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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #306758

Title: Development of Japonica mapping populations to validate GWAS in the rice diversity panel 1

item HANCOCK, TERESA - University Of Arkansas
item ALI, LIAKAT - University Of Arkansas
item MCCOUCH, SUSAN - Cornell University
item Eizenga, Georgia

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/2/2014
Publication Date: 12/15/2014
Citation: Hancock T.A., Ali M.L., McCouch, S.R., Eizenga, G.C. 2014. Development of Japonica mapping populations to validate GWAS in the rice diversity panel 1. Proc. 35th Rice Tech. Work. Group Meet., New Orleans, LA, pp. 64-65. Feb. 18-21, 2014. CDROM.

Interpretive Summary:

Technical Abstract: In order to validate associations identified in the Rice Diversity Panel 1 (RDP1) between SNP markers and 34 phenotypic traits, four bi-parental recombinant inbred line (RIL) populations were developed from Oryza sativa L. ssp. japonica accessions that were phenotypically and genotypically diverse. Three of these populations were grown in the field in Stuttgart, Arkansas to determine the range of phenotypic variation within each population. Two of the populations, Estrela (tropical japonica)/NSF-TV199 (tropical japonica) and Norin 20 (temperate japonica)/Fortuna (tropical japonica) were grown during summer 2012. The third population, L-202 (tropical japonica)/Trembese (tropical japonica), was grown during the summer 2013. Each population was represented by over 250 F6 progeny lines grown in an unreplicated field study with phenotypic data for days to heading, plant type, and plant height collected on each progeny line. One panicle was collected from a single, typical plant in each row for each line to use for generation advancement and for additional phenotypic evaluation of the panicle. Panicles from 20% of the progeny were randomly chosen for phenotyping. Data were collected on panicle length, panicle branching, awn presence, shattering tendency, number of seeds per panicle, weight of seeds per panicle, number of blank florets per panicle, seed length and seed width. Transgressive variation was most apparent where data was collected from every progeny line. However, the extreme range in variation noted in the parents for plant, panicle and seed traits was reflected in the progeny, although data were taken from only 20% of the progeny. The Estrela/NSFTV199 parents were extremely divergent for all traits evaluated except panicle length and this population was selected for a replicated field trial during the summer 2013 with a second season of data collection planned for 2014. The three populations have been advanced and F8 progeny seed is being produced in the greenhouse to develop RILs. Leaf tissue has been collected from each F7 RIL progenitor plant for genotyping, most likely using genotype-by-sequencing (GBS) technology. Currently, F6 is being produced from a fourth population, Kamenoo (temperate japonica)/Estrela (tropical japonica).