Genomic architecture of complex traits in loblolly pine
Genomic architecture of complex traits in loblolly pine
复制标题
DOI：
10.1111/nph.15535
复制
发表时间：
2019-03-01
期刊：
影响因子：
9.4
通讯作者：
Neale, David B.
中科院分区：
文献类型：
--
作者：
De La Torre, Amanda R.;Puiu, Daniela;Neale, David B.
剖析复杂性状的遗传和基因组结构对于理解维持具有生态和经济重要性的表型性状变异的力量是必不可少的。全基因组重测序数据被用来产生高分辨率的多态性单核苷酸多态性（SNP）标记和基因型个体从常见的花园火炬松（火炬松）的自然范围。全基因组的关联进行了测试与一个大型的表型数据集，包括409个变量，包括形态性状（高度，直径，碳同位素的歧视，沥青溃疡病抗性），和分子性状，如代谢产物和木质部发育基因的表达。我们的研究确定了该物种的2335个新的SNP x性状关联，其中许多SNP位于该物种基因组中的物理簇中;以及代谢x基因型关联的热点的基因组位置。我们发现了一个高度多基因的数量遗传的基础上，显着差异的数量，影响大小，基因组位置和频率的等位基因有助于在不同性状的表型变异。虽然突变选择平衡可能塑造代谢性状的遗传变异，平衡选择更有可能塑造木质部发育基因表达的变异。我们的工作有助于非模式植物物种的复杂性状的研究，确定协会在全基因组水平。
Dissecting the genetic and genomic architecture of complex traits is essential to understand the forces maintaining the variation in phenotypic traits of ecological and economical importance. Whole-genome resequencing data were used to generate high-resolution polymorphic single nucleotide polymorphism (SNP) markers and genotype individuals from common gardens across the loblolly pine (Pinus taeda) natural range. Genome-wide associations were tested with a large phenotypic dataset comprising 409 variables including morphological traits (height, diameter, carbon isotope discrimination, pitch canker resistance), and molecular traits such as metabolites and expression of xylem development genes. Our study identified 2335 new SNP x trait associations for the species, with many SNPs located in physical clusters in the genome of the species; and the genomic location of hotspots for metabolic x genotype associations. We found a highly polygenic basis of quantitative inheritance, with significant differences in number, effects size, genomic location and frequency of alleles contributing to variation in phenotypes in the different traits. While mutation-selection balance might be shaping the genetic variation in metabolic traits, balancing selection is more likely to shape the variation in expression of xylem development genes. Our work contributes to the study of complex traits in nonmodel plant species by identifying associations at a whole-genome level.