Two-stage identification of SNP effects on dynamic poplar growth

Jingyuan Liu, Meixia Ye, Sheng Zhu, Libo Jiang, Mengmeng Sang, Jingwen Gan, Qian Wang, Minren Huang, Rongling Wu

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

This project proposes an approach to identify significant single nucleotide polymorphism (SNP) effects, both additive and dominant, on the dynamic growth of poplar in diameter and height. The annual changes in yearly phenotypes based on regular observation periods are considered to represent multiple responses. In total 156,362 candidate SNPs are studied, and the phenotypes of 64 poplar trees are recorded. To address this ultrahigh dimensionality issue, this paper adopts a two-stage approach. First, the conventional genome-wide association studies (GWAS) and the distance correlation sure independence screening (DC-SIS) methods (Li et al., 2012) were combined to reduce the model dimensions at the sample size; second, a grouped penalized regression was applied to further refine the model and choose the final sparse SNPs. The multiple response issue was also carefully addressed. The SNP effects on the dynamic diameter and height growth patterns of poplar were systematically analyzed. In addition, a series of intensive simulation studies was performed to validate the proposed approach.

Original languageEnglish (US)
Pages (from-to)286-296
Number of pages11
JournalPlant Journal
Volume93
Issue number2
DOIs
StatePublished - Jan 2018

Fingerprint

single nucleotide polymorphism
Single Nucleotide Polymorphism
phenotype
Growth
additive effect
screening
Phenotype
Genome-Wide Association Study
Sample Size
Observation
sampling
methodology
genome-wide association study

All Science Journal Classification (ASJC) codes

  • Genetics
  • Plant Science
  • Cell Biology

Cite this

Liu, J., Ye, M., Zhu, S., Jiang, L., Sang, M., Gan, J., ... Wu, R. (2018). Two-stage identification of SNP effects on dynamic poplar growth. Plant Journal, 93(2), 286-296. https://doi.org/10.1111/tpj.13777
Liu, Jingyuan ; Ye, Meixia ; Zhu, Sheng ; Jiang, Libo ; Sang, Mengmeng ; Gan, Jingwen ; Wang, Qian ; Huang, Minren ; Wu, Rongling. / Two-stage identification of SNP effects on dynamic poplar growth. In: Plant Journal. 2018 ; Vol. 93, No. 2. pp. 286-296.
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Liu, J, Ye, M, Zhu, S, Jiang, L, Sang, M, Gan, J, Wang, Q, Huang, M & Wu, R 2018, 'Two-stage identification of SNP effects on dynamic poplar growth', Plant Journal, vol. 93, no. 2, pp. 286-296. https://doi.org/10.1111/tpj.13777

Two-stage identification of SNP effects on dynamic poplar growth. / Liu, Jingyuan; Ye, Meixia; Zhu, Sheng; Jiang, Libo; Sang, Mengmeng; Gan, Jingwen; Wang, Qian; Huang, Minren; Wu, Rongling.

In: Plant Journal, Vol. 93, No. 2, 01.2018, p. 286-296.

Research output: Contribution to journalArticle

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AU - Liu, Jingyuan

AU - Ye, Meixia

AU - Zhu, Sheng

AU - Jiang, Libo

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AU - Gan, Jingwen

AU - Wang, Qian

AU - Huang, Minren

AU - Wu, Rongling

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Liu J, Ye M, Zhu S, Jiang L, Sang M, Gan J et al. Two-stage identification of SNP effects on dynamic poplar growth. Plant Journal. 2018 Jan;93(2):286-296. https://doi.org/10.1111/tpj.13777