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QTL mapping of 1000-kernel weight, kernel length, and kernel width in bread
wheat (Triticum aestivum L.)

Article  in  Journal of applied genetics · December 2010

DOI: 10.1007/BF03208872 · Source: PubMed

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J Appl Genet 51(4), 2010, pp. 421–429

Original article

QTL mapping of 1000-kernel weight, kernel length, and kernel

width in bread wheat (Triticum aestivum L.)

P. Ramya1, A. Chaubal1, K. Kulkarni1, L. Gupta1, N. Kadoo1, H. S. Dhaliwal2, 3, P. Chhuneja3,

M. Lagu1, V. Gupta1

1
Plant Molecular Biology Group, Division of Biochemical Sciences, National Chemical Laboratory, Pune 411008, Maharashtra,
India
2
Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
3
School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana 141004, Punjab, India

Abstract. Kernel size and morphology influence the market value and milling yield of bread wheat (Triticum
aestivum L.). The objective of this study was to identify quantitative trait loci (QTLs) controlling kernel traits in
hexaploid wheat. We recorded 1000-kernel weight, kernel length, and kernel width for 185 recombinant inbred
lines from the cross Rye Selection 111 × Chinese Spring grown in 2 agro-climatic regions in India for many years.
Composite interval mapping (CIM) was employed for QTL detection using a linkage map with 169 simple se-
quence repeat (SSR) markers. For 1000-kernel weight, 10 QTLs were identified on wheat chromosomes 1A, 1D,
2B, 2D, 4B, 5B, and 6B, whereas 6 QTLs for kernel length were detected on 1A, 2B, 2D, 5A, 5B and 5D. Chromo-
somes 1D, 2B, 2D, 4B, 5B and 5D had 9 QTLs for kernel width. Chromosomal regions with QTLs detected con-
sistently for multiple year-location combinations were identified for each trait. Pleiotropic QTLs were found on
chromosomes 2B, 2D, 4B, and 5B. The identified genomic regions controlling wheat kernel size and shape can be
targeted during further studies for their genetic dissection.

Keywords: composite interval mapping, kernel shape, kernel size, quantitative trait loci, stable QTLs, Triticum
aestivum.

Introduction wheat genotypes were segregated based on kernel

Wheat kernel size is important in view of both
yield and quality, and its improvement has re-
mained an important objective in ancient and
modern plant breeding initiatives. Larger and uni-
formly sized kernels are visually appealing and
command a higher market price. One of yield
traits and a wheat grading parameter is
1000-kernel weight (TKW), which can be mea-
sured easily and used to approximate the agro-
nomic yield of a wheat genotype (Baril 1992).
Kernel length (KL) and width (KW) have also
been tested as non-invasive and cheap predictors
of milling quality of bread wheat genotypes
(Berman et al. 1996). When grains from individual
size, large-grained samples had significantly
higher flour yield than those of smaller grains
(Marshall et al. 1986). Similarly, selection for in-
creased kernel size resulted in higher flour yield in
the studies conducted by Wiersma et al. (2001).
Breseghello and Sorrells (2006) reported positive
correlations of KL, weight and area with milling
score, i.e. a parameter derived from flour yield, en-
dosperm separation index and friability, whereas
Baker et al. (1999) and Morgan et al. (2000) re-
ported the association of kernel size with
flour-water dough quality. In durum wheat
(Triticum durum Desf.), Novaro et al. (2001)
found that kernel volume, together with TKW or
test weight, was the best predictor of semolina

Received: September 24, 2009. Accepted: October 22, 2009.

