Multivariate genome-wide association study of leaf shape in a Populus deltoides and P. simonii F1 pedigree

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....

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Autores principales:	Wenguo Yang, Dan Yao, Hainan Wu, Wei Zhao, Yuhua Chen, Chunfa Tong
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/02ac3d3e042245fbb2a14b8bdf67acc4
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spelling	oai:doaj.org-article:02ac3d3e042245fbb2a14b8bdf67acc42021-11-04T06:49:34ZMultivariate genome-wide association study of leaf shape in a Populus deltoides and P. simonii F1 pedigree1932-6203https://doaj.org/article/02ac3d3e042245fbb2a14b8bdf67acc42021-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8553126/?tool=EBIhttps://doaj.org/toc/1932-6203Leaf 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.Wenguo YangDan YaoHainan WuWei ZhaoYuhua ChenChunfa TongPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wenguo Yang Dan Yao Hainan Wu Wei Zhao Yuhua Chen Chunfa Tong Multivariate genome-wide association study of leaf shape in a Populus deltoides and P. simonii F1 pedigree
description	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.
format	article
author	Wenguo Yang Dan Yao Hainan Wu Wei Zhao Yuhua Chen Chunfa Tong
author_facet	Wenguo Yang Dan Yao Hainan Wu Wei Zhao Yuhua Chen Chunfa Tong
author_sort	Wenguo Yang
title	Multivariate genome-wide association study of leaf shape in a Populus deltoides and P. simonii F1 pedigree
title_short	Multivariate genome-wide association study of leaf shape in a Populus deltoides and P. simonii F1 pedigree
title_full	Multivariate genome-wide association study of leaf shape in a Populus deltoides and P. simonii F1 pedigree
title_fullStr	Multivariate genome-wide association study of leaf shape in a Populus deltoides and P. simonii F1 pedigree
title_full_unstemmed	Multivariate genome-wide association study of leaf shape in a Populus deltoides and P. simonii F1 pedigree
title_sort	multivariate genome-wide association study of leaf shape in a populus deltoides and p. simonii f1 pedigree
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/02ac3d3e042245fbb2a14b8bdf67acc4
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Multivariate genome-wide association study of leaf shape in a Populus deltoides and P. simonii F1 pedigree

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