RiceWiki - User contributions [en]

Os03g0646900

2014-06-06T07:31:22Z

Shilulu: /* Annotated Information */

The rice ''GL3.1; qGL3-1; qGL3; OsPPKL1'' gene controls the grain length and yield of rice.
== Annotated Information ==
=== Function ===
[[File:qGL3-OsPPKL1 grain length.jpg|right|thumb|200px|''Fig. 3. Comparison of different traits between 93-11 and NIL-qgl3. (from reference <ref name="ref3" />).'']]

The gene loci of GL3.1 in the paper of Qi (2012), the gene loci of qGL3-1 in the paper of Hu (2012) and the loci of qGL3 of Zhang (2013) are the same loci.

''GL3.1'' encodes a protein phosphatase kelch (PPKL) family — Ser/Thr phosphatase.GL3.1 regulates grain length and yield in rice. GL3.1 regulates grain length by mediating cell cycle progression through affecting the phosphorylation status of cell cycle proteins, such as Cyclin-T1;3, thereby controlling grain yield. GL3.1 directly dephosphorylates its substrate, Cyclin-T1;3, which has only been rarely studied in plants. The downregulation of Cyclin-T1;3 in rice resulted in a shorter grain, which indicates a novel function for Cyclin-T in cell cycle regulation <ref name="ref2" />.

''qGL3'', encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1), which has two functional domains. The rice genome has other two OsPPKL1 homologs, OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator. The rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1 <ref name="ref1" /> <ref name="ref3" />.
These findings provide insight into seed development and establish a new tool for improved crop breeding.

=== Expression ===
''GL3.1'' is a widespread gene that influences protein phosphorylation in vivo. A quantitative proteomic analysis using two-dimensional difference gel electrophoresis (2-D DIGE) indicated that 21 proteins were differentially expressed in FAZ1 and NIL, of which 18 were upregulated in NIL . Mass spectrometry revealed that the 21 proteins were associated with cellular metabolic processes. Interestingly, actin was upregulated in NIL, which is consistent with the observation that ''GL3.1'' influences the rate of cell proliferation. The phosphopeptides from the young spikelets of FAZ1 and NIL were enriched on the TiO2 beads and quantified using iTRAQ, which confirmed that ''GL3.1'' is a phosphatase. 556 phosphopeptides were detected, and 464 of these molecules were quantified. Proteins showing a 1.5-fold difference between FAZ1 and NIL and demonstrating the same trend when quantified using two different labelling systems were chosen for further analysis. At least 130 proteins demonstrated a different phosphorylation status between FAZ1 and NIL during spikelet development. Gene ontology analysis revealed that these proteins are primarily involved in processes related to nucleic acid metabolism and protein complex assembly.The molecular functions of these proteins include nucleotide binding and the activities of phosphotransferases, helicases and the RNA polymerase II transcription factor. These results strongly suggest that ''GL3.1'' could influence DNA duplication. Thus, ''GL3.1'' may regulate the expression and phosphorylation of a variety of genes involved in metabolism and cell division <ref name="ref2" />.

=== Evolution ===
Phylogenetic analyzes based on genomic BLAST searches demonstrated the widespread existence of ''GL3.1'' in plants , which suggests that ''GL3.1'' has an important conserved function in plants <ref name="ref2" />.

== Labs working on this gene ==
*State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
*Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of sciences, Beijing 100101, China
*State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
*Ministry of Education Key Laboratory for Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China, Jiangxi Super Rice Engineering Technology Research Center, Jiangxi Agricultural University, Nanchang 330045, China
*Institute of Rice Research, Shandong Academy of Agricultural Sciences, Jinan 250100,China
*National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
*School of Life Sciences, Centre for Cell and Developmental Biology, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China