Correspondence: V. Gupta, Scientist ‘G’, Plant Molecular Biology Group, Division of Biochemical Sciences, National Chemi-
cal Laboratory, Dr. Homi Bhabha Road, Pashan, Pune 411 008, Maharashtra, India; e-mail: vs.gupta@ncl.res.in,
vidyagene@gmail.com
422 P. Ramya et al.
yield. Because of their importance, kernel size and
shape characters are subjects of investigations also
in other cereals, like oat, barley and rice (Groh et
al. 2001; Ayoub et al. 2002; Fan et al. 2006; Song
et al. 2007). In a complex system like hexaploid
wheat, quantitative trait locus (QTL) mapping can
serve as an initial step in discovering the molecu-
lar bases of kernel size and shape. Identification of
tightly linked markers to QTLs governing these
traits will be useful in their coordinated selection
in segregating generations. Understanding the ge-
netic bases of kernel characters is, therefore, an es-
sential milestone in the development of improved
wheat varieties.
In earlier studies, genomic regions associated
with kernel weight and dimensions have been
identified using monosomic (Giura and Saulescu
1996; Varshney et al. 2000) and QTL analysis
(Campbell et al. 1999; Ammiraju et al. 2001 and
2004; Dholakia et al. 2003; Kumar et al. 2006;
Breseghello and Sorrells 2007). Breseghello and
Sorrells (2006) studied the association of these
kernel traits with simple sequence repeat (SSR)
markers in a collection of wheat cultivars, whereas
Röder et al. (2008) performed fine mapping of a
grain weight QTL at the telomeric region of chro-
mosomal arm 7DS. QTLs associated with TKW in
wheat were also identified by studies related to ag-
ronomic yield components (Börner et al. 2002;
Groos et al. 2003; Huang et al. 2006; Wang et al.
2009). In spite of these efforts, there are very few
studies that address traits of kernel size and mor-
phology in the same genetic background across
different environments (Giura and Saulescu 1996;
Campbell et al. 1999; Dholakia et al. 2003;
Ammiraju et al. 2004; Breseghello and Sorrells
2007). Hence, we performed QTL mapping of
TKW, KL, and KW using a hexaploid wheat
population of recombinant inbred lines (RILs)
with phenotypic evaluations conducted in
2 agro-climatic zones for many years, to identify
the genetic and environmental influences on these
traits.
Materials and methods
Plant material and phenotypic analysis
The RIL mapping population of 185 lines used in
this study was derived from the cross Rye Selec-
tion 111 (RS) × Chinese Spring (CS). The parents
and the RIL population were grown for 4 years in a
randomized block design with 2 replications at
Ludhiana, Punjab (1999–2000, 2002–2003,
2004–2005, and 2006–2007) and for 3 years at
Pune, Maharashtra (2004–2005, 2005–2006, and
2006–2007). The study sites at Ludhiana
(30°52’N, 75°56’E, altitude 255 m, North-western
Plain Zone) and Pune (18°32’N, 73°51’E, altitude
559 m altitude, Peninsular Zone) represent 2 dif-
ferent wheat-growing agro-climatic regions in In-
dia.
TKW was recorded using an electronic balance
for all the years at both locations. KL and KW
were recorded for 20 random kernels from each
line in each replication using Vernier calipers, and
the average value was used for further analysis.
KL and KW were recorded for 2003 and 2005 har-
vests at Ludhiana and for all the 3 years at Pune.
Mean trait values of the 2 replications were used
for QTL analysis. Each year-location combination
was considered as one environment, designated by
its trait, year, and location information. For exam-
ple, TKW2003Lud indicated TKW assessed for
the harvest of the season 2002–2003 at Ludhiana.
Pearson’s correlation coefficients (r) between
pairs of traits was calculated using Microsoft Ex-
cel 2000 for the years in which all the 3 traits were
recorded and also for the average trait value across
environments for each trait. Analysis of variance
(ANOVA) was performed using IRRISTAT ver.
5.0 (International Rice Research Institute, Manila,
Philippines), for the data from all the environ-
ments for each trait. Heritability was estimated us-
ing the formula:
h2 = 1 - [M2/M1],
where M1 and M2 are the mean squares of genotype
and genotype × environment, respectively (Huang
et al. 2006).
Construction of genetic linkage map and QTL
analysis
Genomic DNA was extracted from 15-day-old
seedlings of parents and F9 RILs as described by
Stein et al. (2001). Ten wheat chromosomes were
initially targeted for map construction and QTL
analysis due to their repeated association with the
traits of interest in earlier reports (Giura and
Saulescu 1996; Campbell et al. 1999; Ammiraju
et al. 2001 and 2004; Börner et al. 2002; Dholakia
et al. 2003; Groos et al. 2003; Breseghello and
Sorrells 2006 and 2007; Huang et al. 2006 and
Kumar et al. 2006). Microsatellite polymorphism
was determined using parental DNA with 600
primer pairs (gwm, gdm, barc, cfa, cfd, psp and
wmc; see the GrainGenes website ). These also in-
cluded 21 pairs obtained from the Leibniz Institute
of Plant Genetics and Crop Plant Research or from
 QTL mapping of wheat kernel traits 423

