It has approximately 1,500 mapped DNA markers comprised of approximately 700 mapped unigenes with the remainder amplified fragment length polymorphisms (AFLPs), restriction fragment length polymorphisms (RFLPs) and simple sequence repeats (SSRs) [ 14].
The sizes of the bands resolved by T-RFLP were determined by comparing their relative position with known size markers, comprised of bands equivalent to 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900 and 1000 bases of single-stranded DNA (microSTEP 15a [700 nm], Microzone, Lewes, UK).
A set of 1063 markers comprising of 521 Rice Microsatellite (RM), 139 Genic Non Coding Microsatellite (GNMS), 388 Hypervariable Simple Sequence Repeat (HvSSR) and 15 gene based markers were used for polymorphism survey between Pusa1266 and Jaya.
As an additional validation step we examined the expression profiles of a panel of 39 known cell-specific markers, comprised predominantly of CD antigens [see Additional file 1].
This sub-set of markers comprised 2,508.4 Mb of the genome, with a mean distance between markers of 4.90 ± 2.89 kb.
The combined dataset of the three genetic markers comprised the sequences of three outgroup species, 38 Burkholderia species, five nodulating endophytes and the endophytes of 28 gousiekte-inducing plants.
Interestingly, genotyped markers comprised over 95% of all selected features, with many (60) SMP response predictions based solely on marker features.
The final set of markers comprised 23 SNPs and 11 INDELs, which were arrayed in a hierarchical assay structure in 68 wells of a 96-well plate (one primer pair per well was used) (Figure 2).
Moreover, the number of markers comprising bins of common frequency (6,894,397 markers with MAF > 0.05) is much lower than the number of markers comprising bins of low frequency (23,178,341 markers with MAF < 0.05), which usually have low imputation quality.
H e t e r o z y g o c i t y H = 1 - ∑ i n P i 2 P r o b a b i l i t y o fi d e n t i t y P I = ∑ i = 1 n x i 2 P r o b a b i l i t y o f r a n d o m m a t c h P M = 1 x i f o r a s i n g l e m a r k e r The vervet multiplex assay was developed by including eight human STR markers, all comprised of tetranucleotide repeats.
The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA) and three non-coding (trnH-psbA, atpF atpH, and psbK psbI) loci.
