Abstract
Leaf morphology exhibits tremendous diversity between and within species, and is likely related to adaptation to environmental factors. Most poplar species are of great economic and ecological values and their leaf morphology can be a good predictor for wood productivity and environment adaptation. It is important to understand the genetic mechanism behind variation in leaf shape. Although some initial efforts have been made to identify quantitative trait loci (QTLs) for poplar leaf traits, more effort needs to be expended to unravel the polygenic architecture of the complex traits of leaf shape. Here, we performed a genome-wide association analysis (GWAS) of poplar leaf shape traits in a randomized complete block design with clones from F1 hybrids of Populus deltoides and Populus simonii. A total of 35 SNPs were identified as significantly associated with the multiple traits of a moderate number of regular polar radii between the leaf centroid and its edge points, which could represent the leaf shape, based on a multivariate linear mixed model. In contrast, the univariate linear mixed model was applied as single leaf traits for GWAS, leading to genomic inflation; thus, no significant SNPs were detected for leaf length, measures of leaf width, leaf area, or the ratio of leaf length to leaf width under genomic control. Investigation of the candidate genes showed that most flanking regions of the significant leaf shape-associated SNPs harbored genes that were related to leaf growth and development and to the regulation of leaf morphology. The combined use of the traditional experimental design and the multivariate linear mixed model could greatly improve the power in GWAS because the multiple trait data from a large number of individuals with replicates of clones were incorporated into the statistical model. The results of this study will enhance the understanding of the genetic mechanism of leaf shape variation in Populus. In addition, a moderate number of regular leaf polar radii can largely represent the leaf shape and can be used for GWAS of such a complicated trait in Populus, instead of the higher-dimensional regular radius data that were previously considered to well represent leaf shape.
Highlights
Leaves are the most fundamental photosynthetic organs in plants; they are responsible for absorbing solar energy to generate power for plant growth and provide food for many species on earth [1, 2]
We used the multiple traits of different numbers of regular radii across −π/2 to π/2 to find Single nucleotide polymorphism (SNP) associated with leaf shape, which was implemented with the multivariate linear mixed model (mvLMM) as follows: yijkl 1⁄4 ml þ Bil þ Mjl þ Gjl þ eijkl ð1Þ
The coefficient of variation (CV) for the leaf length and different leaf widths were similar, ranging from 20.79% for L to 25.14% for W2/3, while the CV for leaf area reached a maximum value of 42.25% and the CV for the length/width ratio had a minimum value of 10.12%
Summary
Leaves are the most fundamental photosynthetic organs in plants; they are responsible for absorbing solar energy to generate power for plant growth and provide food for many species on earth [1, 2]. Leaf size and shape are evolutionarily adapted to environmental changes in response to water and light stress [3, 4], making it possible to reconstruct the paleoclimate [5, 6]. Quantitative trait loci have been detected for leaf morphological traits in species such as tomato [12], Arabidopsis [13], Brassica [14], maize [15], barley [16], and Populus [17, 18]. Despite advances made in these studies, the identified genes or loci may only cover a portion of the leaf morphological variation observed in nature because the variation is considered to be under polygenic control [11, 19]
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