QTL detection for wheat kernel size and quality and
the response of these traits to low nitrogen stress
Fa Cui · Xiaoli Fan · Mei Chen · Na Zhang · Chunhua Zhao · Wei Zhang · Jie Han · Jun
Ji · Xueqiang Zhao · Lijuan Yang · Zongwu Zhao · Yiping Tong · Tao Wang · Junming Li
1
Supplementary information
1 Results
1.1 Phenotypic variation and correlations between traits
In nearly all cases, all 11 kernel-related traits (KRTs) widely varied, showed transgressive
segregation and were normally distributed, with absolute values of skewness and kurtosis of less than 1
for the 188 KJ-recombinant inbred lines (RILs). The average coefficients of variation (CVs) among the
ten environments ranged from 1.23 % (test weight (TW), 0.94–1.58 %) to 14.90 % (Zeleny
sedimentation value (ZEL), 10.90–19.92 %) (Supplementary Table S3). These results indicated that all
the 11 traits were typical quantitative traits suitable for analysis of quantitative trait loci (QTLs).
Kernel length (KL) showed a positive correlation with kernel width (KW) under high-nitrogen
(HN) and low-nitrogen (LN) conditions, although this correlation was statistically non-significant
under HN. All seven kernel quality-related traits, except for TW, were significantly positively
correlated with each other. Although statistically non-significant under HN, TW showed negative
correlations with water absorption (ABS), ZEL, and kernel hardness (KH) under HN and LN, and TW
was negatively correlated with grain protein content (GPC) and wet gluten content (WGC) under HN,
but these correlations were positive under LN. Although statistically non-significant under both LN and
HN, positive correlations existed between KL and GPC and between KW and ZEL. KL showed a
positive correlation with DT, ABS, ZEL, and KH under both LN (significant) and HN (non-significant),
and KW showed positive correlations with GPC and TW under both LN (non-significant) and HN
(significant), as did thousand-kernel weight (TKW) with GPC, WGC, and ZEL. Although
non-significant in some cases, KL and kernel diameter ratio (KDR) were negatively correlated with
TW and dough tractility (DT), respectively. The remaining factors showed inconsistent correlations
with each other under LN and HN, including either a negative correlation under LN but a positive
correlation under HN or a positive correlation under LN but a negative correlation under HN. Theses
correlations were statistically non-significant in the majority of cases.
1.2 Genotypic analysis of the ten genes related to kernel size and quality traits and the novel
genetic linkage map
Concerning the three high-molecular-weight (HMW) glutenin loci, the diagnostic markers of Glu-B1
showed polymorphisms between KN9204 and J411. ZSBy9aF1/R3, the dominant marker of By9, was
detected by the presence of a diagnostic fragment (662 bp) in KN9204, but no corresponding
amplification product was observed in J411. For Glu-A1, KN9204 had the Ax-null allele, whereas J411
had Ax-2* (Cui et al. 2014a). In addition, sodium dodecyl sulfate polyacrylamide gel electrophoresis
(SDS-PAGE) revealed that KN9204 carried the null, 7+9, and 2+12 alleles, whereas J411 carried the
2*, 6+8, and 2+12 alleles at the Glu-A1, Glu-B1 and Glu-D1 loci, respectively (data not shown). These
findings were consistent with the results identified by assessment of the functional markers of the three
HMW glutenin loci. Concerning the three low-molecular-weight (LMW) glutenin subunits, the
diagnostic markers of Glu-A3 showed polymorphisms between KN9204 and J411. Of them,
LA3F/SA2R and LA3F/SA4R, the dominant markers of Glu-A3b and Glu-A3d, respectively, were
detected by the amplification of 894 bp and 967 bp diagnostic fragments, respectively, in KN9204,
but no corresponding amplification products were obtained in J411. LA1F/SA3R, the dominant marker
of Glu-A3a and Glu-A3c, was detected by amplification of the diagnostic fragment (573 bp) in J411,
but no corresponding amplification product was observed in KN9204. These findings indicated that
KN9204 had the Glu-A3b or Glu-A3d alleles and that J411 had the Glu-A3a or Glu-A3c alleles. In
addition, J411 had the Glu-B3h allele, whereas KN9204 had a 1BL.1RS translocation that resulted in
the loss of Glu-B3 (Cui et al. 2014a). The two parents had the same Glu-D3 allele.
1.3 QTLs for the 11 kernel-related traits
Nine putative additive QTLs for GPC were identified in an individual environment QTL mapping
analysis and were distributed on chromosomes 1A, 1B (2 QTLs), 2A, 2B, 3B, 4A (2 QTLs), and 4B.
These QTLs individually explained an average of 4.27–8.08 % of the phenotypic variance with average
LOD values ranging from 2.07 to 3.66. All of these QTLs were verified in at least two of the ten
environments. QGpc-1A and QGpc-1B.2 were stable QTLs that were identified reproducibly in six and
five environments, respectively; QGpc-2A, QGpc-2B, and QGpc-4B were all verified in four of the ten
environments. Five and four favorable alleles that increased GPC were contributed by J411 and
KN9204, respectively (Table 3; Supplementary Table S4; Fig. 2).
For WGC, nine QTLs were significant together in ten individual environments and were
2
distributed on chromosomes 1A, 1B (2 QTLs), 2A, 2B, 3B, 4B, 5D, and 7D. These QTLs individually
explained an average of 4.27–9.83 % of the phenotypic variance, with average LOD values ranging
from 2.17 to 4.91. All of these QTLs were significant in at least two of the ten environments. QWgc-1A,
QWgc-1B.1, and QWgc-5D were stable QTLs that were all identified reproducibly in five environments,
and both QWgc-1B.2 and QWgc-2A were significant in four of the ten environments. KN9204 and J411
contributed favorable alleles that increased WGC at five and four QTLs, respectively (Table 3;
Supplementary Table S4; Fig. 2).
For DT, nine putative additive QTLs were detected together in ten individual environments and
were distributed on chromosomes 1A (2 QTLs), 2A, 2D, 3B, 4A, 4B, 5D, and 7D. These QTLs
individually accounted for an average of 3.90–11.44 % of the phenotypic variance, with average LOD
values ranging from 2.66 to 6.03. All of these QTLs were detected reproducibly in at least two of the
ten environments. QDt-1A.2, QDt-2A, QDt-4A, QDt-4B, and QDt-5D were stable QTLs that were
verified in six, eight, five, nine, and eight environments, respectively, and QDt-7D was detected
reproducibly in four of the ten environments; in addition, QDt-4B was a major stable QTL for DT that
individually explained 11.44 % (6.59–15.78 %) of the phenotypic variance with a LOD value of 6.03
(2.68–9.63). KN9204 and J411 contributed to increased DT at five and four chromosomal regions,
respectively (Table 3; Supplementary Table S4; Fig. 2).
Eight QTLs for TW were mapped to chromosomes 2B, 2D, 3B, 4A, 4B (2 QTLs), 5D, and 7A,
and they individually explained an average of 4.57–11.91 % of the phenotypic variance, with average
LOD values of 2.28–5.61. All of these QTLs were verified in two of the ten environments, with the
exception of QTw-4B, which was significant in six environments and individually explained 11.91 %
(9.36–14.97 %) of the phenotypic variance as the only major stable QTL for TW. Two and six QTL
alleles that increased TW were contributed by KN9204 and J411, respectively (Table 3; Supplementary
Table S4; Fig. 2).
Eight QTLs for ABS were mapped to chromosomes 1B, 2A, 2B, 2D (2 QTLs), 3B, 5D, and 6B
and they individually accounted for an average of 2.85–32.75 % of the phenotypic variance with
average LOD values of 2.55–18.23. They all could be verified in at least two different environments.
QAbs-1B.1, QAbs-3B, and QAbs-5D were stable QTLs that could be verified in nine, six, and ten
environments, respectively, and QAbs-2B could be verified in four environments; in addition, QAbs-5D
individually explained 32.75 % (11.78–49.06 %) of the phenotypic variance, with a LOD value of
18.23 (4.58–26.41), and it was the only stable QTL for ABS. Four and four QTL alleles that increased
ABS were donated by KN9204 and J411, respectively (Table 3; Supplementary Table S4; Fig. 2).
In the ten environments, six QTLs for ZEL were identified and were distributed on chromosomes
1B, 2A, 3B (2 QTLs), 4B, and 5D. These QTLs individually explained an average of 5.04–16.54 % of
the phenotypic variance, with average LOD values of 2.88–7.71. Both QZel-2A and QZel-5D were
stable QTLs that were significant in eight of the ten environments. In addition, QZel-5D individually
explained 16.54 % (10.96–30.54 %) of the phenotypic variance, with a LOD value of 7.71 (5.23–14.4),
and it was the only major stable QTL for ZEL. The remaining four QTLs were verified in at least two
of the ten environments. All six QTL alleles that increased ZEL were contributed by J411 (Table 3;
Supplementary Table S4; Fig. 2).
A total of six QTLs for KH were identified in the ten environments and were mapped to
chromosomes 1B, 2A, 2D (2 QTLs), 5D, and 6B. These QTLs individually accounted for an average of
2.92–35.57 % of the phenotypic variance, with average LOD values of 2.33–18.14. QKh-5D, the only
major stable QTL for KH, was mapped to chromosome 5DS in the vicinity of the known location of Ha,
and it was confirmed in all ten environments. QKh-2D was significant in four different environments
and the remaining QTLs were significant in only two different environments. Equal number of
favorable alleles that increased KH were contributed by KN9204 and J411 (Table 3; Supplementary
Table S4; Fig. 2).
In total, 11 putative additive QTLs for KL were identified and were distributed on chromosomes
1A, 1B, 1D, 2A (2 QTLs), 2B, 3B, 4A (3 QTLs), and 7A. These QTLs individually accounted for an
average of 4.91–17.64 % of the phenotypic variance, with average LOD values of 2.38–6.33. QKl-1B
and QKl-2A.1 were stable QTLs that could be detected reproducibly in seven and six environments,
respectively. Moreover, QKl-1B individually exhibited 13.47 % (5.48–18.28 %) of the phenotypic
variance, with a LOD value of 6.33 (2.22–9.48), as the only major stable QTL. Both QKl-1A and
QKl-2A.2 were major QTLs that individually caused 13.47 and 10.20 % of the phenotypic variance,
respectively; however, they were only significant in one and two environments, respectively. The
remaining QTLs had a moderate additive effect and could be identified in only two or three different
environments. Five and six QTL alleles that increased KL were contributed by KN9204 and J411,
respectively (Table 3; Supplementary Table S4; Fig. 2).
