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Since mapping was based on different population designs (i.e. F1 or F2) and the total number of mapped markers varied between populations, a consensus order of loci common between mapping populations was determined and used as fixed order for mapping.
It is noteworthy that no difference in R2 values for qMel-1 and qMel-3 between the 2 mapping populations was observed.
The DNA of the mapping populations was extracted according to the experimental protocols of Rice Genome Research Program (RGP) (http://rgp.dna.affrc.go.jp/E/rgp/protocols/index.html, written in Japanese) with some modifications.
We found that the reproducibility of clustering profiles among two mapping populations was very high.
Linkage analysis for both mapping populations was performed with the JoinMap® 4.0 software [ 55].
Marker segregation distortion in each of the mapping populations was investigated employing Joinmap 4.0 software [ 29].
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Three bi-parental mapping populations were used to develop the genetic map for organizing scaffolds into pseudomolecules.
Large mapping populations are being used to study the genetics of a range of viticultural and resistance traits.
The genotypic data for the two mapping populations were downloaded from http://ricediversity.org/data.org/data
The main limitation with QTL detection in these mapping populations is the large size of the confidence interval.
The parental lines of two mapping populations were exposed to a pulse stress of 1,000 mg L−1 Fe2+ in hydroponics.
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