Barley is an economically important cereal crop grown under diverse environmental conditions and ranked fourth in terms of production volume. Barley is a diploid self-fertilizing plant with seven chromosomes, and has a 5.1 Gbp genome with more than 80% repeat sequences. Whole genome re-sequencing (WGR) has provided substantial information on sequence variation distributed on all chromosomes, such as single nucleotide polymorphisms, insertions, and deletions, which are used in the development of DNA markers. In this study, we performed WGR to detect sequence variations among six Korean malting varieties. An average of 92,552 insertions and deletions (InDels) were detected in these varieties in comparison to the high-quality reference genome sequences. The InDel density of the six Korean malting varieties ranged from 17 to 19 InDel/1Mbp with an average of 18 InDel/1Mbp. No InDel could be detected in 193 regions in all chromosomes except chr. unassigned. One interval with high-density InDel, more than 150 InDel/1Mbp, was located on the 1H, 3H, 6H, and 7H chromosomes. A total of 145 InDel markers were developed using 225 large-InDel markers, longer than 50 bp. Seventeen large-InDel makers showed polymorphisms among 31 malting barley varieties. These 31 malting barley varieties were divided into four groups based on phylogenetic analysis. These results presented a development method of agarose-resolvable large-InDel markers using WGR. Seventeen polymorphic large-InDel markers were used to conserve and identify barley germplasms. This vast information on sequence variation in six Korean malting barleys could be used for the development of DNA markers and marker-assisted selection.

The next generation sequencing (NGS) has been developed rapidly in recent years, paving ways of discovering vast sequence variations among germplasms. Whole-genome sequencing was performed on the genomic DNA of Milyang23 and Gihobyeo using NGS and developed new CAPS (cleaved amplified polymorphic sequence) markers based on the single nucleotide polymorphisms (SNPs) in coding sequence between these varieties. The NGS sequencing yielded sequences of 60x coverage of the Nipponbare reference genome on average. A molecular genetic map was constructed with the recombinant inbred population derived from Milyang23/Gihobyeo cross (MGRIL) integrating the newly developed 146 CAPS makers and previously reported 219 PCR-based DNA markers. This map was applied to the detection of quantitative trait loci (QTLs) for stem internode diameters, culm length and panicle length in rice with MGRIL population. A total of 4 new QTLs were detected for stem diameter traits including the first internode diameter (I1D), second internode diameter (I2D), third internode diameter (I3D), and fourth internode diameter (I4D). Among stem diameter QTLs, qI1D5 had relatively 6.09 LOD (likelihood of odds) score and explained 8.99% of total variation. Only very small portion of SNPs through re-sequencing were used in this study. Much more markers can be developed by using SNP information acquired in this study, which will enable construction of high-density genetic map and more accurate QTL analysis of important agronomical traits with MGRIL population.