The libraries were subsequently quantified using the 2100 Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA, USA) and diluted to 100 p
Online PR News – 04-February-2018 – IA – The libraries were subsequently quantified using the 2100 Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA, USA) and diluted to 100 pM for emulsion PCR amplification. We multiplexed between 12 and 14 samples per run. The libraries were sequenced on the Ion Proton PI? Chips according to the manufacturer's protocol (Life Technologies, Grand Island, NY, USA). Raw reads were de-multiplexed according to their barcodes and the adapter/barcode sequences were removed using the standard Ion Torrent? Suite Software. Clean reads were mapped to the oil Kinase Inhibitor Library palm reference genome  using the Ion Torrent? Suite Software Alignment Plugin (Torrent Mapping Alignment Program Version 4.0.6) and the variants were called using the Ion Torrent VariantCaller (GATK v1.4-749-g8b996e2; Life Technologies, Grand Island, NY, USA). The following (default) parameter setting was applied: minimum sequence match on both sides of the variants ï¿½ï¿½ 5, minimum support for a variant to be evaluated ï¿½ï¿½ 6, minimum frequency of the variant to be reported ï¿½ï¿½ 0.15, and maximum relative strand bias ï¿½ï¿½ 0.8. The uniformity of base coverage was determined using the Ion Torrent Suite Software Coverage Analysis Plugin (Life Technologies, Grand Island, NY, USA), and it is defined as the percentage of bases in all targeted regions (or whole genome) covered by at least 0.2?ï¿½ï¿½ the average base coverage depth. To analyze the types of mutations from the GBS data caused by single nucleotide variations in the coding regions, we used the program SNPEff  Selleckchem BI 2536 with oil palm reference genome sequence and GFF annotation input files . Isotretinoin Since the mapping population was derived from a self-pollination of the F1 progeny, we first selected SNPs that were heterozygous in the F1 (clone A43/9) to ensure that they segregated in the F2 progeny. Moreover, we included only markers that were homozygous in the female parent (clone A) for mapping, so that the information on paternally inherited alleles could be inferred. The informative markers were expected to segregate in a 1:2:1 ratio and those that deviated significantly from the expected Mendelian segregation ratios (ï¿½ï¿½2 test P-value?0.01) were removed from further analysis. Linkage analysis was performed with JoinMap v 3.0  using the parameters set for the F2 population type. Initial assignment to linkage groups was based on the logarithm of the odds (LOD) threshold of 7.0 for each marker pair. We used linkages with a recombination rate (REC)?0.4, a map LOD value of 0.05 and a goodness-of-fit jump threshold of 5 for inclusion into the map and for the calculation of the linear order of the markers within a linkage group. Loci that were completely linked (i.e.