieties, Pei'ai64S, 93-11 and Taiziyuzhu. The population from the crossbetween ysa and Taiziyuzhu, which includes 7,760 normal green individuals and 2,240mutant plants, was used for fine mapping of the YSA locus. 474 Genomic DNA was extracted from F2 plants and analyzed for cosegregation using available SSR markers. New markers were developed based on the entire genomic sequences of the Nipponbare variety and the indica variety 93-11.dCAPS markers were designed using the Web server program dCAPS Finder 2.0(http://helix.wustl.edu/dcaps/dcaps.html). Full-length cDNAs for candidate genes were amplified using the GeneRacer Kit following the manufacturer's instructions.		For genetic analysis, F2 populations were generated from crosses between the ysa mutant and three wild-type varieties, Pei'ai64S, 93-11 and Taiziyuzhu. The population from the crossbetween ysa and Taiziyuzhu, which includes 7,760 normal green individuals and 2,240mutant plants, was used for fine mapping of the YSA locus. 474 Genomic DNA was extracted from F2 plants and analyzed for cosegregation using available SSR markers. New markers were developed based on the entire genomic sequences of the Nipponbare variety and the indica variety 93-11.dCAPS markers were designed using the Web server program dCAPS Finder 2.0(http://helix.wustl.edu/dcaps/dcaps.html). Full-length cDNAs for candidate genes were amplified using the GeneRacer Kit following the manufacturer's instructions.
		+
		+	Complementation of the ysa Mutant
		+	Plasmids for transgenic plants were constructed using standard molecular techniques. To
		+	create the complementation construct pYSA, the genomic fragment encoding YSA was
		+	amplified by RT-PCR from Pei'ai64S with the primers
		+	5'-cgcaagcttctagagggacgacgacatcgccggcggg-3'
		+	5'-ctggatcctcggtaactccattgagggttg-3'.
		+	Tocreate the pYSAT construct, the frameshifted coding region of ysa was amplified by RT-PCRwith the primers
		+	5'-cgcaagcttctagagggacgacgacatcgccggcggg-3'
		+	5'-ctggatccttatatgtaattgtacttcgaggacaacc-3'.
		+	The resulting fragments were inserted into the binary vector pCUbi1390 in which the YSA gene was under the control of the constitutive maize ubiquitin promoter. The constructs were introduced into ysa mutant by A.tumefaciens-mediated transformation as described previously