All ESTs with only a single BLASTN match to the Mus genome, and therefore specific enough to be markers useful for mapping, were screened for simple sequence repeats (SSRs) using msatCommander 0.8.1 [ 37].
In this study, the finished complete genome of Mycobacterium avium subsp. paratuberculosis (Map) was screened for specific coding sequences that could be very valuable in the design of a sensitive and specific Map detection serological assay.
The mapping results were screened using a 500-nt sliding window, to identify genomic regions where ⩾3 different mapped positions were found for sRNA reads, and where each mapped position was separated from the next one by <24 nt (suggesting a possible phased locus).
Two pairs of parents from mapping populations were screened initially for tolerance to an Fe pulse stress at the vegetative growth stage: IR29/Pokkali, and Nipponbare/Kasalath.
Figure 1 Parents of two mapping populations were screened after a pulse stress of 1,000 mg L −1 Fe 2+ for 5 days.
The parents of the mapping population were screened for ESTPs (length polymorphism).
Ten genotypes from each mapping population were screened by PCR and all amplicons sequenced, thus allowing identification of polymorphic markers.
Entries from the diversity panel and from the KxO mapping population were screened separately on the three discovery arrays.
All but one of the 205 lines of the mapping population were screened for root growth in a hydroponics experiment under conditions essentially identical to those described in [ 23] except that it was a growth chamber with 12 hr day at 200 μMol s-1 m-2 PAR and temperatures 25/28°C day/night (unpublished).
Ten genotypes from each mapping population were screened on a PCR of 15 μl volume containing 12.2 μl water, 2 μl 10X DNA polymerase buffer, 1.6 μl dNTPs (2.5 mM each), 1 μl 5 μM of each primer, 0.2 μl Taq polymerase (MBI, Fermentas, USA) and 2 μl of genomic DNA (~50 ng).
