Re-sequencing Resources to Improve Starch and Grain Quality in Rice

Gopala Krishnan Subbaiyan, Ardashir K. Masouleh, Agnelo Furtado, Daniel L.E. Waters, Robert J. Henry

Research output: Book chapter/Published conference paperChapter (peer-reviewed)

Abstract

Next-generation sequencing can identify differences in the rice genome that explain the genetic basis of grain quality variation. Differences in rice grain quality are mainly associated with differences in the major component of the grain, starch. Association of rice quality variation with rice genome variation can be conducted at the gene or whole-genome level. Re-sequencing of specific genes or whole genomes can be used depending on the extent to which candidate genes for the traits of interest are known. Amplicon sequencing of genes involved in starch metabolism can help in targeted discovery of the molecular genetic basis of differences in starch related quality attributes. Whole-genome re-sequencing can complement this, when the genetic basis of the trait is expected to be outside the coding region of starch metabolism genes. These approaches have been used successfully to understand the rice genome at specific loci and over the whole genome.
Original languageEnglish
Title of host publicationRice Grain Quality
Subtitle of host publicationMethods and Protocols
EditorsNese Sreenivasulu
Place of PublicationNew York
PublisherHumana Press Inc.
Chapter12
Pages201-240
Number of pages40
Edition1st
ISBN (Electronic)9781493989140
ISBN (Print)9781493989126
DOIs
Publication statusPublished - 01 Jan 2019

Publication series

NameMethods in Molecular Biology
Volume1892
ISSN (Print)1064-3745

Fingerprint

Starch
Genome
Genes
Oryza
Molecular Biology

Cite this

Subbaiyan, G. K., Masouleh, A. K., Furtado, A., Waters, D. L. E., & Henry, R. J. (2019). Re-sequencing Resources to Improve Starch and Grain Quality in Rice. In N. Sreenivasulu (Ed.), Rice Grain Quality : Methods and Protocols (1st ed., pp. 201-240). (Methods in Molecular Biology; Vol. 1892). New York: Humana Press Inc.. https://doi.org/10.1007/978-1-4939-8914-0_12
Subbaiyan, Gopala Krishnan ; Masouleh, Ardashir K. ; Furtado, Agnelo ; Waters, Daniel L.E. ; Henry, Robert J. / Re-sequencing Resources to Improve Starch and Grain Quality in Rice. Rice Grain Quality : Methods and Protocols. editor / Nese Sreenivasulu. 1st. ed. New York : Humana Press Inc., 2019. pp. 201-240 (Methods in Molecular Biology).
@inbook{934c7a7acd724ad7a9a3739ede9cf37e,
title = "Re-sequencing Resources to Improve Starch and Grain Quality in Rice",
abstract = "Next-generation sequencing can identify differences in the rice genome that explain the genetic basis of grain quality variation. Differences in rice grain quality are mainly associated with differences in the major component of the grain, starch. Association of rice quality variation with rice genome variation can be conducted at the gene or whole-genome level. Re-sequencing of specific genes or whole genomes can be used depending on the extent to which candidate genes for the traits of interest are known. Amplicon sequencing of genes involved in starch metabolism can help in targeted discovery of the molecular genetic basis of differences in starch related quality attributes. Whole-genome re-sequencing can complement this, when the genetic basis of the trait is expected to be outside the coding region of starch metabolism genes. These approaches have been used successfully to understand the rice genome at specific loci and over the whole genome.",
keywords = "Amplicon sequencing, Association analysis, Genotyping, Grain quality, Re-sequencing, Rice, SNPs, Starch",
author = "Subbaiyan, {Gopala Krishnan} and Masouleh, {Ardashir K.} and Agnelo Furtado and Waters, {Daniel L.E.} and Henry, {Robert J.}",
year = "2019",
month = "1",
day = "1",
doi = "10.1007/978-1-4939-8914-0_12",
language = "English",
isbn = "9781493989126",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "201--240",
editor = "Nese Sreenivasulu",
booktitle = "Rice Grain Quality",
edition = "1st",

