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With genotyped data of the markers, we constructed phylogenies of these populations with both DA and DC measures and performed a principal component analysis, as well as a clustering analysis by structure.
Using these markers, we constructed high-density genome-wide linkage maps, which we used to anchor, reorient, and rearrange scaffolds and to examine genome-wide recombination patterns.
In the present study, based on common biochemical parameters including routine and serum markers, we constructed a three-layer neural network which extended a back-propagation learning algorithm by introducing probabilistic treatment of the Bayesian inference technique for the synaptic weight[ 31].
To saturate the wheat genome with genetic markers, we constructed two genomic libraries generated using the methylation sensitive RE PstI combined with either the six base-pair cutting RE MluI (ACGCGT, methylation sensitive) or the four base-pair cutting RE MseI (AATT, methylation insensitive).
To facilitate the access and effective utilization of the Brassica SSR markers, we constructed an integrative database (http://oilcrops.info/SSRdb), which has search tools to obtain much useful information for the newly developed genome-wide SSR markers from the sequenced Brassica species and the previously developed publicly available Brassica SSR markers (Fig. 4).
Based on the calculated matrices of rm and rf values for all pairs of markers, we constructed the corresponding female and male maps using the algorithm described in Mester et al. (2003), with some modifications caused by the special features of intercross data.
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It was because of these early initial results that we chose pporRFP to include as the scorable FP marker when we constructed the versatile large pANIC vector set for Gateway-enabled monocot transformation [ 27].
To determine whether placing a miRNA in an intron can improve the expression of the miRNA and the marker gene, we constructed an artificial intron and placed the pre-miRNA in this intron (pCAG-RFP-miRint, Figure 2A; also see methods).
With the 398 individuals typed at 10,091 markers, we then constructed an initial genetic map by estimating recombination fractions calculated under the excess heterozygosity model and R/qtl's implemented Haldane mapping function with markers grouped and ordered by their physical position on the Sbi1 reference genome.
Together with the previously published SSR and CAPS markers [ 11], we constructed a linkage map with a total length of 289 cM consisting of 90 markers.
Using the 868 segregating markers defined above, we constructed an integrated linkage map for M. sinensis using JoinMap 4.1.
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