SNP markers for panicle architecture and grain traits developed from GWA-QTL and available for japonica rice improvement

Authors: Eizenga, Georgia; Jackson, Aaron; Jia, Melissa; Edwards, Jeremy; McClung, Anna

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/14/2019
Publication Date: 12/16/2019
Citation: Eizenga, G.C., Jackson, A.K., Jia, M.H., Edwards, J., McClung, A.M. 2019. SNP markers for panicle architecture and grain traits developed from GWA-QTL and available for japonica rice improvement. Abstract, Plant and Animal Genome Conference XXVIII, San Diego, California, January 11-15, 2020.

Interpretive Summary:

Technical Abstract: Panicle architecture, grain size and grain weight are important yield component traits to consider when breeding rice (Oryza sativa L.). Having SNP markers for these traits would expedite breeding efforts through marker assisted selection. Previously, the Rice Diversity Panel 1 (RDP1), representing the five major rice subpopulations, was phenotyped for these yield related traits and genome-wide association mapping (GWA)-QTL were identified. Most southern U.S. cultivars are classified as tropical japonica and California cultivars as temperate japonica; thus, these subpopulations are of particular interest to U.S. breeders. To develop markers and dissect the variation underlying these GWA-QTLs for rice improvement, diverse japonica RDP1 accessions were selected as parents to develop biparental recombinant inbred line (RIL) mapping populations. All 276 progeny from the Estrela (admixture of japonica) × NSFTV199 (tropical japonica) cross have been evaluated for panicle architecture and grain traits. The QTL analyses with 256 RILs revealed 38 RIL-QTL which overlapped with the previously identified GWA-QTL and regions on chromosomes 3, 4, 5, 6, 7, 8 and 9 were selected for marker development. To develop markers, the sequence variation in regions surrounding the significant SNPs identified in GWA studies was assessed in rice genomic databases to find optimum sites to target for marker development. Once developed, the markers were tested in the Estrela × NSFTV199 population for amplification and polymorphism, and in two additional biparental japonica populations developed from RDP1 accessions. Polymorphic marker data were analyzed in these populations to identify marker-trait associations. Six Estrela × NSFTV199 RILs with desirable panicle architecture traits along with acceptable grain size, maturity, plant height and grain yield were selected for evaluation in a replicated field trial conducted over two years. The targeted SNP markers corresponded well with the panicle architecture and grain size data from the field studies. These SNP genotypes will be used to select RILs with the best agronomic and grain quality traits that are suited for the U.S. market along with QTL for desirable panicle architecture traits. The selected RILs will be released as improved germplasm for U.S. breeders.