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The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance


Most biological traits vary in natural populations, and understanding the genetic basis of this variation remains an important challenge. Genome-wide association (GWA) studies have emerged as a powerful tool to address this challenge by dissecting the genetic architecture of trait variation into the contribution of individual genes. This contribution has traditionally been measured as the difference in the phenotypic means between groups of individuals with alternative genotypes at one, or multiple loci. However, instead of altering the trait mean, certain loci alter the variability of the trait. Here, we describe the genetic dissection of one such variance-controlling locus that drives variation in leaf molybdenum concentrations amongst natural accessions of Arabidopsis thaliana. The variance-controlling locus was found to result from the contributions of multiple alleles at multiple loci that are closely linked on the chromosome and is a major contributor to the “missing heritability” for this trait identified in previous studies. This illustrates that multi-allelic genetic architectures can hide large amounts of additive genetic variation, and that it is possible to uncover this hidden variation using the appropriate experimental designs and statistical methods described here.


Vyšlo v časopise: The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance. PLoS Genet 11(11): e32767. doi:10.1371/journal.pgen.1005648
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005648

Souhrn

Most biological traits vary in natural populations, and understanding the genetic basis of this variation remains an important challenge. Genome-wide association (GWA) studies have emerged as a powerful tool to address this challenge by dissecting the genetic architecture of trait variation into the contribution of individual genes. This contribution has traditionally been measured as the difference in the phenotypic means between groups of individuals with alternative genotypes at one, or multiple loci. However, instead of altering the trait mean, certain loci alter the variability of the trait. Here, we describe the genetic dissection of one such variance-controlling locus that drives variation in leaf molybdenum concentrations amongst natural accessions of Arabidopsis thaliana. The variance-controlling locus was found to result from the contributions of multiple alleles at multiple loci that are closely linked on the chromosome and is a major contributor to the “missing heritability” for this trait identified in previous studies. This illustrates that multi-allelic genetic architectures can hide large amounts of additive genetic variation, and that it is possible to uncover this hidden variation using the appropriate experimental designs and statistical methods described here.


Zdroje

1. Guo J, Jorjani H, Carlborg Ö. A genome-wide association study using international breeding-evaluation data identifies major loci affecting production traits and stature in the Brown Swiss cattle breed. BMC Genet. 2012;13: 82. doi: 10.1186/1471-2156-13-82 23031427

2. Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, et al. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 2010;465: 627–631. doi: 10.1038/nature08800 20336072

3. Baxter I, Brazelton JN, Yu D, Huang YS, Lahner B, Yakubova E, et al. A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1. PLoS Genet. 2010;6: e1001193. doi: 10.1371/journal.pgen.1001193 21085628

4. Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, et al. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat Genet. 2012;44: 212–216. doi: 10.1038/ng.1042 22231484

5. Chao D-Y, Silva A, Baxter I, Huang YS, Nordborg M, Danku J, et al. Genome-wide association studies identify heavy metal ATPase3 as the primary determinant of natural variation in leaf cadmium in Arabidopsis thaliana. PLoS Genet. 2012;8: e1002923. doi: 10.1371/journal.pgen.1002923 22969436

6. Chao D-Y, Chen Y, Chen J, Shi S, Chen Z, Wang C, et al. Genome-wide association mapping identifies a new arsenate reductase enzyme critical for limiting arsenic accumulation in plants. Plos Biol. 2014;12: e1002009. doi: 10.1371/journal.pbio.1002009 25464340

7. Shen X, De Jonge J, Forsberg SKG, Pettersson ME, Sheng Z, Hennig L, et al. Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality. PLoS Genet. 2014;10: e1004842. doi: 10.1371/journal.pgen.1004842 25503602

8. Nelson RM, Pettersson ME, Carlborg Ö. A century after Fisher: time for a new paradigm in quantitative genetics. Trends Genet. 2013;29: 669–676. doi: 10.1016/j.tig.2013.09.006 24161664

9. Hill WG, Mulder HA. Genetic analysis of environmental variation. Genet Res. 2010;92: 381–395. doi: 10.1017/S0016672310000546

10. Rönnegård L, Valdar W. Detecting major genetic loci controlling phenotypic variability in experimental crosses. Genetics. 2011;188: 435–447. doi: 10.1534/genetics.111.127068 21467569

11. Dworkin I. Canalization, Cryptic Variation and Developmental Buffering: A Critical Examination and Analytical Perspective. In: Hallgrimsson B, Hall B, editors. Variation, A Central Concept in Biology. 1st ed. Elsevier; 2005. pp. 138–158.

