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GWAS 분석을 이용한 벼 지엽각 관련 SNP 동정 및 발현 분석

Gene expression and SNP identification related to leaf angle traits using a genome-wide association study in rice (Oryza sativa L.)

조용구|강권규|김미선|유의수
한국식물생명공학회 (Korean Society for Plant Biotechnology)|2018.03|Journal of Plant Biotechnology|제45권 제1호|pp. 17-29

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참고문헌

키워드

riceSNPGWAScore-collectionleaf angle
주제분류농학

초록

본 연구에서는 국내외에서 수집한 벼 294개 유전자원 핵심집단을 대상으로 벼의 지엽각 특성에 대한 조사를 수행하였고, GWAS를 이용하여 지엽각 연관 유전자를 추출 및 분석하였다. 표현형 데이터를 이용한 GWAS의 Manhattan plot 결과 분석을 통해, 각 집단에서 염색체를 대상으로 표현형과통계적 유의성을 나타내 연관성을 보이는 SNP를 발굴하였다. 지엽각 관련 특성에 대하여 선행 연구된 QTL region과의비교를 통하여 본 연구에서 발굴된 SNP간의 유의성을 조사한 결과, 지엽각과 유의성이 있는 SNP (S8-19815442)가 이미확인된 QTL region에 위치하는 것으로 나타났으며, 후보유전자 Os08g31950 대해 연관 유전자 변이를 관찰하기 위해서형질 특이적 품종군 간의 염기서열을 비교한 결과 1개의 지역에서 단일염기변이가 검출되었다. Os08g31950의 조직별RNA의 상대적 발현량 수준을 비교한 결과, Os08g31950 유전자는 모든 조직에서 높은 발현량을 확인할 수 있었으며 조직별로 다양한 발현 양상을 관찰할 수 있었다. 또한, 모두 직립형 품종군에서 상대적으로 발현량이 높게 나타났으며 뿌리보다 잎에서의 발현율이 높게 나타났다. 본 연구를 통해 동정된 지엽각 연관 후보유전자 Os08g31950는 벼 생육 및 수량증대에 이용할 수 있는 마커제작 및 육종의 기초자료가 될것으로 기대된다.

Abstract

This study was conducted to investigate a morphological trait in 294 rice accessions including Korean breeding lines. We also carried out a genome-wide association study (GWAS) to detect significant single nucleotide polymorphism markers and candidate genes affecting major agronomic traits. A Manhattan plot analysis of GWAS using morphological traits showed that phenotypic and statistical significance was associated with a chromosome in each group. The significance of SNPs that were detected in this study was investigated by comparing them with those found previously studied QTL regions related to agronomic traits. As a result, SNP (S8-19815442), which is significant with regard to leaf angle, was located in the known QTL regions. To observe gene mutations related to leaf angle in a candidate gene, Os08g31950, its sequences were compared with sequences in previously selected rice varieties. In Os08g31950, a single nucleotide mutation occurred in one region. To compare relative RNA expression levels of candidate gene Os08g31950, obtained from GWAS analysis of 294 rice accessions and related to lateral leaf angle, we investigated relative levels by selecting 10 erect leaf angle varieties and 10 horizontal leaf angle varieties and examining real-time PCR. In Os08g31950, a high level of expression and various expression patterns were observed in all tissues. Also, Os08g31950 showed higher expression levels in the erect leaf angle variety group and higher expression rates in the leaf than in the root. The candidate gene detected through GWAS would be useful in developing new rice varieties with improved yield potential through future molecular breeding.

