Mixed linear model approach for mapping quantitative trait loci underlying crop seed traits

doi:10.1038/hdy.2014.17

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	Mixed linear model approach for mapping quantitative trait loci underlying crop seed traits
	Qi, T.1; Jiang, B.1; Zhu, Z.1; Wei, C.1; Gao, Y.2; Zhu, S.1; Xu, H.1; Lou, X.3
刊名	HEREDITY
	2014
卷号	113 期号:3 页码:224-232
ISSN号	0018-067X
DOI	10.1038/hdy.2014.17
通讯作者	Qi, T.
英文摘要	The crop seed is a complex organ that may be composed of the diploid embryo, the triploid endosperm and the diploid maternal tissues. According to the genetic features of seed characters, two genetic models for mapping quantitative trait loci (QTLs) of crop seed traits are proposed, with inclusion of maternal effects, embryo or endosperm effects of QTL, environmental effects and QTL-by-environment (QE) interactions. The mapping population can be generated either from double back-cross of immortalized F-2 (IF2) to the two parents, from random-cross of IF2 or from selfing of IF2 population. Candidate marker intervals potentially harboring QTLs are first selected through one-dimensional scanning across the whole genome. The selected candidate marker intervals are then included in the model as cofactors to control background genetic effects on the putative QTL(s). Finally, a QTL full model is constructed and model selection is conducted to eliminate false positive QTLs. The genetic main effects of QTLs, QE interaction effects and the corresponding P-values are computed by Markov chain Monte Carlo algorithm for Gaussian mixed linear model via Gibbs sampling. Monte Carlo simulations were performed to investigate the reliability and efficiency of the proposed method. The simulation results showed that the proposed method had higher power to accurately detect simulated QTLs and properly estimated effect of these QTLs. To demonstrate the usefulness, the proposed method was used to identify the QTLs underlying fiber percentage in an upland cotton IF2 population. A computer software, QTLNetwork-Seed, was developed for QTL analysis of seed traits.
学科主题	Ecology ; Evolutionary Biology ; Genetics & Heredity
语种	英语
出版者	NATURE PUBLISHING GROUP
WOS记录号	WOS:000341087900005
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/4842]
专题	作物科学研究所
作者单位	1.Zhejiang Univ, Inst Bioinformat, Coll Agr & Biotechnol, Hangzhou 310058, Zhejiang, Peoples R China 2.Chinese Acad Agr Sci, Inst Crop Sci, Beijing 100193, Peoples R China 3.Univ Alabama Birmingham, Dept Biostat, Birmingham, AL 35294 USA
推荐引用方式 GB/T 7714	Qi, T.,Jiang, B.,Zhu, Z.,et al. Mixed linear model approach for mapping quantitative trait loci underlying crop seed traits[J]. HEREDITY,2014,113(3):224-232.
APA	Qi, T..,Jiang, B..,Zhu, Z..,Wei, C..,Gao, Y..,...&Lou, X..(2014).Mixed linear model approach for mapping quantitative trait loci underlying crop seed traits.HEREDITY,113(3),224-232.
MLA	Qi, T.,et al."Mixed linear model approach for mapping quantitative trait loci underlying crop seed traits".HEREDITY 113.3(2014):224-232.