12. Kitano H. Biological robustness. Nat Rev Genet. 2004;5: 826–837. doi: 10.1038/nrg1471 15520792

13. Rutherford SL, Lindquist S. Hsp90 as a capacitor for morphological evolution. Nature. 1998;396: 336–342. doi: 10.1038/24550 9845070

14. Dworkin I, Palsson A, Birdsall K, Gibson G. Evidence that Egfr Contributes to Cryptic Genetic Variation for Photoreceptor Determination in Natural Populations of Drosophila melanogaster. Current Biology. 2003;13: 1888–1893. doi: 10.1016/j.cub.2003.10.001 14588245

15. Mackay TF, Lyman RF. Drosophila bristles and the nature of quantitative genetic variation. Philos Trans R Soc Lond, B, Biol Sci. 2005;360: 1513–1527. doi: 10.1098/rstb.2005.1672 16108138

16. Weller JI, Soller M, Brody T. Linkage analysis of quantitative traits in an interspecific cross of tomato (lycopersicon esculentum x lycopersicon pimpinellifolium) by means of genetic markers. Genetics. 1988;118: 329–339. 17246412

17. Hall MC, Dworkin I, Ungerer MC, Purugganan M. Genetics of microenvironmental canalization in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America. 2007;104: 13717–13722. doi: 10.1073/pnas.0701936104 17698961

18. Ordas B, Malvar RA, Hill WG. Genetic variation and quantitative trait loci associated with developmental stability and the environmental correlation between traits in maize. Genet Res. 2008;90: 385–395. doi: 10.1017/S0016672308009762

19. Jimenez-Gomez JM, Corwin JA, Joseph B, Maloof JN, Kliebenstein DJ. Genomic analysis of QTLs and genes altering natural variation in stochastic noise. PLoS Genet. 2011;7: e1002295. doi: 10.1371/journal.pgen.1002295 21980300

20. Rönnegård L, Valdar W. Recent developments in statistical methods for detecting genetic loci affecting phenotypic variability. BMC Genet. 2012;13: 63. doi: 10.1186/1471-2156-13-63 22827487

21. Struchalin MV, Dehghan A, Witteman JCM, Duijn CV, Aulchenko YS. Variance heterogeneity analysis for detection of potentially interacting genetic loci: method and its limitations. BMC Genet. 2010;11: 92. doi: 10.1186/1471-2156-11-92 20942902

22. Shen X, Pettersson M, Rönnegård L, Carlborg Ö. Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana. PLoS Genet. 2012;8: e1002839. doi: 10.1371/journal.pgen.1002839 22876191

23. Ayroles JF, Buchanan SM, O'Leary C, Skutt-Kakaria K, Grenier JK, Clark AG, et al. Behavioral idiosyncrasy reveals genetic control of phenotypic variability. Proceedings of the National Academy of Sciences. 2015;112: 6706–6711. doi: 10.1073/pnas.1503830112

24. Nelson RM, Pettersson ME, Li X, Carlborg Ö. Variance Heterogeneity in Saccharomyces cerevisiae Expression Data: Trans-Regulation and Epistasis. PLoS ONE. 2013;8: e79507. doi: 10.1371/journal.pone.0079507 24223957

25. Mendel RR, Leimkühler S. The biosynthesis of the molybdenum cofactors. J Biol Inorg Chem. 2015;20: 337–347. doi: 10.1007/s00775-014-1173-y 24980677

26. Kaiser BN, Gridley KL, Ngaire Brady J, Phillips T, Tyerman SD. The role of molybdenum in agricultural plant production. Ann Bot. 2005;96: 745–754. doi: 10.1093/aob/mci226 16033776

27. Williams L, Salt DE. The plant ionome coming into focus. Curr Opin Plant Biol. 2009;12: 247–249. doi: 10.1016/j.pbi.2009.05.009 19524481

28. Bentsink L, Alonso-Blanco C, Vreugdenhil D, Tesnier K, Groot SP, Koornneef M. Genetic analysis of seed-soluble oligosaccharides in relation to seed storability of Arabidopsis. Plant Physiology. 2000;124: 1595–1604. 11115877

29. Bentsink L, Yuan K, Koornneef M, Vreugdenhil D. The genetics of phytate and phosphate accumulation in seeds and leaves of Arabidopsis thaliana, using natural variation. Theor Appl Genet. 2003;106: 1234–1243. doi: 10.1007/s00122-002-1177-9 12748774

30. Payne KA, Bowen HC, Hammond JP, Hampton CR, Lynn JR, Mead A, et al. Natural genetic variation in caesium (Cs) accumulation by Arabidopsis thaliana. New Phytologist. 2004;162: 535–548. doi: 10.1111/j.1469-8137.2004.01026.x

