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)peer-review


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.
Number of pages40
ISBN (Electronic)9781493989140
ISBN (Print)9781493989126
Publication statusPublished - 01 Jan 2019

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745

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