Re-sequencing resources to improve starch and grain quality in rice

Document Type

Book chapter

Publication details

Subbaiyan G, 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 (Methods in molecular biology), Humana Press, New York, pp. 201-240. ISBN 9781493989140

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Peer Reviewed



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.