Genic and nongenic contributions to natural variation of quantitative traits in maize

Genome Research

Volumn 22, Issue 12, 2012, Pages 2436-2444

  Li, Xianran ^a   Zhu, Chengsong ^a   Yeh, Cheng Ting ^b   Wu, Wei ^b   Takacs, Elizabeth M ^c   Petsch, Katherine A ^d   Tian, Feng ^c   Bai, Guihua ^a,e   Buckler, Edward S ^c,e   Muehlbauer, Gary J ^f   Timmermans, Marja C P ^d   Scanlon, Michael J ^c   Schnable, Patrick S ^b   Yu, Jianming ^a  

^a KANSAS STATE UNIVERSITY   (United States)

^b IOWA STATE UNIVERSITY   (United States)

^c Cornell University ^*  (United States)

^d Simons Center for Quantitative Biology   (United States)

^e U S DEPARTMENT OF AGRICULTURE   (United States)

^f UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ADAPTATION; ARTICLE; CROP PRODUCTION; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC VARIABILITY; MAIZE; PLANT GENOME; PRIORITY JOURNAL; PROMOTER REGION; QUANTITATIVE TRAIT; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; GENES, PLANT; GENETIC VARIATION; LINKAGE DISEQUILIBRIUM; MUTATION; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; RNA, PLANT; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION INITIATION SITE; TRANSCRIPTOME; ZEA MAYS;

ZEA MAYS;

EID: 84870495767     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.140277.112     Document Type: Article

References (54)