31. Vreugdenhil D, Aarts MGM, Koornneef M, Nelissen H, Ernst WHO. Natural variation and QTL analysis for cationic mineral content in seeds of Arabidopsis thaliana. Plant Cell Environ. 2004;27: 828–839. doi: 10.1111/j.1365-3040.2004.01189.x

32. Harada H, Leigh RA. Genetic mapping of natural variation in potassium concentrations in shoots of Arabidopsis thaliana. Journal of Experimental Biology. 2006;57: 953–960. doi: 10.1093/jxb/erj081

33. Zeng C, Han Y, Shi L, Peng L, Wang Y, Xu F, et al. Genetic analysis of the physiological responses to low boron stress in Arabidopsis thaliana. Plant Cell Environ. 2008;31: 112–122. doi: 10.1111/j.1365-3040.2007.01745.x 17999661

34. Ghandilyan A, Barboza L, Tisné S, Granier C, Reymond M, Koornneef M, et al. Genetic analysis identifies quantitative trait loci controlling rosette mineral concentrations in Arabidopsis thaliana under drought. New Phytologist. 2009;184: 180–192. doi: 10.1111/j.1469-8137.2009.02953.x 19656307

35. Morrissey J, Baxter IR, Lee J, Li L, Lahner B, Grotz N, et al. The ferroportin metal efflux proteins function in iron and cobalt homeostasis in Arabidopsis. The Plant Cell. 2009;21: 3326–3338. doi: 10.1105/tpc.109.069401 19861554

36. Baxter I, Muthukumar B, Park HC, Buchner P, Lahner B, Danku J, et al. Variation in molybdenum content across broadly distributed populations of Arabidopsis thaliana is controlled by a mitochondrial molybdenum transporter (MOT1). PLoS Genet. 2008;4: e1000004. doi: 10.1371/journal.pgen.1000004 18454190

37. Poormohammad Kiani S, Trontin C, Andreatta M, Simon M, Robert T, Salt DE, et al. Allelic heterogeneity and trade-off shape natural variation for response to soil micronutrient. PLoS Genet. 2012;8: e1002814. doi: 10.1371/journal.pgen.1002814 22807689

38. Rus A, Baxter I, Muthukumar B, Gustin J, Lahner B, Yakubova E, et al. Natural variants of AtHKT1 enhance Na+ accumulation in two wild populations of Arabidopsis. PLoS Genet. 2006;2: e210. doi: 10.1371/journal.pgen.0020210 17140289

39. Kobayashi Y, Kuroda K, Kimura K, Southron-Francis JL, Furuzawa A, Kimura K, et al. Amino Acid Polymorphisms in Strictly Conserved Domains of a P-Type ATPase HMA5 Are Involved in the Mechanism of Copper Tolerance Variation in Arabidopsis. Plant Physiology. 2008;148: 969–980. doi: 10.1104/pp.108.119933 18701674

40. Loudet O, Saliba-Colombani V, Camilleri C, Calenge F, Gaudon V, Koprivova A, et al. Natural variation for sulfate content in Arabidopsis thaliana is highly controlled by APR2. Nat Genet. 2007;39: 896–900. doi: 10.1038/ng2050 17589509

41. Koprivova A, Giovannetti M, Baraniecka P, Lee B-R, Grondin C, Loudet O, et al. Natural variation in the ATPS1 isoform of ATP sulfurylase contributes to the control of sulfate levels in Arabidopsis. Plant Physiology. 2013;163: 1133–1141. doi: 10.1104/pp.113.225748 24027241

42. Chao D-Y, Baraniecka P, Danku J, Koprivova A, Lahner B, Luo H, et al. Variation in sulfur and selenium accumulation is controlled by naturally occurring isoforms of the key sulfur assimilation enzyme ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE2 across the Arabidopsis species range. Plant Physiology. 2014;166: 1593–1608. doi: 10.1104/pp.114.247825 25245030

43. Baxter I, Hermans C, Lahner B, Yakubova E, Tikhonova M, Verbruggen N, et al. Biodiversity of mineral nutrient and trace element accumulation in Arabidopsis thaliana. PLoS ONE. 2012;7: e35121. doi: 10.1371/journal.pone.0035121 22558123

44. Tomatsu H, Takano J, Takahashi H, Watanabe-Takahashi A, Shibagaki N, Fujiwara T. An Arabidopsis thaliana high-affinity molybdate transporter required for efficient uptake of molybdate from soil. Proceedings of the National Academy of Sciences. 2007;104: 18807–18812. doi: 10.1073/pnas.0706373104

45. Friedman J, Hastie T, Tibshirani R. Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw. 2010;33: 1–22. 20808728

46. Billard V, Ourry A, Maillard A, Garnica M, Coquet L, Jouenne T, et al. Copper-Deficiency in Brassica napus Induces Copper Remobilization, Molybdenum Accumulation and Modification of the Expression of Chloroplastic Proteins. PLoS ONE. 2014;9: e109889. doi: 10.1371/journal.pone.0109889 25333918

