A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits.
BACKGROUND
Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers.


RESULTS
The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 +/- 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 +/- 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits.


CONCLUSIONS
Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.
Wenzl
Peter
P
Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia. peter@DiversityArrays.com
Li
Haobing
H
Carling
Jason
J
Zhou
Meixue
M
Raman
Harsh
H
Paul
Edie
E
Hearnden
Phillippa
P
Maier
Christina
C
Xia
Ling
L
Caig
Vanessa
V
Ovesná
Jaroslava
J
Cakir
Mehmet
M
Poulsen
David
D
Wang
Junping
J
Raman
Rosy
R
Smith
Kevin P
KP
Muehlbauer
Gary J
GJ
Chalmers
Ken J
KJ
Kleinhofs
Andris
A
Huttner
Eric
E
Kilian
Andrzej
A
D002874:Chromosome Mapping / Q000379:methods*; D018556:Crops, Agricultural / Q000235:genetics; D005819:Genetic Markers; D018745:Genome, Plant; D001467:Hordeum / Q000235:genetics*; D012150:Polymorphism, Restriction Fragment Length; D012091:Repetitive Sequences, Nucleic Acid; D016324:Sequence Tagged Sites
D005819:Genetic Markers