온대자포니카 벼 품종의 등숙기 종자 내 카드뮴 함량에 관한 전장유전체연관분석
Genome-wide Association Study on Cadmium Contents of Temperate Japonica Varieties
2
조회
0
다운로드
1
인용
0
참고문헌
키워드
초록
본 연구는 비오염지 논에서 재배된 벼 품종 280점의 카드뮴함량의 차이를 조사하고 카드뮴 함량과 관련된 유전자를 확인하고자 수행하였다. 벼 종자를 산분해법으로 전처리 한 뒤 유도결합플라즈마질량분석기(ICP-MS)로 카드뮴 함량을 분석한 결과평균 0.943 (0.050~5.699) ㎍/㎏ 수준이었다. 그리고 국내외에서 수집한 유전자원 280점을 선발하여 생태형 (온대자포니카, 열대자포니카, 인디카, Aus, Aromatic 및 Admixture) 별로 구분한 뒤, 전장유전체(whole genome)에 대한 유전자 분석 및 각각의 염색체에 대한 단일염기다형성(SNP)을 분석한 후 온대자포니카 계통 182점의 등숙기 종자 내 카드뮴 함량을 전장유전체분석하여 카드뮴과 연관된 후보유전자를 확인하였다. 그리고Os01g0611300, Os01g0611900, Os01g0611950, Os01g0612 000, Os01g0612200, Os11g0444400, Os11g0444700, Os11g 0444800 및 Os11g0444900 등의 후보유전자가 쌀알 중의 카드뮴 함량과 강한 상관관계가 있음을 확인하였다. 후보유전자들에대한 haplotype 분석 결과 온대자포니카 임에도 allele들을 갖는염색체 1번의 9개 품종과 염색체 11번의 33개 품종은 인디카에서 유래되어 온 품종들일 가능성이 높을 것으로 판단되었고, 인디카가 대체적으로 자포니카에 비해 등숙기 종자 내 카드뮴함량이 높다는 기존의 보고들과 유사하였다.
Abstract
Objective of this study was to investigate the difference of cadmium (Cd) levels in rice grains from non-polluted fields and to define the gene associated with Cd uptake for producing safety food. Cd was analyzed by Inductively Coupled Plasma Mass Spectrometer (ICP-MS). The average concentration of Cd in rice grains was 0.943 ㎍/㎏ and Cd levels ranged from 0.050 to 5.699 ㎍/㎏. Genome-Wide Association study (GWAS) based on phenotype data for Cd levels was performed. However, results of GWAS were affected by subpopulation structure and caused false positive. Therefore, GWAS for rice ecotypes (temperate Japonica, tropical Japonica, Indica, Aus, Aromatic, and Admixture) was performed to minimize false positive. GWAS results showed that Os01g0611300, Os01g0611900, Os01g0611950, Os01g0612000, Os01g0612200, Os11g0444400, Os11g0444700, Os11g0444800, and Os11g0444900 genes have significant correlation with Cd levels in rice grains. The sequences of these genes were compared to sequence positions of each other gene (haplotype analysis). According to the results of haplotype analysis, Cd levels of non-synonymous group were higher than other groups and sequence of non-synonymous group was similar to that of Indica. These results were corresponding to the previous research result that Cd levels of Indica were higher than Japonica. Therefore, candidate genes detected through GWAS need to be examined by knock-out or cross breeding.
참고문헌 (17)
- Arao T., "Genotypic variations in cadmium levels of rice grain", Soil Sci. Plant Nutr, 49, pp.473~479 (2003)
- Arao T, "Genotypic differences in cadmium concentration and distribution of soybean and rice", JARQ, 40, pp.21~30 (2006)
- Horiguchi H, "Latest status of cadmium accumulation and its effects on kidneyes, bone, and erythropoiesis in inhabitants of the formerly cadmium-polluted Jinzu River Basin in Toyama, Japan, after restoration of rice paddies", Int.Arch.Occup. Environ. Health, 83, pp.953~970 (2010)
- Huang X, "Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm", Nature genetics, 44, pp.32~39 (2012)
- "Joint FAO", WHO Expert Committee on Food Additives, 2010, pp.73~
- Kim KW, "PowerCore:a program applying the advanced M strategy with a heuristic search for establishing core sets", Bioinformatics, 23, pp.2371~2162 (2007)
- Kim TS, "Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era", BMC Genomics, 17, pp.408~ (2016)
- 김원일, "광산인근 논토양의 카드뮴 존재형태와 쌀의 카드뮴의 함량과의 관계", 한국토양비료학회지(Korean Journal of Soil Science and Fertilizer), 41(3), pp.184~189 (2008), 한국토양비료학회
- Lee S, "Over-expression of OsIRT1 leads to increased iron and zinc accumulations in rice", Plant Cell Environ, 32, pp.408~416 (2009)
- Lipka AE, "GAPIT: genome association and prediction integrated tool", Bioinformatics, 28, pp.2397~2399 (2012)
- Morishita T, "Varietal differences in cadmium levels of rice grains of Japonica, Indica, Javanica, and hybrid varieties produced in the same plot of a field", Soil Sci. Plant Nutr, 33, pp.629~637 (1986)
- Setakis E, "Logistic regression protects against population structure in genetic association studies", Genome Res, 16, pp.290~296 (2006)
- Takijima Y, "Cadmium contamination of soils and rice plants caused by zinc mining. Ⅲ. Effects of water management and applied organic manures on the control of Cd uptake by plants", Soil Sci. Plant Nutr, 19, pp.183~193 (1973)
- Uraguchi S, "Cadmium transport and tolerance in rice: perspectives for reducing grain cadmium accumulation", Rice, 5, pp.5~ (2012)
- Yoon MY., "Genome-wide Association studies (GWAS) of related genes for flowering time in rice core set", pp.2016
- Yuko AK, "Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing", Plant Cell Physiol, 52, pp.274~282 (2011)
- Zhang Z, "Mixed linear model approach adapted for genome-wide association studies", Nature genetics, 42, pp.355~360 (2010)