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Roadmap of Genome wide survey in rice project

1536 SNP chip genome coverage. Association test : Phenotyping. SNP Analysis Pipeline. Short heading & Yield component. Heading date & Yield component were characterized under green house and field condition across season. iScan :. GenomeStudio: Preliminary analysis.

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Roadmap of Genome wide survey in rice project

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  1. 1536 SNP chip genome coverage Association test : Phenotyping SNP Analysis Pipeline Short heading & Yield component Heading date & Yield component were characterized under green house and field condition across season iScan: GenomeStudio:Preliminary analysis Validate functional SNPs for allele target needed for breeding program GENOME WIDE SURVEY IN INDONESIAN RICE LINES Roadmap of Genome wide survey in rice project Association Mapping Program Rice genomic research in BB Biogen • Initiation : 2010 • iScan-Illumina with GoldenGate reader • Operational : 2011 • 1536 SNP bead chip disigned for trait targets : Short heading and Yield components • 192 rice germplasm presenting putative patterns of introgression Indica-Japonica-O.rufipogon • - Local varieties • - Introduction lines (IRRI) • - Improved lines / elite varieties • - Wild species Accelerate breeding process : precise selection, improved screening, fewer generation Downstream applications Clusters pattern for each SNP Final 1536-plex 384-plex (Thomson et al, 2011) 384 (Feltus et al, 2004) 44K (Tung et al, in prep) 1536-plex (Zhao et al, 2010) 61 : 97.495-27.728.824 Good SNP: well-defined clusters 64 : 1.473.671-30.575.776 45 : 158.129-23.030.605 47 : 800.369-23.571.010 57: 6.348-28.465.614 101 : 336.771-30.297.837 TBGI336542 194 : 296.743-31.686.494 Roadmap of Genome wide survey in rice project 112 : 22.254-29.633,213 69 : 348.610-35.742.807 215 : 288.984-37.233.286 102 : 201.495-36.820856 469:422.520-45.027.302 AA AB BB 86 3 7 raw data output Call rate : 0.79 – 0.99 Gene Train (Locus) : 0.27 – 0.97 Rice Genome Research Teams Indonesian Centre Agriculture Biotechnology R&D, Ministry of Agriculture Jl. Tentara Pelajar 3A, Bogor, West Java 16111 Indonesia

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