A total of 13 QTLs for KW were mapped to chromosomes 1A, 1B, 2A, 2B, 2D, 4A (2 QTLs), 4B
3
(2 QTLs), 5D, 6A, 6B, and 7A. These QTLs individually explained an average of 4.32–21.70 % of the
phenotypic variation, with average LOD values of 2.65–6.61. QKw-1A, QKw-1B, QKw-2A, and
QKw-4A.2 were major QTLs that could be identified in only one environment. QKw-4B.1, QKw-4B.2,
and QKw-6B were major QTLs that could be identified reproducibly in two, four, and four different
environments, respectively. QKw-2D, the only stable QTL for KW, was verified in nine of the ten
environments and individually explained 9.05 % (5.11–15.36 %) of the phenotypic variation, with
LOD values ranging from 2.12 to 10.54. The remaining QTLs showed moderate additive effects and
were unstable across the environments. Seven and six QTL alleles that increased KW were contributed
by KN9204 and J411, respectively (Table 3; Supplementary Table S4; Fig. 2).
Thirteen QTLs associated with KDR were detected that individually explained an average of
4.12–12.36 % of the phenotypic variation, with average LOD values of 2.20–6.37. These QTLs were
located on chromosomes 1B, 2A, 2B (2 QTLs), 2D, 3D, 4A (2 QTLs), 4B (2 QTLs), 5B, 6B, and 7A.
QKdr-2A, QKdr-2D, and QKdr-4B.2 were stable QTLs that were detected reproducibly in six, six, and
five environments, respectively. Additionally, QKdr-4B.2 individually explained 12.36 %
(4.82–18.82 %) of the phenotypic variation, with a LOD value of 6.37 (2.88–10.98), as the only major
stable QTL for KDR. Although QKdr-7A individually explained an average of 10.92% of the
phenotypic variance with an average LOD value of 3.05, it could be identified in only two different
environments. The remaining QTLs had moderate additive effects and were unstable across
environments. KN9204 and J411 contributed six and seven QTL alleles that increased KDR,
respectively (Table 3; Supplementary Table S4; Fig. 2).
Up to 17 QTLs for TKW were identified in the ten individual environment QTL mapping analyses.
These QTLs were located on chromosomes 1A, 1B (2 QTLs), 2A (2 QTLs), 2B, 2D, 3B, 4A, 4B (2
QTLs), 5D, 6A, 6B (2 QTLs), 7A, and 7D, and they individually explained an average of 3.19–13.85 %
of the phenotypic variation, with average LOD values of 2.15–7.99. QTkw-2D, QTkw-4A, QTkw-4B.2,
and QTkw-5D were stable QTLs that were verified in ten, eight, five, and five different environments,
respectively. Moreover, both QTkw-2D and QTkw-4B.2 were major stable QTLs individually
accounting for an average of > 10.00 % of the phenotypic variance, with average LOD values of > 3.00.
QTkw-6B.2 was the third major QTL, but it was unstable across the environments. QTkw-6A could be
verified in four different environments with a moderate additive effect. The remaining QTLs
individually explained < 10.00 % of the phenotypic variance and were unstable across the
environments. Nine and eight QTLs alleles that increased TKW were contributed by KN9204 and J411,
respectively (Table 3; Supplementary Table S4; Fig. 2).
2 Discussion
2.1 Would indirect selection of superior genotypes under normal conditions maximize the genetic
gain in breeding programs designed to improve tolerance to nitrogen deficient conditions?
In the present study, indirect selection for TKW under HN resulted in the selection of seven of nine
(77.8 %), 12 of 19 (63.2 %), and 15 of 28 (53.6 %) common RILs at 5, 10, and 15 % selection
intensities, respectively. The Spearman’s rank correlation coefficient calculated for TKW between the
treatments was second (0.79) to that of KL among the 11 traits investigated (Table 2, Fig. 1). In
addition, TKW showed higher heritability under both HN and LN and was less significantly or not
significantly negatively affected by N stress (Supplementary Tables S2 and S3). The top five RILs had
identical or similar TWK under LN and HN (50.78–53.71 and 50.10–53.64 g, respectively). This
finding indicates that indirect selection under HN can maximize the genetic gain for the improvement
of tolerance to N stress for TKW. Similar inferences were also made for KL, KW, and KDR because
they showed strong correlations with TKW, but indirect selection under HN resulted in the selection of
50 % or fewer common RILs selected at the three selection intensities (Tables 1 and 2; Fig. 1).
Despite the moderate Spearman’s rank correlation coefficients between the N treatments for DT
and WGC, direct selection under each N treatment resulted in the selection of one-half or more of the
RILs as common RILs at all three selection intensities (Table 2; Fig. 1). In addition, both traits showed
higher heritabilities under both HN and LN, and they were consistently negatively affected by N stress
across the tested environments (Supplementary Tables S2 and S3). The top five RILs had higher DTs
and higher WGCs under HN than under LN (173.38–177.79 vs. 155.27–163.73 for DT and
35.84–37.03 vs. 27.87–33.33 for WGC, respectively). This finding indicates that indirect selection
under HN allows for the genetic improvement of DT and WGC under LN in most cases; however, the
negative effects of N stress on both DT and WGC were difficult to counteract.
Although the Spearman’s rank correlation coefficient for ABS was relatively high (0.70) between
the treatments, direct selection under each N treatment resulted in the selection of more than half of the
RILs as common at only a 15 % selection intensity (15 of the 28 lines were selected as common).
4
However, ABS was less negatively affected by N stress, and the top five RILs had a slightly higher or
similar ABS under HN compared with that under LN, (61.96–63.16 under HN and 60.96–62.34 under
LN, respectively) (Supplementary Tables S2 and S3). This finding indicates that indirect selection
under HN allows for the genetic improvement of ABS under LN to some extent.
For GPC, TW, ZEL, and KH, indirect selection under HN resulted in the selection of fewer than
50 % of the RILs as common at the three selection intensities, indicating the lower efficiency of
indirect selection under HN for the genetic improvement of these traits under LN (Tables 1 and 2; Fig.
1).
2.2 QTL co-segregation with known genes
KN9204 and J411 differed at two HMW glutenin loci (Glu-A1 and Glu-B1) and two LMW glutenin
loci (Glu-A3 and Glu-B3). Only one moderately stable QTL for DT (QDt-1A.2) mapped to a location
near the Glu-A1 locus, which was likely due to the positive effect of the 2*-HMW subunit encoded by
the Glu-1Ab allele on J411. QGpc-1B.2 and QWgc-1B.2 mapped to chromosome 1BL in the vicinity of
Glu-B1. Additionally, three QTLs for kernel size (QKl-1B, QKdr-1B, and QTkw-1B.2) also mapped to
this region, and alleles from KN9204 in this region (Bx7+By9) increased GPC and WGC but reduced
kernel size, which might have contributed to the increase in the grain nitrogen concentration at the
expense of grain biomass accumulation (Kunert et al. 2007). Moreover, the Bx7+By9 allele from
KN9204 increased the tolerances of GPC, WGC, KL, and KDR to low N stress (Table 5). Two stable
QTLs, QGpc-1A and QWgc-1A, along with an environmentally sensitive QTL, QDt-1A.1, mapped to
locations near the Glu-A3 locus. The alleles from KN9204 in this region (Glu-A3b or Glu-A3d)
simultaneously increased GPC, WGC, and DT. In addition, J411 had the Glu-B3h alleles, whereas
KN9204 had a translocation of 1BL.1RS, resulting in the loss of Glu-B3. However, no QTLs for KRTs
mapped to any locations near the Glu-B3 locus, indicating that this translocation had no adverse effects
on the quality traits. In fact, Johnson et al. (1999) have concluded that genetic background and
environmental factors likely affect the milling and baking quality to a greater extent than the 1BL.1RS
translocation.
TaCwi was mapped to 164.7 cM on chromosome 2AL in C3, which was found to harbor ten QTLs
for both kernel size and kernel quality, and alleles from J411 enhanced all ten kernel related-traits,
including ABS, WGC, KH, GPC, DT, ZEL, KDR, KW, KL, and TKW (Table 6; Supplementary Fig.
S1). These findings indicate that the TaCwi-A1a allele may be associated with not only a greater kernel
size but also enhanced kernel milling and baking quality. Moreover, TaCwi-A1a from J411 enhanced
the tolerances of ABS, ZEL, and KH to low N stress and reduced those of KDR and TKW (Table 5).
However, a QTL for sensitivity of wheat yield per plant to N stress (QYddv-2A.1-2) was mapped to this
region, with alleles from J411 enhancing N stress tolerance (Cui et al. 2014a). These findings indicate
that TaCwi-A1a enhances the tolerances of both quality and yield to N stress.
TaSus2 was mapped to 95.2 cM on chromosome 2BS in C4, which was found to harbored five
QTLs for both kernel size and kernel quality. Alleles from KN9204 increased KW and TKW but
decreased GPC, WGC, and KDR (Table 6; Supplementary Fig. S1). In addition, a QTL for the
per-plant wheat yield (QYd-2B) was mapped to this region, and alleles from KN9204 contributed to an
increased phenotypic value (Cui et al. 2014a). This finding indicates that TaSus2 has opposing effects
on yield and quality traits, which might contribute to the dilution effect between grain nitrogen
concentration and grain biomass accumulation (Kunert et al. 2007). Two QTLs for KLDV (QKldv-2B)
and KWDV (QKwdv-2B) were identified in this chromosomal region, and alleles from KN9204
increased the phenotypic value for both KLDV and KWDV. These results indicate that TaSus2 can
influence the responses of KL and KW to N stress. However, no QTL for differences between the
values for per-plant wheat yield under HN and LN was identified within this chromosomal region (Cui
et al. 2014a). These results indicate that TaSus2 has no effect on the response of per-plant yield to N
stress (Table 5; Supplementary Table S5).
TaGS2-D1 and PPO-D1 were mapped to 210.3 and 214.8 cM on chromosome 2DL on the KJ-RIL
map, respectively (Cui et al. 2014a). Both genes were located in C5, which harbored seven QTLs for
kernel size and quality (ABS, KH, TW, DT, KW, KDR, and TKW). Alleles from KN9204 (TaGS2-D1a
for TaGS2-D1 and PPO-D1a for PPO-D1) increased both kernel size and quality (Table 6). The
average LOD peak positions for QKw-2D (209.3 cM), QTkw-2D (211.0 cM), and QKdr-2D (211.8 cM)
across the environments were close to TaGS2-D1, whereas for QDt-2D (214.0 cM) and QAbs-2D.2
(217.0 cM) were close to that for PPO-D1; in addition, the average LOD peak positions for QKh-2D.1
and QTw-2D were 186.8 and 223.0 cM, respectively. These findings indicate that the associations with
QKw-2D, QTkw-2D, and QKdr-2D likely resulted from a positive effect of TaGS2-D1a on KN9204,
whereas those with QDt-2D and QAbs-2D.2 resulted from a positive effect of PPO-D1 on KN9204.