== References ==
<references>
<ref name="ref1">Zejun Hu, Haohua He, Shiyong Zhang, Fan Sun, Xiaoyun Xin, Wenxiang Wang, Xi Qian, Jingshui Yang, Xiaojin Luo. (2012) A Kelch Motif-Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice. Journal of Integrative Plant Biology 54(12): 979-990.</ref>
<ref name="ref2">Peng Qi, You-Shun Lin, Xian-Jun Song, Jin-Bo Shen, Wei Huang, Jun-Xiang Shan, Mei-Zhen Zhu, Liwen Jiang, Ji-Ping Gao, Hong-Xuan Lin. (2012) The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1,3. Cell Research 22(12): 1666-1680.</ref>
<ref name="ref3">Xiaojun Zhang, Jianfei Wang, Ji Huang, Hongxia Lan, Cailin Wang, Congfei Yin, Yunyu Wu, Haijuan Tang, Qian Qian, Jiayang Li, Hongsheng Zhang. (2012) Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proceedings of the National Academy of Sciences 109(52): 21534-21539.</ref>
</references>

File:QGL3-OsPPKL1 grain length.jpg

2014-06-06T07:28:31Z

Shilulu: uploaded a new version of "File:QGL3-OsPPKL1 grain length.jpg": Fig. 3. Comparison of different traits between 93-11 and NIL-qgl3.

Fig. 3. Comparison of different traits between 93-11 and NIL-qgl3.

Os03g0646900

2014-06-06T07:24:57Z

Shilulu: /* Function */

The rice ''GL3.1; qGL3-1; qGL3; OsPPKL1'' gene controls the grain length and yield of rice.
== Annotated Information ==
=== Function ===
[[File:Example.jpg|right|thumb|150px|''Fig. 3. Comparison of different traits between 93-11 and NIL-qgl3. (from reference <ref name="ref3" />).'']]

The gene loci of GL3.1 in the paper of Qi (2012), the gene loci of qGL3-1 in the paper of Hu (2012) and the loci of qGL3 of Zhang (2013) are the same loci.

''GL3.1'' encodes a protein phosphatase kelch (PPKL) family — Ser/Thr phosphatase.GL3.1 regulates grain length and yield in rice. GL3.1 regulates grain length by mediating cell cycle progression through affecting the phosphorylation status of cell cycle proteins, such as Cyclin-T1;3, thereby controlling grain yield. GL3.1 directly dephosphorylates its substrate, Cyclin-T1;3, which has only been rarely studied in plants. The downregulation of Cyclin-T1;3 in rice resulted in a shorter grain, which indicates a novel function for Cyclin-T in cell cycle regulation <ref name="ref2" />.

''qGL3'', encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1), which has two functional domains. The rice genome has other two OsPPKL1 homologs, OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator. The rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1 <ref name="ref1" /> <ref name="ref3" />.
These findings provide insight into seed development and establish a new tool for improved crop breeding.

=== Expression ===
''GL3.1'' is a widespread gene that influences protein phosphorylation in vivo. A quantitative proteomic analysis using two-dimensional difference gel electrophoresis (2-D DIGE) indicated that 21 proteins were differentially expressed in FAZ1 and NIL, of which 18 were upregulated in NIL . Mass spectrometry revealed that the 21 proteins were associated with cellular metabolic processes. Interestingly, actin was upregulated in NIL, which is consistent with the observation that ''GL3.1'' influences the rate of cell proliferation. The phosphopeptides from the young spikelets of FAZ1 and NIL were enriched on the TiO2 beads and quantified using iTRAQ, which confirmed that ''GL3.1'' is a phosphatase. 556 phosphopeptides were detected, and 464 of these molecules were quantified. Proteins showing a 1.5-fold difference between FAZ1 and NIL and demonstrating the same trend when quantified using two different labelling systems were chosen for further analysis. At least 130 proteins demonstrated a different phosphorylation status between FAZ1 and NIL during spikelet development. Gene ontology analysis revealed that these proteins are primarily involved in processes related to nucleic acid metabolism and protein complex assembly.The molecular functions of these proteins include nucleotide binding and the activities of phosphotransferases, helicases and the RNA polymerase II transcription factor. These results strongly suggest that ''GL3.1'' could influence DNA duplication. Thus, ''GL3.1'' may regulate the expression and phosphorylation of a variety of genes involved in metabolism and cell division <ref name="ref2" />.