}

Subbaiyan, GK, Masouleh, AK, Furtado, A, Waters, DLE & Henry, RJ 2019, Re-sequencing Resources to Improve Starch and Grain Quality in Rice. in N Sreenivasulu (ed.), Rice Grain Quality : Methods and Protocols. 1st edn, Methods in Molecular Biology, vol. 1892, Humana Press Inc., New York, pp. 201-240. https://doi.org/10.1007/978-1-4939-8914-0_12

Re-sequencing Resources to Improve Starch and Grain Quality in Rice. / Subbaiyan, Gopala Krishnan; Masouleh, Ardashir K.; Furtado, Agnelo; Waters, Daniel L.E.; Henry, Robert J.

Rice Grain Quality : Methods and Protocols. ed. / Nese Sreenivasulu. 1st. ed. New York : Humana Press Inc., 2019. p. 201-240 (Methods in Molecular Biology; Vol. 1892).

Research output: Book chapter/Published conference paperChapter (peer-reviewed)

TY - CHAP

T1 - Re-sequencing Resources to Improve Starch and Grain Quality in Rice

AU - Subbaiyan, Gopala Krishnan

AU - Masouleh, Ardashir K.

AU - Furtado, Agnelo

AU - Waters, Daniel L.E.

AU - Henry, Robert J.

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Next-generation sequencing can identify differences in the rice genome that explain the genetic basis of grain quality variation. Differences in rice grain quality are mainly associated with differences in the major component of the grain, starch. Association of rice quality variation with rice genome variation can be conducted at the gene or whole-genome level. Re-sequencing of specific genes or whole genomes can be used depending on the extent to which candidate genes for the traits of interest are known. Amplicon sequencing of genes involved in starch metabolism can help in targeted discovery of the molecular genetic basis of differences in starch related quality attributes. Whole-genome re-sequencing can complement this, when the genetic basis of the trait is expected to be outside the coding region of starch metabolism genes. These approaches have been used successfully to understand the rice genome at specific loci and over the whole genome.

AB - Next-generation sequencing can identify differences in the rice genome that explain the genetic basis of grain quality variation. Differences in rice grain quality are mainly associated with differences in the major component of the grain, starch. Association of rice quality variation with rice genome variation can be conducted at the gene or whole-genome level. Re-sequencing of specific genes or whole genomes can be used depending on the extent to which candidate genes for the traits of interest are known. Amplicon sequencing of genes involved in starch metabolism can help in targeted discovery of the molecular genetic basis of differences in starch related quality attributes. Whole-genome re-sequencing can complement this, when the genetic basis of the trait is expected to be outside the coding region of starch metabolism genes. These approaches have been used successfully to understand the rice genome at specific loci and over the whole genome.

KW - Amplicon sequencing

KW - Association analysis

KW - Genotyping

KW - Grain quality

KW - Re-sequencing

KW - Rice

KW - SNPs

KW - Starch

UR - http://www.scopus.com/inward/record.url?scp=85056280172&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85056280172&partnerID=8YFLogxK

U2 - 10.1007/978-1-4939-8914-0_12

DO - 10.1007/978-1-4939-8914-0_12

M3 - Chapter (peer-reviewed)

SN - 9781493989126

T3 - Methods in Molecular Biology

SP - 201

EP - 240

BT - Rice Grain Quality

A2 - Sreenivasulu, Nese

PB - Humana Press Inc.

CY - New York

ER -

Subbaiyan GK, Masouleh AK, Furtado A, Waters DLE, Henry RJ. Re-sequencing Resources to Improve Starch and Grain Quality in Rice. In Sreenivasulu N, editor, Rice Grain Quality : Methods and Protocols. 1st ed. New York: Humana Press Inc. 2019. p. 201-240. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-8914-0_12