We performed genome-wide association mapping analysis in maize for 41 different phenotypes in order to identify which types of variants are more likely to be important for controlling traits. We took advantage of a large mapping population (roughly 5000 recombinant inbred lines) and nearly 30 million segregating variants to identify ∼4800 variants that were significantly associated with at least one phenotype. While these variants are enriched in genes, most of them occur outside of genes, often in regions where regulatory elements likely lie. We also found a significant enrichment for paralogous (duplicated) genes, implying that functional divergence after gene duplication plays an important role in trait variation. Overall these analyses provide important insight into the unifying patterns of variation in traits across maize, and the results will likely also apply to other organisms with similarly large, complex genomes.
Vyšlo v časopise: Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize. PLoS Genet 10(12): e32767. doi:10.1371/journal.pgen.1004845 Kategorie: Research Article prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004845
1. HainesJL, HauserMA, SchmidtS, ScottWK, OlsonLM, et al. (2005) Complement factor H variant increases the risk of age-related macular degeneration. Science 308 : 419–421.
2. Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447 : 661–678.
3. RipkeS, O'DushlaineC, ChambertK, MoranJL, KählerAK, et al. (2013) Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat Genet 45 : 1150–1159.
4. CARDIoGRAMplusC4D Consortium, DeloukasP, KanoniS, WillenborgC, FarrallM, et al. (2013) Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet 45 : 25–33.
5. MorrisAP, VoightBF, TeslovichTM, FerreiraT, SegrèAV, et al. (2012) Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet 44 : 981–990.
6. WrayGA (2007) The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8 : 206–216.
7. SchaubMA, BoyleAP, KundajeA, BatzoglouS, SnyderM (2012) Linking disease associations with regulatory information in the human genome. Genome Res 22 : 1748–1759.
8. VernotB, StergachisAB, MauranoMT, VierstraJ, NephS, et al. (2012) Personal and population genomics of human regulatory variation. Genome Res 22 : 1689–1697.
9. ChurchillGA, AireyDC, AllayeeH, AngelJM, AttieAD, et al. (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet 36 : 1133–1137.
10. KoverPX, ValdarW, TrakaloJ, ScarcelliN, EhrenreichIM, et al. (2009) A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5: e1000551.
11. McMullenMD, KresovichS, VilledaHS, BradburyP, LiH, et al. (2009) Genetic Properties of the Maize Nested Association Mapping Population. Science 325 : 737–740.
12. BrownPJ, UpadyayulaN, MahoneGS, TianF, BradburyPJ, et al. (2011) Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genet 7: e1002383.
13. KumpKL, BradburyPJ, WisserRJ, BucklerES, BelcherAR, et al. (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43 : 163–168.
14. BucklerES, HollandJB, BradburyPJ, AcharyaCB, BrownPJ, et al. (2009) The Genetic Architecture of Maize Flowering Time. Science 325 : 714–718.
15. HungH-Y, ShannonLM, TianF, BradburyPJ, ChenC, et al. (2012) ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proc Natl Acad Sci U S A 109: E1913–21.
16. PeifferJA, Flint-GarciaSA, De LeonN, McMullenMD, KaepplerSM, et al. (2013) The genetic architecture of maize stalk strength. PLoS One 8: e67066.
17. PeifferJA, RomayMC, GoreMA, Flint-GarciaSA, ZhangZ, et al. (2014) The genetic architecture of maize height. Genetics 196 : 1337–1356.
18. PolandJA, BradburyPJ, BucklerES, NelsonRJ (2011) Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci U S A 108 : 6893–6898.
19. TianF, BradburyPJ, BrownPJ, HungH, SunQ, et al. (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43 : 159–162.
20. GoreMA, ChiaJ-M, ElshireRJ, SunQ, ErsozES, et al. (2009) A first-generation haplotype map of maize. Science 326 : 1115–1117.
21. ChiaJ-M, SongC, BradburyPJ, CostichD, de LeonN, et al. (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 44 : 803–807.
22. ElshireRJ, GlaubitzJC, SunQ, PolandJA, KawamotoK, et al. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6: e19379.
23. McLarenW, PritchardB, RiosD, ChenY, FlicekP, et al. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26 : 2069–2070.
24. SchorkAJ, ThompsonWK, PhamP, TorkamaniA, RoddeyJC, et al. (2013) All SNPs Are Not Created Equal: Genome-Wide Association Studies Reveal a Consistent Pattern of Enrichment among Functionally Annotated SNPs. PLoS Genet 9(4): e1003449 doi: 10.1371/journal.pgen.1003449
25. DicksonSP, WangK, KrantzI, HakonarsonH, GoldsteinDB (2010) Rare variants create synthetic genome-wide associations. PLoS Biol 8: e1000294.