=== Evolution ===
Phylogenetic analyzes based on genomic BLAST searches demonstrated the widespread existence of ''GL3.1'' in plants , which suggests that ''GL3.1'' has an important conserved function in plants <ref name="ref2" />.

== Labs working on this gene ==
*State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
*Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of sciences, Beijing 100101, China
*State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
*Ministry of Education Key Laboratory for Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China, Jiangxi Super Rice Engineering Technology Research Center, Jiangxi Agricultural University, Nanchang 330045, China
*Institute of Rice Research, Shandong Academy of Agricultural Sciences, Jinan 250100,China
*National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
*School of Life Sciences, Centre for Cell and Developmental Biology, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China

== References ==
<references>
<ref name="ref1">Zejun Hu, Haohua He, Shiyong Zhang, Fan Sun, Xiaoyun Xin, Wenxiang Wang, Xi Qian, Jingshui Yang, Xiaojin Luo. (2012) A Kelch Motif-Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice. Journal of Integrative Plant Biology 54(12): 979-990.</ref>
<ref name="ref2">Peng Qi, You-Shun Lin, Xian-Jun Song, Jin-Bo Shen, Wei Huang, Jun-Xiang Shan, Mei-Zhen Zhu, Liwen Jiang, Ji-Ping Gao, Hong-Xuan Lin. (2012) The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1,3. Cell Research 22(12): 1666-1680.</ref>
<ref name="ref3">Xiaojun Zhang, Jianfei Wang, Ji Huang, Hongxia Lan, Cailin Wang, Congfei Yin, Yunyu Wu, Haijuan Tang, Qian Qian, Jiayang Li, Hongsheng Zhang. (2012) Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proceedings of the National Academy of Sciences 109(52): 21534-21539.</ref>
</references>

File:QGL3-OsPPKL1 grain length.jpg

2014-06-06T07:22:54Z

Shilulu: Replaced content with "Fig. 3. Comparison of different traits between 93-11 and NIL-qgl3."

Fig. 3. Comparison of different traits between 93-11 and NIL-qgl3.

File:QGL3-OsPPKL1 grain length.jpg

2014-06-06T07:20:43Z

Shilulu: uploaded a new version of "File:QGL3-OsPPKL1 grain length.jpg": Fig. 3. Comparison of different traits between 93-11 and NIL-qgl3.

Fig. 3. Comparison of different traits between 93-
11 and NIL-qgl3. (A) Grains of 93-11 and NIL-qgl3.
(Scale bar: 10 mm.) (B) Panicles of 93-11 and NILqgl3.
(Scale bar: 2 cm.) (C) Plants of 93-11 and NILqgl3.
(Scale bar: 10 cm.) (D) Scanning electron and
light microscope photos of glume outer surfaces of
93-11 and NIL-qgl3 spikelets at three stages. Stage 1,
spikelet = 2 mm; stage 2, spikelet = 5 mm; stage 3,
maturity. (Scale bars: yellow, 50 μm; blue, 1.0 mm.)
(E) Cell density of glume outer surfaces of 93-11 and
NIL-qgl3 spikelets at three stages. (F) Grain filling
rate of 93-11 and NIL-qgl3 after fertilization, indicated
by dry weight of 1,000 grains.

Os03g0646900

2014-06-06T07:16:37Z

Shilulu: /* Function */

The rice ''GL3.1; qGL3-1; qGL3; OsPPKL1'' gene controls the grain length and yield of rice.
== Annotated Information ==
=== Function ===
[[File:QGL3-OsPPKL1 grain length.jpg ‎ (uploaded a new version of "File:QGL3-OsPPKL1 grain length.jpg" (from reference <ref name="ref3" />).'']]