참고문헌 (50)

  1. Sailila E Abdula, "Development and Identification of Transgenic Rice Lines with Abiotic Stress Tolerance by using a Full-length Overexpressor Gene Hunting System", Plant Breeding and Biotechnology, 1(1), pp.33~48 (2013), 한국육종학회[DOI]
  2. Abe A, "Genome sequencing reveals agronomically important loci in rice using MutMap", Nature Biotechnology, 30, pp.174~178 (2012)[DOI]
  3. Alexandrov N, "SNP-seek database of SNPs derived from 3000 rice genomes", Nucleic Acids Research, 43(D1), pp.1023~1027 (2015)[DOI]
  4. Altshule D, "Genetic mapping in human disease", Science, 322, pp.881~888 (2008)
  5. Asano K, "Genetic and molecular analysis of utility of sd1 alleles in rice breeding", Korean Journal of Breeding Science, 57, pp.53~58 (2007)[DOI]
  6. Ashikari M, "Cytokinin oxidase regulates rice grain production", Science, 309, pp.741~745 (2005)[DOI]
  7. Blawid R, "Discovering and sequencing new plant viral genomes by next-generation sequencing: description of a practical pipeline", Annals of Applied Biology, 170, pp.301~314 (2017)[DOI]
  8. Cai J, "QTLs for rice flag leaf traits in doubled haploid populations in different environments", Genetics and Molecular Research, 14(2), pp.6786~6795 (2015)[DOI]
  9. Castillo-Davis CI, "Selection for short introns in highly expressed genes", Nature Genetics, 31(4), pp.415~418 (2002)[DOI]
  10. Cheong HS, "Growth hormone-releasing hormone (GHRH) polymorphisms associated with carcass traits of meat in Korean cattle", BMC Genetics, 7, pp.35~40 (2006)
  11. Cho DS, "Studies on the productivity of individual leaf blade of paddy rice", Korean Journal of Breeding Science, 18, pp.1~27 (1975)
  12. Cho YG, "Integrated map of AFLP, SSLP, and RFLP markers using a recombinant inbred population of rice (Oryza sativa L.)", Theoretical and Applied Genetics, 97, pp.370~380 (1998)
  13. Dong Y, "Mapping of QTLs for leaf developmental behavior in rice (Oryza sativa L.)", Euphytica, 138, pp.169~175 (2004)[DOI]
  14. Feng Z, "SLG controls grain size and leaf angle by modulating brassinosteroid homeostasis in rice", Journal of Experimental Botany, 16(14), pp.4341~4253 (2016)
  15. Fujino K, "Diversification of the plantspecific hybrid glycine-rich protein (HyGRP) genes in cereals", Plant Science, 24, pp.489~ (2014)
  16. Garg AK, "Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses", Proceedings of the National Academy of Sciences of the United States of America, 99(25), pp.15898~15903 (2002)[DOI]
  17. Grandori G, "The Myc", Max, Annual Review of Cell and Developmental Biology, pp.2000, 16[DOI]
  18. Heang D, "Antagonistic actions of HLH", bHLH proteins are involved in grain length and weight in rice, 2012, pp.7, e31325~
  19. Hu WD, "Genetic analysis and QTL mapping of large flag leaf angle trait in Japonica rice", Rice Scienc, 19(4), pp.277~285 (2012)[DOI]
  20. Huang X, "High-throughput genotyping by whole-genome resequencing", Genome Research, 19, pp.1068~1076 (2009)
  21. Huang X, "Natural variation at the DEP1 locus enhances grain yield in rice", Nature Genetics, 41, pp.494~497 (2009)[DOI]
  22. Hunter KW, "The future of mouse QTL mapping to diagnose disease in mice in the age of whole-genome association studies", Annual Review of Genetics, 42, pp.131~141 (2008)[DOI]
  23. Jang S, "Rice leaf angle and grain size are affected by the OsBUL1 transcriptional activator complex", Plant Physiology, 173(1), pp.688~702 (2017)[DOI]
  24. Jung KH, "Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy", PLoS ONE, 3, pp.e3337~ (2008)[DOI]
  25. 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)[DOI]
  26. Kobayashi S, "Quantitative trait loci affecting flag leaf development in rice (Oryza sativa L.)", Breeding Science, 53, pp.255~262 (2003)[DOI]
