Du Qingzhang, Gong Chenrui, Wang Qingshi, Zhou Daling, Yang Haijiao, Pan Wei, Li Bailian, Zhang Deqiang
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, 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, No. 35, Qinghua East Road, Beijing, 100083, China.
New Phytol. 2016 Feb;209(3):1067-82. doi: 10.1111/nph.13695. Epub 2015 Oct 26.
Deciphering the genetic architecture underlying polygenic traits in perennial species can inform molecular marker-assisted breeding. Recent advances in high-throughput sequencing have enabled strategies that integrate linkage-linkage disequilibrium (LD) mapping in Populus. We used an integrated method of quantitative trait locus (QTL) dissection with a high-resolution linkage map and multi-gene association mapping to decipher the nature of genetic architecture (additive, dominant, and epistatic effects) of potential QTLs for growth traits in a Populus linkage population (1200 progeny) and a natural population (435 individuals). Seventeen QTLs for tree height, diameter at breast height, and stem volume mapped to 11 linkage groups (logarithm of odds (LOD) ≥ 2.5), and explained 2.7-18.5% of the phenotypic variance. After comparative mapping and transcriptome analysis, 187 expressed genes (10 046 common single nucleotide polymorphisms (SNPs)) were selected from the segmental homology regions (SHRs) of 13 QTLs. Using multi-gene association models, we observed 202 significant SNPs in 63 promising genes from 10 QTLs (P ≤ 0.0001; FDR ≤ 0.10) that exhibited reproducible associations with additive/dominant effects, and further determined 11 top-ranked genes tightly linked to the QTLs. Epistasis analysis uncovered a uniquely interconnected gene-gene network for each trait. This study opens up opportunities to uncover the causal networks of interacting genes in plants using an integrated linkage-LD mapping approach.
解析多年生植物多基因性状的遗传结构有助于分子标记辅助育种。高通量测序技术的最新进展使整合杨树连锁不平衡（LD）图谱的策略成为可能。我们采用了一种综合的数量性状基因座（QTL）剖析方法，结合高分辨率连锁图谱和多基因关联图谱，来解析杨树连锁群体（1200个子代）和自然群体（435个个体）中生长性状潜在QTL的遗传结构性质（加性、显性和上位性效应）。17个与树高、胸径和材积相关的QTL定位到11个连锁群上（优势对数（LOD）≥2.5），解释了2.7%-18.5%的表型变异。经过比较图谱分析和转录组分析，从13个QTL的片段同源区域（SHR）中筛选出187个表达基因（10046个常见单核苷酸多态性（SNP））。使用多基因关联模型，我们在来自10个QTL的63个有前景的基因中观察到202个显著SNP（P≤0.0001；错误发现率≤0.10），这些SNP表现出与加性/显性效应的可重复关联，并进一步确定了11个与QTL紧密连锁的顶级基因。上位性分析揭示了每个性状独特的相互连接的基因-基因网络。本研究为利用整合的连锁-LD图谱方法揭示植物中相互作用基因的因果网络提供了机会。
