메뉴 건너뛰기




Volumn 112, Issue 39, 2015, Pages E5411-E5419

Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

Author keywords

Breeding signature; GWAS; Resequencing; Rice improvement

Indexed keywords

AGRONOMIC TRAIT; ARTICLE; ASIA; BREEDING; CHINA; CROP IMPROVEMENT; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOMICS; GRAIN YIELD; NONHUMAN; PLANT GENOME; POPULATION GENETIC STRUCTURE; PRIORITY JOURNAL; RICE; RICE IMPROVEMENT; BIOLOGY; GENETIC MARKER; GENETIC SELECTION; GENETIC VARIATION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GROWTH, DEVELOPMENT AND AGING; HISTORY; ORYZA; PLANT BREEDING; PROCEDURES; REGRESSION ANALYSIS;

EID: 84942845644     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1515919112     Document Type: Article
Times cited : (166)

References (49)
  • 2
    • 84867875610 scopus 로고    scopus 로고
    • A map of rice genome variation reveals the origin of cultivated rice
    • Huang X, et al. (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490(7421): 497-501.
    • (2012) Nature , vol.490 , Issue.7421 , pp. 497-501
    • Huang, X.1
  • 3
    • 78049332150 scopus 로고    scopus 로고
    • Genome-wide association studies of 14 agronomic traits in rice landraces
    • Huang X, et al. (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42(11): 961-967.
    • (2010) Nat Genet , vol.42 , Issue.11 , pp. 961-967
    • Huang, X.1
  • 4
    • 84655176647 scopus 로고    scopus 로고
    • Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm
    • Huang X, et al. (2012) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44(1): 32-39.
    • (2012) Nat Genet , vol.44 , Issue.1 , pp. 32-39
    • Huang, X.1
  • 5
    • 84903595019 scopus 로고    scopus 로고
    • Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism
    • Chen W, et al. (2014) Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nat Genet 46(7): 714-721.
    • (2014) Nat Genet , vol.46 , Issue.7 , pp. 714-721
    • Chen, W.1
  • 6
    • 84946080193 scopus 로고    scopus 로고
    • RiceVarMap: A comprehensive database of rice genomic variations
    • Zhao H, et al. (2015) RiceVarMap: A comprehensive database of rice genomic variations. Nucleic Acids Res 43(Database issue): D1018-D1022.
    • (2015) Nucleic Acids Res , vol.43 , Issue.DATABASE ISSUE , pp. D1018-D1022
    • Zhao, H.1
  • 7
    • 69749099417 scopus 로고    scopus 로고
    • Fast model-based estimation of ancestry in unrelated individuals
    • Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19(9): 1655-1664.
    • (2009) Genome Res , vol.19 , Issue.9 , pp. 1655-1664
    • Alexander, D.H.1    Novembre, J.2    Lange, K.3
  • 9
    • 0028191783 scopus 로고
    • A diallel analysis of heterosis in elite hybrid rice based on RFLPs and microsatellites
    • Zhang Q, et al. (1994) A diallel analysis of heterosis in elite hybrid rice based on RFLPs and microsatellites. Theor Appl Genet 89(2-3): 185-192.
    • (1994) Theor Appl Genet , vol.89 , Issue.2-3 , pp. 185-192
    • Zhang, Q.1
  • 11
    • 33745516652 scopus 로고
    • Rice breeding in China
    • (International Rice Research Institute, Philippines)
    • Shen J (1980) Rice breeding in China. Rice Improvement in China and Other Asian Countries (International Rice Research Institute, Philippines), pp 9-30.
    • (1980) Rice Improvement in China and Other Asian Countries , pp. 9-30
    • Shen, J.1
  • 13
    • 84877851614 scopus 로고    scopus 로고
    • Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
    • Cavanagh CR, et al. (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci USA 110(20): 8057-8062.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.20 , pp. 8057-8062
    • Cavanagh, C.R.1
  • 14
    • 77649260327 scopus 로고    scopus 로고
    • Population differentiation as a test for selective sweeps
    • Chen H, Patterson N, Reich D (2010) Population differentiation as a test for selective sweeps. Genome Res 20(3): 393-402.
    • (2010) Genome Res , vol.20 , Issue.3 , pp. 393-402
    • Chen, H.1    Patterson, N.2    Reich, D.3