47. Carlborg Ö, Haley CS. Opinion: Epistasis: too often neglected in complex trait studies? Nat Rev Genet. 2004;5: 618–625. doi: 10.1038/nrg1407 15266344

48. Weigel D. Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiology. 2012;158: 2–22. doi: 10.1104/pp.111.189845 22147517

49. Barboza L, Effgen S, Alonso-Blanco C, Kooke R, Keurentjes JJB, Koornneef M, et al. Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution dwarf alleles in rice and barley. Proceedings of the National Academy of Sciences. 2013;110: 15818–15823. doi: 10.1073/pnas.1314979110

50. Saez-Aguayo S, Rondeau-Mouro C, Macquet A, Kronholm I, Ralet M-C, Berger A, et al. Local Evolution of Seed Flotation in Arabidopsis. Bomblies K, editor. PLoS Genet. 2014;10: e1004221. doi: 10.1371/journal.pgen.1004221 24625826

51. Johanson U, West J, Lister C, Michaels S, Amasino R, Dean C. Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science. 2000;290: 344–347. 11030654

52. Li P, Filiault D, Box MS, Kerdaffrec E, van Oosterhout C, Wilczek AM, et al. Multiple FLC haplotypes defined by independent cis-regulatory variation underpin life history diversity in Arabidopsis thaliana. Genes & Development. 2014;28: 1635–1640. doi: 10.1101/gad.245993.114 25035417

53. Kijas JM, Wales R, Törnsten A, Chardon P, Moller M, Andersson L. Melanocortin receptor 1 (MC1R) mutations and coat color in pigs. Genetics. 1998;150: 1177–1185. 9799269

54. Kijas JMH, Moller M, Plastow G, Andersson L. A Frameshift Mutation in MC1R and a High Frequency of Somatic Reversions Cause Black Spotting in Pigs. Genetics. 2001;158: 779–785. 11404341

55. Pielberg G, Olsson C, Syvänen AC, Andersson L. Unexpectedly High Allelic Diversity at the KIT Locus Causing Dominant White Color in the Domestic Pig. Genetics. 2002;160: 305–311. 11805065

56. Grobet L, Poncelet D, Royo LJ, Brouwers B, Pirottin D, Michaux C, et al. Molecular definition of an allelic series of mutations disrupting the myostatin function and causing double-muscling in cattle. Mamm Genome. 1998;9: 210–213. 9501304

57. Ciobanu D, Bastiaansen J, Malek M, Helm J, Woollard J, Plastow G, et al. Evidence for new alleles in the protein kinase adenosine monophosphate-activated gamma(3)-subunit gene associated with low glycogen content in pig skeletal muscle and improved meat quality. Genetics. 2001;159: 1151–1162. 11729159

58. Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. Rare variants create synthetic genome-wide associations. Plos Biol. 2010;8: e1000294. doi: 10.1371/journal.pbio.1000294 20126254

59. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, et al. Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet. 2010;11: 446–450. doi: 10.1038/nrg2809 20479774

60. Meyers BC, Kaushik S, Nandety RS. Evolving disease resistance genes. Curr Opin Plant Biol. 2005;8: 129–134. doi: 10.1016/j.pbi.2005.01.002 15752991

61. Kroymann J, Mitchell-Olds T. Epistasis and balanced polymorphism influencing complex trait variation. Nature. 2005;435: 95–98. doi: 10.1038/nature03480 15875023

62. R Development Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria; 2015.

63. Struchalin MV, Amin N, Eilers PHC, van Duijn CM, Aulchenko YS. An R package “VariABEL” for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity. BMC Genet. 2012;13: 4. doi: 10.1186/1471-2156-13-4 22272569

64. Belonogova NM, Svishcheva GR, van Duijn CM, Aulchenko YS, Axenovich TI. Region-based association analysis of human quantitative traits in related individuals. PLoS ONE. 2013;8: e65395. doi: 10.1371/journal.pone.0065395 23799013

65. Aulchenko YS, Ripke S, Isaacs A, van Duijn CM. GenABEL: an R package for genome-wide association analysis. Bioinformatics. 2007;23: 1294–1296. 17384015

66. Smyth GK. Generalized linear models with varying dispersion. Journal of the Royal Statistical Society, Series B. 1989;51: 47–60.

67. Dunn PK, Smyth GK. dglm: Double Generalized Linear Models. 1st ed. http://CRAN.R-project.org/package=dglm; 2014 Apr. Report No.: R-package.

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Genetika Reprodukčná medicína

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PLOS Genetics


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