The effects of QKh-2D.1 and QTw-2D might have resulted from the presence of other linked genes.
5
Eight QTLs for both kernel size and quality were mapped to chromosome 4B near Rht-B1,
coincident with a major stable QTL for plant height (PH) (data not shown). To analyze the effect of
Rht-B1 on kernel size and quality in further detail, we performed an analysis of covariate (ANCOVA)
using plant height (PH) as a co-variable. The removal of PH effects from statistical analyses by
considering this trait as a covariate in ANCOVA resulted in decreases in the differences in TKW, KW,
KDR, TW, DT, and ZEL between the lines with Rht-B1a and Rht-B1b; however, the differences in
GPC and WGC did not change (Supplementary Fig. S2). These findings indicate that Rht-B1b has
negative effects on TKW, KW, KDR, TW, DT, and ZEL. The effects of QGpc-4B and QWgc-4B might
have resulted from the presence of other linked genes. In addition, Rht-B1b enhanced the tolerances of
TW, KW, and TKW to N deficiency (Table 5).
The hardness (Ha) locus was mapped to 0.0 cM on chromosome 5DS in C10, which was found to
harbor eight QTLs for both kernel size and quality traits, including a major stable QTL for KH
(QKh-5D) (Table 6; Supplementary Fig. S1). To analyze the effects of Ha on kernel size and quality in
further detail, we performed ANCOVA using KH as a covariate. The removal of KH effects from
statistical analyses by considering this trait as a covariate in ANCOVA resulted in decreases in the
differences in WGC, DT, ABS, ZEL, KW, and TKW between the lines with Pinb-D1b and Pinb-D1a
but an increase in that of TW (Supplementary Fig. S3). These findings indicate that Pinb-D1b has
pleiotropic effects on increasing KH and thus increasing WGC, DT, ABS, ZEL, KW, and TKW but
decreasing TW, consistent with the additive effects listed in Table 6. Moreover, the Pinb-D1b alleles
from KN9204 enhanced the tolerances of KH, ABS, and ZEL to N deficiency but reduced the tolerance
of KW (Table 5). QTkw-5D was insensitive to N deficiency because no QTL for the response to LN of
TKW was detected in that region.
6
Trait
Bread and
noodle-ma
king
quality
Kernel
weight
Grain
hardness
Yellow
pigment
content
Supplementary Table S1 The eleven functional markers of kernel size- and quality-related traits
Marker
Primer sequence (5’-3’)
Allele
Expected
fragment
size (bp)
Glu-B1
ZSBy9aF1/R3
Forward: TTCTCTGCATCAGTCAGGA
By9
662
Reverse: AGAGAAGCTGTGTAATGCC
nonBy9
707
Glu-A3
GluA3b
LA3F: TTCAGATGCAGCCAAACAA
Glu-A3b
894
SA2R: GCTGTGCTTGGATGATACTCTA
GluA3ac
LA1F: AAACAGAATTATTAAAGCCGG
Glu-A3a
573
SA3R: GTGGCTGTTGTGAAAACGA
Glu-A3c
GluA3d
LA3F: TTCAGATGCAGCCAAACAA
Glu-A3d
967
SA4R: TGGGGTTGGGAGACACATA
TaCwi-A1
CWI22
Forward: GGTGATGAGTTCATGGTTAAT
TaCwi-A1a
402
Reverse: AGAAGCCCAACATTAAATCAAC
CWI21
Forward: GTGGTGATGAGTTCATGGTTAAG
TaCwi-A1b
404
Reverse: AGAAGCCCAACATTAAATCAAC
TaSus2-2B
Sus2-SNP-185/5 Sus2-SNP-185: TAAGCGATGAATTATGGC
Hap-H
423
89H2
Sus2-SNP-589H2: GGTGTCCTTGAGCTTCTGG
Pin-b
Forward: ATGAAGACCTTATTCCTCCTA
Pinb-D1a
250
Reverse: CTCATGCTCACAGCCGCC
Forward: ATGAAGACCTTATTCCTCCTA
Pinb-D1b
250
Reverse: CTCATGCTCACAGCCGCT
Psy-B1
YP7B-1
Forward: GCCACAACTTGAATGTGAAAC
Psy-B1a
151
Reverse: ACTTCTTCCATTTGAACCCC
Psy-B1b
156
YP7B-2
Forward: GCCACCCACTGATTACCACTA
Psy-B1c
428
Reverse: CCAAGGTGAGGGTCTTCAAC
Locus
Chrom.
Reference
1BL
Lei et al. 2006
1AS
Wang
2010
2AL
Ma et al. 2012
2BS
Jiang et al.
2010
Giroux et al.
1997
5DS
7BL
et
al.
He et al. 2009
7
Supplementary Table S2 Analysis of variance (ANOVA) for the investigated traits
Traits
VG
VT
VL
VG×T
VG×L
GPC
0.16***
1.85***
1.21***
0.09***
0.28***
WGC
1.13***
9.54***
1.72***
0.66***
1.72***
DT
23.04***
109.54***
112.31***
8.32***
28.26***
***
***
***
***
TW
9.17
4.76
31.99
15.02
28.25***
ABS
1.94***
0.15***
1.79***
0.74***
2.14***
ZEL
5.56***
32.47***
4.61***
6.23***
9.84***
KH
5.44***
10.19***
3.39***
7.49***
0.04**
KL
0.041***
0.050***
0.003***
0.011***
0.001**
KW
0.018***
0.095***
0.109***
0.000
0.000
KDR
0.008***
0.022***
0.010***
0.000
0.000
TKW
11.00***
0.53***
13.40***
1.69***
3.21***
VG variance induced by genetic factors (the 188 KJ-RILs); VT variance induced by nitrogen treatment (HN and LN); VL variance
induced by locations (L1, L2, L3, L4, and L5), VG×T variance induced by the interaction of genetic factors with nitrogen treatment;
and VG×L variance induced by the interaction of genetic factors with location
GPC grain protein content, WGC wet gluten content, DT dough tractility, TW test weight, ABS water absorption, ZEL Zeleny
sedimentation value, KH kernel hardness, KL kernel length, KW kernel width, KDR kernel diameter ratio, TKW thousand-kernel
weight
**
Indicates significance at a P < 0.01
***
Indicates significance at a P < 0.001
8
Traits
GPC
(%)
WGC
(%)
DT
(%)
TW
g/L
ABS
(%)
ZEL
(ml)
KH
(%)
KL
Supplementary Table S3 Phenotypic values for 11 kernel-related traits of two parents and the KJ-RIL population in
environments in wheat
Locations
En.a
N plots
Parents
KJ–Population
KN9204
J411
Mean
SD
CVs (%)
Min.
Max.
Skewness
L1
E1
LN
14.33
12.46
12.11
0.76
6.26
10.23
13.94
0.17
E2
HN
16.29
13.38
14.58
0.68
4.65
12.33
16.84
0.11
L2
E3
LN
14.03
12.83
12.71
0.84
6.58
10.78
15.03
0.23
E4
HN
15.53
13.28
14.75
0.71
4.81
13.12
16.58
0.36
L3
E5
LN
13.17
12.61
13.23
1.06
7.99
9.95
18.50
0.62
E6
HN
15.31
14.78
15.50
0.82
5.32
13.76
18.55
0.62
L4
E7
LN
11.23
10.69
15.81
1.22
7.72
12.80
19.50
0.72
E8
HN
15.68
14.33
16.76
1.18
7.50
12.68
19.85
0.79
L5
E9
LN
10.61
10.54
12.97
0.82
6.29
11.39
16.70
0.82
E10
HN
14.42
13.66
15.12
0.68
4.49
13.66
17.56
0.36
L1
E1
LN
29.46
27.48
26.59
1.99
7.48
22.08
31.11
0.17
E2
HN
31.68
30.02
32.11
1.70
5.29
26.98
36.73
–0.18
L2
E3
LN
31.33
27.72
27.70
2.10
7.59
23.03
33.84
0.19
E4
HN
33.09
30.87
32.61
1.84
5.65
28.39
37.43
0.32
L3
E5
LN
28.81
26.68
28.76
2.62
9.12
20.80
41.04
0.52
E6
HN
34.06
31.79
34.16
2.10
6.15
29.54
41.67
0.51
L4
E7
LN
29.22
28.16
34.87
2.92
8.38
28.60
44.43
0.61
E8
HN
35.11
30.86
36.77
2.83
8.15
28.23
44.51
0.70
L5
E9
LN
22.97
