QTL mapping for leaf morphology traits in a large maize-teosinte population

Fu, Yuhua; Xu, Guiyun; Chen, Huafeng; Wang, Xufeng; Chen, Qiuyue; Huang, Cheng; Li, Dan; Xu, Dongxiao; Tian, Jinge; Wu, Weihao; Lü, Sijia; Liu, Cong; Tian, Feng

doi:10.1007/s11032-019-1012-5

Cited by 22 publications

(11 citation statements)

References 67 publications

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“…This RIL population has also been widely used to fine-map QTL, and identify causal or candidate genes for many traits, including seed shattering (Lin et al 2012), leaf number (Li et al 2016), kernel row number (KRN) (Calderón et al 2016), shoot apical meristem morphology (Leiboff et al 2016), vascular bundle number (Huang et al 2016), tassel-related traits (G. Xu et al 2017), nodal root number (Zhang et al 2018), and leaf morphological traits (Fu et al 2019). Using this population, several QTL have been fine-mapped to single genes including grassy tillers1 ( gt1 ) for controlling prolificacy (PROL) (Wills et al 2013), prolamin box-binding factor1 ( pbf1 ) for kernel weight (Lang et al 2014), glossy15 ( gl15 ) for vegetative phase changes (D.…”

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TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize

et al. 2019

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Recombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple teosinte inbred lines as parents has been lacking. Here, we report a teosinte nested association mapping (TeoNAM) population, derived from crossing five teosinte inbreds to the maize inbred line W22. The resulting 1257 BC1S4 RILs were genotyped with 51,544 SNPs, providing a high-density genetic map with a length of 1540 cM. On average, each RIL is 15% homozygous teosinte and 8% heterozygous. We performed joint linkage mapping (JLM) and a genome-wide association study (GWAS) for 22 domestication and agronomic traits. A total of 255 QTL from JLM were identified, with many of these mapping near known genes or novel candidate genes. TeoNAM is a useful resource for QTL mapping for the discovery of novel allelic variation from teosinte. TeoNAM provides the first report that PROSTRATE GROWTH1, a rice domestication gene, is also a QTL associated with tillering in teosinte and maize. We detected multiple QTL for flowering time and other traits for which the teosinte allele contributes to a more maize-like phenotype. Such QTL could be valuable in maize improvement.

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TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize

et al. 2019

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“…Among these rice QTL, qFW4-2 was located to a 37-kb region, with the most possible candidate gene which previously detected NAL1 . Moreover, 17 and 14 QTL, respectively, for FLL and FLW have been identified in a maize-teosinte BC 2 S 3 RIL population ( Fu et al, 2019 ). Many mutants with leaf size phenotypes have been characterized, and their relevant genes have been cloned in rice ( Fujino et al, 2008 ; Hu et al, 2010 ; Xiang et al, 2012 ; Liu et al, 2016 ).…”

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confidence: 99%

QTL-Seq and Transcriptome Analysis Disclose Major QTL and Candidate Genes Controlling Leaf Size in Sesame (Sesamum indicum L.)

et al. 2021

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Leaf size is a crucial component of sesame (Sesamum indicum L.) plant architecture and further influences yield potential. Despite that it is well known that leaf size traits are quantitative traits controlled by large numbers of genes, quantitative trait loci (QTL) and candidate genes for sesame leaf size remain poorly understood. In the present study, we combined the QTL-seq approach and SSR marker mapping to identify the candidate genomic regions harboring QTL controlling leaf size traits in an RIL population derived from a cross between sesame varieties Zhongzhi No. 13 (with big leaves) and ZZM2289 (with small leaves). The QTL mapping revealed 56 QTL with phenotypic variation explained (PVE) from 1.87 to 27.50% for the length and width of leaves at the 1/3 and 1/2 positions of plant height. qLS15-1, a major and environmentally stable pleiotropic locus for both leaf length and width explaining 5.81 to 27.50% phenotypic variation, was located on LG15 within a 408-Kb physical genomic region flanked by the markers ZMM6185 and ZMM6206. In this region, a combination of transcriptome analysis with gene annotations revealed three candidate genes SIN_1004875, SIN_1004882, and SIN_1004883 associated with leaf growth and development in sesame. These findings provided insight into the genetic characteristics and variability for sesame leaf and set up the foundation for future genomic studies on sesame leaves and will serve as gene resources for improvement of sesame plant architecture.

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“…In model systems, several genes and networks have been identified to affect initial leaf development and pattern formation [ 2 , 7 , 8 ] as well as leaf length and width [ 9 – 11 ] using the mutagenesis screening method. Moreover, quantitative trait loci have also 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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confidence: 99%

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

Yang

Yao

et al. 2021

PLoS ONE

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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.

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QTL mapping for leaf morphology traits in a large maize-teosinte population

Cited by 22 publications

References 67 publications

TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize

TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize

QTL-Seq and Transcriptome Analysis Disclose Major QTL and Candidate Genes Controlling Leaf Size in Sesame (Sesamum indicum L.)

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

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