Plant Molecular Biology (2019) 99:1–15

https://doi.org/10.1007/s11103-018-0797-7

Genome-wide association study of maize plant architecture using ­F1

populations
Yang Zhao1,2 · Hengsheng Wang1,2 · Chen Bo1,2 · Wei Dai1,2 · Xingen Zhang1,2 · Ronghao Cai1,2 · Longjiang Gu1,2 ·
Qing Ma1,2 · Haiyang Jiang1,2 · Jun Zhu3 · Beijiu Cheng1,2 

Received: 5 January 2018 / Accepted: 10 November 2018 / Published online: 5 December 2018
© Springer Nature B.V. 2018

Abstract
Key message  Genome-wide association study of maize plant architecture using F ­ 1 populations can better dissect
various genetic effects that can provide precise guidance for genetic improvement in maize breeding.
Abstract  Maize grain yield has increased at least eightfold during the past decades. Plant architecture, including plant
height, leaf angle, leaf length, and leaf width, has been changed significantly to adapt to higher planting density. Although
the genetic architecture of these traits has been dissected using different populations, the genetic basis remains unclear in
the ­F1 population. In this work, we perform a genome-wide association study of the four traits using 573 ­F1 hybrids with a
mixed linear model approach and QTXNetwork mapping software. A total of 36 highly significant associated quantitative
trait SNPs were identified for these traits, which explained 51.86–79.92% of the phenotypic variation and were contributed
mainly by additive, dominance, and environment-specific effects. Heritability as a result of environmental interaction was
more important for leaf angle and leaf length, while major effects (a, aa, and d) were more important for leaf width and
plant height. The potential breeding values of the superior lines and superior hybrids were also predicted, and these values
can be applied in maize breeding by direct selection of superior genotypes for the associated quantitative trait SNPs. A total
of 108 candidate genes were identified for the four traits, and further analysis was performed to screen the potential genes
involved in the development of maize plant architecture. Our results provide new insights into the genetic architecture of the
four traits, and will be helpful in marker-assisted breeding for maize plant architecture.

Keywords  Maize · GWAS · QTSs · Plant architecture · F1 population

Abbreviations LW Leaf width

PH Plant height GWAS Genome-wide association study
LA Leaf angle QTSs Quantitative trait SNPs
LL Leaf length SNP Single nucleotide polymorphism
RNA-Seq RNA sequencing
Electronic supplementary material  The online version of this GE Genotype × environment interaction
article (https​://doi.org/10.1007/s1110​3-018-0797-7) contains a Additive
supplementary material, which is available to authorized users. d Dominance
aa Epistasis
* Jun Zhu
jzhu@zju.edu.cn
* Beijiu Cheng
bjchengahau@163.com Introduction
1
National Engineering Laboratory of Crop Stress Resistance Maize (Zea mays L.) is one of the most important cereal
Breeding, School of Life Sciences, Anhui Agricultural crops worldwide and has become a model plant for study of
University, Hefei, China
genetics, evolution and basic biology. After a long domesti-
2
Key Laboratory of Crop Biology of Anhui Province, School cation history of about 10,000 years from teosinte (Z. mays
of Life Sciences, Anhui Agricultural University, Hefei, China
ssp. Parviglumis) and subsequently a long breeding pro-
3
Institute of Bioinformatics, Zhejiang University, Hangzhou, cess under natural and human selection, modern maize has
China