TraitGenetics, Gatersleben, Germany. The poly- conducted using QTL Cartographer ver. 2.5, to de-
merase chain reaction (PCR) was performed in tect the pleiotropic QTLs. MapChart ver. 2.0
15-mL reaction volumes according to Ammiraju et (Voorrips 2002) was used to depict the linkage
al. (2002) with minor modifications. The PCR groups and QTLs.
products were resolved using 6% denaturing
PAGE gels containing 7.5 M urea in 1× TBE
buffer. The bands were visualized by silver stain- Results
ing of the gels as described by Sanguinetti et al.
(1994) and scored twice to eliminate interpretation TKW, KL and KW values for the parental geno-
errors. The polymorphic microsatellite markers types and summary statistics for RILs for all the
were used for genotyping of the RIL population. years and locations are presented in Table 1. The
The genetic linkage map was constructed using parental genotype RS showed higher trait values
JoinMap ver. 4.0 (Van Ooijen 2006) at LOD score than CS for all the traits and environments. Fre-
4.0, using the Kosambi mapping function quency distributions of the traits showed continu-
(Kosambi 1944) and subsequently employed for ous variation (data not shown). This fact, along
QTL analysis. with the presence of transgressive segregants
QTL analysis was carried out for each trait by among the RILs, suggested that the traits are con-
using the data from all the environments and their trolled by multiple loci. The coefficient of varia-
average. Composite interval mapping (CIM) using tion (CV) values were comparable for the same
QTL Cartographer ver. 2.5 (Wang et al. 2007) was traits in different environments (Table 1).
performed to determine the positions and effects Pearson’s correlation coefficients (r) were posi-
of the QTLs. QTLs with LOD value ³ threshold tive and highly significant for all the trait combi-
LOD, as determined by 1000 permutation tests at nations (Table 2). ANOVA indicated significant
P £ 0.05 (Churchill and Doerge 1994; Doerge and differences (P < 0.0001) among RIL genotypes
Churchill 1996), were declared as significant and and among environments (Table 3). Heritability
reached 0.879 for TKW, 0.865 for KL, and 0.796
those with LOD ³ 2.0 but less than the threshold
for KW.
LOD were considered as suggestive QTLs. The Out of the 600 SSR primer pairs, 175 were
proportion of observed phenotypic variance ex- polymorphic between the parental genotypes and
plained by a QTL was estimated as the coefficient yielded 193 markers, as 12 primers generated
of determination (R2). Multi-trait composite inter- more than one polymorphic locus. Of these, 169
val mapping (MCIM) (Jiang and Zeng 1995) was markers formed 24 linkage groups, while 24 mark-
Table 1. Phenotypic performance of wheat genotypes Rye Selection 111 (RS), Chinese Spring (CS) and
recombinant inbred lines (RILs) in diverse environments for 1000-kernel weight (TKW), kernel length (KL), and
kernel width (KW). The environment is designated by the trait, year and location.
Trait Environment Parental genotypes RILs
RS CS mean SD range CV (%)
TKW (g) TKW2000Lud 54.6 19.6 31.15 7.39 15.4–52.1 23.7
TKW2003Lud 52.2 20.5 29.32 7.08 11.5–46.0 24.1
TKW2005Lud 50.3 17.6 24.57 5.44 10.0–40.3 22.1
TKW2007Lud 54.4 22.2 28.99 7.22 10.8–44.2 24.9
TKW2005Pun 52.8 16.1 31.61 7.40 15.5–55.5 23.4
TKW2006Pun 51.5 14.5 25.65 6.41 13.3–52.3 24.9
TKW2007Pun 51.0 16.6 27.03 5.56 13.4-–52.4 20.5
KL (mm) KL2003Lud 7.66 5.31 5.96 0.39 5.14–7.14 6.5
KL2005Lud 6.70 5.10 5.92 0.30 5.10–6.60 5.1
KL2005Pun 7.61 5.20 6.38 0.34 5.40–7.50 5.3
KL2006Pun 7.53 5.35 6.22 0.38 5.40–7.65 6.1
KL2007Pun 7.52 5.37 6.12 0.33 5.27–7.41 5.4
KW (mm) KW2003Lud 3.64 2.97 2.95 0.32 2.10–3.61 10.8
KW2005Lud 3.30 2.20 2.82 0.34 2.00–3.50 12.1
KW2005Pun 3.36 2.38 3.01 0.29 2.20–3.60 9.6
KW2006Pun 3.19 2.35 2.65 0.29 2.00–3.35 10.9
KW2007Pun 3.20 2.17 2.56 0.22 2.07–3.15 8.6
424 P. Ramya et al.