  • 15
    • 0037173012 scopus 로고    scopus 로고
    • Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene
    • Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci USA 99(13): 9043-9048.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.13 , pp. 9043-9048
    • Spielmeyer, W.1    Ellis, M.H.2    Chandler, P.M.3
  • 16
    • 79960616753 scopus 로고    scopus 로고
    • Artificial selection for a green revolution gene during japonica rice domestication
    • Asano K, et al. (2011) Artificial selection for a green revolution gene during japonica rice domestication. Proc Natl Acad Sci USA 108(27): 11034-11039.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.27 , pp. 11034-11039
    • Asano, K.1
  • 17
    • 0002760245 scopus 로고
    • Breeding rice for resistance to bacterial blight
    • (International Rice Research Institute, Philippines)
    • Khush G, Mackill D, Sidhu G (1989) Breeding rice for resistance to bacterial blight. Bacterial Blight of Rice (International Rice Research Institute, Philippines), pp 207-217.
    • (1989) Bacterial Blight of Rice , pp. 207-217
    • Khush, G.1    Mackill, D.2    Sidhu, G.3
  • 18
    • 1342333402 scopus 로고    scopus 로고
    • Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein
    • Sun X, et al. (2004) Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. Plant J 37(4): 517-527.
    • (2004) Plant J , vol.37 , Issue.4 , pp. 517-527
    • Sun, X.1
  • 19
    • 84863049130 scopus 로고    scopus 로고
    • Ortholog alleles at Xa3/Xa26 locus confer conserved race-specific resistance against Xanthomonas oryzae in rice
    • Li HJ, Li XH, Xiao JH, Wing RA, Wang SP (2012) Ortholog alleles at Xa3/Xa26 locus confer conserved race-specific resistance against Xanthomonas oryzae in rice. Mol Plant 5(1): 281-290.
    • (2012) Mol Plant , vol.5 , Issue.1 , pp. 281-290
    • Li, H.J.1    Li, X.H.2    Xiao, J.H.3    Wing, R.A.4    Wang, S.P.5
  • 20
    • 84863260667 scopus 로고    scopus 로고
    • The rice pentatricopeptide repeat protein RF5 restores fertility in Hong-Lian cytoplasmic male-sterile lines via a complex with the glycine-rich protein GRP162
    • Hu J, et al. (2012) The rice pentatricopeptide repeat protein RF5 restores fertility in Hong-Lian cytoplasmic male-sterile lines via a complex with the glycine-rich protein GRP162. Plant Cell 24(1): 109-122.
    • (2012) Plant Cell , vol.24 , Issue.1 , pp. 109-122
    • Hu, J.1
  • 21
    • 56549095978 scopus 로고    scopus 로고
    • Pentatricopeptide repeat proteins: A socket set for organelle gene expression
    • Schmitz-Linneweber C, Small I (2008) Pentatricopeptide repeat proteins: A socket set for organelle gene expression. Trends Plant Sci 13(12): 663-670.
    • (2008) Trends Plant Sci , vol.13 , Issue.12 , pp. 663-670
    • Schmitz-Linneweber, C.1    Small, I.2
  • 22
    • 23044455690 scopus 로고    scopus 로고
    • Cytokinin oxidase regulates rice grain production
    • Ashikari M, et al. (2005) Cytokinin oxidase regulates rice grain production. Science 309(5735): 741-745.
    • (2005) Science , vol.309 , Issue.5735 , pp. 741-745
    • Ashikari, M.1
  • 23
    • 80955166184 scopus 로고    scopus 로고
    • Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice
    • Li M, et al. (2011) Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice. Plant Biotechnol J 9(9): 1002-1013.
    • (2011) Plant Biotechnol J , vol.9 , Issue.9 , pp. 1002-1013
    • Li, M.1
  • 24
    • 0033784150 scopus 로고    scopus 로고
    • Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint
    • Yamamuro C, et al. (2000) Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint. Plant Cell 12(9): 1591-1606.
    • (2000) Plant Cell , vol.12 , Issue.9 , pp. 1591-1606
    • Yamamuro, C.1
  • 25
    • 84862993359 scopus 로고    scopus 로고
    • Comparative population genomics of maize domestication and improvement
    • Hufford MB, et al. (2012) Comparative population genomics of maize domestication and improvement. Nat Genet 44(7): 808-811.