23.10
28.23
2.06
7.30
24.04
36.70
0.66
E10
HN
32.45
30.42
33.38
1.77
5.30
29.96
38.93
0.30
L1
E1
LN
142.56
140.21
135.40
7.65
5.65
115.15
152.88
0.10
E2
HN
162.89
152.35
156.31
6.87
4.39
135.30
173.78
–0.08
L2
E3
LN
146.81
144.49
141.76
8.66
6.11
118.03
161.57
0.08
E4
HN
155.41
154.40
158.17
7.95
5.03
138.56
186.02
0.37
L3
E5
LN
145.51
143.77
147.16
10.18
6.92
117.76
194.20
0.45
E6
HN
151.73
156.23
158.85
9.35
5.88
135.57
189.08
0.48
L4
E7
LN
140.21
135.12
169.58
11.71
6.91
136.66
209.90
0.46
E8
HN
166.66
158.07
179.18
11.27
6.66
135.63
210.08
0.42
L5
E9
LN
120.85
117.25
144.46
8.31
5.75
121.32
175.43
0.42
E10
HN
154.26
144.17
158.51
7.96
5.02
137.38
187.55
0.48
L1
E1
LN
782.23
796.78
782.70
7.36
0.94
765.04
804.56
0.10
E2
HN
779.48
791.73
777.39
7.82
1.01
759.01
795.99
0.09
L2
E3
LN
786.30
793.67
786.42
11.03
1.40
753.54
813.89
–0.34
E4
HN
764.47
792.89
781.79
11.49
1.47
743.72
808.68
–0.16
L3
E5
LN
779.59
790.50
778.46
7.48
0.96
755.13
796.22
–0.45
E6
HN
767.81
784.73
778.93
12.28
1.58
744.67
809.52
–0.33
L4
E7
LN
782.12
789.23
790.67
10.71
1.36
762.19
834.70
0.05
E8
HN
781.61
791.72
790.50
9.77
1.24
761.55
827.49
–0.09
L5
E9
LN
778.77
787.07
782.44
7.74
0.99
758.43
801.12
–0.45
E10
HN
769.63
767.53
780.36
10.12
1.30
745.32
806.84
–0.17
L1
E1
LN
59.76
56.76
57.86
2.25
3.89
50.87
62.69
–0.23
E2
HN
61.46
54.89
58.85
1.74
2.95
53.06
63.30
–0.25
L2
E3
LN
60.02
55.58
56.30
2.72
4.84
49.64
62.56
–0.15
E4
HN
59.43
53.19
57.06
2.42
4.24
50.51
63.68
0.00
L3
E5
LN
58.58
54.07
58.08
3.01
5.18
50.48
65.48
–0.12
E6
HN
59.87
54.65
57.97
2.62
4.52
52.04
65.01
0.10
L4
E7
LN
58.23
56.15
59.70
2.66
4.45
50.92
65.49
–0.33
E8
HN
61.29
55.77
59.62
2.52
4.23
50.09
64.41
–0.54
L5
E9
LN
59.80
58.09
57.19
2.66
4.65
51.90
63.14
–0.13
E10
HN
61.95
60.72
57.52
2.29
3.98
52.16
63.77
0.08
L1
E1
LN
40.56
36.89
34.31
6.22
18.13
19.62
51.42
0.01
E2
HN
48.23
41.25
47.43
5.17
10.90
35.29
60.38
0.08
L2
E3
LN
43.61
40.98
34.97
6.96
19.92
18.23
52.48
0.04
E4
HN
49.35
41.28
43.73
6.82
15.60
27.77
60.18
0.08
L3
E5
LN
41.80
39.35
44.27
6.73
15.21
30.11
63.73
0.20
E6
HN
45.05
44.03
45.55
6.06
13.30
25.60
59.68
–0.14
L4
E7
LN
36.23
32.15
43.60
6.73
15.45
23.19
61.27
0.28
E8
HN
44.22
43.04
45.38
6.25
14.40
27.57
60.55
0.36
L5
E9
LN
31.89
30.71
39.62
5.58
14.08
25.69
52.29
–0.19
E10
HN
54.86
42.71
44.64
5.34
11.97
28.24
55.20
–0.22
L1
E1
LN
68.89
63.56
65.18
4.54
6.96
53.43
75.72
0.06
E2
HN
71.56
68.52
66.02
3.49
5.29
56.34
74.88
–0.03
L2
E3
LN
66.65
62.90
61.94
5.98
9.66
46.11
77.06
0.08
E4
HN
70.39
65.28
63.75
5.23
8.46
48.71
76.22
0.14
L3
E5
LN
66.19
59.20
61.69
4.86
7.87
46.78
73.60
–0.09
E6
HN
68.63
62.52
66.13
5.47
8.27
53.96
76.72
–0.13
L4
E7
LN
62.28
60.19
61.51
5.22
8.48
45.61
73.74
0.13
E8
HN
65.60
63.60
63.52
4.97
8.08
45.30
73.00
0.07
L5
E9
LN
71.60
67.54
64.04
5.14
8.02
51.53
74.73
–0.09
E10
HN
74.26
68.68
65.72
4.44
7.19
49.75
73.85
–0.04
L1
E1
LN
6.18
6.32
6.48
0.23
3.54
5.83
7.07
–0.11
ten
Kurtosis
–0.48
0.64
–0.40
–0.14
2.94
0.92
0.56
1.05
1.63
0.04
–0.75
0.32
–0.41
–0.33
2.14
0.42
0.54
1.00
0.90
–0.33
–0.54
0.03
–0.49
0.26
2.05
0.79
0.45
0.62
0.66
0.90
–0.39
–0.32
0.18
0.04
0.08
–0.17
0.75
0.93
0.05
0.10
–0.04
0.32
–0.55
0.26
–0.77
–0.55
–0.13
0.23
–0.91
–0.31
–0.37
–0.59
–0.31
–0.58
–0.31
–0.11
0.02
–0.06
–0.58
–0.41
–0.27
–0.18
–0.42
0.05
–0.29
–0.91
–0.28
–0.04
–0.88
–0.21
–0.18
9
hB2 (%)
69.98
57.33
44.17
49.67
50.51
68.37
82.56
71.87
62.01
70.09
71.42
65.58
46.67
52.93
51.76
69.22
82.85
72.84
63.74
72.05
63.27
69.46
51.33
61.49
60.63
73.29
82.87
72.52
70.24
81.29
48.04
69.46
36.22
27.82
42.73
43.04
47.52
24.29
51.76
47.12
71.16
69.25
66.21
63.90
74.48
56.65
88.66
57.95
81.32
74.05
60.54
51.52
35.01
27.39
39.22
32.69
84.37
43.55
56.14
41.98
62.55
51.82
58.35
38.83
67.13
43.56
64.68
46.43
74.93
57.00
46.00
(mm)
L2
L3
L4
L5
KW
(mm)
L1
L2
L3
L4
L5
KDR
L1
L2
L3
L4
L5
TKW
(g)
L1
L2
L3
L4
L5
E2
HN
6.16
6.53
6.52
0.25
3.87
5.43
7.13
–0.47
1.14
E3
LN
6.46
6.81
6.75
0.34
5.07
5.83
8.30
0.28
1.59
E4
HN
6.15
7.13
6.66
0.35
5.29
5.48
7.40
–0.45
0.37
E5
LN
6.51
6.75
6.91
0.33
4.76
5.50
7.81
–0.40
1.12
E6
HN
6.91
6.92
7.07
0.28
4.01
6.24
7.78
–0.33
0.08
E7
LN
6.73
7.20
6.89
0.29
4.25
6.09
7.73
0.34
0.04
E8
HN
6.58
7.03
6.89
0.38
5.54
4.15
7.70
–2.04
12.95
E9
LN
6.01
6.05
6.48
0.27
4.11
5.24
7.20
–0.45
2.11
E10
HN
6.33
6.50
6.50
0.28
4.27
5.60
7.24
–0.16
0.33
E1
LN
3.46
3.43
3.40
0.12
3.40
3.11
3.68
–0.18
–0.10
E2
HN
3.32
3.19
3.33
0.12
3.63
2.75
3.85
–0.58
4.42
E3
LN
3.34
3.21
3.24
0.15
4.55
2.80
3.63
–0.18
0.03
E4
HN
3.24
3.18
3.17
0.18
5.78
2.10
3.55
–1.16
5.13
E5
LN
4.91
5.02
3.09
0.20
3.84
4.40
5.56
–0.34
0.40
E6
HN
3.06
3.01
3.05
0.18
6.03
2.43
3.53
–0.11
0.04
E7
LN
3.64
3.46
3.46
0.14
4.14
2.93
3.86
–0.39
0.61
E8
HN
3.54
3.44
3.47
0.26
7.49
2.99
5.38
4.42
27.86
E9
LN
3.48
3.52
3.45
0.15
4.31
3.00
4.10
–0.03
1.81
E10
HN
3.48
3.55
3.45
0.20
5.78
2.83
4.05
–0.36
0.34
E1
LN
1.78
1.84
1.91
0.09
4.46
1.71
2.18
0.08
0.20
E2
HN
1.86
2.05
1.96
0.09
4.69
1.77
2.26
0.30
0.15
E3
LN
1.93
2.13
2.09
0.13
6.17
1.79
2.54
0.14
0.21
E4
HN
1.90
2.12
2.11
0.16
7.79
1.71
3.00
0.94
3.96
E5
LN
1.33
1.34
1.36
0.03
2.32
1.25
1.42
–0.29
0.18
E6
HN
2.26
2.30
2.33
0.16
7.03
1.86
2.77
0.21
–0.10
E7
LN
1.85
2.08
2.00
0.10
5.09
1.78
2.55
1.09
4.24
E8
HN
1.86
2.04
2.00
0.15
7.41
1.21
2.35
–1.71
7.44
E9
LN
1.73
1.89
1.88
0.11
5.94
1.54
2.18
0.18
0.22
E10
HN
1.82
1.84
1.89
0.13
6.82
1.59
2.28
0.45
0.33
E1
LN
43.41
45.18
45.99
3.51
7.63
36.38
54.07
–0.25
–0.10
E2
HN
45.31
40.94
45.61
3.88
8.51
31.34
54.55
–0.76
1.65
E3
LN
40.17
42.46
41.95
4.46
10.64
30.40
54.10
0.18
–0.02
E4
HN
38.71
41.83
40.72
5.19
12.75
22.68
53.56
–0.05
0.33
E5
LN
39.56
39.82
40.81
4.68
11.47
27.01
53.13
–0.16
0.32
E6
HN
34.85
34.65
36.75
5.70
15.51
20.76
49.82
–0.12
–0.24
E7
LN
47.02
47.50
46.16
4.13
8.95
32.15
57.71
–0.34
0.28
E8
HN
46.33
44.13
47.04
4.81
10.23
30.04
64.47
–0.22
2.22
E9
LN
43.25
50.07
46.40
4.38
9.45
29.23
67.96
0.35
3.18
E10
HN
46.44
50.83
47.74
5.49
11.50
25.47
59.28
–0.70
1.01
a