13
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2 Plant Molecular Biology (2019) 99:1–15
maintained a large degree of genetic variation, which has
resulted in significant phenotypic variation (Doebley 2004;
Wright et al. 2005). Increasing grain yield is an important
long-term goal of maize breeding. During the past 80 years,
maize grain yield has increased eightfold (Duvick 2005).
The increased yield of maize was not a result of advanced
technological and management, but rather attributed to cur-
rent selection and hybrid breeding (Cardwell 1982). Study
also indicated that the increasing of gain yield was attributed
mainly to the newer hybrids that can adapt to higher plant-
ing density and higher tolerance to various stresses (Duvick
2005). Duvick (2005) reported the average plant density
of maize in the United States increased from 30,000 plants
­ha−1 of the pre-1930s to the current 80,000 plants ­ha−1 or
higher in the major maize producing regions. During the
same period, maize plant architecture, including plant height
(PH), leaf angle (LA), leaf length (LL), and leaf width (LW),
have changed significantly as a result of selection to adapt
to the higher planting density (Ku et al. 2010; Lambert and
Johnson 1978). These agronomic traits are important for
maize hybrids and can influence canopy morphology and
photosynthetic efficiency, thus affecting the overall yield
(Sinclair and Sheehy 1999; Tian et al. 2011). Breeding new
hybrids with optimized plant architecture has been regarded
as one of the most effective methods to improve maize yield.
Dissecting the genetic architecture of maize plant architec-
ture may provide important clues to identify key genes or
quantitative trait loci (QTLs) for improving complex traits
by molecular breeding.
Plant architecture in natural populations is a quantita-
tive trait (Mackay 2001). To understand the genetic basis
of maize plant architecture, a large number of QTLs distrib-
uted throughout the genome have been identified through
construction of different mapping populations (Ku et al.
2010; Mickelson et al. 2002; Peiffer et al. 2014). The results
have strengthened the understanding of the heredity of tar-
get traits. However, the identified QTLs generally had large
confidence intervals, and it is a time-consuming process to
clone the related genes, especially given the complexity of
the maize genome (Li et al. 2015; Mackay et al. 2009; Tian
et al. 2011; Xiao et al. 2016). In recent years, genome-wide
association study (GWAS) has been extensively applied to
dissect the genetic basis of complex traits in plants and ani-
mals (Burton et al. 2007; Flint-Garcia et al. 2003; Huang
et al. 2010). In maize, a nested association mapping pop-
ulation has been constructed by McMullen et al. (2009),
which composed of 5000 recombinant inbred lines. Based
on this population, genetic architectures of leaf traits, PH,
and flowering time have been dissected based on the pheno-
typic variation (Buckler et al. 2009; Peiffer et al. 2014; Tian
et al. 2011). In particular, a maize natural population that
included 368 inbred lines was constructed with high-quality
single nucleotide polymorphism (SNP) markers, and this
13
population has been used to dissect the genetic architectures
of maize complex traits (Li et al. 2013; Liu et al. 2013a; Wen
et al. 2014; Xue et al. 2013; Yang et al. 2011).
Although a large number of related genes and quantita-
tive trait SNPs (QTSs) of plant architecture were identified
by GWAS, the genetic architecture of complex traits is still
far from being understood in maize. Phenotypic variation
of complex traits is usually controlled by multiple genes
with gene × gene (epistasis) and genotype × environment
interactions in multiple environments (Carlborg and Haley
2004; Zhang et al. 2015a). Many studies indicated that geno-
type × environment or epistasis interactions could explain a
considerable proportion of phenotypic variations (Caicedo
et al. 2004; Sambandan et al. 2008; Uwatoko et al. 2008).
However, detecting two-locus and environmental interac-
tions in multiple environments is still a major challenge in
the current GWAS because of the large amount of data to
be computed (Yang et al. 2007). Indeed, maize ­F1 hybrids
have been used extensively in current maize production pro-
gram, and planting density of maize F ­ 1 hybrids are mainly
affected by PH, LA, LL, and LW. Thus, using ­F1 hybrids
as the association population for GWAS may help to bet-
ter dissect the genetic architecture of genotypic effects and
their environment interactions, especially for epistasis and
dominance. Importantly, QTSs identified based on the F ­1
populations can also provide precise molecular selection in
modern maize breeding.
In this study, a maize F ­ 1 population containing 573
hybrids was constructed through incomplete diallel crosses
using 87 maize inbred lines genotyped with high density
SNPs (Xie et al. 2013), and PH, LA, LL, and LW were phe-
notyped in three environments for 2 years. Then, a mixed lin-
ear model (MLM) approach and newly developed mapping
software of QTXNetwork based on GPU parallel comput-
ing were used to dissect the genetic architecture of the four
traits (Zhang et al. 2015a). Candidate genes significantly
associated with the target traits were further screened and
analyzed. The results presented in this study provide new
insights into the genetic architecture of maize plant architec-
ture and also provide reliable information for maize molecu-
lar breeding.
Materials and methods
Construction of maize ­F1 populations and SNP
genotyping
A total of 87 diverse inbred lines, including 40 temperate
lines and 47 tropical lines representing modern maize elite
inbred lines in China, were used to construct the maize ­F1
population by an incomplete diallel crosses method. To
­ 1 hybrids, the sowing dates of the inbred lines
obtain the F
Plant Molecular Biology (2019) 99:1–15 3
were adjusted according to our previous record because of
the large differences in flowering time. To obtain the geno-
typing of the 87 lines, the whole genomes were re-sequenced
with a mean sequencing depth of 10 × per individual. SNP
calling and data analysis were referenced to Xie et al. (2013).
All the SNP locations were obtained by mapping the re-
sequenced reads onto the B73 reference sequence (AGPv3).
SNP genotyping of the ­F1 hybrids was generated according
to the genotypes of their parents with the following formu-
las: (1) for male and female parents with the same SNP gen-
otype at the individual loci, the genotype of the ­F1 hybrids
was the same as their two parents at these individual loci; (2)
for male and female parents with different SNP genotypes at
the individual loci, a heterozygous genotype was assigned
to the ­F1 hybrids at these individual loci. Each SNP locus of
the hybrids was designated a number as follows. Homozy-
gote loci of high and low frequency were coded 0 and 2,
respectively, and the heterozygote loci were coded 1. The
numerically coded genotype was used in the GWAS analysis.
Trait evaluations of maize plant architecture
All hybrids were grown in Suzhou (Anhui Province),
Liaocheng (Shandong Province) and Gongzhuling (Jilin
Province) during the summer in 2015 and 2016. Each hybrid
was planted in a 6.0 m row with 0.25 m plant spacing and
with 0.6 m spacing between rows, and normal agronomic
practices were used in field management. Each field experi-
ment followed a randomized complete block design with
three replications. Phenotypic measurements were per-
formed at 8–10 day after anthesis, and 3–5 middle plants
were selected randomly form each row. The PH was scored
from ground to the tassel tip of the selected plants. The LA
was measured as the acute angle between the vertical stem
and midrib of the leaf. The LL was measured as the distance
from the base of the ligula to the tip of the leaf. The LW was
measured by taking the width of the widest section of the
leaf. The first leaf above the primary ear was selected for the
measurements and used for GWAS analysis. The trait value
for each ­F1 hybrids was averaged for the measured plants.
Models and statistical methods
Generalized multifactor dimensionality reduction method (Zhu
et al. 2013) was used to scan all the SNP markers for 1D (single
SNP) and 2D (two SNPs epistasis) significant SNP markers,
using the parameters of 400 best SNP selection limit and 1­ 03
