Rice genome sequence accelerates the discovery of commercially important genes and polymorphisms

Daniel LE Waters, Louis MT Bradbury, Russell F Reinke, Melissa A Fitzgerald, Qingsheng Jin, Robert J Henry

Research output: Other contribution to conferenceOther

Abstract

Traditionally, identification of genes which control important traits has been labour intensive and time consuming. We have demonstrated the annotated rice genome sequence used in combination with re-sequencing by PCR greatly facilitates the discovery of both genes and polymorphisms within genes, which control commercially important traits. Identification of the gene which controls fragrance was achieved using a relatively small mapping population of 168 F2 individuals. Analysis of the recombination data and the relatively large tract (385 kbp) of annotated genome sequence between the flanking markers revealed a candidate gene in this region which plausibly explained the known biochemistry of fragrance. Re-sequencing the gene in a fragrant variety found a mutation which was in accord with the known genetics of fragrance. In the absence of a genome sequence, a much larger mapping population, a genome library and more sequencing would have been necessary. Likewise, availability of the rice genome sequence greatly simplified the task of re-sequencing the SSIIa encoding gene which allowed us to identify single nucleotide polymorphisms (SNP) in soluble starch synthase IIa which explain gelatinisation temperature (GT). This important quantitative trait seems to be determined by two SNP in the 3’ end of the coding sequence. Because starch bio-synthetic genes display high levels of interspecific conservation, it is likely this knowledge will have utility in other species.
Original languageUndefined/Unknown
Publication statusPublished - 2006
EventPlant and Animal Genomes Conference XIV -
Duration: 14 Jan 200618 Jan 2006

Conference

ConferencePlant and Animal Genomes Conference XIV
Period14/01/0618/01/06

Cite this

Waters, D. LE., Bradbury, L. MT., Reinke, R. F., Fitzgerald, M. A., Jin, Q., & Henry, R. J. (2006). Rice genome sequence accelerates the discovery of commercially important genes and polymorphisms. Plant and Animal Genomes Conference XIV, .
Waters, Daniel LE ; Bradbury, Louis MT ; Reinke, Russell F ; Fitzgerald, Melissa A ; Jin, Qingsheng ; Henry, Robert J. / Rice genome sequence accelerates the discovery of commercially important genes and polymorphisms. Plant and Animal Genomes Conference XIV, .
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title = "Rice genome sequence accelerates the discovery of commercially important genes and polymorphisms",
abstract = "Traditionally, identification of genes which control important traits has been labour intensive and time consuming. We have demonstrated the annotated rice genome sequence used in combination with re-sequencing by PCR greatly facilitates the discovery of both genes and polymorphisms within genes, which control commercially important traits. Identification of the gene which controls fragrance was achieved using a relatively small mapping population of 168 F2 individuals. Analysis of the recombination data and the relatively large tract (385 kbp) of annotated genome sequence between the flanking markers revealed a candidate gene in this region which plausibly explained the known biochemistry of fragrance. Re-sequencing the gene in a fragrant variety found a mutation which was in accord with the known genetics of fragrance. In the absence of a genome sequence, a much larger mapping population, a genome library and more sequencing would have been necessary. Likewise, availability of the rice genome sequence greatly simplified the task of re-sequencing the SSIIa encoding gene which allowed us to identify single nucleotide polymorphisms (SNP) in soluble starch synthase IIa which explain gelatinisation temperature (GT). This important quantitative trait seems to be determined by two SNP in the 3’ end of the coding sequence. Because starch bio-synthetic genes display high levels of interspecific conservation, it is likely this knowledge will have utility in other species.",
author = "Waters, {Daniel LE} and Bradbury, {Louis MT} and Reinke, {Russell F} and Fitzgerald, {Melissa A} and Qingsheng Jin and Henry, {Robert J}",
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Waters, DLE, Bradbury, LMT, Reinke, RF, Fitzgerald, MA, Jin, Q & Henry, RJ 2006, 'Rice genome sequence accelerates the discovery of commercially important genes and polymorphisms', Plant and Animal Genomes Conference XIV, 14/01/06 - 18/01/06.

Rice genome sequence accelerates the discovery of commercially important genes and polymorphisms. / Waters, Daniel LE; Bradbury, Louis MT; Reinke, Russell F; Fitzgerald, Melissa A; Jin, Qingsheng; Henry, Robert J.

2006. Plant and Animal Genomes Conference XIV, .

Research output: Other contribution to conferenceOther

TY - CONF

T1 - Rice genome sequence accelerates the discovery of commercially important genes and polymorphisms

AU - Waters, Daniel LE

AU - Bradbury, Louis MT

AU - Reinke, Russell F

AU - Fitzgerald, Melissa A

AU - Jin, Qingsheng

AU - Henry, Robert J

PY - 2006

Y1 - 2006

N2 - Traditionally, identification of genes which control important traits has been labour intensive and time consuming. We have demonstrated the annotated rice genome sequence used in combination with re-sequencing by PCR greatly facilitates the discovery of both genes and polymorphisms within genes, which control commercially important traits. Identification of the gene which controls fragrance was achieved using a relatively small mapping population of 168 F2 individuals. Analysis of the recombination data and the relatively large tract (385 kbp) of annotated genome sequence between the flanking markers revealed a candidate gene in this region which plausibly explained the known biochemistry of fragrance. Re-sequencing the gene in a fragrant variety found a mutation which was in accord with the known genetics of fragrance. In the absence of a genome sequence, a much larger mapping population, a genome library and more sequencing would have been necessary. Likewise, availability of the rice genome sequence greatly simplified the task of re-sequencing the SSIIa encoding gene which allowed us to identify single nucleotide polymorphisms (SNP) in soluble starch synthase IIa which explain gelatinisation temperature (GT). This important quantitative trait seems to be determined by two SNP in the 3’ end of the coding sequence. Because starch bio-synthetic genes display high levels of interspecific conservation, it is likely this knowledge will have utility in other species.

AB - Traditionally, identification of genes which control important traits has been labour intensive and time consuming. We have demonstrated the annotated rice genome sequence used in combination with re-sequencing by PCR greatly facilitates the discovery of both genes and polymorphisms within genes, which control commercially important traits. Identification of the gene which controls fragrance was achieved using a relatively small mapping population of 168 F2 individuals. Analysis of the recombination data and the relatively large tract (385 kbp) of annotated genome sequence between the flanking markers revealed a candidate gene in this region which plausibly explained the known biochemistry of fragrance. Re-sequencing the gene in a fragrant variety found a mutation which was in accord with the known genetics of fragrance. In the absence of a genome sequence, a much larger mapping population, a genome library and more sequencing would have been necessary. Likewise, availability of the rice genome sequence greatly simplified the task of re-sequencing the SSIIa encoding gene which allowed us to identify single nucleotide polymorphisms (SNP) in soluble starch synthase IIa which explain gelatinisation temperature (GT). This important quantitative trait seems to be determined by two SNP in the 3’ end of the coding sequence. Because starch bio-synthetic genes display high levels of interspecific conservation, it is likely this knowledge will have utility in other species.

M3 - Other

ER -

Waters DLE, Bradbury LMT, Reinke RF, Fitzgerald MA, Jin Q, Henry RJ. Rice genome sequence accelerates the discovery of commercially important genes and polymorphisms. 2006. Plant and Animal Genomes Conference XIV, .