En. = environments, E1, E2, E3, E4, E5, E6, E7, E8, E9 and E10 represent the low and high nitrogen environments in
2011–2012 in Shijiazhuang (L1), 2012–2013 in Shijiazhuang (L2), 2012–2013 in Beijing (L3), 2012–2013 in Xinxiang (L4), and
2013–2014 in Shijiazhuang (L5), respectively
GPC grain protein content, WGC wet gluten content, DT dough tractility, TW test weight, ABS water absorption, ZEL Zeleny
sedimentation value, KH kernel hardness, KL kernel length, KW kernel width, KDR kernel diameter ratio, TKW thousand-kernel
weight, KN9204 Kenong 9204, J411 Jing 411, LN low nitrogen treatment, HN high nitrogen treatment, SD standard deviation,
CVs coefficients of variation, h2 the estimated broad-sense heritability of the corresponding traits
10
69.25
42.60
52.03
54.01
77.61
59.64
39.19
40.77
52.50
39.51
27.45
48.73
62.55
49.42
73.08
71.70
29.72
47.42
55.38
41.84
36.83
49.78
71.50
54.44
60.59
68.60
44.03
44.78
49.70
70.42
60.88
74.21
75.19
83.03
85.11
51.80
60.75
57.78
78.76
1
Supplementary Table S4 Putative additive QTLs associated with 11 kernel-related traits, as detected using IciMapping 4.0
Traits
QTL a
Left markers
Right markers Environments b
LOD value
Range
Mean
GPC
QGpc-1A
Xcnl137
BE425125
E1/E3/E6/E7/E8/E10 2.03/3.35/2.57/3.15/3.61/2.53
2.87
QGpc-1B.1
Xgwm374
Xcinau172
E5/E10
3.39/3.57
3.48
QGpc-1B.2
Glu-B1
Xme23em15.1 E2/E3/E4/E7/E9
2.60/3.07/2.74/2.21/5.45
3.21
QGpc-2A
Xwmc522
TaCwi-A1
E1/E3/E4/E9
2.55/4.27/2.37/3.54
3.18
QGpc-2B
Xksum053
Xcfe212
E1/E4/E6/E10
2.10/4.43/2.83/5.24
3.66
QGpc-3B
wPt-0021
wPt-9368
E3/E9
2.13/2.22
2.17
QGpc-4A.1
Xgpw2331
wPt-4230
E4/E8
2.03/2.12
2.07
QGpc-4A.2
wPt-8271
Xmag974
E3/E9
2.40/2.57
2.49
QGpc-4B
Rht-B1
Xmag4087
E3/E7/E8/E9
2.02/3.87/4.78/2.07
3.18
WGC
QWgc-1A
Xcnl137
BE425125
E1/E3/E6/E7/E8
2.89/3.23/2.20/2.62/3.06
2.80
QWgc-1B.1
Xgwm374
Xissr811.3
E2/E4/E5/E6/E10
2.72/2.71/3.82/3.29/3.99
3.11
QWgc-1B.2
Glu-B1
wPt-2315
E3/E7/E8/E9
3.59/2.48/2.54/5.02
3.41
QWgc-2A
Xwmc522
Xme9em20
E1/E3/E4/E9
2.19/3.08/2.66/2.98
2.73
QWgc-2B
Xgwm148
Xcfe274
E4/E6/E10
5.95/3.03/5.76
4.91
QWgc-3B
wPt-0021
wPt-9368
E3/E9
2.13/2.22
2.17
QWgc-4B
Rht-B1
Xcnl10
E7/E8
3.16/3.93
3.54
QWgc-5D
Ha
Xcfd18
E3/E4/E6/E9/E10
5.13/2.98/2.57/3.56/4.66
3.78
QWgc-7D
wPt-666095
Xcfd5
E4/E6/E10
2.11/2.33/3.43
2.62
DT
QDt-1A.1
Xcnl137
wPt-6538
E1/E3
2.94/3.59
3.26
QDt-1A.2
wPt-6046
Xwmc312
E1/E3/E4/E6/E9/E10 2.34/5.20/4.56/4.05/3.22/4.88
4.05
TW
QDt-2A
Xcfe67
Xme9em20
3.56/2.21/4.91/2.50/2.40/2.13/3.9
6/2.20
2.10/3.23
3.49/2.15
2.25/4.26/2.00/2.20/3.08
2.68/5.16/5.76/6.48/8.71/4.48/5.2
4/6.16/9.63
3.22/3.00/6.53/6.66/2.58/2.85/6.3
5/7.49
2.39/2.02/2.83/3.40
3.90/3.56
2.10/2.90
2.50/2.59
2.43/2.14
4.14/4.36
3.95/6.02/6.85/5.00/4.97/6.84
2.98
Xwmc824
wPt-0462
Xgpw5215.1
wPt-5836
Xmag1140
Xcfe89
Xmag2055
E1/E2/E3/E4/E5/E6/
E9/E10
E4/E10
E7/E8
E1/E4/E7/E9/E10
E2/E3/E4/E5/E6/E7/
E8/E9/E10
E1/E2/E3/E4/E5/E6/
E9/E10
E4/E5/E9/E10
E6/E10
E4/E10
E7/E8
E5/E9
E6/E10
E1/E4/E5/E6/E9/E10
QDt-2D
QDt-3B
QDt-4A
QDt-4B
Xswes61
Xgwm285
Xgpw2331
Rht-B1
wPt-671737
Xme12em20.1
Xgpw7543
Xmag4087
QDt-5D
Ha
Xcfd18
QDt-7D
QTw-2B
QTw-2D
QTw-3B
QTw-4A
QTw-4B.1
QTw-4B.2
Xcfd5
Xbarc200
wPt-671737
Xbarc101
Xgwm160
Xwmc657
Rht-B1
QTw-5D
QTw-7A
Ha
Xgpw2264
Xcfd18
Xbarc174
E2/E3
E2/E3
3.45/2.01
2.02/2.65
2.73
2.33
2.66
2.83
2.76
6.03
4.83
2.66
3.73
2.50
2.55
2.28
4.25
5.61
PVE % c
Range
4.90/6.27/5.68/7.85/8.86/5.03
8.44/7.27
6.29/6.34/7.04/4.96/11.77
6.95/9.34/6.10/7.73
5.78/9.83/6.46/10.27
4.24/4.30
5.88/4.28
4.01/4.90
3.34/9.21/11.16/3.77
6.94/5.78/4.23/6.65/7.65
6.86/5.56/9.39/5.09/7.79
7.48/6.68/6.32/11.41
5.63/6.70/4.96/6.65
12.38/6.62/10.49
4.24/4.30
7.66/9.39
10.95/5.41/5.26/6.88/8.23
5.69/9.47/14.33
5.85/4.80
5.50/7.33/8.43/8.12/5.90/8.11
7.30/4.99/7.44/4.01/7.33/6.12/1
1.20/4.80
3.09/4.72
7.19/4.33
4.85/7.49/3.89/3.40/4.95
6.59/7.11/10.5/10.54/13.95/15.7
8/9.62/11.98/10.74/11.68
6.31/6.72/9.06/10.90/5.03/4.49/
10.69/10.96
6.10/6.85/7.40/7.95
6.81/5.89
4.40/4.74
6.16/6.41
6.90/4.75
7.54/7.30
9.36/14.94/14.97/9.39/10.36/12.
46
8.08/4.42
8.84/9.43
Mean
6.43
7.85
7.29
7.53
8.08
4.27
5.08
4.45
6.87
6.25
6.94
7.97
5.99
9.83
4.27
8.52
7.35
9.83
5.33
7.23
6.65
3.90
5.76
4.92
11.44
8.02
7.03
6.35
4.57
6.28
5.83
7.25
11.91
6.25
9.13
Additive effect d
Range
0.15/0.21/0.20/0.34/0.35/0.15
0.33/0.20
0.19/0.21/0.19/0.27/0.28
–0.18/–0.25/–0.18/–0.23
–0.16/–0.22/–0.21/–0.22
–0.43/–0.43
0.17/0.24
–0.17/–0.18
–0.15/–0.37/–0.40/–0.16
0.45/0.51/0.43/0.75/0.78
0.53/0.47/0.85/0.51/0.53
0.58/0.75/0.71/0.70
–0.40/–0.54/–0.41/–0.53
–0.65/–0.55/–0.58
–0.43/–0.43
–0.81/–0.87
0.70/0.43/0.48/0.54/0.51
0.35/0.64/0.67
1.67/1.89
–1.61/–2.36/–2.32/–2.67/–2.0
3/–2.28
–1.86/–1.71/–2.36/–1.61/–2.7
7/–2.32/–2.79/–1.76
1.39/1.73
3.15/2.35
1.51/2.17/2.31/1.53/1.77
–1.96/–2.32/–2.58/–3.81/–3.7
2/–3.63/–3.91/–2.72/–3.24
1.73/1.99/2.62/2.64/2.30/1.99/
2.73/2.65
1.96/2.66/2.26/2.24
3.20/2.45
2.42/2.20
–2.66/–2.47
–1.95/–1.69
–3.40/–2.75
–2.39/–4.45/–2.90/–3.77/–2.4
9/–3.57
–2.13/–2.35
–2.18/–3.38
Mean
0.23
0.26
0.23
–0.21
–0.20
–0.43
0.21
–0.18
–0.27
0.58
0.58
0.68
–0.47
–0.59
–0.43
–0.84
0.53
0.56
1.78
–2.21
–2.15
1.56
2.75
1.86
–3.10
2.27
2.15
2.82
2.31
–2.57
–1.82
–3.08
–3.26
–2.24
–2.78
11
ABS
ZEL
KH
KL
KW
QAbs-1B.1
wPt-5312
Xwmc402.2
QAbs-2A
QAbs-2B
QAbs-2D.1
QAbs-2D.2
QAbs-3B
QAbs-5D
Xgwm372
Xwmc154
Xgwm484
Xmag3947
Xwmc777
Ha
Xme9em20
Xksum053
Xcau15
wPt-671737
Xme12em20.1
Xcfd18
QAbs-6B
QZel-1B
QZel-2A
wPt-9642
wPt-5765
Xwmc598
wPt-5037
Xissr811.3
Xbarc89
QZel-3B.1
QZel-3B.2
QZel-4B
QZel-5D
Xbarc101
Xwmc687
Rht-B1
Ha
Xgwm566
wPt-667746
Xcnl10
Xcfd18
QKh-1B
Xme16em12.1
QKh-2A
QKh-2D.1
QKh-2D.2
QKh-5D
Xme11em12.
2
Xme6em12
XwmpE08
wPt-731134
Ha
QKh-6B
QKl-1A
QKl-1B
Xbarc198
wPt-6538
wPt-2315
wPt-5037
Xwmc402.1
Xwmc766
QKl-1D
QKl-2A.1
wPt-9380
Xwmc522
QKl-2A.2
QKl-2B
QKl-3B
QKl-4A.1
QKl-4A.2
QKl-4A.3
QKl-7A
QKw-1A
QKw-1B
Xbarc89
Xbarc200
Xgwm285
Xgpw2331
Xmag3886
wPt-7354
Xbarc219
wPt-6538
Xme23em15.
3
Xgwm372
QKw-2A
E1/E3/E4/E5/E6/E7/
E8/E9/E10
E3/E5/E9
E5/E6/E9/E10
E2/E6
E4/E6/E10
E4/E6/E7/E8/E9/E10
E1/E2/E3/E4/E5/E6/
E7/E8/E9/E10
2.20/3.23/10.42/6.44/7.81/3.58/4.
