Migratory plant parasitic nematodes from the genus Pratylenchus are major pests in
agriculture and attack a wide spectrum of crops leading to heavy losses up to 16% of grain yield
in barley. Breeding resistant varieties is the most effective and environmentally friendly
approach to control root lesion nematodes. A doubled haploid population derived from a cross
between the Turkish accession Beysehir and the old German variety Valentina were used for
genetic mapping of P. neglectus resistance QTLs. A genetic linkage map was constructed using
226 DH lines with 388 AFLP, SSR and CAPS markers that cover 1,051 cM on seven linkage
groups. Using nematode numbers which were counted 7 weeks after artificial infection, eight
QTLs were mapped by composite interval mapping on six linkage groups (2H, 3H, 4H, 5H, 6H
and 7H). Comparative QTL analysis revealed that two major QTLs are located at the same
position as previously described Pratylenchus resistance QTLs on chromosomes 5 and 6
(Rlnnp5H and Rlnnp6H) which had been mapped with two different. Two markers flanking
Rlnnp6H are being used to identify DH lines with recombinations within the QTL regions in a
large DH population of Beysehir × Valentina. Currently, 760 DH lines have been genotyped
with the two flanking markers and 35 recombinant DHs were identified. Recombinant DH lines
will be used for fine mapping of the QTL taking the markers selected by whole genome
sequencing of two phenotypic bulks. Two phenotypic bulks representing the distributional
extremes of the mapping population were subjected to whole genome sequencing using
Illumina HiSeq 2000 technology. Short reads from the susceptible bulk were aligned to the
barley reference genome sequence, and a consensus reference sequence was obtained. Reads
from the resistant bulk were mapped to the consensus reference sequence and variants between
the two bulks were identified. Homozygous variants densities were calculated across all
chromosomes in a sliding window of 1Mb using CLC Genomics Workbench 6.5. Preliminary
results show that a unique region with the highest variant density was localized at the same
position as one of the resistance QTL. Sequence analysis to identify resistance candidates is in
progress.