Rice SNP Consortium; Bala, Azucena; 3/2012
Natural variation in strigolactone biosynthesis in rice is associated with deletion of two MAX1 orthologs"
BALA: Young leaf tissue from rice cultivar BALA was sent from Adam Price’s lab at the University of Aberdeen to the McCouch lab at Cornell University. High quality nuclear DNA was extracted from the young leaf tissue in the McCouchlab and paired-end (PE) libraries consisting of 350-450 bp fragments were prepared. The DNA samples were processed using Illumina GAII re-sequencing technology (~88-120 bp PE reads) to achieve ~20-30x genome coverage at the Cornell University Life Sciences Core Laboratories Center (CLC).     Using an automated informatics pipeline in the McCouch/Bustamante labs at Cornell, the data was aligned to the Nipponbare genome, SNPs were called, and digital datasets consisting of allele calls and SNP positional information was made available to Price lab at the University of Aberdeen for further analysis and manuscript preparation.     The data from BALA is part of the “SNP discovery” dataset developed in theMcCouch lab as part of the part of the "International Rice SNP Consortium" activities..      AZUCENA: Young leaf tissue from rice cultivar AZUCENA was harvested from plants grown in the Guterman Greenhouse at Cornell University. High quality nuclear DNA was extracted from the young leaf tissue in the McCouch lab and paired-end (PE) libraries consisting of 350-450 bp fragments were prepared. The DNA samples were processed using Illumina GAII re-sequencing technology (~88-120 bp PE reads) to achieve ~20-30x genome coverage at the Cornell University Life Sciences Core Laboratories Center (CLC).     Using an automated informatics pipeline in the McCouch/Bustamante labs at Cornell, the data were aligned to the Nipponbare genome, SNPs were called, digital datasets consisting of allele calls and SNP positional information were made available to the Price lab at the University of Aberdeen for futher analysis and manuscript preparation.     The data from AZUCENA-AP is part of the “SNP discovery” dataset developed in the McCouch lab as part of the part of the "International Rice SNP Consortium" activities.
BALA:  The scope of this study was to re-sequence the rice variety BALA to approximately 20-30x genome coverage using Illumina GAII technology, align the re-sequencing data to the Nipponbare genome and call SNPs using a pipeline developed at Cornell University, compare the BALA sequence to other Indica and Japonica cultivars being re-sequenced in the McCouch lab, and prepare a publication to be co-authored by members of the Price lab at the University of Aberdeen, the McCouch lab at Cornell, and other contributors to the project.   AZUCENA: The scope of this study was to re-sequence the rice variety AZUCENA to approximately 20-30x genome coverage using Illumina GAII technology, align the re-sequencing data to the Nipponbare genome and call SNPs using a pipeline developed at Cornell University, compare the BALA sequence to other Indica and Japonica cultivars being re-sequenced in the McCouch lab, and prepare a publication to be co-authored by members of the Price lab at the University of Aberdeen, the McCouch lab at Cornell, and other contributors to the project.