Composite map marker details, component map(s) marker origins and multicopy DArT marker information is presented in Additional file 1. Marker-order correlations between composite map and component map linkage groups; the GU-SA component map is not shown as this map was used as the seed-map (i.e. provided a fixed-order and all correlations were 1.0).
Second, it divides the data into (1) markers with information present in both the reference and the test set (the T part), and (2) markers with information present only in the reference set ("untyped", the U part).
Based on these two types of additive genetic relationships, both pedigree-based, marker-based and combined relationships based on both pedigree and marker information are presented.
Maps for the 29 chromosomes including marker information, informative meioses and map positions are presented in Additional file 1 (SalmonLinkageMapSept2010.txt).
The marker information generated in the present study was made publicly accessible through a user-friendly web-resource, "Chickpea ISM-ILP Marker Database".
To take into account the additional information present in adjacent markers, Dijk for all markers on a chromosome were analyzed jointly using a likelihood-based interval mapping (IA) method [ 40], as implemented by Heifetz et al. [ 18] for a backcross but with additional adjustments for autosomal and Z chromosomes in an F6 population.
Using SNP marker information in rat, it was already shown that this effect was present [ 5, 6] and here we confirm this observation on a genome-wide scale.
This so-called interval mapping approach and its extensions [3] [5] is robust and powerful for the detection of major QTL and presents the most efficient way to utilize marker information when marker maps are sparse [6].
For a scenario with a large number of genotyped animals whose marker information does not provide information for the parameter estimation, Appendix B presents a method for breeding value estimation where only part of the needs to be computed.
This clone has been submitted to transcriptome sequencing in the present work, with the aim to augment the available gene sequence and marker information for this crop.