permutation power for each trait. Then, a set of 9503 prelimi-
nary filtered SNPs were used in the second step to dissect the
genetic architecture of the four traits using a saturated MLM
implemented in QTXNetwork (http://ibi.zju.edu.cn/softw​are/
QTXNe​twork​/) (Zhang et al. 2015a). The genetic model for
association mapping used the MLM including genetic main
effects (a, d, aa, ad, da, and dd) as fixed effect, environment
(e) and loci by environment interaction (ae, de, aae, ade, dae,
and dde) as random effects. The phenotypic value of the k-th
line in the h-th environment ( yhk ) was expressed by the MLM
as described in our previous study (Luo et al. 2017). In this
model, there are constraints for random variables with normal
distributions of zero mean and variances 𝜎v2.
The phenotypic variance (VP ) was defined as the sum of
additive variance (VA ) , dominance variance (VD ) , epistasis
variance (VI = VAA + VAD + VDA + VDD ) , additive by envi-
ronment interaction variance (VAE ) , dominance by environ-
ment interaction variance (VDE ) , epistasis by environment
interaction variance (VIE = VAAE + VADE + VDAE + VDDE ) ,
and residual variance (V𝜀 ) as follows.
VP = VA + VD + (VAA + VAD + VDA + VDD )
+ VAE + VDE + (VAAE + VADE + VDAE + VDDE ) + V𝜀
= VA + VD + VI + VAE + VDE + VIE + V𝜀
Total heritability was estimated by
h2T = h2G + h2GE
= (h2A + h2D + h2AA + h2AD + h2DA + h2DD )
+ (h2AE + h2DE + h2AAE + h2ADE + h2DAE + h2DDE )
= (h2A + h2D + h2I ) + (h2AE + h2DE + h2IE )
where h2T is the total heritability; h2A = i h2a is the herit-
∑
ability due to additive effects contributed by the sum of
individual loci, h2D = i h2d is the heritability due to domi-
∑
nance effects contributed by the sum of individual loci,
h2AA = i<j h2aa is the heritability contributed by the sum of
∑
pair-wise additive by additive (aa) epistasis, h2AD = i<j h2ad
∑
is the heritability contributed by the sum of pair-wise addi-
tive by dominance (ad) epistasis, h2DA = i<j h2da is the her-
∑
itability contributed by the sum of pair-wise dominance by
additive (da) epistasis, h2DD = i<j h2dd is the heritability
∑
contributed by the sum of pair-wise dominance by domi-
nance (dd) epistasis, h2AE = i h2ae is additive by environment
∑
interaction heritability contributed by the sum of individual
additive by environment interaction effects, h2DE = i h2de is
∑
dominance by environment interaction heritability contrib-
uted by the sum of individual dominance by environment
interaction effects, h2AAE = i<j h2aae is aa epistasis by envi-
∑
ronment interaction heritability contributed by the sum of
pair-wise aa epistasis by environment interaction effects,
h2ADE = i<j h2ade is ad epistasis by environment interaction
∑
heritability contributed by the sum of pair-wise ad epistasis
by environment interaction effects, h2DAE = i<j h2dae is da
∑
epistasis by environment interaction heritability contrib-
uted by the sum of pair-wise da epistasis by environment
interaction effects, and h2DDE = i<j h2dde is dd epistasis by
∑
13
4 Plant Molecular Biology (2019) 99:1–15
environment interaction heritability contributed by the sum
of pair-wise dd epistasis by environment interaction effects.
The MLM framework with Henderson method III
(Searle et al. 1992) was used to construct the F-statistic
test for association analysis. The permutation test was set
for a total of 2000 times to calculate the critical F-value to
control the experiment-wise type I error (𝛼EW < 0.05) . The
QTS effects were estimated using the Markov Chain Monte
Carlo algorithm with 20,000 Gibbs sample iterations (Yang
et al. 2007). Based on the information of genetic effects of
the detected QTSs of the four traits, we calculated breeding
values (̂𝜇 +̂e+G ̂ for the best lines and best hybrids
̂ + GE)
in the mapping population (Yang and Zhu 2005). Breeding
values for the superior lines and superior hybrids were also
calculated.
QTS mapping and associated gene annotation
To further understand the genetic basis of maize plant
architecture, QTSs with significant effects (− LogP-
2
experiment-wise(EW) > 3.00,) and large heritability (h  > 0.50%)
were mapped to the B73 reference genome (AGPv3) to
determine whether these QTSs were located in or near
associated genes involved for regulating the four traits. The
locations of candidate QTSs were extended 50 kb upstream
and downstream to infer the associated genome regions, and
genes located in those regions were considered as candidate
gens and used for further analysis. Expression levels were
transformed by ­log2 (FPKM + 1) based on the transcriptome
data of maize at different developmental stages and in differ-
ent tissues (Stelpflug et al. 2016), and a heatmap was gener-
ated using R and Bioconductor program (http://www.bioco​
nduct​or.org/). All candidate genes were annotated for gene
ontology (GO) enrichment analysis and pathway analysis.
For the GO analysis, the candidate genes were assigned
to GO terms under the three main categories of molecular
function, cellular component, and biological process using
the GO database (http://www.geneo​ntolo​gy.org/). Kyoto
Encyclopedia of Genes and Genomes (KEGG) (http://
www.genom​e.jp/kegg/) was used to identify the statistically
enriched pathways that candidate genes involved (Kanehisa
et al. 2008). To further explore the biological function of
the candidate genes, functional annotation was performed
using the MaizeGDB (https​://www.maize​gdb.org/), Pfam
(http://pfam.sange​r.ac.uk), and Phytozome online websites
(https​://phyto​zome.jgi.doe.gov/pz/porta​l.html). Homologs
of the candidate genes were also identified in Arabidopsis
by comparative genomics, and the GO terms assigned to
Arabidopsis genes were downloaded from TAIR (http://
www.arabi​dopsi​s.org/).
13
Co‑expression network construction
Weighted gene co-expression network analysis (WGCNA)
in the R-package was used to construct a gene co-expres-
sion network to further explore the possible functions of
the candidate genes in regulating the development of PH
(Langfelder and Horvath 2008; Zhang and Horvath 2005).
Genes used for the network were based on our previous
RNA sequencing (RNA-Seq) data from nine different stem
developmental stages (jointing stage, big flare period and
tasseling stage) of low, middle and high hybrids in maize
PH (accession number: GSE115796). To construct networks
with approximate scale-free topology, a power of nine was
chosen (model fitting index R ­ 2 = 0.8). The topological
overlap-based dissimilarity measure was used to cluster
all the coding sequences hierarchically. Finally, the result-
ing gene dendrogram was used for module detection using
the dynamic tree cut method (minModuleSize = 100 and
mergeCutHeight = 0.25). In a weighted gene co-expression
network, any two genes are connected; the topology overlap
measure provided in WGCNA was used to determine edge
weight. The weights ranged from 0 to 1, and reflected the
strength of the communication between the two connected
genes. Only weights > 0.2 between any two genes were con-
sidered to indicate a strong co-expression relationship. Con-
nectivity was defined as the sum of the weights across all
the edges of a node. Genes that shared a similar expression
pattern were clustered into a modules based on their correla-
tion. Each module was searched and filtered by interesting
genes, including reported maize PH genes and the 24 candi-
date genes identified in this study, and Cytoscape software
was used to display the co-expression network (Smoot et al.
2011).
Results
Genetic and phenotypic variations of the ­F1
population
To construct the ­F1 population used for GWAS analysis,
the 87 tenfold re-sequencing lines were used as the par-
ents, including 40 temperate lines and 47 tropical lines.
The genetic representative of the 87 tropical and temper-
ate inbred lines was selected based on previously published
studies (Lu et al. 2009; Xie et al. 2007, 2013). Due to the
large genetic difference, the sowing dates were adjusted to
ensure the similar flowering time. A total of 573 ­F1 hybrid
combinations were obtained through an incomplete diallel
crosses method. These F ­ 1 hybrids were planted in three dif-
ferent locations for 2 years. The results indicated that the
four traits (PH, LA, LW, and LL) had significantly differ-
ent phenotypes across different environments. The average
Plant Molecular Biology (2019) 99:1–15 5

