Genetic variants and underlying mechanisms influencing variance heterogeneity in maize.
gene × gene interactions
maize
mean-effect SNP
vGWAS
variance heterogeneity
Journal
The Plant journal : for cell and molecular biology
ISSN: 1365-313X
Titre abrégé: Plant J
Pays: England
ID NLM: 9207397
Informations de publication
Date de publication:
08 2020
08 2020
Historique:
received:
11
11
2019
revised:
04
04
2020
accepted:
20
04
2020
pubmed:
29
4
2020
medline:
2
3
2021
entrez:
29
4
2020
Statut:
ppublish
Résumé
Traditional genetic studies focus on identifying genetic variants associated with the mean difference in a quantitative trait. Because genetic variants also influence phenotypic variation via heterogeneity, we conducted a variance-heterogeneity genome-wide association study to examine the contribution of variance heterogeneity to oil-related quantitative traits. We identified 79 unique variance-controlling single nucleotide polymorphisms (vSNPs) from the sequences of 77 candidate variance-heterogeneity genes for 21 oil-related traits using the Levene test (P < 1.0 × 10
Substances chimiques
Corn Oil
8001-30-7
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1089-1102Informations de copyright
© 2020 Society for Experimental Biology and John Wiley & Sons Ltd.
Références
Aulchenko, Y.S., Stephan, R., Aaron, I. et al. (2007) GenABEL: an R library for genome-wide association analysis. Bioinformatics, 23, 1294-1296.
Ayroles, J.F., Buchanan, S.M., O'Leary, C. et al. (2015) Behavioral idiosyncrasy reveals genetic control of phenotypic variability. Proc. Natl. Acad. Sci. USA, 112, 6706-6711.
Ashburner, M., Ball, C.A., Blake, J.A. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29.
Carlborg, Ö. and Haley, C.S. (2004) Epistasis:too often neglected in complex trait studies? Nat. Rev. Genet. 5, 618-625.
Cook, J.P., Mcmullen, M.D., Holland, J.B. et al. (2012) Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiol. 158, 824-834.
Deng, T., Yao, H., Wang, J. et al. (2016) GhLTPG1, a cotton GPI-anchored lipid transfer protein, regulates the transport of phosphatidylinositol monophosphates and cotton fiber elongation. Sci. Rep. 6, 26829.
Du, Z., Zhou, X., Ling, Y. et al. (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38, W64-70.
Ek, W.E., Rask-Andersen, M., Karlsson, T. et al. (2018) Genetic variants influencing phenotypic variance heterogeneity. Hum. Mol. Genet. 27, 799-810.
Forsberg, S.K., Andreatta, M.E., Huang, X.Y. et al. (2015) 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, e1005648.
Forsberg, S.K.G. and Carlborg, O. (2017) On the relationship between epistasis and genetic variance heterogeneity. J. Exp. Bot. 68, 5431-5438.
Fu, J., Cheng, Y., Linghu, J. et al. (2013) RNA sequencing reveals the complex regulatory network in the maize kernel. Nat. Commun. 4, 2832.
Fu, W., Shen, Y., Hao, J. et al. (2015) Acyl-CoA N-acyltransferase influences fertility by regulating lipid metabolism and jasmonic acid biogenesis in cotton. Sci. Rep. 5, 11790.
Hill, W.G. and Mulder, H.A. (2010) Genetic analysis of environmental variation. Genet. Res. 92, 381-395.
Hothorn, L.A., Libiger, O. and Gerhard, D.J.B.G. (2012) Model-specific tests on variance heterogeneity for detection of potentially interacting genetic loci. BMC Genet. 13, 59-59.
Hulse, A.M. and Cai, J.J. (2013) Genetic variants contribute to gene expression variability in humans. Genetics, 193, 95-108.
Lawrence, C.J., Harper, L.C., Schaeffer, M.L. et al. (2008) MaizeGDB: The maize model organism database for basic, translational, and applied research. Int. J. Plant Genomics, 2008, 496957.
Leal, S.M. (1998) Genetics and ANALYSIS OF QUANTITATIVE Traits. Am. J. Hum. Genet. 68, 548-549.
Lee S.H., Li C.W. and Koh K.W., et al. (2014) MSRB7 reverses oxidation of GSTF2/3 to confer tolerance of Arabidopsis thaliana to oxidative stress. J Exp Bot, 65, 5049-5062.