The gene loci of GL3.1 in the paper of Qi (2012), the gene loci of qGL3-1 in the paper of Hu (2012) and the loci of qGL3 of Zhang (2013) are the same loci.

''GL3.1'' encodes a protein phosphatase kelch (PPKL) family — Ser/Thr phosphatase.GL3.1 regulates grain length and yield in rice. GL3.1 regulates grain length by mediating cell cycle progression through affecting the phosphorylation status of cell cycle proteins, such as Cyclin-T1;3, thereby controlling grain yield. GL3.1 directly dephosphorylates its substrate, Cyclin-T1;3, which has only been rarely studied in plants. The downregulation of Cyclin-T1;3 in rice resulted in a shorter grain, which indicates a novel function for Cyclin-T in cell cycle regulation <ref name="ref2" />.

''qGL3'', encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1), which has two functional domains. The rice genome has other two OsPPKL1 homologs, OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator. The rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1 <ref name="ref1" /> <ref name="ref3" />.
These findings provide insight into seed development and establish a new tool for improved crop breeding.

=== Expression ===
''GL3.1'' is a widespread gene that influences protein phosphorylation in vivo. A quantitative proteomic analysis using two-dimensional difference gel electrophoresis (2-D DIGE) indicated that 21 proteins were differentially expressed in FAZ1 and NIL, of which 18 were upregulated in NIL . Mass spectrometry revealed that the 21 proteins were associated with cellular metabolic processes. Interestingly, actin was upregulated in NIL, which is consistent with the observation that ''GL3.1'' influences the rate of cell proliferation. The phosphopeptides from the young spikelets of FAZ1 and NIL were enriched on the TiO2 beads and quantified using iTRAQ, which confirmed that ''GL3.1'' is a phosphatase. 556 phosphopeptides were detected, and 464 of these molecules were quantified. Proteins showing a 1.5-fold difference between FAZ1 and NIL and demonstrating the same trend when quantified using two different labelling systems were chosen for further analysis. At least 130 proteins demonstrated a different phosphorylation status between FAZ1 and NIL during spikelet development. Gene ontology analysis revealed that these proteins are primarily involved in processes related to nucleic acid metabolism and protein complex assembly.The molecular functions of these proteins include nucleotide binding and the activities of phosphotransferases, helicases and the RNA polymerase II transcription factor. These results strongly suggest that ''GL3.1'' could influence DNA duplication. Thus, ''GL3.1'' may regulate the expression and phosphorylation of a variety of genes involved in metabolism and cell division <ref name="ref2" />.

=== Evolution ===
Phylogenetic analyzes based on genomic BLAST searches demonstrated the widespread existence of ''GL3.1'' in plants , which suggests that ''GL3.1'' has an important conserved function in plants <ref name="ref2" />.

== Labs working on this gene ==
*State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
*Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of sciences, Beijing 100101, China
*State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
*Ministry of Education Key Laboratory for Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China, Jiangxi Super Rice Engineering Technology Research Center, Jiangxi Agricultural University, Nanchang 330045, China
*Institute of Rice Research, Shandong Academy of Agricultural Sciences, Jinan 250100,China
*National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
*School of Life Sciences, Centre for Cell and Developmental Biology, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China

== References ==
<references>
<ref name="ref1">Zejun Hu, Haohua He, Shiyong Zhang, Fan Sun, Xiaoyun Xin, Wenxiang Wang, Xi Qian, Jingshui Yang, Xiaojin Luo. (2012) A Kelch Motif-Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice. Journal of Integrative Plant Biology 54(12): 979-990.</ref>
<ref name="ref2">Peng Qi, You-Shun Lin, Xian-Jun Song, Jin-Bo Shen, Wei Huang, Jun-Xiang Shan, Mei-Zhen Zhu, Liwen Jiang, Ji-Ping Gao, Hong-Xuan Lin. (2012) The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1,3. Cell Research 22(12): 1666-1680.</ref>
<ref name="ref3">Xiaojun Zhang, Jianfei Wang, Ji Huang, Hongxia Lan, Cailin Wang, Congfei Yin, Yunyu Wu, Haijuan Tang, Qian Qian, Jiayang Li, Hongsheng Zhang. (2012) Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proceedings of the National Academy of Sciences 109(52): 21534-21539.</ref>
</references>

