Long range PCR, deep parallel sequencing and multiplexed Maldi-TOF mass spectrometry reveals new SNP variants associated with starch functional properties

Daniel LE Waters, Ardashir K Masouleh, Russell F Reinke, Robert J Henry

Research output: Other contribution to conferenceOther

Abstract

The barley genome sequence will be available soon, allowing barley to follow the rice model of genetic analysis, accelerating the rate of knowledge acquisition surrounding the genetic control of important traits. We have used the rice genome sequence to understand the genetic control of rice starch quality within the Australian rice breeding program. Illumina GAIIx sequencing of 17 rice starch synthesis genes from 233 genotypes within the Australian rice breeding program detected 501 SNPs and 113 Indels in both coding and non-coding regions. Five genes encoding the enzymes AGPL2a, Isoamylase1, SPHOL, SSIIb and SSIVb showed no polymorphism. Associations between 52 of the 110 functional SNP and the pasting and cooking quality of the rice were detected. GBSSI and SSIIa had a major influence on starch properties and the genes encoding other enzymes had minor associations. The ´G/T´ SNP at the boundary site of exon1/intron1 of GBSSI showed the strongest association with retrogradation and amylose content. The GC/TT SNP at exon 8 of SSIIa showed a very significant association with pasting temperature, gelatinisation temperature and peak time. A new ´C/T´ SNP was found at position 1188 in the GPT encoding gene which alters Leu24 to Phe. This SNP may be associated with retrogradation and amylose content. These associations provide new tools for deliberate selection of rice genotypes for specific functional and nutritional outcomes.

Acknowledgements: This project was funded by NSW DPI and the Australian Research Council. Thanks to Rachelle Ward NSW DPI for provision of rice starch phenotypic data and Stirling Bowen and Mark Edwards for technical assistance with Illumina GAIIx sequencing and MALDI-TOF MS (Sequenom MassARRAY) analysis.
Original languageEnglish
Publication statusPublished - 2011
Event15th Australian Barley Technical Symposium: Barley for Business - Adelaide, Australia
Duration: 18 Sep 201121 Sep 2011

Conference

Conference15th Australian Barley Technical Symposium
CountryAustralia
CityAdelaide
Period18/09/1121/09/11

Fingerprint

functional properties
mass spectrometry
starch
rice
rice starch
retrogradation
pasting properties
amylose
genes
barley
genome
genotype
breeding
cooking quality
enzymes
exons
genetic techniques and protocols
genetic polymorphism
synthesis
temperature

Cite this

Waters, D. LE., Masouleh, A. K., Reinke, R. F., & Henry, R. J. (2011). Long range PCR, deep parallel sequencing and multiplexed Maldi-TOF mass spectrometry reveals new SNP variants associated with starch functional properties. 15th Australian Barley Technical Symposium, Adelaide, Australia.
Waters, Daniel LE ; Masouleh, Ardashir K ; Reinke, Russell F ; Henry, Robert J. / Long range PCR, deep parallel sequencing and multiplexed Maldi-TOF mass spectrometry reveals new SNP variants associated with starch functional properties. 15th Australian Barley Technical Symposium, Adelaide, Australia.
@conference{13f0f87fec73461f849bfee3958cb912,
title = "Long range PCR, deep parallel sequencing and multiplexed Maldi-TOF mass spectrometry reveals new SNP variants associated with starch functional properties",
abstract = "The barley genome sequence will be available soon, allowing barley to follow the rice model of genetic analysis, accelerating the rate of knowledge acquisition surrounding the genetic control of important traits. We have used the rice genome sequence to understand the genetic control of rice starch quality within the Australian rice breeding program. Illumina GAIIx sequencing of 17 rice starch synthesis genes from 233 genotypes within the Australian rice breeding program detected 501 SNPs and 113 Indels in both coding and non-coding regions. Five genes encoding the enzymes AGPL2a, Isoamylase1, SPHOL, SSIIb and SSIVb showed no polymorphism. Associations between 52 of the 110 functional SNP and the pasting and cooking quality of the rice were detected. GBSSI and SSIIa had a major influence on starch properties and the genes encoding other enzymes had minor associations. The ´G/T´ SNP at the boundary site of exon1/intron1 of GBSSI showed the strongest association with retrogradation and amylose content. The GC/TT SNP at exon 8 of SSIIa showed a very significant association with pasting temperature, gelatinisation temperature and peak time. A new ´C/T´ SNP was found at position 1188 in the GPT encoding gene which alters Leu24 to Phe. This SNP may be associated with retrogradation and amylose content. These associations provide new tools for deliberate selection of rice genotypes for specific functional and nutritional outcomes.Acknowledgements: This project was funded by NSW DPI and the Australian Research Council. Thanks to Rachelle Ward NSW DPI for provision of rice starch phenotypic data and Stirling Bowen and Mark Edwards for technical assistance with Illumina GAIIx sequencing and MALDI-TOF MS (Sequenom MassARRAY) analysis.",
author = "Waters, {Daniel LE} and Masouleh, {Ardashir K} and Reinke, {Russell F} and Henry, {Robert J}",
year = "2011",
language = "English",
note = "15th Australian Barley Technical Symposium : Barley for Business ; Conference date: 18-09-2011 Through 21-09-2011",