28/9.17/8.41
2.05/2.01/3.60
2.87/2.52/3.80/2.77
2.22/4.14
3.10/5.89/3.52
2.30/2.50/3.71/4.21/2.84/2.54
4.58/7.58/26.41/23.81/20.25/13.8
4/14.15/17.14/31.56/22.93
6.17
E3/E9
E7/E8/E10
E1/E2/E3/E4/E5/E7/
E8/E9
E4/E5/E10
E5/E6/E10
E7/E8
E2/E3/E4/E5/E7/E8/
E9/E10
E6/E9
3.30/3.43
4.05/3.08/3.06
2.69/3.65/4.31/3.50/3.85/2.49/3.2
1/5.94
2.01/2.03/4.60
3.22/5.24/2.19
4.83/4.63
6.18/8.85/5.06/8.49/5.23/5.68/14.
42/7.79
2.21/2.45
3.36
3.40
3.70
2.20/2.96
3.83/2.79/3.26/3.87
5.84/6.06
6.13/7.51/21.51/19.08/28.07/14.3
9/15.27/16.34/41.33/11.77
2.31/3.14
3.07
6.90/9.23/5.15/9.48/6.59/2.22/4.7
0
2.84/2.78/3.10
2.20/3.58/8.50/2.24/5.00/2.26
2.58
3.43
5.95
18.14
Xwmc429
Xksum052
E5/E9
E6/E7/E8/E10
E6/E10
E1/E2/E3/E4/E5/E6/
E7/E8/E9/E10
E3/E9
E5
E1/E2/E3/E4/E6/E7/
E10
E3/E4/E10
E1/E3/E5/E6/E9/E10
wPt-665330
wPt-0462
wPt-8096
Xwmc760
wPt-9418
Xmag974
Xbarc174
Xwmc402.1
Xme16em12.1
E2/E6
E5/E9
E1/E3/E4
E1/E8/E10
E6/E10
E5/E9
E4/E6
E5
E6
Xme9em20
E5
Xme9em20
Xcfd233
wPt-671737
Xcfd18
5.16/4.09/15.25/9.58/12.27/5.71
/6.40/9.90/12.17
2.44/2.46/3.65
3.78/6.17/3.94/5.11
4.61/8.57
3.95/8.86/4.55
3.57/3.62/6.01/6.39/2.88/3.32
11.78/20.39/49.06/41.32/34.88/2
3.53/29.18//33.62/45.53/38.22/3
2.75
4.51/3.53
9.45/6.86/5.15
9.03/8.15/9.78/8.85/7.74/8.37/1
1.13/10.47
4.01/3.40/7.71
6.25/11.22/3.94
9.62/9.13
15.60/20.67/12.40/16.19/10.96/1
1.66/30.54/14.28
3.95/2.27
8.95
2.92
6.45
9.35
35.57
2.91
3.96
2.94/2.89
8.82/5.45/6.25/5.22
10.49/8.22
13.96/17.67/45.59/40.00/55.93/
29.79/34.55/35.45/65.36/17.43
3.47/3.34
17.64
13.38/18.28/15.61/19.31/12.23/
5.48/10.04
5.54/5.64/6.46
4.04/7.50/17.23/4.32/9.83/5.33
4.28/5.28
2.63/2.33
7.62/3.48/4.02
3.03/3.65/2.08
2.99/2.68
4.56/3.27
2.30/2.46
4.04
6.91
4.78
2.48
5.04
2.92
2.84
3.91
2.38
4.04
6.91
7.75/12.65
4.82/7.50
15.11/6.96/7.45
7.09/8.69/5.11
6.28/5.48
8.57/6.16
4.01/5.80
21.70
10.85
5.81
5.81
11.88
2.55
2.99
3.18
4.17
3.02
18.23
2.88
3.55
4.73
7.71
2.33
2.73
3.07
6.33
0.40/0.55/0.99/1.01/0.99/0.64/
0.65/0.84/0.86
–0.43/–0.47/–0.51
–0.58/–0.65/–0.53/–0.52
–0.48/–0.77
0.48/0.78/0.49
0.46/0.51/0.65/0.64/0.46/0.42
0.55/1.03/1.92/1.57/1.79/1.28/
1.45/1.47/1.81/1.42
0.77
–0.58/–0.50
–2.11/–1.67/–1.25
–1.55/–1.77/–2.18/–2.03/–1.8
8/–1.96/–2.10/–1.81
–1.36/–1.24/–1.48
–1.68/–2.02/–1.06
–2.09/–1.89
2.49/3.20/2.42/2.72/2.24/2.15/
3.11/2.03
0.98/0.78
–0.54
–1.68
–1.91
–0.91
–1.23
1.42
2.96
10.20
6.16
9.84
6.96
5.88
7.37
4.91
21.70
10.85
–0.94/–0.88
–1.44/–1.22/–1.24/–1.01
1.57/1.27
1.31/1.93/4.07/3.34/4.12/2.66/
3.09/2.98/4.19/1.86
–1.11/–0.94
0.14
–0.084/–0.108/–0.135/–0.154/
–0.099/–0.068/–0.088
–0.081/–0.084/–0.071
–0.046/–0.093/–0.136/–0.059/
–0.084/–0.064
–0.070/–0.100
–0.073/–0.073
–0.090/–0.091/–0.096
0.061/0.112/0.063
0.072/0.066
0.100/0.069
0.071/0.068
0.091
0.061
11.88
–0.068
–0.068
2.85
4.75
6.59
5.79
4.30
32.75
4.02
7.15
9.19
5.04
7.14
9.37
16.54
3.11
3.41
17.64
13.47
5.88
8.04
–0.47
–0.57
–0.62
0.58
0.52
1.43
–1.36
–1.59
–1.99
2.54
0.88
–1.02
0.14
–0.105
–0.079
–0.080
–0.085
–0.073
–0.092
0.079
0.069
0.084
0.069
0.091
0.061
12
KDR
TKW
QKw-2B
QKw-2D
TaSus2
Xwmpe08
Xwmc344
Xgpw5215.1
3.02
2.42/4.18/4.41/3.98/10.54/2.51/2.
12/5.89/6.10
2.12/3.56
4.04
7.06/4.87
3.79/5.12/2.85/14.69
2.21/4.11/4.19
2.28/3.51
4.52/5.67/5.91/3.41
2.65
4.13/3.42/3.40
6.58/2.22/3.18/3.44/4.45/3.73
3.02
4.68
Xgpw2331
Xgpw3079
Xcfe89
Xmag2055
Xcfd189
wPt-731413
Xcau10
Xme12em26.2
Xme26em26.1
Xme9em20
E6
E1/E2/E3/
E4/E6/E7/E8/E9/E10
E2/E6
E5
E4/E6
E2/E6/E9/E10
E5/E6/E10
E9/E10
E3/E5/E9/E10
E10
E4/E6/E8
E1/E2/E3/E5/E6/E9
4.32
9.05
2.84
4.04
5.96
6.61
3.50
2.89
4.88
2.65
3.65
3.93
4.32
6.00/9.83/9.99/8.90/15.36/5.83/
5.11/11.62/8.80
6.50/6.40
10.04
9.57/10.98
8.83/7.53/5.29/24.99
4.00/5.34/6.05
3.92/4.99
15.17/13.99/14.61/8.23
7.33
8.24/8.80/10.02
13.84/4.76/7.84/5.17/6.35/6.35
QKw-4A.1
QKw-4A.2
QKw-4B.1
QKw-4B.2
QKw-5D
QKw-6A
QKw-6B
QKw-7A
QKdr-1B
QKdr-2A
Xwmc161
wPt-4424
Xwmc657
Xbarc199
Ha
Xwmc201
Xcnl64
Xwmc809
wPt-2315
Xme6em12
QKdr-2B.1
QKdr-2B.2
QKdr-2D
wPt-6932
Xksum053
Xswes61
wPt-0462
Xcfe274
Xmag4089
E5/E6
E5/E9
E1/E4/E5/E6/E8/E9
QKdr-3D
QKdr-4A.1
QKdr-4A.2
QKdr-4B.1
QKdr-4B.2
Xgdm72
Xmag3886
wPt-7354
Xwmc657
Xbarc199
wPt-730660
wPt-9418
Xgwm160
wPt-6149
Xcnl10
QKdr-5B
QKdr-6B
QKdr-7A
QTkw-1A
QTkw-1B.1
QTkw-1B.2
QTkw-2A.1
QTkw-2A.2
QTkw-2B
QTkw-2D
Xcfd156
Xcnl64
Xwmc809
wPt-6538
Xme23em15.
