Finding the sources of missing heritability in a yeast cross

被引:302
作者
Bloom, Joshua S. [1 ,2 ]
Ehrenreich, Ian M. [1 ,3 ]
Loo, Wesley T. [1 ,2 ]
Thuy-Lan Vo Lite [1 ,2 ]
Kruglyak, Leonid [1 ,4 ,5 ]
机构
[1] Princeton Uniyers, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08540 USA
[2] Princeton Univ, Dept Mol Biol, Princeton, NJ 08540 USA
[3] Univ So Calif, Mol & Computat Biol Sect, Los Angeles, CA 90089 USA
[4] Princeton Univ, Dept Ecol & Evolutionary Biol, Princeton, NJ 08540 USA
[5] Princeton Univ, Howard Hughes Med Inst, Princeton, NJ 08540 USA
基金
美国国家卫生研究院; 美国国家科学基金会;
关键词
GENETIC INTERACTIONS; COMPLEX DISEASES; HUMAN HEIGHT; VARIANTS; TRAITS; EXPRESSION; EVOLUTION;
D O I
10.1038/nature11867
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
For many traits, including susceptibility to common diseases in humans, causal loci uncovered by genetic-mapping studies explain only a minority of the heritable contribution to trait variation. Multiple explanations for this 'missing heritability' have been proposed(1). Here we use a large cross between two yeast strains to accurately estimate different sources of heritable variation for 46 quantitative traits, and to detect underlying loci with high statistical power. We find that the detected loci explain nearly the entire additive contribution to heritable variation for the traits studied. We also show that the contribution to heritability of gene-gene interactions varies among traits, from near zero to approximately 50 per cent. Detected two-locus interactions explain only a minority of this contribution. These results substantially advance our understanding of the missing heritability problem and have important implications
引用
收藏
页码:234 / 237
页数:4
相关论文
共 30 条
[1]   Hundreds of variants clustered in genomic loci and biological pathways affect human height [J].
Allen, Hana Lango ;
Estrada, Karol ;
Lettre, Guillaume ;
Berndt, Sonja I. ;
Weedon, Michael N. ;
Rivadeneira, Fernando ;
Willer, Cristen J. ;
Jackson, Anne U. ;
Vedantam, Sailaja ;
Raychaudhuri, Soumya ;
Ferreira, Teresa ;
Wood, Andrew R. ;
Weyant, Robert J. ;
Segre, Ayellet V. ;
Speliotes, Elizabeth K. ;
Wheeler, Eleanor ;
Soranzo, Nicole ;
Park, Ju-Hyun ;
Yang, Jian ;
Gudbjartsson, Daniel ;
Heard-Costa, Nancy L. ;
Randall, Joshua C. ;
Qi, Lu ;
Smith, Albert Vernon ;
Maegi, Reedik ;
Pastinen, Tomi ;
Liang, Liming ;
Heid, Iris M. ;
Luan, Jian'an ;
Thorleifsson, Gudmar ;
Winkler, Thomas W. ;
Goddard, Michael E. ;
Lo, Ken Sin ;
Palmer, Cameron ;
Workalemahu, Tsegaselassie ;
Aulchenko, Yurii S. ;
Johansson, Asa ;
Zillikens, M. Carola ;
Feitosa, Mary F. ;
Esko, Tonu ;
Johnson, Toby ;
Ketkar, Shamika ;
Kraft, Peter ;
Mangino, Massimo ;
Prokopenko, Inga ;
Absher, Devin ;
Albrecht, Eva ;
Ernst, Florian ;
Glazer, Nicole L. ;
Hayward, Caroline .
NATURE, 2010, 467 (7317) :832-838
[2]   Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines [J].
Atwell, Susanna ;
Huang, Yu S. ;
Vilhjalmsson, Bjarni J. ;
Willems, Glenda ;
Horton, Matthew ;
Li, Yan ;
Meng, Dazhe ;
Platt, Alexander ;
Tarone, Aaron M. ;
Hu, Tina T. ;
Jiang, Rong ;
Muliyati, N. Wayan ;
Zhang, Xu ;
Amer, Muhammad Ali ;
Baxter, Ivan ;
Brachi, Benjamin ;
Chory, Joanne ;
Dean, Caroline ;
Debieu, Marilyne ;
de Meaux, Juliette ;
Ecker, Joseph R. ;
Faure, Nathalie ;
Kniskern, Joel M. ;
Jones, Jonathan D. G. ;
Michael, Todd ;
Nemri, Adnane ;
Roux, Fabrice ;
Salt, David E. ;
Tang, Chunlao ;
Todesco, Marco ;
Traw, M. Brian ;
Weigel, Detlef ;
Marjoram, Paul ;
Borevitz, Justin O. ;
Bergelson, Joy ;
Nordborg, Magnus .
NATURE, 2010, 465 (7298) :627-631
[3]   Genetic analysis of complex traits in the emerging Collaborative Cross [J].