    • (2012) Nat Genet , vol.44 , Issue.7 , pp. 808-811
    • Hufford, M.B.1
  • 26
    • 84867129056 scopus 로고    scopus 로고
    • Plant nitrogen assimilation and use efficiency
    • Xu G, Fan X, Miller AJ (2012) Plant nitrogen assimilation and use efficiency. Annu Rev Plant Biol 63(63): 153-182.
    • (2012) Annu Rev Plant Biol , vol.63 , Issue.63 , pp. 153-182
    • Xu, G.1    Fan, X.2    Miller, A.J.3
  • 27
    • 31944446171 scopus 로고    scopus 로고
    • Over-expression of the rice OsAMT1-1 gene increases ammonium uptake and content, but impairs growth and development of plants under high ammonium nutrition
    • Hoque MS, Masle J, Udvardi MK, Ryan PR, Upadhyaya NM (2006) Over-expression of the rice OsAMT1-1 gene increases ammonium uptake and content, but impairs growth and development of plants under high ammonium nutrition. Funct Plant Biol 33(2): 153-163.
    • (2006) Funct Plant Biol , vol.33 , Issue.2 , pp. 153-163
    • Hoque, M.S.1    Masle, J.2    Udvardi, M.K.3    Ryan, P.R.4    Upadhyaya, N.M.5
  • 28
    • 79959241413 scopus 로고    scopus 로고
    • Genomic inflation factors under polygenic inheritance
    • Yang J, et al.; GIANT Consortium (2011) Genomic inflation factors under polygenic inheritance. Eur J Hum Genet 19(7): 807-812.
    • (2011) Eur J Hum Genet , vol.19 , Issue.7 , pp. 807-812
    • Yang, J.1
  • 29
    • 0036937858 scopus 로고    scopus 로고
    • Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice
    • Xing Z, et al. (2002) Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theor Appl Genet 105(2-3): 248-257.
    • (2002) Theor Appl Genet , vol.105 , Issue.2-3 , pp. 248-257
    • Xing, Z.1
  • 30
    • 0037418206 scopus 로고    scopus 로고
    • Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid
    • Hua J, et al. (2003) Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 100(5): 2574-2579.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.5 , pp. 2574-2579
    • Hua, J.1
  • 31
    • 79952299301 scopus 로고    scopus 로고
    • Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers
    • Yu H, et al. (2011) Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS One 6(3): e17595.
    • (2011) PLoS One , vol.6 , Issue.3
    • Yu, H.1
  • 32
    • 77953796079 scopus 로고    scopus 로고
    • Parent-independent genotyping for constructing an ultrahighdensity linkage map based on population sequencing
    • Xie W, et al. (2010) Parent-independent genotyping for constructing an ultrahighdensity linkage map based on population sequencing. Proc Natl Acad Sci USA 107(23): 10578-10583.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.23 , pp. 10578-10583
    • Xie, W.1
  • 33
    • 84922203325 scopus 로고    scopus 로고
    • Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice
    • Yang W, et al. (2014) Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Nat Commun 5: 5087.
    • (2014) Nat Commun , vol.5 , pp. 5087
    • Yang, W.1
  • 34
    • 84898720249 scopus 로고    scopus 로고
    • A high-density SNP genotyping array for rice biology and molecular breeding
    • Chen H, et al. (2014) A high-density SNP genotyping array for rice biology and molecular breeding. Mol Plant 7(3): 541-553.
    • (2014) Mol Plant , vol.7 , Issue.3 , pp. 541-553
    • Chen, H.1
  • 35
    • 84891153631 scopus 로고    scopus 로고
    • A whole-genome SNP array (RICE6K) for genomic breeding in rice
    • Yu H, Xie W, Li J, Zhou F, Zhang Q (2014) A whole-genome SNP array (RICE6K) for genomic breeding in rice. Plant Biotechnol J 12(1): 28-37.
    • (2014) Plant Biotechnol J , vol.12 , Issue.1 , pp. 28-37
    • Yu, H.1    Xie, W.2    Li, J.3    Zhou, F.4    Zhang, Q.5
  • 36
    • 0030829363 scopus 로고    scopus 로고
    • Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid
    • Yu SB, et al. (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 94(17): 9226-9231.
    • (1997) Proc Natl Acad Sci USA , vol.94 , Issue.17 , pp. 9226-9231
    • Yu, S.B.1
  • 37
    • 84866876710 scopus 로고    scopus 로고
    • Genetic composition of yield heterosis in an elite rice hybrid