Os03g0646900

2014-06-06T07:13:47Z

Shilulu: /* Labs working on this gene */

The rice ''GL3.1; qGL3-1; qGL3; OsPPKL1'' gene controls the grain length and yield of rice.
== Annotated Information ==
=== Function ===
[[File:QGL3-OsPPKL1 grain length.jpg ‎ (uploaded a new version of "File:QGL3-OsPPKL1 grain length.jpg" (from reference <ref name="ref3" />).'']]

The gene loci of GL3.1 in the paper of Qi (2012), the gene loci of qGL3-1 in the paper of Hu (2012) and the loci of qGL3 of Zhang (2013) are the same loci.

''GL3.1'' encodes a protein phosphatase kelch (PPKL) family — Ser/Thr phosphatase.GL3.1 regulates grain length and yield in rice. GL3.1 regulates grain length by mediating cell cycle progression through affecting the phosphorylation status of cell cycle proteins, such as Cyclin-T1,3, thereby controlling grain yield. GL3.1 directly dephosphorylates its substrate, Cyclin-T1,3, which has only been rarely studied in plants. The downregulation of Cyclin-T1,3 in rice resulted in a shorter grain, which indicates a novel function for Cyclin-T in cell cycle regulation <ref name="ref2" />.

''qGL3'', encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1), which has two functional domains. The rice genome has other two OsPPKL1 homologs, OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator. The rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1 <ref name="ref1" /> <ref name="ref3" />.
These findings provide insight into seed development and establish a new tool for improved crop breeding.

=== Expression ===
''GL3.1'' is a widespread gene that influences protein phosphorylation in vivo. A quantitative proteomic analysis using two-dimensional difference gel electrophoresis (2-D DIGE) indicated that 21 proteins were differentially expressed in FAZ1 and NIL, of which 18 were upregulated in NIL . Mass spectrometry revealed that the 21 proteins were associated with cellular metabolic processes. Interestingly, actin was upregulated in NIL, which is consistent with the observation that ''GL3.1'' influences the rate of cell proliferation. The phosphopeptides from the young spikelets of FAZ1 and NIL were enriched on the TiO2 beads and quantified using iTRAQ, which confirmed that ''GL3.1'' is a phosphatase. 556 phosphopeptides were detected, and 464 of these molecules were quantified. Proteins showing a 1.5-fold difference between FAZ1 and NIL and demonstrating the same trend when quantified using two different labelling systems were chosen for further analysis. At least 130 proteins demonstrated a different phosphorylation status between FAZ1 and NIL during spikelet development. Gene ontology analysis revealed that these proteins are primarily involved in processes related to nucleic acid metabolism and protein complex assembly.The molecular functions of these proteins include nucleotide binding and the activities of phosphotransferases, helicases and the RNA polymerase II transcription factor. These results strongly suggest that ''GL3.1'' could influence DNA duplication. Thus, ''GL3.1'' may regulate the expression and phosphorylation of a variety of genes involved in metabolism and cell division <ref name="ref2" />.

=== Evolution ===
Phylogenetic analyzes based on genomic BLAST searches demonstrated the widespread existence of ''GL3.1'' in plants , which suggests that ''GL3.1'' has an important conserved function in plants <ref name="ref2" />.