26. PlattA, VilhjálmssonBJ, NordbordM (2010) Conditions under which genome-wide association studies will be positively misleading. Genetics 186 : 1045–1052.
27. ShabalinaSA, SpiridonovNA, KashinaA (2013) Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res 41 : 2073–2094.
28. OrrHA (1998) The Population Genetics of Adaptation: The Distribution of Factors Fixed during Adaptive Evolution. Evolution 52 : 935–949.
29. Fisher RA (1930) The genetical theory of natural selection. Oxford University Press.
30. SekhonRS, BriskineR, HirschCN, MyersCL, SpringerNM, et al. (2013) Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One 8: e61005.
31. TaylorJS, RaesJ (2004) Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 38 : 615–643.
32. LiX, ZhuC, YehC-T, WuW, TakacsEM, et al. (2012) Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res 22 : 2436–2444.
33. ENCODE Project Consortium (2012) BernsteinBE, BirneyE, DunhamI, GreenED, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489 : 57–74.
34. Mouse ENCODE Consortium (2012) StamatoyannopoulosJA, SnyderM, HardisonR, RenB, et al. (2012) An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol 13 : 418.
35. CelnikerSE, DillonLAL, GersteinMB, GunsalusKC, HenikoffS, et al. (2009) Unlocking the secrets of the genome. Nature 459 : 927–930.
36. GeigenbergerP, LerchiJ, StittM, SonnewaldU (1996) Phloem-specific expression of pyrophosphatase inhibits long distance transport of carbohydrates and amino acids in tobacco plants. Plant Cell Environ 19 : 43–55.
37. HendriksJHM, KolbeA, GibonY, StittM, GeigenbergerP (2003) ADP-glucose pyrophosphorylase is activated by posttranslational redox-modification in response to light and to sugars in leaves of Arabidopsis and other plant species. Plant Physiol 133 : 838–849.
38. BradfordMM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72 : 248–254.
39. ArnonDI (1949) Copper Enzymes in Isolated Chloroplasts. Polyphenoloxidase in Beta vulgaris. Plant Physiol 24 : 1–15.
40. Bantan-PolakT, KassaiM, GrantKB (2001) A comparison of fluorescamine and naphthalene-2,3-dicarboxaldehyde fluorogenic reagents for microplate-based detection of amino acids. Anal Biochem 297 : 128–136.
41. TschoepH, GibonY, CarilloP, ArmengaudP, SzecowkaM, et al. (2009) Adjustment of growth and central metabolism to a mild but sustained nitrogen-limitation in Arabidopsis. Plant Cell Environ 32 : 300–318.
42. Nunes-NesiA, CarrariF, GibonY, SulpiceR, LytovchenkoA, et al. (2007) Deficiency of mitochondrial fumarase activity in tomato plants impairs photosynthesis via an effect on stomatal function. Plant J 50 : 1093–1106.
43. JelittoT, SonnewaldU, WillmitzerL, HajirezeaiM, StittM (1992) Inorganic pyrophosphate content and metabolites in potato and tobacco plants expressing E. coli pyrophosphatase in their cytosol. Planta 188 : 238–244.
44. Holm S (1979) A simple sequentially rejective multiple test procedure. Scand Stat Theory Appl. Available: http://www.jstor.org/stable/4615733.
45. LiH, BradburyP, ErsozE, BucklerES, WangJ (2011) Joint QTL linkage mapping for multiple-cross mating design sharing one common parent. PLoS One 6: e17573.
46. BradburyPJ, ZhangZ, KroonDE, CasstevensTM, RamdossY, et al. (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23 : 2633–2635.
47. ValdarW, HolmesCC, MottR, FlintJ (2009) Mapping in structured populations by resample model averaging. Genetics 182 : 1263–1277.
48. RobinsonMD, McCarthyDJ, SmythGK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26 : 139–140.
49. AbyzovA, UrbanAE, SnyderM, GersteinM (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 21 : 974–984.
50. R Core Team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available: http://www.R-project.org/.
51. DuZ, ZhouX, LingY, ZhangZ, SuZ (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38: W64–70.
52. SchnableJC, FreelingM (2011) Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize. PLoS One 6: e17855.
Zvýšte si kvalifikáciu online z pohodlia domova
Nemáte účet? Registrujte sa
Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.