3
wPt-2315
Xwmc522
Xbarc89
Xbarc13
Xcfd233
QTkw-3B
QTkw-4A
Xcft3530
Xgpw2331
Xbarc131
Xwmc760
QTkw-4B.1
QTkw-4B.2
QTkw-5D
QTkw-6A
Xwmc657
Rht-B1
Ha
Xwmc553
Xcfe89
Xmag2055
Xcfd189
Xwmc754
6.46/3.32
2.25/3.38
2.34/3.79/5.44/5.52/3.81/3.81
4.89
2.81
4.12
9.09/4.57
3.46/6.04
4.33/7.94/7.81/7.79/8.97/6.70
6.83
4.75
7.26
E5/E6/E9
E6
E1/E2/E5
E2
E4/E5/E6/E9/E10
3.51/2.76/2.22
2.95
4.30/2.78/2.71
3.46
6.59/5.01/10.98/2.88/6.37
2.83
2.95
3.26
3.46
6.37
4.73/3.88/7.31
4.37
8.48/6.36/3.61
8.53
14.34/7.93/18.82/4.82/15.90
5.31
4.37
6.15
8.53
12.36
Xwmc75
Xcau10
Xme12em26.2
Xgwm164
Xme16em12.1
E5/E10
E9/E10
E9/E10
E5/E7/E10
E5/E6
4.72/2.33
2.05/2.35
3.84/2.25
2.79/2.13/2.08
4.17/4.54
3.53
2.20
3.05
2.33
4.35
6.85/7.08
3.37/4.86
11.38/10.46
11.82/6.94/7.74
7.86/6.41
6.97
4.12
10.92
8.83
7.00
Xme26em26.1
Xme13em23.2
Xme16em19.2
Xcfe212
Xgpw5215.1
E1/E4
E6
E3/E10
E5/E6
E1/E2/E3/
E4/E5/E6/E7/E8/E9/
E10
E5/E6
E1/E2/E3/
E4/E5/E6/E9/E10
E5/E6
E2/E3/E4/E6/E10
E2/E4/E6/E7/E10
E3/E5/E9/E10
4.41/4.78
3.50
5.53/3.48
2.12/2.29
6.02/5.64/7.36/2.23/6.53/9.26/4.5
7/2.75/7.12/4.32
4.60
3.50
4.51
2.20
5.58
7.89/8.97
4.75
10.21/5.62
3.04/3.35
11.63/11.78/10.15/5.94/10.18/11
.69/10.80/6.93/14.10/8.44
2.04/2.27
6.43/7.33/6.82/2.01/6.17/4.17/3.5
0/2.05
7.25/4.82
4.30/4.93/6.33/11.02/13.39
2.03/3.03/3.83/2.81/2.51
2.63/2.76/2.12/2.17
2.15
4.81
4.87/5.25
15.00/15.08/9.83/3.39/9.79/6.10
/7.45/4.34
12.32/5.61
8.85/6.62/12.96/15.07/25.75
3.49/6.09/5.41/5.96/4.08
3.77/5.05/4.06/3.70
6.04
7.99
2.84
2.42
0.038
0.028/0.038/0.047/0.055/0.07
2/0.035/0.059/0.051/0.059
0.031/0.046
0.062
–0.057/–0.061
–0.036/–0.051/–0.034/–0.100
0.039/0.043/0.050
–0.030/–0.045
–0.058/–0.074/–0.057/–0.050
–0.054
–0.047/–0.048/–0.047
–0.032/–0.020/–0.036/–0.007/
–0.041/–0.028
–0.010/–0.035
–0.006/–0.028
–0.018/–0.046/–0.009/–0.046/
–0.044/–0.029
–0.007/–0.032/–0.030
0.035
0.026/0.024/0.006
0.027
0.062/0.009/0.071/0.025/0.05
2
–0.008/–0.034
0.021/0.029
0.038/0.042
1.62/1.10/1.53
1.30/1.46
0.038
0.049
8.43
4.75
7.92
3.19
10.16
–0.98/–1.55
–1.24
–1.43/–1.30
0.82/0.86
1.19/1.33/1.42/1.03/1.49/1.94/
1.35/1.17/1.64/1.49
–1.27
–1.24
–1.36
0.84
1.41
5.06
8.87
1.03/1.31
1.36/1.50/1.40/0.95/1.46/1.41/
1.19/1.14
–1.65/–1.36
–1.16/–1.15/–1.88/–2.22–2.79
0.73/1.29/1.33/1.02/1.12
–0.88/–1.06/–0.91/–1.06
1.17
1.30
6.45
10.04
10.27
11.66
5.13
4.45
13.00
7.33
9.02
7.39
8.96
13.85
5.01
4.15
0.039
0.062
–0.059
–0.055
0.044
–0.040
–0.060
–0.054
–0.047
–0.027
–0.022
–0.017
–0.032
–0.023
0.035
0.019
0.027
0.044
–0.021
0.025
0.040
1.42
1.38
–1.51
–1.84
1.10
–0.98
13
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
QTkw-6B.1
Xcnl113
Xme9em2.2
E1/E6/E9
3.29/4.71/3.81
3.94
6.81/5.63/7.45
6.63
–0.91/–1.35/–1.19
–1.15
Xcnl64
Xcau10
E3/E5
8.27/6.52
–1.59/–1.57
–1.58
7.40
12.50/11.02
11.76
QTkw-6B.2
QTkw-7A
wPt-4553
Xissr807.1
E2/E4/E8
2.15/3.58/2.83
2.85
3.71/6.79/6.23
5.57
0.75/1.35/1.20
1.10
QTkw-7D
Xmag2931.2
Xgdm88.2
E3/E8
3.17/2.19
2.68
3.91/4.57
4.24
0.88/1.03
0.96
a
A putative major QTL is marked in bold typeface and is characterized by a mean LOD > 3.0 and a mean PVE > 10 %; a putative stable QTL is underlined when this locus was detected in at least five of the ten
environments; and a QTL for a kernel related-trait that was co-localized, with its corresponding difference between HN and LN, is presented in red color
b
E1, E2, E3, E4, E5, E6, E7, E8, E9, and E10 indicate trial 1 (2011–2013, Shijiazhuang) LN, trial 1 HN, trial 2 (2012–2013, Shijiazhuang) LN, trial 2 HN, trial 3 (2012–2013, Beijing) LN, trial 3 HN, trial 4
(2012–2013, Xinxiang) LN, trial 4 HN, trial 5 (2013–2014, Shijiazhuang) LN, and trial 5 HN, respectively
c
PVE indicates the percentage of explained phenotypic variation
d
A positive sign indicates that the alleles from the Kenong9204 parent increased the corresponding trait value; and a negative sign indicates that the alleles from the Jing411 parent increased the corresponding trait
value
GPC grain protein content, WGC wet gluten content, DT dough tractility, TW test weight, ABS water absorption, ZEL Zeleny sedimentation value, KH kernel hardness, KL kernel length, KW kernel width, KDR
kernel diameter ratio, TKW thousand-kernel weight
14
1
Traits
GPCDV
WGCDV
DTDV
TWDV
ABSDV
ZELDV
KHDV
KLDV
KWDV
KDRDV
Supplementary Table S5 Putative additive QTLs associated with the differences in the values for the 11 kernel related traits under high nitrogen and low nitrogen conditions in each trial, as detected by IciMapping 4.0
QTL a
Left markers
Right markers
Trials b
LOD value
PVE % c
Additive effect d
Range
Mean
Range
Mean
Range
Mean
QGpcdv-1B
Xme9em25
Glu-B1
L4
2.87
2.87
7.08
7.08
–0.06
–0.06
QGpcdv-2D
Xksum174.4
Xgwm539
L3
2.23
2.23
14.93
14.93
0.36
0.36
Xwmc125
Xmag2055
L1/L2/L3/L5/M
3.28/3.11/2.19/2.87/4.66
3.22
11.47/7.47/9.02/7.14/15.11
10.04
0.31/0.21/0.28/0.18/0.19
0.24
QGpcdv-4B
QWgcdv-1B
Xme9em25
Glu-B1
L4
3.21
3.21
7.89
7.89
–0.16
–0.16
QWgcdv-2D
Xksum174.4
Xgwm539
L3/L5
2.61/2.21
2.41
17.40/15.38
16.39
0.63/0.92
0.77
Xwmc125
Xmag2055
L1/L2/L3/L5/M
2.29/2.54/2.53/3.44/4.26
3.01
8.61/6.90/10.02/12.26/14.03
10.36
0.65/0.47/0.70/0.56/0.46
0.57
QWgcdv-4B
QDtdv-1B
wPt-3451
Xissr811.3
L3
2.27
2.27
5.44
5.44
–1.80
–1.80
QDtdv-2A
Xksum193
Xwmc658
M
2.31
2.31
6.15
6.15
0.98
0.98
QDtdv-2D
Xksum174.4
Xgwm539
L3
2.46
2.45
15.75
15.75
3.03
3.03
QTwdv-1B
Xme11em12.2
Xme26em26.3
L1/L2
2.33/2.33
2.33
6.07/6.97
6.02
2.49/3.24
2.87
Xwmc598
Xwmc522
L3/L5
5.03/2.37
3.70
19.51/7.41
13.46
–4.60/–2.52
–3.56
QTwdv-2A
QTwdv-4B
Xbarc199
Rht-B1
L3/L5/M
4.22/3.15/3.18
3.52
8.96/8.14/7.77
8.29
–3.09/–2.61/–1.97
–2.56
QTwdv-7A
Xbarc219
Xbarc174
L1/L2/L5/M
2.09/2.14/2.14/2.51
2.22
9.36/10.45/5.37/7.24
8.11
3.06/4.27/3.12/1.91
2.84
QAbsdv-1A
wPt-6654
Xgwm497
L4
2.19
2.19
21.45
21.45
0.47
0.47
QAbsdv-2A.1
Xwmc522
Xme13em23.2
L3
2.83
2.83
6.95
6.95
0.50
0.50
QAbsdv-2A.2
Xksum193
Xwmc658
L3/L5/M
3.83/3.82/3.02
3.55
8.49/9.17/7.32
8.33
0.56/0.47/0.32
0.98
QAbsdv-2D
Xksum174.1
Xksum174.4
L3/L5
2.37/2.05
2.21
8.69/5.84
7.26
0.58/0.39
0.48
QAbsdv-5D
Ha
Xcfd18
L3/L5/M
5.02/3.45/3.03
3.83
11.59/8.65/7.73
9.32
–0.66/–0.46/–0.33
–0.48
QAbsdv-6B
wPt-9952
wPt-3045
L2/M
2.85/2.12
2.48
6.86/4.00
5.43
0.55/0.24
0.39
QZeldv-1B
Xme11em12.2
Xme26em26.3
L1/L2/L5/M
3.10/2.28/2.97/3.46
2.96
7.75/5.88/7.55/8.74
7.48
–2.08/–1.89/–1.46/–1.25
–1.67
Qzeldv-2A
Xwmc522
Xme13em23.2
L3
2.81
2.81
7.85
7.85
1.68
1.68
QZeldv-5D
Ha
Xcfd18
L3
2.67
2.67
5.99
5.99
–1.48
–1.48
QKhdv-2A
Xme13em23.2
Xgwm448
L3
2.46
2.46
6.61
6.61
1.17
1.17
QKhdv-5D
Ha
Xcfd18
L3/L5/M
4.18/2.20/2.24
2.87
11.28/5.96/5.21
7.48
–1.55/–1.02/–0.72
–1.10
QKhdv-6B
Xedm149.2
wPt-3045
L1/L2/L5/M
2.18/2.88/2.25/2.31
2.40
4.92/6.90/5.99/5.63
5.86
1.15/1.56/1.02/0.75
1.12
QKldv-1A
Xksum174.2
wPt-6654
L5/M
2.12/2.12
2.12
4.87/9.16
7.02
0.071/0.064
0.067
QKldv-1B.1
wPt-2315
Xme23em15.1
L1
2.95
2.95
11.32
11.32
–0.064
–0.064
Xwmc44
Xcfa2219
M
3.59
3.59
11.05
11.05
–0.046
–0.046
QKldv-1B.2
QKldv-2B
wPt-4301
Xksum053
L2/M
2.01/2.80
2.41
4.80/6.15
5.47
0.077/0.035
0.056
QKldv-3B
Xbarc101
wPt-1940
L1/L5
2.98/2.18
2.58
6.67/5.86
6.26
0.049/0.063
0.060
Xksum174.2
wPt-6654
L3/L4
2.67/14.47
8.57
4.42/49.19
26.81
0.060/0.808
0.434
QKwdv-1A
QKwdv-1B.1
Glu-B1
wPt-2315
M
2.33
2.33
5.15
5.15
0.024
0.024
QKwdv-1B.2
Xwmc44
Xcfa2219
L4
2.43
2.43
5.87
5.87
–0.070
–0.070
QKwdv-2B
wPt-4301
Xksum053
L3/M
2.70/2.23
2.46
8.51/7.38
7.95
0.067/0.028
0.048
Xwmc657
Xcnl10
L1/L2/L3/L5/M
2.03/3.67/8.04/7.06/7.59
5.68
4.86/9.45/15.79/16.93/17.08
12.82
–0.027/–0.050/–0.092–0.