1. Alonso-Blanco C, Aarts MG, Bentsink L, Keurentjes JJ, Reymond M, Vreugdenhil D, Koornneef M. 2009. What has natural variation taught us about plant development, physiology, and adaptation? Plant Cell 21: 1877-1896.
2. Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M. 2005. Cytokinin oxidase regulates rice grain production. Science 309: 741-745. (Pubitemid 41077314)
3. Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, et al. 2010. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
4. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS. 2007. SNP discovery via 454 transcriptome sequencing. Plant J 51: 910-918. (Pubitemid 47301664)
5. Bernardo R, Yu J. 2007. Prospects for genomewide selection for quantitative traits in maize. Crop Sci 47: 1082-1090. (Pubitemid 47309157)
6. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, et al. 2009. The genetic architecture of maize flowering time. Science 325: 714-718.
7. Chang BL, Cramer SD, Wiklund F, Isaacs SD, Stevens VL, Sun J, Smith S, Pruett K, Romero LM, Wiley KE, et al. 2009. Fine mapping association study and functional analysis implicate a SNP in MSMB at 10q11 as a causal variant for prostate cancer risk. Hum Mol Genet 18: 1368-1375.
8. Cirulli ET, Goldstein DB. 2010. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 11: 415-425.
9. Cirulli ET, Singh A, Shianna KV, Ge D, Smith JP, Maia JM, Heinzen EL, Goedert JJ, Goldstein DB. 2010. Screening the human exome: A comparison of whole genome and whole transcriptome sequencing. Genome Biol 11: R57. doi: 10.1186/gb-2010-11-5-r57.
10. Clark RM, Wagler TN, Quijada P, Doebley J. 2006. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat Genet 38: 594-597.
11. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, et al. 2008. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5: 613-619. (Pubitemid 351911866)
12. Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. 2010. Rare variants create synthetic genome-wide associations. PLoS Biol 8: e1000294. doi: 10.1371/journal.pbio.1000294.
13. Doebley JF, Gaut BS, Smith BD. 2006. The molecular genetics of crop domestication. Cell 127: 1309-1321. (Pubitemid 44960415)
14. Emrich SJ, Barbazuk WB, Li L, Schnable PS. 2007. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 17: 69-73. (Pubitemid 46041667)
15. Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD. 2000. fw2.2: A quantitative trait locus key to the evolution of tomato fruit size. Science 289: 85-88. (Pubitemid 30463294)
16. Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, et al. 2009. A first-generation haplotype map of maize. Science 326: 1115-1117.
17. Harper L, Freeling M. 1996. Interactions of liguleless1 and liguleless2 function during ligule induction in maize. Genetics 144: 1871-1882. (Pubitemid 26427931)
18. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci 106: 9362-9367.
19. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, et al. 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42: 961-967.
20. Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, et al. 2010. Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42: 1027-1030.
21. Lee JY, Baum SF, Alvarez J, Patel A, Chitwood DH, Bowman JL. 2005. Activation of CRABS CLAWin the nectaries and carpels of Arabidopsis. Plant Cell 17: 25-36. (Pubitemid 41672985)
22. Li P, Ponnala L, Gandotra N, Wang L, Si Y, Tausta SL, Kebrom TH, Provart N, Patel R, Myers CR, et al. 2010. The developmental dynamics of the maize leaf transcriptome. Nat Genet 42: 1060-1067.
23. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, et al. 2009. Finding the missing heritability of complex diseases. Nature 461: 747-753.
24. McMullen MD, Kresovich S, Villeda HS, Bradbury P, LiH, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, et al. 2009. Genetic properties of the maize nested association mapping population. Science 325: 737-740.
25. Mena M, Mandel MA, Lerner DR, Yanofsky MF, Schmidt RJ. 1995. A characterization of the MADS-box gene family in maize. Plant J 8: 845-854. (Pubitemid 3009644)
26. Meyer KB, Maia AT, O'Reilly M, Teschendorff AE, Chin SF, Caldas C, Ponder BA. 2008. Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer. PLoS Biol 6: e108. doi: 10.1371/journal.pbio.0060108.
27. Miura K, Ashikari M, Matsuoka M. 2011. The role of QTLs in the breeding of high-yielding rice. Trends Plant Sci 16: 319-326.
28. Nogueira FT, Madi S, Chitwood DH, Juarez MT, Timmermans MC. 2007. Two small regulatory RNAs establish opposing fates of a developmental axis. Genes Dev 21: 750-755. (Pubitemid 46572355)
29. Plotkin JB, Kudla G. 2011. Synonymous but not the same: The causes and consequences of codon bias. Nat Rev Genet 12: 32-42.
30. Rice WR. 1989. Analyzing tables of statistical tests. Evolution 43: 223-225.
31. Riedelsheimer C, Czedik-Eysenberg A, Grieder C, Lisec J, Technow F, Sulpice R, Altmann T, Stitt M, Willmitzer L, Melchinger AE. 2012. Genomic and metabolic prediction of complex heterotic traits in hybrid maize. Nat Genet 44: 217-220.
32. Salvi S, Sponza G, Morgante M, Tomes D, Niu X, Fengler KA, Meeley R, Ananiev EV, Svitashev S, Bruggemann E, et al. 2007. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci 104: 11376-11381. (Pubitemid 47175148)
33. Scheet P, Stephens M. 2006. A fast and flexible statistical model for largescale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78: 629-644.
34. Schnable JC, Freeling M. 2011. Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize. PLoS ONE 6: e17855. doi: 10.1371/journal.pone.0017855.
35. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, et al. 2009. The B73 maize genome: Complexity, diversity, and dynamics. Science 326: 1112-1115.
36. Schnable JC, Springer NM, Freeling M. 2011. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci 108: 4069-4074.
37. Schneeberger RG, Becraft PW, Hake S, Freeling M. 1995. Ectopic expression of the knox homeo box gene rough sheath1 alters cell fate in the maize leaf. Genes Dev 9: 2292-2304.
38. Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, de Leon N, Kaeppler SM. 2011. Genome-wide atlas of transcription during maize development. Plant J 66: 553-563.
39. Singleton AB, Hardy J, Traynor BJ, Houlden H. 2010. Towards a complete resolution of the genetic architecture of disease. Trends Genet 26: 438-442.
40. Stam M, Belele C, Ramakrishna W, Dorweiler JE, Bennetzen JL, Chandler VL. 2002. The regulatory regions required for B′ paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics 162: 917-930. (Pubitemid 35365051)
41. Stenson PD, Mort M, Ball EV, Howells K, Phillips AD, Thomas NS, Cooper DN. 2009. The Human Gene Mutation Database: 2008 update. Genome Med 1: 13. doi: 10.1186/gm13.
42. Storey JD, Tibshirani R. 2003. Statistical significance for genomewide studies. Proc Natl Acad Sci 100: 9440-9445. (Pubitemid 37033947)
43. Sun G, Zhu C, Kramer MH, Yang SS, Song W, Piepho HP, Yu J. 2010. Variation explained in mixed-model association mapping. Heredity 105: 333-340.
44. Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM. 2010. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res 20: 1689-1699.
45. Teslovich TM, Musunuru K, Smith AV, Edmondson AC, Stylianou IM, Koseki M, Pirruccello JP, Ripatti S, Chasman DI, Willer CJ, et al. 2010. Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466: 707-713.
46. Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES. 2011. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43: 159-162.
47. Timmermans MC, Schultes NP, Jankovsky JP, Nelson T. 1998. Leafbladeless1 is required for dorsoventrality of lateral organs in maize. Development 125: 2813-2823. (Pubitemid 28410206)
48. Waldman YY, Tuller T, Keinan A, Ruppin E. 2011. Selection for translation efficiency on synonymous polymorphisms in recent human evolution. Genome Biol Evol 3: 749-761.
49. Walsh J, Waters CA, Freeling M. 1998. The maize gene liguleless2 encodes a basic leucine zipper protein involved in the establishment of the leaf blade-sheath boundary. Genes Dev 12: 208-218. (Pubitemid 28060451)
50. Wu TD, Nacu S. 2010. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.
51. Yang J, Manolio TA, Pasquale LR, Boerwinkle E, Caporaso N, Cunningham JM, de Andrade M, Feenstra B, Feingold E, Hayes MG, et al. 2011. Genome partitioning of genetic variation for complex traits using common SNPs. Nat Genet 43: 519-525.
52. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, et al. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203-208. (Pubitemid 43177234)
53. Yu J, Holland JB, McMullen MD, Buckler ES. 2008. Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551. (Pubitemid 351398767)
54. Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, et al. 2010. Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42: 355-360.