== Labs working on this gene ==
*State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
*Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of sciences, Beijing 100101, China
*State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
*Ministry of Education Key Laboratory for Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China, Jiangxi Super Rice Engineering Technology Research Center, Jiangxi Agricultural University, Nanchang 330045, China
*Institute of Rice Research, Shandong Academy of Agricultural Sciences, Jinan 250100,China
*National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
*School of Life Sciences, Centre for Cell and Developmental Biology, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China

== References ==
<references>
<ref name="ref1">Zejun Hu, Haohua He, Shiyong Zhang, Fan Sun, Xiaoyun Xin, Wenxiang Wang, Xi Qian, Jingshui Yang, Xiaojin Luo. (2012) A Kelch Motif-Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice. Journal of Integrative Plant Biology 54(12): 979-990.</ref>
<ref name="ref2">Peng Qi, You-Shun Lin, Xian-Jun Song, Jin-Bo Shen, Wei Huang, Jun-Xiang Shan, Mei-Zhen Zhu, Liwen Jiang, Ji-Ping Gao, Hong-Xuan Lin. (2012) The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1,3. Cell Research 22(12): 1666-1680.</ref>
<ref name="ref3">Xiaojun Zhang, Jianfei Wang, Ji Huang, Hongxia Lan, Cailin Wang, Congfei Yin, Yunyu Wu, Haijuan Tang, Qian Qian, Jiayang Li, Hongsheng Zhang. (2012) Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proceedings of the National Academy of Sciences 109(52): 21534-21539.</ref>
</references>

Os03g0646900

2014-06-06T07:12:43Z

Shilulu: /* Labs working on this gene */

The rice ''GL3.1; qGL3-1; qGL3; OsPPKL1'' gene controls the grain length and yield of rice.
== Annotated Information ==
=== Function ===
[[File:QGL3-OsPPKL1 grain length.jpg ‎ (uploaded a new version of "File:QGL3-OsPPKL1 grain length.jpg" (from reference <ref name="ref3" />).'']]

The gene loci of GL3.1 in the paper of Qi (2012), the gene loci of qGL3-1 in the paper of Hu (2012) and the loci of qGL3 of Zhang (2013) are the same loci.

''GL3.1'' encodes a protein phosphatase kelch (PPKL) family — Ser/Thr phosphatase.GL3.1 regulates grain length and yield in rice. GL3.1 regulates grain length by mediating cell cycle progression through affecting the phosphorylation status of cell cycle proteins, such as Cyclin-T1,3, thereby controlling grain yield. GL3.1 directly dephosphorylates its substrate, Cyclin-T1,3, which has only been rarely studied in plants. The downregulation of Cyclin-T1,3 in rice resulted in a shorter grain, which indicates a novel function for Cyclin-T in cell cycle regulation <ref name="ref2" />.

''qGL3'', encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1), which has two functional domains. The rice genome has other two OsPPKL1 homologs, OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator. The rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1 <ref name="ref1" /> <ref name="ref3" />.
These findings provide insight into seed development and establish a new tool for improved crop breeding.

=== Expression ===
''GL3.1'' is a widespread gene that influences protein phosphorylation in vivo. A quantitative proteomic analysis using two-dimensional difference gel electrophoresis (2-D DIGE) indicated that 21 proteins were differentially expressed in FAZ1 and NIL, of which 18 were upregulated in NIL . Mass spectrometry revealed that the 21 proteins were associated with cellular metabolic processes. Interestingly, actin was upregulated in NIL, which is consistent with the observation that ''GL3.1'' influences the rate of cell proliferation. The phosphopeptides from the young spikelets of FAZ1 and NIL were enriched on the TiO2 beads and quantified using iTRAQ, which confirmed that ''GL3.1'' is a phosphatase. 556 phosphopeptides were detected, and 464 of these molecules were quantified. Proteins showing a 1.5-fold difference between FAZ1 and NIL and demonstrating the same trend when quantified using two different labelling systems were chosen for further analysis. At least 130 proteins demonstrated a different phosphorylation status between FAZ1 and NIL during spikelet development. Gene ontology analysis revealed that these proteins are primarily involved in processes related to nucleic acid metabolism and protein complex assembly.The molecular functions of these proteins include nucleotide binding and the activities of phosphotransferases, helicases and the RNA polymerase II transcription factor. These results strongly suggest that ''GL3.1'' could influence DNA duplication. Thus, ''GL3.1'' may regulate the expression and phosphorylation of a variety of genes involved in metabolism and cell division <ref name="ref2" />.

