Du Qingzhang, Tian Jiaxing, Yang Xiaohui, Pan Wei, Xu Baohua, Li Bailian, Ingvarsson Pär K, Zhang Deqiang
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China.
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P. R. China Department of Forestry, North Carolina State University, Raleigh, NC 27695-8203, USA.
DNA Res. 2015 Feb;22(1):53-67. doi: 10.1093/dnares/dsu040. Epub 2014 Nov 26.
Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R(2)). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q ≤ 0.10), representing 38 SNPs from nine genes, and its average effect (R(2) = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene-gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding.
许多物种中具有经济重要性的性状通常表现为多基因的数量遗传。由共享生物途径中的多个基因赋予的这些性状的遗传变异成分（加性、显性和上位性效应）仍有待确定。在这里，我们通过多基因关联研究了460个无亲缘关系的毛白杨个体群体中纤维素生物合成中的11个全长基因，涉及10个生长和木材性质性状。为了验证正相关关系，我们在一个由1200个个体组成的连锁群体中进行了单标记分析。我们分别鉴定出118、121和43个与加性、显性和上位性效应相对应的关联（P<0.01），其表型变异比例（R²）低至中等。上位性相互作用模型揭示了来自三个独特基因的三个非同义位点的组合，这对胸径和树干体积具有显著的上位性。单标记分析验证了61个关联（错误发现率，Q≤0.10），代表来自九个基因的38个单核苷酸多态性（SNP），其平均效应（R² = 3.8%）比多基因关联鉴定出的效应高出近2倍，这表明多基因关联可以捕获较小的个体变异。此外，基于组织特异性转录本丰度的结构基因-基因网络能够更好地理解影响树木生长和木质纤维素生物合成的多基因途径。我们的研究强调了基于途径的多基因关联对于揭示数量性状遗传变异本质的重要性，并可能推动分子育种的新进展。