Table 2. Pearson’s correlation coefficients (r) between somes 1A, 2B, 2D, 5A, 5B, and 5D showed the
1000-kernel weight (TKW), kernel length (KL), and presence of QTLs for KL. Similarly, KW QTLs
kernel width (KW) were observed on chromosomes 1D, 2B, 2D, 4B,
Year, location TKW-KL TKW-KW KL-KW 5B, and 5D. Chromosomes 1A, 2B, 2D, and 5B for
2003, Ludhiana 0.556*** 0.868*** 0.432*** TKW, 2D for KL, and 2D, 4B, and 5B for KW
2005, Ludhiana 0.209** 0.560*** 0.284***
showed marker intervals with QTLs in multiple
2005, Pune 0.538*** 0.701*** 0.458***
environments from both the agro-climatic zones,
2006, Pune 0.648*** 0.771*** 0.437***
2007, Pune 0.493*** 0.405*** 0.334***
while chromosomes 1A, 1D, 2B, 2D, 4B, 5B, and
Average 0.524*** 0.790*** 0.365*** 5D showed QTLs for more than one trait. Notably,
Significance: ** P < 0.01; *** P < 0.001
chromosomes 2B, 2D and 5B were associated with
all the 3 traits, and 5B showed overlapping regions
of TKW, KL, and KW QTLs. Chromosome 1A
showed overlapping QTL regions for TKW and
Table 3. Analysis of variance for 1000-kernel weight KL, while 2D showed coincidence between KL
(TKW), kernel length (KL), and kernel width (KW)
and KW QTLs. Chromosomes 2B, 2D, and 4B
Source of TKW KL KW showed common regions harbouring QTLs for
variation # #
df F df F df F# TKW and KW.
Genotype (G) 184 8.27 184 7.43 184 3.65 MCIM using individual environment data and
Environment (E) 6 60.52 4 123.48 4 118.54 average data across environments indicated 27
G×E 1104 – 736 – 736 – QTLs in total. QTLs for TKW were on chromo-
#
P < 0.0001 somes 1A, 2B, 4B and 5B, for KL on 1A, 2D and
4B, while for KW on 1A, 2B, 2D, 4B, 5B and 5D
(Table 5). Joint-MCIM indicated 64 peaks that in-
ers remained unlinked (Figure 1). The combined cluded the QTLs also detected by MCIM analysis.
map of the linkage groups was 1070 cM long, with When MCIM and joint–MCIM were performed
an average interval of 6.33 cM between markers. using the data from the years in which all the
The marker order in the present map was com- 3 traits were recorded, pleiotropic QTLs were de-
pared with relative marker positions in the maps tected for Ludhiana and Pune in the years 2003
reported by Röder et al. (1998) and Somers et al. and 2005, respectively. In addition, average data
(2004), and the linkage groups were arranged ac- across environments indicated pleiotropic QTLs
cordingly to represent parts of different wheat for TKW and KW on chromosomes 2B and 5B
chromosomes (Figure 1). The linkage groups rep- (Table 6).
resented chromosomes 1A, 1B, 1D, 2B, 2D, 4B,
5A, 5B, 5D, 6B, 7A, and 7B.
All the chromosomes except 1B, 7A, and 7B Discussion
included QTLs for at least one of the 3 kernel
traits. CIM indicated a total of 47 QTL peaks with In crop plants such as wheat, which contain large
LOD scores ³ 2.0 for the 3 traits under study (Ta- and complex genomes, QTL mapping can provide
ble 4, Figure 1). Among these, 14 were significant, initial information regarding the molecular basis
14 had LOD scores between 2.5 and threshold of determination of quality–related traits. In view
LOD and the rest had LOD scores between 2.0 and of this, we performed CIM of kernel characters
2.5. The QTLs for a trait with identical, overlap- and identified QTLs for TKW, KL, and KW on
ping or adjacent marker intervals in a linkage chromosomes 1A, 1D, 2B, 2D, 4B, 5A, 5B, 5D,
group were treated as the same and given a com- and 6B. Earlier studies for QTL analysis of kernel
mon name according to McIntosh et al. (2003). characters have yielded preliminary information
Based on this, 10 detected QTLs for TKW ex- on their genetic basis (Campbell et al. 1999;
plained 4.15–15.53% of phenotypic variation, 6 Dholakia et al. 2003; Ammiraju et al. 2004;
QTLs for KL explained 4.36–10.6%, and 9 QTLs Breseghello and Sorrells 2007). The population
for KW explained 4.42–11.54%. The additive ef- size in those efforts ranged from 78 to 115, and the
fect of individual QTLs indicated that both RS- maximum number of phenotypic trials for a popu-
and CS-derived positive alleles contributed to the lation at a single location was for 2 consecutive
3 traits. A total of 22 QTL peaks were observed at years by Campbell et al. (1999). However, in our
Ludhiana and 19 at Pune. study, we employed a bigger population of 185
TKW QTLs were detected on chromosomes RILs and phenotypic data for 7 (TKW) and 5 (KL
1A, 1D, 2B, 2D, 4B, 5B, and 6B, while chromo- and KW) year-location combinations from 2 dis-
 QTL mapping of wheat kernel traits 425

