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Two‐stage identification of SNP effects on dynamic poplar growth
Author(s) -
Liu Jingyuan,
Ye Meixia,
Zhu Sheng,
Jiang Libo,
Sang Mengmeng,
Gan Jingwen,
Wang Qian,
Huang Minren,
Wu Rongling
Publication year - 2018
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13777
Subject(s) - snp , single nucleotide polymorphism , genome wide association study , biology , sample size determination , curse of dimensionality , computational biology , statistics , mathematics , genetics , genotype , gene
Summary 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 SNP s 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 SNP s. 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.