=== Evolution ===
Phylogenetic analyzes based on genomic BLAST searches demonstrated the widespread existence of ''GL3.1'' in plants , which suggests that ''GL3.1'' has an important conserved function in plants <ref name="ref2" />.

== Labs working on this gene ==
*State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
*Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy
of Sciences, Beijing 100101, China
*State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
*Ministry of Education Key Laboratory for Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China,
Jiangxi Super Rice Engineering Technology Research Center, Jiangxi Agricultural University, Nanchang 330045, China
*Institute of Rice Research, Shandong Academy of Agricultural Sciences, Jinan 250100,China
*National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Shanghai Institute of Plant Physiology
and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
*School of Life Sciences, Centre for Cell and Developmental Biology, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China

== References ==
<references>
<ref name="ref1">Zejun Hu, Haohua He, Shiyong Zhang, Fan Sun, Xiaoyun Xin, Wenxiang Wang, Xi Qian, Jingshui Yang, Xiaojin Luo. (2012) A Kelch Motif-Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice. Journal of Integrative Plant Biology 54(12): 979-990.</ref>
<ref name="ref2">Peng Qi, You-Shun Lin, Xian-Jun Song, Jin-Bo Shen, Wei Huang, Jun-Xiang Shan, Mei-Zhen Zhu, Liwen Jiang, Ji-Ping Gao, Hong-Xuan Lin. (2012) The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1,3. Cell Research 22(12): 1666-1680.</ref>
<ref name="ref3">Xiaojun Zhang, Jianfei Wang, Ji Huang, Hongxia Lan, Cailin Wang, Congfei Yin, Yunyu Wu, Haijuan Tang, Qian Qian, Jiayang Li, Hongsheng Zhang. (2012) Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proceedings of the National Academy of Sciences 109(52): 21534-21539.</ref>
</references>

Os03g0646900

2014-06-06T07:10:06Z

Shilulu: Created page with "The rice ''GL3.1; qGL3-1; qGL3; OsPPKL1'' gene controls the grain length and yield of rice. == Annotated Information == === Function === [[File:QGL3-OsPPKL1 grain length.jp..."

The rice ''GL3.1; qGL3-1; qGL3; OsPPKL1'' gene controls the grain length and yield of rice.
== Annotated Information ==
=== Function ===
[[File:QGL3-OsPPKL1 grain length.jpg ‎ (uploaded a new version of "File:QGL3-OsPPKL1 grain length.jpg" (from reference <ref name="ref3" />).'']]

The gene loci of GL3.1 in the paper of Qi (2012), the gene loci of qGL3-1 in the paper of Hu (2012) and the loci of qGL3 of Zhang (2013) are the same loci.

''GL3.1'' encodes a protein phosphatase kelch (PPKL) family — Ser/Thr phosphatase.GL3.1 regulates grain length and yield in rice. GL3.1 regulates grain length by mediating cell cycle progression through affecting the phosphorylation status of cell cycle proteins, such as Cyclin-T1,3, thereby controlling grain yield. GL3.1 directly dephosphorylates its substrate, Cyclin-T1,3, which has only been rarely studied in plants. The downregulation of Cyclin-T1,3 in rice resulted in a shorter grain, which indicates a novel function for Cyclin-T in cell cycle regulation <ref name="ref2" />.

''qGL3'', encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1), which has two functional domains. The rice genome has other two OsPPKL1 homologs, OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator. The rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1 <ref name="ref1" /> <ref name="ref3" />.
These findings provide insight into seed development and establish a new tool for improved crop breeding.

