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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #358274

Research Project: Gene Discovery and Crop Design for Current and New Rice Management Practices and Market Opportunities

Location: Dale Bumpers National Rice Research Center

Title: Prototype for developing SNP markers from GWAS and biparental QTL for rice panicle and grain traits

item Eizenga, Georgia
item Jackson, Aaron
item Edwards, Jeremy

Submitted to: Agricultural and Environmental Letters
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/23/2021
Publication Date: 6/5/2021
Citation: Eizenga, G.C., Jackson, A.K., Edwards, J. 2021. Prototype for developing SNP markers from GWAS and biparental QTL for rice panicle and grain traits. Agricultural and Environmental Letters.

Interpretive Summary: With the development of advanced genotyping methods, together with advances in computing power, it is now possible to identify the actual genes controlling many important agronomic traits that are related to improving rice yield and quality. From this information, DNA markers can be developed that are linked to these genes and used to assist rice breeding programs. The objective of this study was to develop DNA markers to assist rice breeders in incorporating genes controlling grain shape; grain appearance and cooking quality (chalkiness); panicle (seed head) traits which affect yield; and days to maturity, into variety development programs. This study developed 18 new DNA markers of which 14 markers were shown to be useful in selecting for the previously mentioned genes. These DNA markers are now available to rice researchers for breeding and further research. The goal is to accelerate breeding selections for the desired panicle architecture, plant maturity, translucent grains, and the required seed dimensions as mandated by rice market classes, i.e. short grain, medium grain or long grain

Technical Abstract: Rice (Oryza sativa L.) genome-wide association (GWA) mapping studies have been conducted to identify SNPs controlling traits associated with yield and quality improvement. Unfortunately, there is a large gap in developing SNP markers for these traits which can be utilized in marker-assisted selection programs to select the desired trait(s) and develop improved varieties to feed the world’s population. The objective of this study was to develop SNP markers from significant marker-trait associations identified by GWA mapping with 700,00 SNPs in the Rice Diversity Panel 1 (RDP1) which also overlapped with QTL regions found in the mapping population Estrela/NSFTV199 for grain size, weight and chalkiness, panicle architecture traits affecting grain yield like number of primary branches and florets, and photoperiod sensitivity. To develop SNP markers, the region surrounding the significant SNPs was evaluated in rice databases to identify the most appropriate SNPs for marker development. Once developed, the utility of the SNP markers was tested in the tropical japonica Estrela/NSFTV199 mapping population and if polymorphic, in two other Japonica populations to determine the traits the marker was associated with. As further validation, these 18 markers were included with the original 132 markers used for QTL mapping in the Estrela/NSFTV199 population and a new QTL analysis was conducted. This updated QTL analysis better defined the QTL regions for the targeted traits. Based on these analyses, 14 of the 18 SNP markers had significant associations with the targeted trait(s) and are available for additional validation in genotyping studies and use in marker-assisted selection by both geneticists and breeders.