    • Zhou G, et al. (2012) Genetic composition of yield heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 109(39): 15847-15852.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.39 , pp. 15847-15852
    • Zhou, G.1
  • 38
    • 84906663723 scopus 로고    scopus 로고
    • Predicting hybrid performance in rice using genomic best linear unbiased prediction
    • Xu S, Zhu D, Zhang Q (2014) Predicting hybrid performance in rice using genomic best linear unbiased prediction. Proc Natl Acad Sci USA 111(34): 12456-12461.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.34 , pp. 12456-12461
    • Xu, S.1    Zhu, D.2    Zhang, Q.3
  • 39
    • 78651096904 scopus 로고    scopus 로고
    • A core collection and mini core collection of Oryza sativa L. in China
    • Zhang H, et al. (2011) A core collection and mini core collection of Oryza sativa L. in China. Theor Appl Genet 122(1): 49-61.
    • (2011) Theor Appl Genet , vol.122 , Issue.1 , pp. 49-61
    • Zhang, H.1
  • 40
    • 9144233515 scopus 로고    scopus 로고
    • Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program
    • Yu SB, et al. (2003) Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program. Theor Appl Genet 108(1): 131-140.
    • (2003) Theor Appl Genet , vol.108 , Issue.1 , pp. 131-140
    • Yu, S.B.1
  • 41
    • 67849085011 scopus 로고    scopus 로고
    • Genetic assessment of a mini-core subset developed from the USDA rice genebank
    • Agrama H, et al. (2009) Genetic assessment of a mini-core subset developed from the USDA rice genebank. Crop Sci 49(4): 1336-1346.
    • (2009) Crop Sci , vol.49 , Issue.4 , pp. 1336-1346
    • Agrama, H.1
  • 42
    • 68149145780 scopus 로고    scopus 로고
    • Genomewide SNP variation reveals relationships among landraces and modern varieties of rice
    • McNally KL, et al. (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci USA 106(30): 12273-12278.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.30 , pp. 12273-12278
    • McNally, K.L.1
  • 43
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of Phylogenetics and Evolution in R language
    • Paradis E, Claude J, Strimmer K (2004) APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20(2): 289-290.
    • (2004) Bioinformatics , vol.20 , Issue.2 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 44
    • 84907150192 scopus 로고    scopus 로고
    • The map-based sequence of the rice genome
    • International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436(7052): 793-800.
    • (2005) Nature , vol.436 , Issue.7052 , pp. 793-800
  • 45
    • 34547110828 scopus 로고    scopus 로고
    • A new approach for using genome scans to detect recent positive selection in the human genome
    • Tang K, Thornton KR, Stoneking M (2007) A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol 5(7): e171.
    • (2007) PLoS Biol , vol.5 , Issue.7 , pp. e171
    • Tang, K.1    Thornton, K.R.2    Stoneking, M.3
  • 46
    • 80053372166 scopus 로고    scopus 로고
    • FaST linear mixed models for genome-wide association studies
    • Lippert C, et al. (2011) FaST linear mixed models for genome-wide association studies. Nat Methods 8(10): 833-835.
    • (2011) Nat Methods , vol.8 , Issue.10 , pp. 833-835
    • Lippert, C.1
  • 47
    • 84862260334 scopus 로고    scopus 로고
    • Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets
    • Li MX, Yeung JM, Cherny SS, Sham PC (2012) Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum Genet 131(5): 747-756.
    • (2012) Hum Genet , vol.131 , Issue.5 , pp. 747-756
    • Li, M.X.1    Yeung, J.M.2    Cherny, S.S.3    Sham, P.C.4
  • 48
  • 49
    • 85136354327 scopus 로고    scopus 로고
    • Ridge regression and other kernels for genomic selection with R package rrBLUP
    • Endelman JB (2011) Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome 4(3): 250-255.
    • (2011) Plant Genome , vol.4 , Issue.3 , pp. 250-255
    • Endelman, J.B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.