phenotypic performance and range in the three environments
are shown in Table S1.
Genetic dissection of maize plant architecture
GWAS analysis was adopted to dissect the genetic archi-
tecture of the four traits (PH, LA, LW, and LL) with a
MLM approach using the maize F ­ 1 population. The total
heritability of the QTSs with significant genetic effects was
estimated, and a total of 41 QTSs significantly associated
with the four traits were identified, including 11 QTSs for
PH, 8 for LA, 10 for LW, and 12 for LL (Fig. 1, Table S2).
These QTSs explained 51.86–79.92% of the phenotypic vari-
ation, which was contributed by various types of genetic
variance effects (Table  1). The total heritability (h2T ) of
PH, LW and LL was attributed mainly to additive effect
( h2A = 20.13–45.28%), especially for PH, suggesting that
single QTS with genotypic effects were more important in
determining these phenotypic variation. These results are
consistent with previous reports for PH and leaf traits (Pei-
ffer et al. 2014; Tian et al. 2011). Dominance effect was
also determined in the four traits, and the results indicated

Fig. 1  Network plot of significant associated QTSs detected for the
four traits. Red dot, QTS with additive effect; black dot, QTS with
epistasis effect but without detected individual effects; green dot,
QTS with environment-specific additive effect; blue dot, QTS with
additive and environment-specific additive effect; red square, QTS
with dominance effect; green square, QTS with environment-specific
dominance effect; blue square, QTS with dominance and environ-
ment-specific dominance effect; black square, environment-specific
epistasis effect (da) without detected individual effects; red lines,
epistasis effect between two QTSs; green line, environment-specific
epistasis effect between two QTSs; PH plant height, LL leaf length,
LW leaf width, LA leaf angle

Table 1  Estimated heritability Trait h2A (%) h2D (%) h2I (%) h2AE (%) h2DE (%) h2IE (%) h2T (%)
of detected QTSs for the four
traits PH 45.28 6.68 0.00 13.04 0.71 0.00 65.71
LA 3.34 2.04 0.00 13.05 22.60 10.83 51.86
LW 20.13 20.52 14.19 4.48 11.18 0.00 70.50
LL 24.54 8.49 0.00 23.89 21.12 1.88 79.92

h2A , heritability of additive effect; h2D , heritability of dominance effect; h2I  , heritability of epistasis effect; h2IE ,
heritability of environment-specific additive effect; h2DE , heritability of environment-specific dominance
effect; h2IE , heritability of environment-specific epistasis effect; h2T  , total heritability of all genetic effects

13
6 Plant Molecular Biology (2019) 99:1–15

that the heritability of LA was significant lower than the Table 3  Predicted genetic effects of highly significant QTSs for
heritability of the other three traits. Additionally, we found maize LA
that QTSs with environmental interacted genetic effects Chr_SNP_Q/q Effect Predict SE − LogPEW h2 (%)
accounted for a large portion ( h2GE = 13.75–46.89%) of the
1_33250364_C/T ae1 − 1.74 0.19 19.99 7.96
estimated total heritability, suggesting that genotype × envi-
ae2 1.39 0.19 12.71
ronment interaction effects were also more important
de1 − 2.70 0.35 14.15 12.15
in determining these traits. LA ( h2GE = 46.48%) and LL
de2 1.69 0.34 6.12
( h2GE = 46.89%) were more sensitive to the environment than
1_105209274_C/T a − 0.85 0.14 9.26 2.30
LW ( h2GE = 15.66%) and PH ( h2GE = 13.75%), which were
de2 0.84 0.23 3.66 1.77
stable across the three environments. No significant epistasis
3_5579454_C/T d − 0.63 0.15 4.83 1.28
effects were detected among three of the traits; LW was the
de2 − 0.92 0.24 3.85 1.78
exception which accounted for 14.19% of the heritability.
6_24178316_C/T ae3 1.09 0.24 5.22 2.80
Overall, these results suggested that phenotypic variations
de2 0.80 0.22 3.51 1.43
of the four traits were controlled by genotypic effects and
9_58862666_G/A a 0.45 0.12 3.69 0.64
genotypic × environment interaction effects.
10_139263527_G/T ae2 − 0.76 0.19 4.39 1.10
1_33250364_C/T × aae1 − 2.03 0.20 23.48 10.83
Highly significant associated QTSs of the four traits 10_139263527_G/T aae2 1.62 0.20 14.68

The associated QTSs of the four traits with highly signifi-

cant genetic effects were screened with − LogPEW > 3.00 and
h2 > 0.50%, and the results are listed in Tables 2, 3, 4 and 5.
A total of 10 highly significant QTSs were detected for PH,
6 for LA, 9 for LW, and 11 for LL across the three environ-
ments. For PH, the total heritability was contributed mainly
by additive effect (Table 2). Five significant QTSs, namely
1_184045560_T/C, 6_135818683_G/C, 6_152679157_G/A,
7_133083644_T/C, and 10_91513471_C/G, showed
only additive heritability of > 3.30 (Table 2), especially
6_135818683_G/C ( h2A = 11.44%). Based on their large
main effects of their positive or negative effects, these QTSs
could be used to improve significantly PH in maize breeding.
We also found that some of the QTSs for PH had multiple
genetic effects. For example, 9_94559983_G/A had posi-
tive environment interaction effects in environment 2, but

Table 4  Predicted genetic effects of highly significant QTSs for

Table 2  Predicted genetic effects of highly significant QTSs for maize LW
maize PH
Chr_SNP_Q/q Effect Predict SE − LogPEW h2 (%)
Chr_SNP_Q/q Effect Predict SE − LogPEW h2 (%)
1_7688471_C/T d − 0.33 0.03 25.84 8.48
1_184045560_T/C a − 6.43 0.45 46.05 7.06
3_136932077_G/A a − 0.34 0.02 86.90 9.08
3_56071815_A/G a − 1.78 0.42 4.59 0.54
d 0.17 0.03 5.84 2.18
d − 4.82 0.64 13.30 3.97
de3 0.22 0.06 3.76 3.93
4_204331702_T/C a − 8.30 0.39 97.14 11.77
3_199126238_G/A a − 0.13 0.02 9.52 1.39
ae1 − 2.67 0.67 4.23 2.53
ae3 − 0.15 0.04 4.48 1.31
ae2 − 2.72 0.68 4.23
5_175651796_A/G a − 0.28 0.02 54.54 6.26
ae3 5.46 0.69 14.73
d − 0.21 0.03 12.71 3.60
5_166902397_C/T ae1 − 2.30 0.70 3.01 1.23
7_104716709_G/A d − 0.22 0.02 21.09 3.69
ae3 3.74 0.72 6.66
7_174262697_C/T a 0.16 0.02 15.44 2.03
6_135818683_G/C a 8.18 0.50 58.97 11.44
8_17971579_T/C a 0.10 0.02 5.73 0.74
6_152679157_G/A a − 5.04 0.51 22.03 4.35
d 0.13 0.02 7.90 1.38
7_133083644_T/C a 5.81 0.43 40.56 5.78
ae3 − 0.14 0.03 4.51 1.29
8_112550109_T/C a 1.65 0.50 3.01 0.47
8_173266113_C/T a − 0.09 0.02 6.18 0.63
ae1 − 3.39 0.84 4.24 2.94
d 0.12 0.03 4.61 1.19
ae3 5.77 0.89 10.14
ae1 − 0.12 0.03 4.56 0.78
9_94559983_G/A a − 1.82 0.48 3.78 0.57
de2 0.17 0.05 3.31 3.59
d 1.83 0.51 3.43
de3 − 0.25 0.05 6.10
ae2 5.07 0.83 9.08 4.55
7_65736590_C/T  aa − 0.42 0.02 70.11 14.19
ae3 − 5.25 0.84 9.30 × 7_104716709
10_91513471_C/G a − 4.39 0.40 26.65 3.30 _G/A

