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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #348337

Title: Genome-wide association study (GWAS) of coleoptile and mesocotyl elongation in rice (Oryza sativa L.)

item SAKHALE, SANDEEP - University Of Illinois
item Eizenga, Georgia
item LIPKA, ALEXANDER - University Of Illinois
item KUMAR, ARVIND - International Rice Research Institute
item SACKS, ERIK - University Of Illinois

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/2/2017
Publication Date: 12/4/2017
Citation: Sakhale, S.A., Eizenga, G.C., Lipka, A.E., Kumar, A., Sacks, E.J. 2017. Genome-wide association study (GWAS) of coleoptile and mesocotyl elongation in rice (Oryza sativa L.). Plant & Animal Genome Conference XXVI, San Diego, CA. 13-17 Jan. 2018.

Interpretive Summary:

Technical Abstract: Direct-seeding of rice without prior pre-germination is gaining popularity in rice growing countries because it requires less water and is less labor than transplanting rice seedlings. Slow emergence and poor seedling establishment of direct-seeded rice are the primary drawback of this method. Adequate shoot length is important for successful direct seeding of rice, especially if seeds are sown deeply to ensure adequate moisture. To assess variation among cultivars and identify the genomic regions associated with shoot length, we studied 238 Japonica accessions from the Rice Diversity Panel 1 (RDP1). Two complementary experiments were conducted, one in an incubator (Expt1) and the other in a greenhouse (Expt 2). For Expt 1, seed was placed on a moist paper towel (ragdoll method), rolled up and placed in a tube for 5 days in the dark at 30C. Subsequently, seedlings were photographed and coleoptile length was measured with the ImageJ software. For Expt 2, seeds were planted 8 cm deep in 3.8 x 18.4 cm pots (Cone-tainers) filled with a 1:1:1 mixture of field soil, peat moss and sand, and subsequently cultured for 21 days at 29 deg C (day) and 29 deg C (night). Highly significant differences were noted among the accessions for coleoptile length in Expt 1, ranging from 0.7 to 5.2 cm; and in Expt 2, total shoot length ranged from 4.2 to 29.0 cm and days to emergence ranged from 4 to 21 days. Genome-wide association analysis was conducted using the high density rice array (HDRA) genotypes which consisted of 700,000 SNPs. The present study will enrich our knowledge as to which genomic regions are associated with the traits, coleoptile and mesocoytl length, which, in turn, will enable rice breeders to develop new cultivars with improved adaptation to direct seeding.