Aylor, David L. ;
Valdar, William ;
Foulds-Mathes, Wendy ;
Buus, Ryan J. ;
Verdugo, Ricardo A. ;
Baric, Ralph S. ;
Ferris, Martin T. ;
Frelinger, Jeff A. ;
Heise, Mark ;
Frieman, Matt B. ;
Gralinski, Lisa E. ;
Bell, Timothy A. ;
Didion, John D. ;
Hua, Kunjie ;
Nehrenberg, Derrick L. ;
Powell, Christine L. ;
Steigerwalt, Jill ;
Xie, Yuying ;
Kelada, Samir N. P. ;
Collins, Francis S. ;
Yang, Ivana V. ;
Schwartz, David A. ;
Branstetter, Lisa A. ;
Chesler, Elissa J. ;
Miller, Darla R. ;
Spence, Jason ;
Liu, Eric Yi ;
McMillan, Leonard ;
Sarkar, Abhishek ;
Wang, Jeremy ;
Wang, Wei ;
Zhang, Qi ;
Broman, Karl W. ;
Korstanje, Ron ;
Durrant, Caroline ;
Mott, Richard ;
Iraqi, Fuad A. ;
Pomp, Daniel ;
Threadgill, David ;
de Villena, Fernando Pardo-Manuel ;
Churchill, Gary A. .
GENOME RESEARCH, 2011, 21 (08) :1213-1222
[4]   Genetic interactions between polymorphisms that affect gene expression in yeast [J].
Brem, RB ;
Storey, JD ;
Whittle, J ;
Kruglyak, L .
NATURE, 2005, 436 (7051) :701-703
[5]   The landscape of genetic complexity across 5,700 gene expression traits in yeast [J].
Brem, RB ;
Kruglyak, L .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (05) :1572-1577
[6]   The Genetic Architecture of Maize Flowering Time [J].
Buckler, Edward S. ;
Holland, James B. ;
Bradbury, Peter J. ;
Acharya, Charlotte B. ;
Brown, Patrick J. ;
Browne, Chris ;
Ersoz, Elhan ;
Flint-Garcia, Sherry ;
Garcia, Arturo ;
Glaubitz, Jeffrey C. ;
Goodman, Major M. ;
Harjes, Carlos ;
Guill, Kate ;
Kroon, Dallas E. ;
Larsson, Sara ;
Lepak, Nicholas K. ;
Li, Huihui ;
Mitchell, Sharon E. ;
Pressoir, Gael ;
Peiffer, Jason A. ;
Rosas, Marco Oropeza ;
Rocheford, Torbert R. ;
Cinta Romay, M. ;
Romero, Susan ;
Salvo, Stella ;
Sanchez Villeda, Hector ;
da Silva, H. Sofia ;
Sun, Qi ;
Tian, Feng ;
Upadyayula, Narasimham ;
Ware, Doreen ;
Yates, Heather ;
Yu, Jianming ;
Zhang, Zhiwu ;
Kresovich, Stephen ;
McMullen, Michael D. .
SCIENCE, 2009, 325 (5941) :714-718
[7]   Genotype to Phenotype: A Complex Problem [J].
Dowell, Robin D. ;
Ryan, Owen ;
Jansen, An ;
Cheung, Doris ;
Agarwala, Sudeep ;
Danford, Timothy ;
Bernstein, Douglas A. ;
Rolfe, P. Alexander ;
Heisler, Lawrence E. ;
Chin, Brian ;
Nislow, Corey ;
Giaever, Guri ;
Phillips, Patrick C. ;
Fink, Gerald R. ;
Gifford, David K. ;
Boone, Charles .
SCIENCE, 2010, 328 (5977) :469-469
[8]   Genetic Dissection of Complex Traits in Yeast: Insights from Studies of Gene Expression and Other Phenotypes in the BYxRM Cross [J].
Ehrenreich, I. M. ;
Gerke, J. P. ;
Kruglyak, L. .
EVOLUTION: THE MOLECULAR LANDSCAPE, 2009, 74 :145-153
[9]   Dissection of genetically complex traits with extremely large pools of yeast segregants [J].
Ehrenreich, Ian M. ;
Torabi, Noorossadat ;
Jia, Yue ;
Kent, Jonathan ;
Martis, Stephen ;
Shapiro, Joshua A. ;
Gresham, David ;
Caudy, Amy A. ;
Kruglyak, Leonid .
NATURE, 2010, 464 (7291) :1039-U101
[10]   VIEWPOINT Missing heritability and strategies for finding the underlying causes of complex disease [J].
Eichler, Evan E. ;
Flint, Jonathan ;
Gibson, Greg ;
Kong, Augustine ;
Leal, Suzanne M. ;
Moore, Jason H. ;
Nadeau, Joseph H. .
NATURE REVIEWS GENETICS, 2010, 11 (06) :446-450