Li-Beisson, Y., Shorrosh, B., Beisson, F. et al. (2013) Acyl-lipid metabolism. Arabidopsis Book, 11, e0161.
Li, H., Peng, Z., Yang, X. et al. (2013) Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat. Genet. 45, 43-50.
Li, H., Thrash, A., Tang, J.D. et al. (2019) Leveraging GWAS data to identify metabolic pathways and networks involved in maize lipid biosynthesis. Plant J. 98, 853-863.
Li, Q.T., Lu, X., Song, Q.X. et al. (2017) Selection for a zinc-finger protein contributes to seed oil increase during soybean domestication. Plant Physiol. 173(4), 2208-2224.
Li, X., Qiu, W., Morrow, J. et al. (2015) A comparative study of tests for homogeneity of variances with application to DNA methylation data. PLoS ONE, 10, e0145295.
Liu, H.J. and Yan, J. (2019) Crop genome-wide association study: a harvest of biological relevance. Plant J. 97, 8-18.
Makowsky, R., Pajewski, N.M., Klimentidis, Y.C., Vazquez, A.I., Duarte, C.W., Allison, D.B. and de los Campos, G. (2011) Beyond missing heritability: prediction of complex traits. PLoS Genet. 7, e1002051.
Raffaele, S., Vailleau, F., Leger, A. et al. (2008) A MYB transcription factor regulates very-long-chain fatty acid biosynthesis for activation of the hypersensitive cell death response in Arabidopsis. Plant Cell, 20, 752-767.
Rask-Andersen, M., Karlsson, T., Ek, W.E. et al. (2017) Gene-environment interaction study for BMI reveals interactions between genetic factors and physical activity, alcohol consumption and socioeconomic status. PLoS Genet. 13, e1006977.
Rönnegård, L. and Valdar, W. (2011) Detecting major genetic loci controlling phenotypic variability in experimental crosses. Genetics, 188, 435-447.
Seo, P.J., Lee, S.B., Suh, M.C. et al. (2011) The MYB96 transcription factor regulates cuticular wax biosynthesis under drought conditions in Arabidopsis. Plant Cell, 23, 1138-1152.
Shen, X., De Jonge, J., Forsberg, S.K. et al. (2014) Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality. PLoS Genet. 10, e1004842.
Shen, X., Pettersson, M., Ronnegard, L. et al. (2012) Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana. PLoS Genet. 8, e1002839.
Struchalin, M.V., Dehghan, A., Witteman, J.C. et al. (2010) Variance heterogeneity analysis for detection of potentially interacting genetic loci: method and its limitations. BMC Genet. 11, 92.
Thompson, J.D., Gibson, T.J. and Plewniak, F. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25.
Waadt, R., Schmidt, L.M., Hashimoto, K. et al. (2010) Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta. Plant J. 56, 505-516.
Wang X.L., Wang H.W., et al. (2016) Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings. Nat Genet, 48, 1233-1241.
Wang, G., Yang, E., Brinkmeyer-Langford, C.L. et al. (2014) Additive, epistatic, and environmental effects through the lens of expression variability QTL in a twin cohort. Genetics, 196, 413-425.
Weller, J.I., Soller, M. and Brody, T. (1988) Linkage analysis of quantitative traits in an interspecific cross of tomato (lycopersicon esculentum × lycopersicon pimpinellifolium) by means of genetic markers. Genetics, 118, 329-339.
Wood, A.R., Esko, T., Yang, J. et al. (2014) Defining the role of common variation in the genomic and biological architecture of adult human height. Nat. Genet. 46, 1173-1186.
Yang, J., Loos, R.J., Powell, J.E. et al. (2012) FTO genotype is associated with phenotypic variability of body mass index. Nature, 490, 267-272.
Yang, N., Liu, J., Gao, Q. et al. (2019) Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nat. Genet. 51, 1052-1059.
Yang, N., Lu, Y., Yang, X., Huang, J., Zhou, Y., Ali, F., Wen, W., Liu, J., Li, J. and Yan, J. (2014) Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel. PLoS Genet. 10, e1004573.
Yang, X., Gao, S., Xu, S. et al. (2011) Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize. Mol. Breeding, 28, 511-526.
Yu, J., Pressoir, G., Briggs, W.H. et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38, 203-208.
Zdobnov, E. and Apweiler, R.J.B. (2001) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847-884.