  27. Kruglyak L, "The road to genome-wide association studies", Nature Reviews Genetics, 9(4), pp.314~318 (2008)
  28. Kump B, "Evaluation of genetic variability among common buckwheat (Fagopyrum esculentum Moench) population by RAPD markers", Plant Science, 114, pp.149~158 (1996)[DOI]
  29. Li J, "A novel strategy for detecting multiple loci in Genome-Wide Association Studies of complex diseases", International Journal of Bioinformatics Research and Applications, 4(2), pp.150~163 (2008)[DOI]
  30. Lipka AE, "GAPIT: genome association and prediction integrated tool", Bioinformatics, 28, pp.2397~2399 (2012)[DOI]
  31. Ma X, "Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing", Scientific Reports, 6, pp.27425~ (2016)[DOI]
  32. Massari ME, "Helix-loop-helix proteins: regulators of transcription in eukaryotic organisms", Molecular and Cellular Biology, 20, pp.429~440 (2000)[DOI]
  33. Nicolae DL, "Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS", PLoS Genetics, 6(4), pp.e1000888~ (2010)[DOI]
  34. 박현수, "자포니카 다수성 벼 드래찬과 보람찬 유래 약배양 계통을 이용한 이삭 및 수량관련 형질 분석 및 다수성 계통 육성", 한국육종학회지, 47(4), pp.384~402 (2015), 한국육종학회[DOI]
  35. Peng B, "OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice", Nature Communications, 5, pp.4847~ (2014)[DOI]
  36. Perez-de-Castro AM, "Application of genomic tools in plant breeding", Current Genomics, 13, pp.179~195 (2012)
  37. Sakai H, "Construction of pseudomolecule sequences of the Aus rice cultivar kasalath for comparative genomics of asian cultivated rice", DNA research, 21(4), pp.397~405 (2014)[DOI]
  38. Schatz MC, "New whole genome de nomo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica", bioRxiv (2014)[DOI]
  39. Shabalina SA, "The mammalian transcriptome and the function of non-coding DNA sequences", Genome Biology, 5(4), pp.105~ (2004)[DOI]
  40. Sladek R, "A genome-wide association study identifies novel risk loci for type 2 diabetes", Nature, 445(7130), pp.881~885 (2007)
  41. Su JJ, "Identification of favorable SNP alleles and candidate genes fortraits related to early maturity via GWAS in upland cotton", BMC Genomics, 17, pp.687~ (2016)[DOI]
  42. Sugimoto K, "Molecular coloning of Sdr4, a regulator incolced in seed dormancy and domestication of rice", Preceedings of the National Academy of Sciences of the United States of America, 107, pp.5792~5797 (2010)
  43. Takagi H, "MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii", New Phytoloist, 200, pp.276~283 (2013)
  44. Tanaka A, "BRASSINOSTEROID UPREGULATED1, encoding a helix-loop-helix protein, is a novel gene involved in brassinosteroid signaling and controls bending of the lamina joint in rice", Plant Physiology, 151, pp.669~680 (2009)[DOI]
  45. Toledo-Ortiz G, "The Arabidopsis basic", helix-loop-helix transcription factor family, 2003, pp.15, 1749~1770
  46. Wallace C, "Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia", American Journal of Human Genetics, 82(1), pp.139~149 (2008)[DOI]
  47. Weedon MN, "A common variant of HMGA2 is associated with adult and childhood height in the general population", Nature Genetics, 39(10), pp.1245~1250 (2007)[DOI]
  48. Y H, "Map-based cloning of qSD1-2 identified a gibberellin synthesis gene regulating the development of endosperm-imposed dormancy in rice", Plant Physiology, 169, pp.152~165 (2015)
  49. Zhang LY, "Antagonistic HLH", bHLH transcription factors mediate brassinosteroid regulation of cell elongation and plant development in rice and Arabidopsis, 2009, pp.21, 3767~3780
  50. Zhang Z, "Mixed linear model approach adapted for genome-wide association studies", Nature Genetics, 42, pp.355~360 (2010)[DOI]

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