Figure 1. QTLs detected by composite interval mapping (CIM) for 1000-kernel weight (TKW, continuous line), kernel
length (KL, dashed line), and kernel width (KW, dotted line) with average data of all year-location combinations (#) or
only at Ludhiana (*) or Pune (+).

tinct agro-climatic zones, which yielded informa-
tion on chromosomal regions consistently
associated with wheat quality traits related to ker-
nel size and shape.
For TKW, KL, and KW, we detected some consis-
tent QTLs in multiple environments from both the
agro-climatic zones. Such QTLs may be declared
to have a consistent effect on the respective traits
and can be considered for fine mapping and vali-
dation in different mapping populations and wheat
genotypes before employing in marker-assisted
selection procedures.
For TKW, QTkw.ncl-2B.1 and QTkw.ncl-5B.2
were consistent. Six overlapping peaks for
QTkw.ncl-2B.1 were detected in different environ-
ments in a 40-cM region corresponding to 2BS.
All the 4 Ludhiana environments indicated the
presence of a QTL in this region on 2B along with
TKW2007Pun and average TKW. While Kumar
et al. (2006) reported a QTL on 2BS in the same
426 P. Ramya et al.

Table 4. Characteristics of QTLs for 1000-kernel weight (TKW), kernel length (KL), and kernel width (KW),
detected by composite interval mapping (CIM). Consistent QTLs are highlighted in bold.
Posi- Markers
Closest LOD Additive
Trait Environment Chr. QTL tion R2
marker left right score effect
(cM)
TKW TKW2000Lud 1A QTkw.ncl-1A.1 Xbarc240x 35 Xbarc148 Xgwm357 2.7 1.7823 0.0539
TKW2007Lud 1A QTkw.ncl-1A.1 Xbarc148 27 Xwmc24 Xbarc240x 2.8 1.7422 0.0568
TKW2006Pun 1A QTkw.ncl-1A.1 Xbarc148 25 Xwmc24 Xwmc278 2.0 1.3571 0.0440
TKW2007Pun 1D QTkw.ncl-1D.1 Xcfd59x 42 Xcfd28 Xcfd65 2.0 1.1437 0.0415
TKW2000Lud 2B QTkw.ncl-2B.1 Xbarc13 18 Xbarc55 Xbarc37 4.3 –2.5981 0.1206
TKW2003Lud 2B QTkw.ncl-2B.1 Xbarc183 4 Xbarc183 Xbarc13 2.5 –2.0746 0.0843
TKW2005Lud 2B QTkw.ncl-2B.1 Xbarc55 8 Xbarc183 Xbarc7 5.5 –1.9960 0.1261
TKW2007Lud 2B QTkw.ncl-2B.1 Xbarc55 8 Xbarc183 Xbarc7 7.4 –2.9535 0.1553
TKW2007Pun 2B QTkw.ncl-2B.1 Xbarc55 8 Xbarc183 Xbarc13 2.3 –1.3233 0.0545
TKW average 2B QTkw.ncl-2B.1 Xbarc55 8 Xbarc183 Xbarc7 4.7 –1.7261 0.1097
TKW2005Pun 2D QTkw.ncl-2D.1 Xgwm4562 24 Xgwm102 Xgwm4756 2.9 2.0796 0.0761
TKW average 2D QTkw.ncl-2D.1 Xgwm4562 22 Xgwm102 Xgwm988 2.2 1.2380 0.0588
TKW2003Lud 2D QTkw.ncl-2D.2 Xgwm539 72 Xwmc181 Xwmc41 2.4 –1.6595 0.0539