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Plant Molecular Biology (2019) 99:1–15 7

Table 5  Predicted genetic effects of highly significant QTSs for selecting 1_33250364_C/T and 1_33250364_C/T × 10_1392
maize LL 63527_G/T genotypes in environments 1 and 2. For LW, the
Chr_SNP_Q/q Effect Predict SE − LogPEW h2 (%) genotypic effects contributed a large portion of the total her-
itability ( h2G = 54.84%). According to the predicted effects
1_225945018_G/A ae2 − 2.97 0.19 53.77 8.26
of QTSs, the 1_7688471_C/T and 5_175651796_A/G loci,
ae3 3.04 0.19 54.18
which had strong additive and dominance effects, could be
de2 − 3.33 0.35 20.72 17.26
used to significantly improve LW (Table 4). Importantly, 7_6
de3 3.79 0.36 25.27
5736590_C/T × 7_104716709_G/A showed 14.19% herit-
3_9955357_A/G a − 1.90 0.12 58.24 4.87
ability for LW, so this QTS should be firstly considered when
ae1 1.17 0.20 8.44 2.51
LW is a target trait in maize breeding. LL had the high-
ae2 0.73 0.20 3.53
est heritability among leaf traits ( h2T = 79.92%) (Table 2),
ae3 − 1.91 0.20 20.08
and environment-specific interacted effects accounted for
3_147041046_A/C a 1.13 0.13 18.78 1.74
a large proportion of the total heritability ( h2GE = 46.89%),
ae3 0.89 0.22 4.47 0.08
suggesting that LL was sensitive to environment, similar to
3_152489669_A/G d 0.92 0.21 4.80 1.14
LA. Among the detected QTSs, locus 1_225945018_G/A
ae1 − 0.91 0.18 6.12 1.40
was detected with strong environment interacted effects
ae3 1.12 0.19 8.32
( h2GE = 25.52%), and locus 3_211687793_G/A had a strong
3_211687793_G/A ae2 − 0.87 0.18 5.63 0.70
additive effect ( h2A = =  10.20%), and could be considered
3_226358454_C/A a − 2.74 0.14 81.40 10.20
the major locus for LL improvement (Table 5).
d 0.67 0.13 6.34 0.60
Similar to PH, QTSs for leaf traits also had multiple
ae1 0.95 0.24 4.21 1.71
genetic effects. For example, 6_153125116_C/G exhibited
ae3 − 1.27 0.25 6.54
six different types of genetic variance effects for LL across
5_93577789_C/T ae1 − 2.21 0.17 36.36 5.21
the three environments. In addition, genetic overlap (plei-
ae2 − 1.67 0.18 20.71
otropy) among the four traits was also analyzed according
5_166972248_G/A a − 1.03 0.14 12.92 1.43
to the detected significant QTSs, and we found that all the
d 0.59 0.14 4.81 0.46
QTSs with significant effects were specific to only one of
5_214196051_C/T a 2.10 0.12 69.83 5.95
the four traits, suggesting the low pleiotropy of these traits
d 1.31 0.17 13.74 2.33
(Fig. 1). This result is consistent with previous results of
ae2 − 0.78 0.20 4.03 1.31
leaf traits reported by Tian et al. (2011). These findings can
ae3 1.15 0.20 7.82
provide a useful genetic basis to the pyramiding of differ-
6_153125116_C/G a 0.51 0.12 4.65 0.35
ent alleles for improving favorable traits in maize genetic
d 1.67 0.16 23.95 3.79
breeding.
ae1 0.94 0.20 5.48 1.14
ae3 − 0.89 0.21 4.75
Prediction of genetic effects for different genotypes
de2 − 1.13 0.28 4.39 2.12
de3 1.36 0.28 5.81
According to the detected associated QTSs, the genetic
7_126086111_C/T ae3 0.78 0.21 3.62 0.69
effects of different genotypes and the superior lines were
predicted in common (G) and different environments (GE).
Additionally, the maize F ­ 1 population provides an oppor-
negative environment interaction effects in environment 3, tunity to predict the superior hybrid, which can be used to
suggesting that this QTS has environment-specific effects, estimate the highest genetic effects in the improvement of
and could be used to increase or decrease PH in specific the four traits. For PH and LW, all of the predicted genetic
environments. effects were negative for homozygote QQ, but positive for
For LA, only one QTS, 9_58862666_G/A, was detected homozygote qq. For LA, the genotypic effects of major-
with single additive effect, and the other five QTSs exhib- allele homozygote QQ were negative in the common envi-
ited significant environment interaction effects, suggesting ronment and in environment 1, but positive in environ-
that LA was more likely to be regulated by the environ- ments 2 and 3. For LL, the positive genotypic effects of
ment (Table 3). We noted that 1_33250364_C/T had very major-allele homozygote QQ were detected only in envi-
strong environment-specific additive and dominance effects ronment 3 (Table 6). These results indicated that these
( h2AE = 7.96%;  h2DE = = 12.15%). Especially, this locus also traits could be further modified by selecting the homozy-
showed strong environment-specific epistasis effects with gote genotype. We noted that the total genetic effects of
locus 10_139263527_G/T ( h2IE = 10.83%). These results sug- the superior lines in each environment were much larger
gested that LA could be expected to improve dramatically by than their optimum homozygote genotypes (QQ, qq).

