Genotyping-by-sequencing (GBS) is a cost-efficient method which can be useful for SNP marker discovery in a population of interest. GBS is genome reduction sequencing method using restriction enzyme. The quality of DNA is a key factor which could have an influence in downstream analysis. However, there have not been many studies which investigated the impact of DNA degradation and the quality of the data on marker discovery. In this study, GBS data of 6 Hanwoo samples (H1~6) showing differing level of DNA degradation were compared. Re-sequencing pipeline was followed to investigate the impact of DNA degradation on marker discovery. As a result, we found that the quantity and quality of SNPs were not affected in the sample H5 and H6 with moderately degraded DNA. On the other hand, marker discovery was greatly affected in samples with severe DNA degradation (H3 and H4). The findings in this study support that GBS is a robust genotyping method towards moderate DNA degradation.

Pepper (Capsicum spp.) germplasm shows diverse phenotypic variations including fruit size, color, pungency, and many other horticultural traits. Traditional markers including SSR, AFLP, and RFLP have been used to construct genetic maps using biparental populations. However to assess the genetic diversity of large number of germplasm, a robust and rapid marker development and genotyping approach is needed. We used six pepper accessions including C. annuum, C. chinense, C. baccatum and C. frutescens and performed genotyping-by-sequencing (GBS). To select the most appropriate condition, eight different 2 bp selective nucleotides were used to make GBS libraries. Selective nucleotide ‘OO’ showed the largest number of reads in all samples, and 11,026 to 47,957 high-quality SNPs were called in six accessions. When C. annuum ‘CM334’ genome sequence was used as a reference, C. annuum showed the smallest number of SNPs, while C. baccatum which was known to be a different Capsicum clade showed the largest number of SNPs. Pepper core collection chosen to represent the genetic diversity of whole germplasm will be genotyped by high-density SNPs developed from GBS. We will perform genome-wide association study (GWAS) using genetic and phenotypic variation to identify the functional genetic loci controlling horticultural traits.

Genotyping-by-sequencing (GBS) is a robust and rapid tool to develop SNP markers. Reduced sequencing complexity and multiplex sequencing of GBS has reduced genotyping cost for complex genome. However multiplex sequencing brings low sequencing depth which can lead to reduced number of markers. Therefore to find the appropriate condition for GBS is needed. In this research we demonstrated the use of ApeKI and selective primers for GBS of pepper (Capsicum spp.). Selective primers which amplify the GBS library with one or two flanking sequences to ApeKI site were used to increase sequencing depth. By in silico digestion, we developed six different selective primers amplify 4,000-400,000 regions. We made the GBS library with eight pepper accessions in four species using six selective primers and sequenced. Proper selective primers and pooling rate for each species will be determined. This approach will be useful for genotyping Capsicum breeding lines or populations by developing high quality SNP markers.

Downy mildew, caused by P. cubensis, is one of the most devastating diseases in cucumber (Cucumis sativus) worldwide. Due to the variation and mutation of the races of P. cubensis, host resistance in cucumber has been lost in recent years, so the identification of new sources of resistance is one of the most important targets in cucumber breeding programs. Moderate levels of resistance against downy mildew has been identified in different cucumber varieties. In this study, we identified new downy 2mildew resistance QTLs in cucumber using F2 mapping populations originated from the hybridization between breeding lines of cucumber. We used both classical QTL mapping based on SSR markers and GBS (gentyping based sequencing) based QTL mapping. In this presentation, detailed information about downy mildew resistance related QTL will be presented

Camelina is a promising energy crop for the biodiesel industry, especially for production of airplane fuel. In addition, its distinctive fatty acid profile and high protein contents satisfy the nutraceutical and animal feed uses. About 200 accession collected from all of the world were selected and evaluated during 2012, 2013 and 2014. The important agricultural traits were detemined by field and greenhouse conditions. In addition, genetic diversity was assessed by GBS approach. a total of 20 Camelina spp. (mostly C. sativa) accessions collected in different locations in Europe and showed different agronomic traits are sequenced. In this section, detail GBS analysis of camelina will be presented.