=== Expression ===
''GL3.1'' is a widespread gene that influences protein phosphorylation in vivo. A quantitative proteomic analysis using two-dimensional difference gel electrophoresis (2-D DIGE) indicated that 21 proteins were differentially expressed in FAZ1 and NIL, of which 18 were upregulated in NIL . Mass spectrometry revealed that the 21 proteins were associated with cellular metabolic processes. Interestingly, actin was upregulated in NIL, which is consistent with the observation that ''GL3.1'' influences the rate of cell proliferation. The phosphopeptides from the young spikelets of FAZ1 and NIL were enriched on the TiO2 beads and quantified using iTRAQ, which confirmed that ''GL3.1'' is a phosphatase. 556 phosphopeptides were detected, and 464 of these molecules were quantified. Proteins showing a 1.5-fold difference between FAZ1 and NIL and demonstrating the same trend when quantified using two different labelling systems were chosen for further analysis. At least 130 proteins demonstrated a different phosphorylation status between FAZ1 and NIL during spikelet development. Gene ontology analysis revealed that these proteins are primarily involved in processes related to nucleic acid metabolism and protein complex assembly.The molecular functions of these proteins include nucleotide binding and the activities of phosphotransferases, helicases and the RNA polymerase II transcription factor. These results strongly suggest that ''GL3.1'' could influence DNA duplication. Thus, ''GL3.1'' may regulate the expression and phosphorylation of a variety of genes involved in metabolism and cell division <ref name="ref2" />.

=== Evolution ===
Phylogenetic analyzes based on genomic BLAST searches demonstrated the widespread existence of ''GL3.1'' in plants , which suggests that ''GL3.1'' has an important conserved function in plants <ref name="ref2" />.

== Labs working on this gene ==
*State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
*Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
* State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life
Sciences, Fudan University, Shanghai 200433, China
* Ministry of Education Key Laboratory for Crop Physiology, Ecology and Genetic
Breeding, Jiangxi Agricultural University, Nanchang 330045, China, Jiangxi Super
Rice Engineering Technology Research Center, Jiangxi Agricultural University,
Nanchang 330045, China
* Institute of Rice Research, Shandong Academy of Agricultural Sciences, Jinan 250100,
China
* National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
*School of Life Sciences, Centre for Cell and Developmental Biology, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China

== References ==
<references>
<ref name="ref1">Zejun Hu, Haohua He, Shiyong Zhang, Fan Sun, Xiaoyun Xin, Wenxiang Wang, Xi Qian, Jingshui Yang, Xiaojin Luo. (2012) A Kelch Motif-Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice. Journal of Integrative Plant Biology 54(12): 979-990.</ref>
<ref name="ref2">Peng Qi, You-Shun Lin, Xian-Jun Song, Jin-Bo Shen, Wei Huang, Jun-Xiang Shan, Mei-Zhen Zhu, Liwen Jiang, Ji-Ping Gao, Hong-Xuan Lin. (2012) The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1,3. Cell Research 22(12): 1666-1680.</ref>
<ref name="ref3">Xiaojun Zhang, Jianfei Wang, Ji Huang, Hongxia Lan, Cailin Wang, Congfei Yin, Yunyu Wu, Haijuan Tang, Qian Qian, Jiayang Li, Hongsheng Zhang. (2012) Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proceedings of the National Academy of Sciences 109(52): 21534-21539.</ref>
</references>

File:QGL3-OsPPKL1 grain length.jpg

2014-06-06T06:27:16Z

Shilulu: uploaded a new version of "File:QGL3-OsPPKL1 grain length.jpg": Fig3 Comparison of different traits between 93-11 and NIL-qgl3.(from reference <ref name="ref3" />)

File:QGL3-OsPPKL1 grain length.jpg

2014-06-06T06:20:31Z

Shilulu: Fig. 3. Comparison of different traits between 93- 11 and NIL-qgl3. (A) Grains of 93-11 and NIL-qgl3. (Scale bar: 10 mm.) (B) Panicles of 93-11 and NILqgl3. (Scale bar: 2 cm.) (C) Plants of 93-11 and NILqgl3. (Scale bar: 10 cm.) (D) Scanning electron and