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8 Plant Molecular Biology (2019) 99:1–15

Table 6  Predicted genetic Trait Environment QQ qq SL (+) SL (−) F1 SH (+) SH (−)

effects for genotype of QQ, qq,
superior lines, ­F1 and superior PH (µ = 244.62) G − 12.11 12.11 43.39 − 43.39 − 0.98 45.23 − 46.43
hybrids of the four traits across
G + GE1 − 22.77 22.77 50.75 − 50.75 1.06 50.76 − 51.74
the three environments
G + GE2 − 15.64 15.64 50.11 − 50.11 − 0.98 50.41 − 53.64
G + GE3 − 2.81 2.81 53.13 − 53.13 − 0.98 53.13 − 56.16
LA (µ = 30.28) G − 0.75 0.75 1.64 − 1.64 − 1.11 1.64 − 1.96
G + GE1 − 5.48 1.42 7.15 − 6.37 − 3.92 7.15 − 6.41
G + GE2 1.49 1.74 3.89 − 5.41 2.67 5.48 − 6.61
G + GE3 0.88 − 0.88 3.27 − 3.27 − 2.17 4.36 − 5.24
LW (µ = 8.22) G − 1.00 0.16 1.51 − 1.51 − 0.33 1.58 − 1.84
G + GE1 − 1.02 0.18 1.75 − 1.75 − 0.24 1.75 − 2.07
G + GE2 − 0.93 0.09 1.44 − 1.44 − 0.19 1.74 − 1.76
G + GE3 − 1.37 0.52 1.54 − 1.54 − 0.43 1.68 − 1.97
LL (µ = 45.03) G − 1.93 1.93 9.41 − 9.41 5.51 11.49 − 9.41
G + GE1 − 3.18 3.18 12.46 − 12.46 4.85 12.69 − 13.13
G + GE2 − 7.10 7.10 13.80 − 13.80 1.05 14.75 − 14.16
G + GE3 0.60 − 0.60 19.80 − 19.80 12.36 24.89 − 20.98

SL (+/−), superior line (+/−), predicted genotypic effect of line in the selecting population with high-
est positive/negative values; SH (+/−), superior hybrid (+/−), predicted genotypic effect of hybrid in the
selecting population with highest positive/negative values; F­ 1, predicted genotypic effect of hybrid in the
mapping population with highest values; µ, estimated mean of the population; G, the genetic effect of the
common environment; GE: the genetic effect of the environment interaction value. QQ, homozygote of all
loci with major-alleles; qq, homozygote of all loci with minor-alleles

Additionally, the potential breeding value of the superior
hybrid across different environments was predicted, and
the total genetic effects of the superior hybrids were sig-
nificantly larger than the total genetic effects of the supe-
rior lines in some environments, which indicated that the
superior hybrids could be selected in the future to improve
the four traits. Based on the predicted superior lines and
superior hybrids, only a few QTSs of genotypic alleles
with significant effects need to be selected in common or
in specific environments for use in the future improve-
ment of the four traits, thereby remarkably reducing the
time and cost of maize breeding (Table S3). For example,
the 6_135818683_G/C (a = 8.18) and 7_133083644_T/C
(a = 5.81) had positive additive effects for PH. Homozy-
gote G/G of 6_135818683 and T/T of 7_133083644 could
be selected to significantly increase PH in the superior
line and superior hybrid, while the minor-alleles (C/C;
C/C) could be selected to decrease PH. Phenotypic vari-
ations of these traits are known to be affected by differ-
ent environments. Thus, the prediction of genetic effects
for different genotypes also provided a useful basis for
environment-specific improvement for maize breeding.
For example, locus 1_33250364_C/T was detected with
strong environment-specific additive and dominance
effects for LA in environments 1 (negative effects) and
2 (positive effects). To obtain a super hybrid with small
LA, homozygote C/C of 1_33250364 should be selected
in environment 1 (ae1 = − 1.74), while the minor-alleles
(T/T) of 1_33250364 (ae 2 = 1.39) should be selected in
environment 2.
Identification and annotation of candidate genes
Genes contained or located near QTSs with highly signifi-
cant genetic effects of the four traits were identified accord-
ing to the B73 reference genome (RefGen_v3) with a 50 kb
flanking region of detected QTSs. A total of 24, 18, 31,
and 35 associated candidate genes were identified for PH,
LA, LW, and LL, respectively (Table S4). The gene expres-
sion patterns of the 108 candidate genes were character-
ized using the genome-wide transcriptome data of differ-
ent developmental stages and tissues. The results indicated
that the candidate genes had different expression patterns in
the examined tissues and organs, and most of the candidate
genes were detected in multiple tissues with relatively high
expression levels (Fig. S1). GO analysis indicated that the
108 candidate were assigned to 15 biological process, 10
cellular component and 7 molecular function (Fig. 2). In the
category of biological process, most candidate genes were
clustered into the GO terms of metabolic process (29 genes),
cellular process (26 genes), and single-organism process (15
genes). In cellular component, candidate genes were mainly
belonged to the GO terms of cell (44 genes), cell part (44
genes), organelle (36 genes) and membrane (12 genes). In
molecular function, candidate genes were mainly assigned
to the GO terms of catalytic activity (34 genes) and binding

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Plant Molecular Biology (2019) 99:1–15 9

Fig. 2  GO classification of the candidate genes. GO terms are shown at the left. Different colors indicated the three GO categories. The numbers
at the right side of each bar indicate the clustered gene number

(28 genes). To identify the metabolic and biological path-
ways in which the candidate genes involved, pathway enrich-
ment analysis was performed using the KEGG database. A
total of 20 main KEGG pathways were identified for the
108 candidates (Fig. 3), and enriched mainly in biosynthe-
sis of secondary metabolites (13 genes), RNA transport (4
genes) and carbon metabolism (4 genes). Especially, one
gene for LA, GRMZM2G143235, was shown to be involved
in brassinosteroid biosynthesis. We also performed separate
GO and KEGG analysis for the genes of each trait, and the
results were shown in Figs. S2 and S3, respectively.
Functional annotations of the candidate genes were
further predicted based on different databases (Table S4).
In maize, a number of important genes related to plant