TKW2005Lud 2D QTkw.ncl-2D.2 Xcfd233 83 Xwmc41 Xgwm349 2.7 –1.2900 0.0537
TKW2005Pun 2D QTkw.ncl-2D.2 Xgwm539 72 Xwmc601 Xwmc41 2.5 –1.7649 0.0520
TKW2005Pun 4B QTkw.ncl-4B.1 Xwmc617 6 Xwmc617 Xwmc710 3.0 2.1983 0.0846
TKW2000Lud 5B QTkw.ncl-5B.1 Xcfd5 14 Xcfd5 Xcfd60 2.8 –2.1394 0.0824
TKW2003Lud 5B QTkw.ncl-5B.2 Xgwm371 58 Xgwm335 Xcfd266 2.0 1.5159 0.0441
TKW2005Lud 5B QTkw.ncl-5B.2 Xgwm371 58 Xgwm335 Xcfd266 2.1 1.1361 0.0429
TKW2007Lud 5B QTkw.ncl-5B.2 Xcfd266 70 Xgwm371 Xgwm499 2.3 1.6155 0.0466
TKW2007Pun 5B QTkw.ncl-5B.2 Xgwm213 48 Xbarc74 Xcfd266 3.2 1.4505 0.0679
TKW average 5B QTkw.ncl-5B.2 Xgwm213 52 Xgwm335 Xcfd266 3.2 1.3815 0.0730
TKW2006Pun 5B QTkw.ncl-5B.3 Xcfd226 70 Xbarc59 Xgwm497 2.0 1.3596 0.0440
TKW2005Pun 6B QTkw.ncl-6B.1 Xbarc178 50 Xgwm889 Xgwm1486 2.7 1.8033 0.0571
KL KL2003Lud 1A QKl.ncl-1A.1 Xwmc469 30 Xwmc24 Xbarc28 3.1 0.1028 0.0656
KL2005Pun 2B QKl.ncl-2B.1 Xwmc317 8 Xwmc317 Xbarc159 2.0 –0.0764 0.0436
KL2003Lud 2D QKl.ncl-2D.1 Xgwm382 110 Xgwm349 Xcfd161 2.3 0.0969 0.0597
KL2005Pun 2D QKl.ncl-2D.1 Xgwm318 104 Xgwm349 Xcfd161 4.6 0.1142 0.1060
KL average 2D QKl.ncl-2D.1 Xgwm382 106 Xgwm349 Xcfd161 2.9 0.0728 0.0633
KL2007Pun 5A QKl.ncl-5A.1 Xcfa2141 0 Xcfa2141 Xcfa2185x 2.5 0.0793 0.0545
KL2005Pun 5B QKl.ncl-5B.1 Xgwm371 58 Xgwm371 Xcfd266 2.8 –0.0974 0.0578
KL2007Pun 5D QKl.ncl-5D.1 Xcfd40 45 Xcfd40 Xbarc143 2.5 –0.0822 0.0555
KW KW2005Lud 1D QKw.ncl-1D.1 Xbarc149 0 Xbarc149 Xgwm458 2.0 –0.0754 0.0442
KW2003Lud 2B QKw.ncl-2B.1 Xbarc183 4 Xbarc183 Xbarc13 3.7 –0.1112 0.1154
KW2005Lud 2B QKw.ncl-2B.2 Xbarc7 27 Xbarc7 Xbarc37 2.0 –0.0813 0.0555
KW2003Lud 2D QKw.ncl-2D.1 Xcfd56 8 Xbarc124 Xwm296 2.2 –0.0870 0.0707
KW2003Lud 2D QKw.ncl-2D.2 Xcfd168 79 Xwmc181 Xwmc41 3.0 –0.0816 0.0597
KW2006Pun 2D QKw.ncl-2D.2 Xgwm539 72 Xwmc181 Xwmc41 2.8 –0.0747 0.0608
KW2005Pun 2D QKw.ncl-2D.3 Xgwm382 102 Xgwm382 Xcfd161 2.3 0.0863 0.0519
KW2003Lud 4B QKw.ncl-4B.1 Xwmc617 12 Xwmc617 Xwmc710 2.2 0.0740 0.0473
KW2005Pun 4B QKw.ncl-4B.1 Xwmc617 10 Xwmc617 Xwmc710 2.5 0.0886 0.0741
KW average 4B QKw.ncl-4B.1 Xwmc617 8 Xwmc617 Xwmc710 2.2 0.0546 0.0656
KW2003Lud 5B QKw.ncl-5B.1 Xgwm371 58 Xgwm335 Xcfd266 3.7 0.0906 0.0741
KW2005Lud 5B QKw.ncl-5B.1 Xgwm213 54 Xgwm335 Xcfd266 2.0 0.0782 0.0480
KW2006Pun 5B QKw.ncl-5B.1 Xbarc74 45 Xgwm67 Xgwm371 2.6 0.0771 0.0666
KW average 5B QKw.ncl-5B.1 Xgwm213 56 Xgwm335 Xcfd266 2.9 0.0540 0.0662
KW2006Pun 5D QKw.ncl-5D.1 Xcfd18 0 Xcfd18 Xgwm1252 2.3 0.0651 0.0486
Chr. = chromosome; R2 = coefficient of determination