}

Waters, DLE, Masouleh, AK, Reinke, RF & Henry, RJ 2011, 'Long range PCR, deep parallel sequencing and multiplexed Maldi-TOF mass spectrometry reveals new SNP variants associated with starch functional properties', 15th Australian Barley Technical Symposium, Adelaide, Australia, 18/09/11 - 21/09/11.

Long range PCR, deep parallel sequencing and multiplexed Maldi-TOF mass spectrometry reveals new SNP variants associated with starch functional properties. / Waters, Daniel LE; Masouleh, Ardashir K; Reinke, Russell F; Henry, Robert J.

2011. 15th Australian Barley Technical Symposium, Adelaide, Australia.

Research output: Other contribution to conferenceOther

TY - CONF

T1 - Long range PCR, deep parallel sequencing and multiplexed Maldi-TOF mass spectrometry reveals new SNP variants associated with starch functional properties

AU - Waters, Daniel LE

AU - Masouleh, Ardashir K

AU - Reinke, Russell F

AU - Henry, Robert J

PY - 2011

Y1 - 2011

N2 - The barley genome sequence will be available soon, allowing barley to follow the rice model of genetic analysis, accelerating the rate of knowledge acquisition surrounding the genetic control of important traits. We have used the rice genome sequence to understand the genetic control of rice starch quality within the Australian rice breeding program. Illumina GAIIx sequencing of 17 rice starch synthesis genes from 233 genotypes within the Australian rice breeding program detected 501 SNPs and 113 Indels in both coding and non-coding regions. Five genes encoding the enzymes AGPL2a, Isoamylase1, SPHOL, SSIIb and SSIVb showed no polymorphism. Associations between 52 of the 110 functional SNP and the pasting and cooking quality of the rice were detected. GBSSI and SSIIa had a major influence on starch properties and the genes encoding other enzymes had minor associations. The ´G/T´ SNP at the boundary site of exon1/intron1 of GBSSI showed the strongest association with retrogradation and amylose content. The GC/TT SNP at exon 8 of SSIIa showed a very significant association with pasting temperature, gelatinisation temperature and peak time. A new ´C/T´ SNP was found at position 1188 in the GPT encoding gene which alters Leu24 to Phe. This SNP may be associated with retrogradation and amylose content. These associations provide new tools for deliberate selection of rice genotypes for specific functional and nutritional outcomes.Acknowledgements: This project was funded by NSW DPI and the Australian Research Council. Thanks to Rachelle Ward NSW DPI for provision of rice starch phenotypic data and Stirling Bowen and Mark Edwards for technical assistance with Illumina GAIIx sequencing and MALDI-TOF MS (Sequenom MassARRAY) analysis.

AB - The barley genome sequence will be available soon, allowing barley to follow the rice model of genetic analysis, accelerating the rate of knowledge acquisition surrounding the genetic control of important traits. We have used the rice genome sequence to understand the genetic control of rice starch quality within the Australian rice breeding program. Illumina GAIIx sequencing of 17 rice starch synthesis genes from 233 genotypes within the Australian rice breeding program detected 501 SNPs and 113 Indels in both coding and non-coding regions. Five genes encoding the enzymes AGPL2a, Isoamylase1, SPHOL, SSIIb and SSIVb showed no polymorphism. Associations between 52 of the 110 functional SNP and the pasting and cooking quality of the rice were detected. GBSSI and SSIIa had a major influence on starch properties and the genes encoding other enzymes had minor associations. The ´G/T´ SNP at the boundary site of exon1/intron1 of GBSSI showed the strongest association with retrogradation and amylose content. The GC/TT SNP at exon 8 of SSIIa showed a very significant association with pasting temperature, gelatinisation temperature and peak time. A new ´C/T´ SNP was found at position 1188 in the GPT encoding gene which alters Leu24 to Phe. This SNP may be associated with retrogradation and amylose content. These associations provide new tools for deliberate selection of rice genotypes for specific functional and nutritional outcomes.Acknowledgements: This project was funded by NSW DPI and the Australian Research Council. Thanks to Rachelle Ward NSW DPI for provision of rice starch phenotypic data and Stirling Bowen and Mark Edwards for technical assistance with Illumina GAIIx sequencing and MALDI-TOF MS (Sequenom MassARRAY) analysis.

M3 - Other

ER -