13

10
Fig. 3  KEGG pathway enrichment analysis of the candidate genes.
Enriched pathways are shown at the left. The color scale indicates the
q-value. The rich factor on the x-axis is the enrichment ratio between
architecture have been identified through mutagenesis
(Multani et al. 2003; Tian et al. 2011); however, none of
the mutated genes were significantly enriched among
the QTSs. Among the 108 candidate genes, two genes
(GRMZM5G832409 for LA and GRMZM2G060536 for
LL) have been reported in previous studies related to plant
development. GRMZM5G832409 encodes a homeobox tran-
scription factor (formerly named KNOX5) that is a homolog
of liguleless3 (lg3), which plays an important role in leaf
development (Bauer et al. 2004). QTS 6_24178316_C/T
had significant genotype × environmental interaction
effects for LA, and was located only about 2.86 kb from
13
Plant Molecular Biology (2019) 99:1–15
the number of candidate gens and all unigenes enriched in a pathway.
The size of the dot indicates the gene number enriched in the pathway
GRMZM5G832409. GRMZM2G060536 encodes a pen-
tatricopeptide repeat-containing protein (named EMP5)
(Liu et al. 2013b), and EMP5 knockdown plants resulted in
slow growth and defective seeds. QTS 3_147041046_A/C
was located about 2.09 kb from EMP5, and was shown to
have significant additive and dominance effects. Most of
the detected genes were annotated with unknown function,
probably because the lower proportion of annotated genes
in the maize genome compared with the model plants. How-
ever, it should be noted that some of the candidate genes
encoded hormone responsive proteins and transcription fac-
tors. These results suggested that the candidate genes may
Plant Molecular Biology (2019) 99:1–15 11
play important roles in different development processes of
the four traits.
Co‑expression analysis of PH candidate genes
To further explore the biological function of the candidate
genes, a co-expression network was constructed using the PH
candidate genes and RNA-Seq data from different develop-
mental stages of stem of low, middle and high hybrid in maize
PH. We investigated the relationships with the PH candidate
genes and reported genes to reveal the regulation relation-
ships of PH. We used the 24 PH candidates and 43 reported
PH genes, which are supported by experimental evidences,
as the guides to build the co-expression network. As shown
in Fig. 4, a total of 10 PH candidate genes and 30 reported
genes were contained in the final co-expression network. Five
genes, including GRMZM2G080912, GRMZM2G044947,
GRMZM2G046331, GRMZM2G088409, and
GRMZM2G080746, were shown in a large cluster with
Fig. 4  Co-expression networks of PH-related candidate genes and
reported PH genes. Each node represents a gene in the network.
Green and red nodes represent PH candidate genes and reported PH
genes, respectively. All other genes are shown as small blue nodes.
Node size represents total connectivity. An edge indicates significant
co-expression between two connected genes. The reported PH genes
were: dwarf3 (D3), dwarf8 (D8), dwarf12 (D12), thick tassel dwarf1
(td1), dwarf1 (D1), scarecrow-like 1 (scl1), Gibberellins insensi-
tive  1 (GAI1), gibberellin 20-oxidase  3 (GA20ox3), dwarf11 (D11),
related genes in the network. Especially, GRMZM2G088409,
a putative homolog of an Arabidopsis gene, was predicted to
be involves in plant hormone signal transduction, suggesting
its possible important roles in the development of PH. The
investigation of co-expression networks can provide useful
information for identifying candidate PH-related genes.
Discussion
Improvement of maize yield to meet continual and increas-
ing demands worldwide is an important long-term goal of
breeding. Plant architectures, such as PH, LA, LL, and LW,
are regarded as the most important traits of maize breed-
ing to adapt to the higher planting density. These traits are
closely related to morphology and photosynthetic efficiency
(Ku et al. 2010; Peiffer et al. 2014; Tian et al. 2011). Analy-
ses of a large number of mutants have identified a number
of functional genes in maize, rice and other species (Multani
ZmMADS3, dwarf1 like  1 (DWF1), brachytic2 (br2), BRI1 kinase
inhibitor 1 (BRI1), dwarf4 (DWF4), cyclin-D2-1 (cycD2), Z. mays
cell number regulator 1 (ZmCNR01), Z. mays cell number regulator 2
(ZmCNR02), D2003-related (D2003), dwarf14 (D14), beta-carotene
hydroxylase (crtRB3), catalase1 (ct1), low phytic acid 1 (lpa1; INO1),
Z. mays reversion-to-ethylene sensitivity 1 like 2 (ZmRTL2), terminal
ear1 (te1;  DT), ZmBHL12 (BHL12), ZmBHL14 (BHL14), Z. mays
growth-regulating factors 10 (ZmGRF10), brevis plant1 (bv1), rotten
ear1 (rte), and tassel-less1 (tls1)
13

