ARS | Publication request: Characterization of grain qulaity in an Oryza sativa/O. nivara advanced backcross and Oyrza spp. with DNA markers

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: November 1, 2006
Publication Date: January 12, 2007
Citation: Eizenga, G.C., Agrama, H.A., Bryant, R.J. 2007. Characterization of grain qulaity in an Oryza sativa/O. nivara advanced backcross and Oyrza spp. with DNA markers [abstract]. Plant and Animal Genome XV, January 13-17, 2007, San Diego, CA. Available: http://intl-pag.org/15/abstracts.

Technical Abstract: Rice wild relatives are a potential source of novel genes for unique rice grain quality traits. Recently, five SNP markers associated with the Waxy gene (granule bound starch synthase) and Alk gene (soluble starch synthase IIa) were reported. These enzymes are important in the synthesis of starch which is composed of amylose and amylopectin, and ultimately affect rice cooking quality. The objective of this study was to survey the allelic diversity in Oryza spp. accessions using five SNP quality markers and conduct a mapping study using an advanced backcross (ABC) population derived from Oryza sativa L./O. nivara Sharma & Shastry. Approximately 60 Oryza spp. accessions and 175 BC2F<sub>3:4 M202 (O. sativa)/O. nivara (IRGC 100195) ABC progeny were evaluated. All ABC progeny and Oryza spp. accessions were genotyped with 150 SSR markers distributed throughout the genome and five SNP markers associated with either the Waxy or Alk genes. The ABC progeny were evaluated for amylose content and alkali spreading value using standard laboratory techniques. Preliminary results from the Oryza spp. survey indicate a novel allele for the Waxy gene may be present. In the ABC progeny, one marker for the Waxy gene and one marker for the Alk gene were polymorphic. SSR markers were mapped into 12 linkage groups representing the rice genome using JoinMap 4.0. QTL linked to these traits were identified using QTLNetwork 2.0. The relationship between the QTL identified in this study, the SNP markers, and previous studies of quality traits will be discussed.