–0.058
QKwdv-4B
078/–0.043
QKwdv-5A
Xmag1241
Xme12em13.1
L1/L5/M
2.10/2.19/3.12
2.47
7.46/6.82/9.40
7.89
–0.033/–0.049/–0.032
–0.038
QKwdv-5D
Ha
Xcfd18
L5
2.07
2.07
4.74
4.74
0.042
0.042
QKwdv-6B.1
Xcnl64
Xgwm282
L3
2.35
2.35
6.02
6.02
0.057
0.057
QKwdv-6B.2
wPt-1325
wPt-6116
M
2.38
2.38
4.76
4.76
0.023
0.023
QKdrdv-1B
wPt-2315
Xme23em15.1
M
3.98
3.98
8.71
8.71
–0.019
–0.019
15
–0.030/–0.015
–0.022
–0.030/–0.028
–0.029
–0.043
–0.043
0.020/0.052/0.038/0.034/
0.035
0.036/0.033
QKdrdv-6B
wPt-9952
wPt-3045
L3
4.14
4.14
5.19
5.19
–0.033
–0.033
QTkwdv-1A
Xksum174.2
wPt-6654
L5
2.68
2.68
20.72
20.72
3.67
3.67
QTkwdv-2A
Xwmc522
Xme13em23.2
L5/M
3.14/2.81
2.98
6.29/4.56
5.42
–1.13/–0.50
–0.81
Xme16em26
Xmag2055
L1/L2/L3/L5/M
2.21/5.05/8.65/9.59/8.29
6.76
8.26/12.26/19.90/20.23/14.33
14.99
–0.78/–1.49/–1.37/–2.03/
–1.31
QTkwdv-4B
–0.89
Xmag1241
Xme12em13.1
L2/L5/M
3.83/3.69/6.50
4.67
12.11/9.11/14.08
11.77
–1.48/–1.36/–0.88
–1.24
QTkwdv-5A
a
A putative major QTL is marked in bold typeface and is characterized by a mean LOD > 3.0 and a mean PVE > 10 %; a putative stable QTL is underlined when this locus was detected in at least three of the six trials;
and a QTL for a kernel-related trait that was co-localized, with its corresponding differences between HN and LN is presented in red color
b
L1, L2, L3 L4, L5, and M indicated location 1 (2011–2013, Shijiazhuang), location 2 (2012–2013, Shijiazhuang), location 3 (2012–2013, Beijing), location 4 (2012–2013, Xinxiang), location 5 (2013–2014,
Shijiazhuang) and the mean of the five trials, respectively
c
PVE indicates the percentage of explained phenotypic variation
d
A positive sign indicates that the alleles from the Kenong9204 parent increased the corresponding trait value; and a negative sign indicates that the alleles from the Jing411 parent increased the corresponding trait
value
GPCDV, WGCDV, DTDV, TWDV, ABSDV, ZELDV, KHDV, KLDV, KWDV, KDRDV, and TKWDV represented the differences in grain protein content between HN and LN, wet gluten content, dough tractility, test
weight, water absorption, Zeleny sedimentation value, kernel hardness, kernel length, kernel width, kernel diameter ratio, and thousand-kernel weight, respectively
QKdrdv-2A
QKdrdv-2B
QKdrdv-2D
QKdrdv-4B
TKWDV
1
2
3
4
5
6
7
8
9
Xwmc598
wPt-6932
Xksum244
Xbarc199
Xksum052
wPt-6576
Xksum174.1
Xmag2055
L3/M
L2/L3
L3
L1/L2/L3/L4/L5/M
3.62/3.03
2.16/2.75
5.97
2.67/5.30/5.28/2.10/3.84/13.15
3.32
2.46
5.97
5.39
4.49/4.92
4.62/3.83
8.99
6.67/14.07/7.15/4.63/8.64/24.88
4.70
4.22
8.99
11.01
16
1A
0.0
6.2
8.2
9.0
10.1
14.0
33.5
82.5
101.1
106.4
108.0
112.3
122.7
123.7
135.3
143.9
159.3
1B
Xgdm33
wPt-730618 wPt-6709
wPt-666537
wPt-665724
Xcnl137
Glu-A3
BE425125
wPt-6358
Xwmc402.1
Xgwm164
Xwmc469
wPt-6046
Xwmc278
wPt-8347
wPt-665590
Xwmc312
Glu-A1
Xme12em12.2
0.0
13.0
Xksum174.2
wPt-6654
42.1
76.1
95.4
Xgwm497
Xbarc17
wPt-668205
wPt-730885 wPt-2847
wPt-667252
wPt-669499
wPt-5316
FM1
121.3
122.0
123.6
135.6
0.0
11.9
12.5
13.4
13.5
14.0
14.4
14.7
15.9
16.5
17.3
18.7
19.9
20.3
20.7
21.3
22.3
22.6
23.2
23.4
23.5
25.3
25.5
27.5
29.1
29.9
30.8
32.0
40.4
55.4
76.4
97.7
106.7
136.5
139.7
160.5
2A
Glu-B3h
wPt-2751
wPt-6117 wPt-6833
wPt-6434 wPt-8616
wPt-6427
wPt-8949 wPt-669239
wPt-5281
wPt-3282
wPt-1684
wPt-2988
wPt-3465
wPt-1176 wPt-9903
wPt-5765
wPt-5745 wPt-7529
wPt-1328
wPt-8930 wPt-4107
wPt-5312
wPt-2052 Xgwm374
Xgwm11 Xwmc406
Xwmc128 Xbarc187
Xcfd59 wPt-2019
wPt-2614
wPt-6985
wPt-4434 wPt-3177
wPt-0974
Xcinau172
wPt-3451
Xissr811.3
Xme10em7 Xme9em2.1
Xme7em19.1 Xme7em10.2
Xme11em12.2
Xme26em26.3
Xme23em15.3
Xme16em12.1
Xwmc402.2
Xme9em25
Glu-B1
wPt-2315
Xme23em15.1
Xme26em26.1
Xwmc766
0.0
6.1
13.5
58.2
60.0
65.4
72.9
88.4
114.5
124.1
130.4
134.8
136.5
136.7
141.6
151.8
164.7
187.1
215.7
224.1
227.6
229.8
242.1
268.8
0.0
6.7
9.5
22.4
30.8
2B
Xbarc1138.3
Xbarc1138.4
Xgwm636
wPt-2448 wPt-669245
wPt-2087
Xme18em11
Xcfe67
Xwmc598
Xwmc522
Xme13em23.2
Xgwm448
Xme6em12
Xksum052
Xgwm372
Xme9em20
TaCwi
Xbarc89
wPt-665330
Xme16em19.2
Xgwm312
Xgwm294
Xksum174.3
Xksum174.5
Xwmc181
Xksum193
Xwmc658
Xgwm311
wPt-6687
Xmag633
0.0
2.9
3.2
3.6
5.3
6.3
7.1
41.2
52.9
54.8
56.1
56.5
82.5
88.4
90.8
92.8
95.2
97.0
102.4
105.4
142.7
149.9
155.4
161.9
163.8
164.1
165.0
176.3
179.5
192.4
229.4
5D
Xcau14.1
Xme26em26.2
Xbarc1138.1
Xbarc1138.2
wPt-0100
Xwmc764
wPt-6627 wPt-3459
wPt-5587 wPt-5934
wPt-6970 wPt-6575 0.0
Xwmc154
8.6
wPt-6932
8.7
wPt-9402 Xbarc200 40.0
wPt-0462
wPt-4301
Xksum053
87.1
wPt-0408 Xgwm148 0.0
Xbarc13
14.5
Xcfe274
TaSus2
Xwmc344
wPt-6576
Xcfe212
Xme4em12
wPt-7004
Xme13em3
Xwmc332
wPt-0473
wPt-9736
wPt-0694
PPO33
wPt-2430
Xme12em26.1
Xwmc317
7B
Xgwm569
Xcfe100
Xgwm46
Xbarc267
wPt-6498
wPt-4025
wPt-0312
Xwmc396
wPt-2305
wPt-3833
wPt-9467
wPt-9925
Xwmc749
Xbarc182
wPt-665293
Psy-B1
wPt-0884
wPt-8598
Xcfe223
Xcau11
wPt-8007
wPt-4038
wPt-0530
wPt-6156
wPt-4814
wPt-7887 wPt-5892
Xcfe127
Xgwm344
0.0
49.8
65.7
67.0
Ha
71.6
Xcfd18
73.4
Xcfd183
73.8
Xcfd189
74.1
74.8
75.6
Xgwm174 77.1
Xwmc765 100.1
Xwmc443 138.1
155.3
158.6
160.1
162.2
167.0
170.4
172.2
194.4
194.7
203.3
205.2
219.8
236.9
246.3
295.3
Supplementary Figure S1 Novel genetic linkage map enriched with functional markers of kernel size and quality traits
17
Supplementary Figure S2 Effects of Rht-B1 (wild type Rht-B1a and mutant Rht-B1b) on traits with QTLs that mapped
close to Rht-B1 in the KJ-RIL population grown under high and low nitrogen conditions
An analysis of covariance (ANCOVA), with removal of the effects of plant height (PH), performed using QGA station
1.0 according to Cui et al. (2011) and Fan et al. (2015); the value for a kernel-related trait (KRT) was obtained from the
average of the five HN and LN values, respectively. KRT|PH indicates KRT without the influence of PH
*
Indicates significance at a P < 0.05
Indicates significance at a P < 0.01
***
Indicates significance at a P < 0.001
**
18
Supplementary Figure S3 Effects of Ha (Pinb-D1b and Pinb-D1a) on traits with QTLs that mapped close to Ha in the
KJ-RIL population grown under high and low nitrogen conditions
Analysis of covariance (ANCOVA), with removal of the effects of kernel hardness (KH), performed using QGA station
1.0 according to Cui et al. (2011) and Fan et al. (2015); the value for a kernel-related trait (KRT) was obtained from the
average of the five HN and LN, respectively. KRT|KH indicates KRT without the influence of KH
*
Indicates significance at a P < 0.05
Indicates significance at aP < 0.01
***
Indicates significance at a P < 0.001
**
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