12
et al. 2003; Wang and Li 2008). However, plant architecture
belongs to quantitative traits controlled by multiple genes,
resulting the unclear understanding of the molecular regula-
tion mechanism for these traits. Especially, the function of
the genetic polymorphisms existed in these genes and many
genomic regions remains largely elusive (Myles et al. 2009;
Xiao et al. 2016). Therefore, dissecting genetic architecture
and identification important genetic variation for these traits
will be useful in the genetic improvement of maize breeding.
In recent years, GWAS has become a fast and effective
method to systematically identify the genetic components
of complex traits in plants (Huang et al. 2010; Poland et al.
2011; Tian et al. 2011). Because of the heavy computational
burden of processing the generated data, a MLM approach
and a newly developed mapping software of QTXNetwork
were used to detect the gene × gene (epistasis) and geno-
type × environment interaction effects across different envi-
ronments (Zhang et al. 2015a) in order to dissect the genetic
architecture of the four complex traits. This approach has
been utilized successfully in dissecting the genetic architec-
ture of cotton and oilseed rape yield-related traits (Jia et al.
2014; Luo et al. 2017; Mei et al. 2017). The 87 re-sequenc-
ing line including 40 temperate and 47 tropical lines, were
used to construct the associated population of 573 maize
­F1 hybrids, and used it to dissect the genetic architecture
of the four traits with the high density markers and pheno-
typic data. In fact, the production and application of temper-
ate–tropical maize hybrids still has considerable application.
Especially, the tropical germplasm have the most abundant
genetic diversity which could be used as elite traits donor
into genetic improvement on temperate inbred lines, such
as disease resistance and abiotic stress resistance. Previous
studies showed that the genetic architecture of PH and leaf
traits was dominated mainly by genetic main effects (addi-
tive and epistasis effects) (Peiffer et al. 2014; Tian et al.
2011). Significant dominance effects were also detected for
the four traits in this study. In addition, epistasis effect was
detected for LW, but not for LA, LL, or PH. These results
indicated that the four traits of maize plant architecture were
contributed by various types of genetic variance effects.
Importantly, the genetic variation of complex traits is often
contributed by significant genotype × environment interac-
tion effects (Caicedo et al. 2004; Sambandan et al. 2008;
Uwatoko et al. 2008). Genotype × environment interaction
is an important component of genetic architecture (Yang
and Zhu 2005), and detecting this interaction for complex
traits will have great importance for maize genetic breeding.
Therefore, we not only examined the genetic main effect of
QTSs across all the three environments but also detected
environment-specific interaction effects. For LA and LL,
the genetic effects of genotype × environment interaction
accounts for a large portion (46.48% and 46.89%) of the
phenotypic variation, whereas only 15.66% and 13.75%
13
Plant Molecular Biology (2019) 99:1–15
environment interaction were detected for LW and PH.
These finding indicate the differences in genetic variance
effects of the four traits, and environment interaction effects
play important roles in controlling the development of these
traits.
Traditional breeding is based mainly on phenotypic selec-
tion of best genotypes among segregating progenies, but its
application is often affected by genotype × environment
interaction. A total of 36 highly significant associated QTSs
(− LogPEW > 3.0 and h2 > 0.5%) were identified for the four
traits. Our results demonstrated that some QTSs had only
major effects (a, aa, and d), such as 1_184045560_T/C for
PH ( h2A = 7.06%), 5_166972248_G/A for LL ( h2A = 1.43%)
and 7_65736590_C/T × 7_104716709_G/A ( h2AA = 14.19%)
for LW. These QTSs could be selected to improve the tar-
get traits across different environments. However, a large
number of the detected QTSs were detected with signifi-
cant environment-specific interaction effects (ae, aae, and
de), especially the QTSs of LA and LL. The genetic effects
of these environment-specific QTSs were detected only in
special conditions. For example, 6_24178316_C/T had a sig-
nificant environment-specific dominance effect for LA in
environment 2 ( h2DE = 1.43%), and a significant environment-
specific additive effect in environment 3 ( h2AE = 2.80%).
Thus, we suggest that breeders should pay more attention
to QTSs with environment-specific interaction effects in
genetic breeding programs (Holloway and Li 2010; Mohan
et al. 1997), and it will be more effective in producing the
ideal phenotype in advanced generations. In fact, mostly F ­1
hybrids are used in currently maize production, and the use
of ­F1 populations in GWAS association population will be
better to detect QTSs with epistasis, dominance and environ-
ment-specific interaction effects, which can be selected for
maker-assisted breeding. Due to the complex genetic basis, it
is often difficult to select ideal plant architecture of the four
traits. For this reason, we estimated the potential breeding
values of the superior lines and superior hybrids using the
current ­F1 population, and the optimum genotypes (QQ, Qq
and qq) were predicted for each significant associated QTS
across different environments. Only a few of the QTSs need
to be selected for the promising prospective of maize trait
improvement, remarkably reducing time and cost.
A total of 108 candidate genes were identified for the
four traits according to the position of highly significant
associated QTSs. However, genes previously identified by
mutagenesis did not overlap with these candidate genes. A
possible reason for this findings is that GWAS is relatively
insensitive to detect low-frequency loci with significant
effects (Xiao et al. 2016), although the low-frequency or
rare allelic variants seem to be important for these complex
traits. To explore the potential function of the candidate
gens in regulating the four traits of plant development, the
expression profiling of the candidates was performed based
Plant Molecular Biology (2019) 99:1–15 13
on the RNA-seq data of different developmental stages. Most
of the genes showed distinct expression patterns, and were
detected in one or more of the tissues, which might sug-
gest their different functions in plant development of the
target traits. GO analysis identified 32 GO classifications
for these genes. It should be noted that some genes were
assigned to the GO terms of biological regulation, signal-
ing and development process. KEGG pathway enrichment
analysis indicated that the candidate genes involved mainly
in 20 different metabolic and biological pathways. Biosyn-
thesis of secondary metabolites, which contained 13 genes,
was the most enriched pathway. GRMZM2G143235 was
involved in the brassinosteroid biosynthesis, and this gene
was identified based on the significant QTS 3_5579454_C/T
in LA. 3_5579454_C/T was detected with significant domi-
nance and environment-specific effects. Plant hormones,
including brassinosteroid, auxin and gibberellin, have
been demonstrated to play important roles in regulating
the development of plant architecture (Wang et al. 2009;
Yamamuro et al. 2000; Zhang et al. 2015b). Thus, selection
of GRMZM2G143235 or this QTS may help to improve
LA in maize breeding. Functional annotation indicated that
most of the candidate genes had unknown function, except
for GRMZM5G832409 (KNOX5) and GRMZM2G060536
(EMP5). Plant hormones regulate many aspects of physi-
ological responses, including both vegetative and repro-
ductive development. Although it is difficult to establish a
direct link to the four traits, some of the candidate genes
were annotated to plant hormone signal transduction and
transcriptional regulation, which suggested their important
functions in different development processes of the four
traits. For example, GRMZM2G045057 encodes an auxin
transported-like protein that mediates responses to plant hor-
mone signal transduction in PH, and GRMZM2G080516 is
an ethylene-responsive element binding protein (EREBP) in
LA. A co-expression network was further constructed using
the 24 PH-related candidate genes based on our previous
RNA-seq data. Ten genes formed close relationships with
the reported PH genes, suggesting a potential role of these
genes in PH, further supporting the results of this study.
Taken together, the candidate genes may provide additional
resources for marker-assisted selection breeding and func-
tional analysis of the four traits in maize.
Conclusions
In the study, we performed a GWAS analysis to dissect the
genetic architecture of the four traits (PH, LA, LL, and LW)
using 573 ­F1 hybrids with a MLM approach and QTXNet-
work mapping software. 36 highly significant associated
QTSs were identified for target traits with total heritabil-
ity varied from 51.86 to 79.92%, which were contributed
by various types of genetic variance effects. Environment
interactions were also important variants for these traits,
especially for LA and LL, while major effects were more
important for LW and PH. The predicted breeding values,
including the superior lines and superior hybrids, lays an
important foundation for the identification of valuable
alleles, especially for the QTSs with environment interaction
effects, which can be used for precise guidance for genetic
improvement during the process of maize breeding.
Acknowledgements  We would like to thank Yunbi Xu and Chuanxiao
Xie for their assistance in providing the genotype data of the 87 inbred
lines.
Author contributions  JBC, JZ and YZ conceived and designed the
experiments; HSW, CB, WD and RHC performed the experiments; JZ,
YZ and LJG analyzed the data; QM and HYJ participated in the design
of the study; YZ and JZ prepared the manuscript.
Funding  This research was supported by grants from the National
Natural Science Foundation of China (91435110), the National Key
Research and Development Program of China (2017YFD01012054)
and the Science and Technology Major Project of Anhui Province
(15czz03119).
Compliance with ethical standards 
Conflict of interest  The authors declare that they have no competing
interests.
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