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SRX278073: Whole genome sequencing of a cultivated indica individual putatively ancestral to SH weeds
1 ILLUMINA (Illumina HiSeq 2000) run: 64.5M spots, 6.5G bases, 3.3Gb downloads

Design: Samples were prepared using an Illumina protocol similar to what is outlined in “TruSeq DNA Sample Preparation Guide” (Ambry Genetics Part# 15005180 Rev. A, Nov. 2010). DNA was fragmented and DNA fragment ends were repaired and phosphorylated using Klenow, T4 DNA Polymerase and T4 Polynucleotide Kinase. Next, an ‘A’ base was added to the 3’ end of the blunted fragments, followed by ligation of Illumina Adapters via T-A mediated ligation. The ligated products were size selected by gel purification and then PCR amplified using Illumina Paired-End primers. The library size and concentration were determined using an Agilent Bioanalyzer.
Submitted by: U MASS AMHERST
Study: Oryza sativa Genome sequencing
show Abstracthide Abstract
Red rice is an aggressive, weedy form of cultivated rice that infests crop fields and is a primary factor limiting rice productivity in the U.S. and worldwide. As the weedy relative of a genomic model species, red rice is supremely suited to serve as a model for understanding the processes by which weediness emerges in agricultural settings. Previous work by this research group has revealed that red rice in the U.S. has arisen twice independently, in both cases from Asian domesticated rice. This study further examines several complementary aspects of red rice evolution in three broad aims. First, leveraging current information about U.S. red rice origins, the project will examine the genetic basis by which weedy traits emerge. Candidate weedy genomic regions will be identified through comparative genomics of U.S. weedy rice strains with their putative cultivated ancestors, and through genetic analyses of weed-crop crosses. Second, the project will determine how the weed''s origin and population structure compare among four world regions that differ in the presence/absence of reproductively compatible wild species and in the predominant locally cultivated rice variety. Third, the project will assess how recent shifts in U.S. agriculture towards the use of imidazolinone (IMI) herbicide-resistant rice varieties is affecting the emergence of herbicide-resistant red rice. Specifically, the project will determine the relative roles of crop-weed gene flow vs. spontaneous mutation in the creation of IMI–resistant weedy rice.
Sample: Oryza sativa sin9
SAMN02117694 • SRS420990 • All experiments • All runs
Instrument: Illumina HiSeq 2000
Strategy: WGS
Selection: unspecified
Layout: PAIRED
Spot descriptor:
forward101  reverse

Runs: 1 run, 64.5M spots, 6.5G bases, 3.3Gb
Run# of Spots# of BasesSizePublished


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