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Nevertheless, there were no significant differences among the 3 PSH accessions by using LSD analysis.
To determine the allelic constitutions at the four loci, we genotyped the 4 genes in each of the 53 photoperiod-insensitive accessions by using previously reported allele-specific DNA markers [ 7, 13, 29- 31].
In this study, association analysis was performed on 162 Tibetan wild accessions by using LDI activity, 835 Diversity Arrays Technology (DArT) markers and single nucleotide polymorphisms (SNPs) of the gene HvLDI encoding LDI.
First, we built a random model to predict the number of absent genes for a certain number of accessions by using data from the identified P/A genes in the 80 accessions.
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Moreover, identifiers or names of PTM proteins extracted from MS/MS papers or external resources were mapped to protein UniProtKB accession numbers by using the ID Mapping Service at UniProt (13).
To knockdown hSOCS7 gene (GenBank Accession: NM_014598.2), by using a hammerhead ribozyme transgene, we designed primers according to secondary structure of the gene generated by using Zuker's RNA mFold programme, targeting at a specific GUC or AUC site (Table 2).
The evolutionary history of these accessions was inferred by using the neighbor-joining tree98.
Nucleotide diversity for the entire regions of Hd6 in five O. sativa varieties and three O. rufipogon accessions was detected by using the program DnaSP that showed π values of 0.0018 and 0.0017, respectively.
Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses.
For development of g-SSR markers, four microsatellite enriched libraries [ CT 14, (AC 10, (GT 12 and (AAC 8] were constructed from genomic DNA of T. cordifolia accession (IC-281965) by using a streptavidin-biotin based enrichment approach.
To better characterize the geographic distribution of P/A polymorphisms, a reconciled tree was constructed to view the evolved P/A tree over an accession tree, built by using all SNPs of non-P/A genes (Additional file 3: Figure S5B).
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