Os07g0585700 - Revision history

Zongyuan at 15:14, 9 June 2014

2014-06-09T15:14:19Z

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Zongyuan: /* Evolution */

2014-06-08T11:06:23Z

‎Evolution

Zongyuan: /* Expression */

2014-06-08T11:03:03Z

‎Expression

Zongyuan: /* Expression */

2014-06-08T11:02:46Z

‎Expression

Zongyuan: /* Expression */

2014-06-08T11:02:28Z

‎Expression

Zongyuan: /* Expression */

2014-06-08T10:58:15Z

‎Expression

Zongyuan: /* Expression */

2014-06-05T15:36:35Z

‎Expression

Zongyuan: /* Expression */

2014-06-05T15:27:07Z

‎Expression

Zongyuan at 10:57, 5 June 2014

2014-06-05T10:57:33Z

Zongyuan: /* Expression */

2014-06-05T10:46:48Z

‎Expression

← Older revision		Revision as of 11:06, 8 June 2014
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	You can also add sub-section(s) at will.		You can also add sub-section(s) at will.
		+	Sequence analysis of 59 cultivars from the world rice core collection revealed the existence of only three haplotypes, Sdr4-n, Sdr4-k, and Sdr4-k′, in the coding sequences. Interestingly, all japonica cultivars had only Sdr4-n, whereas both Sdr4-n and Sdr4-k were found in indica In-2, and all three haplotypes were found in indica In-1. SNP analysis of the chromosomal regions containing Sdr4-n in indica cultivars revealed that in most cases, the japonica haplotypes with Sdr4-n were ﬂanked by indica haplotypes, although some complex haplotypes were found as well . Therefore, we considered the Sdr4-n in indica cultivars to be the result of introgression from japonica sources. The seeds of cultivars with Sdr4-n had lower dormancy than those of cultivars with Sdr4-k (P = 0.012 by the F test). These results strongly suggest that the functional differences in Sdr4 contribute substantially to the variations in dormancy of Asian rice accessions, although the involvement of other loci is suggested by the presence of some indica cultivars with Sdr4-k(k′) showing high germination rates and some indica cultivars with Sdr4-n showing low germination rates.

	==Labs working on this gene==		==Labs working on this gene==

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 　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19)
-  [[File:Figure.jpg|right|thumb|150px|]]
+  [[File:Figure4.jpg|right|thumb|150px|]]
 　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
 　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.

@@ Line 11: / Line 11: @@
 　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19)
-  [[File:Figure.jpgjpg|right|thumb|150px|]]
+  [[File:Figure.jpg|right|thumb|150px|]]
 　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
 　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.

@@ Line 10: / Line 10: @@
 Please input expression information here.
-　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19). [[File:Figure4|right|thumb|150px|]]
+　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19)
 　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
-　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.[[File:Figure5 |right|thumb|150px|]]
+　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.
 ===Evolution===

@@ Line 10: / Line 10: @@
 Please input expression information here.
-　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19).
+　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19). [[File:Figure4|right|thumb|150px|]]
 　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
-　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.
+　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.[[File:Figure5 |right|thumb|150px|]]
 ===Evolution===

@@ Line 21: / Line 21: @@
 ==Labs working on this gene==
 Please input related labs here.
 ==References==
 Please input cited references here.
+<ref name="ref1"> Baumlein H, Nagy I, Villarroel R, Inze D, Wobus U (1992) Cis-analysis of a seed protein gene promoter: The conservative RY repeat CATGCATG within the legumin box is essential for tissue-speciﬁc expression of a legumin gene. Plant J 2:233–239.</ref>
 ==Structured Information==
 {{JaponicaGene|