The results confirmed the existence of two groups: 114 indica and 62 japonica accessions, and 6 admixed accessions (checks excluded).
Abbreviations and accessions double checked and amended.
The 135 Sri Lankan accessions plus five check cultivars (Azucena, Bala, Black Gora, IR 64 and Nipponbare) were sown 5 cm apart in four replicate blocks in a randomised complete block design on the 19th July 2010.
The association study was conducted on 45 accessions including 3 check rice varieties, of which, 18 belonged to tolerant class, 9 moderately tolerant, 7 sensitive and 11 highly sensitive.
All SNP data generated from 326 markers (given in Additional file 3: Table S2) were combined with data for the same markers for 18 accessions from diverse set of 20 rice cultivars and landraces in the OryzaSNP panel (McNally et al. 2009) in order to use them as check accessions of known subpopulation origin in identifying different groups in population structure analysis.
For this reason, the reliability of the herbicide screen to deduce that accessions differ in rooting depth was confirmed by a hydroponic screen on 36 genotypes and a rhizotron screen on 12 where Sri Lankan landraces from high, low and average herbicide scores plus check accessions were used.
MS provided germplasm records and checked accession plants for inconsistencies.
First, we do not want to change an original label of an accession without actually checking the identity of that accession.
Studies excluded were those that provided GISAID [ 31] accession numbers, however checks were made to see if the isolates had also been uploaded to GenBank.
There were 525,997 reviewed protein accession numbers in UniProt (checked on May 4, 2011), from which 5,042 protein accession numbers were chosen randomly.
Fig. 3 Minimum evolution phylogenetic tree of eight HKT genes re-sequenced from representative wild rice accessions and cultivar checks constructed using MEGA 5.1 software.
