DNA Degradation이 Genotyping-by-Sequencing(GBS) 자료 기반 한우 유전적 표지 발굴에 미치는 영향
Effects of DNA Degradation on the Genotyping-by-Sequencing (GBS) Data for Genetic Marker Discovery of Hanwoo Population
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초록
Genotyping-by-sequencing(GBS)은 저렴하면서도 효율적인 유전적 표지 발굴 방법으로, 집단 분석을 통한 SNP(single nucleotide polymorphism) 발굴에 있어 사용될 수 있다. 제한 효소를 이용하여 유전체의 일부분을 sequencing 하는 GBS의 특성상, DNA의 품질은 GBS 연구의 후속 과정에 영향을 끼칠 수 있다. 그러나 DNA degradation 및 품질이 GBS 기반 유전적 지표 발굴에 있어서 끼치는 영향에 대한 연구는 많이 이루어지지 않은 상황이다. 본 연구는 DNA degradation 정도가 다른 한우 집단 GBS 자료를 이용하여 비교분석을 수행하였다. Re-sequencing 파이프라인을 따라서 DNA degradation이 유전적 표지 발굴에 어떠한 영향을 끼치는지 조사하였으며, 그 결과, DNA degradation이 일부 진행된 H5, H6 시료에서는 degradation이 SNP의 양과 품질에 큰 영향을 끼치지 않는다는 것을 확인하였고, 높은 수준으로 DNA degradation이 진행된 경우(H3, H4) 유전적 표지 발굴에 있어서 문제가 된다는 것을 확인하였다. 이는 GBS 연구가 일정 수준의 degradation에 대해서는 강경한 방법이라는 점을 뒷받침 한다.
Abstract
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.
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