population for TKW, it was in a region more distal (2006). Groos et al. (2003), Huang et al. (2006)
on the chromosome arm. The reason for this dif- and Breseghello and Sorrells (2007) also found
ference could be the smaller population size of 100 kernel weight QTLs on 2B by using CIM. Chro-
RILs and AFLP markers used by Kumar et al. mosome 5B indicated QTkw.ncl-5B.2 detected in
 QTL mapping of wheat kernel traits 427

Table 5. Chromosomal regions associated with kernel characters, detected by multi-trait composite interval
mapping (MCIM).
Chromosomal region Environments
Xwmc24-Xpsp3003 (1A) TKW2000Lud, TKW2003Lud and TKW2007Lud; KL2005Pun; KW2003Lud
Xbarc183-Xwmc474 (2B) TKW2000Lud, TKW2003Lud, TKW2005Lud, TKW2007Lud and Average TKW; KW2003Lud,
KW2006Pun and Average KW
Xcfd168-Xcfd161 (2D) KL2003Lud, KL2005Pun and Average KL; KW2005Pun
Xwmc617-Xwmc710 (4B) TKW2005Pun; KL2005Pun; KW2003Lud and KW2005Pun
Xbarc74-Xcfd266 (5B) TKW2003Lud, TKW2007Pun and Average TKW; KW2003Lud and Average KW
Xcfd18-Xgwm1252 (5D) KW2006Pun

Table 6. Pleiotropic QTLs detected by multi-trait
composite interval mapping (MCIM).
Environments Chromosome Marker interval
2B Xbarc183–Xbarc13
TKW2003Lud and
KW2003Lud 2D Xwmc181–Xwmc41
5B Xgwm335–Xcfd266
TKW2005Pun, 4B Xwmc617–Xwmc710
KL2005Pun and
KW2005Pun
Average TKW and 2B Xbarc183–Xwmc474
Average KW 5B Xbarc74–Xcfd266
4 environments, and also for average TKW in a
28-cM region in the proximal long arm region of
5B. In addition, by association mapping,
Breseghello and Sorrells (2006) reported loci con-
trolling kernel weight on chromosome 5B.
For KL, QKl.ncl-2D.1 was detected in a 20-cM
chromosomal region on 2DL in both agro-climatic
zones (KL2003Lud and KL2005Pun) as well as in
the average KL. Campbell et al. (1999) reported an
RFLP marker linked to KL on 2DL, whereas
Breseghello and Sorrells (2006) detected a
KL-associated 2D marker Xgwm539, which is
close to QKl.ncl-2D.1 in our study.
For KW, single consistent QTLs on chromo-
somes 4B and 5B were detected in this study.
Giura and Saulescu (1996) reported the associa-
tion of 4B with KW by monosomic analysis. How-
ever, in the present study, owing to the small
number of markers in the linkage group harbour-
ing QKw.ncl-4B.1, this QTL must be considered
suggestive until the addition of more markers con-
firms its consistency. QKw.ncl-5B.1 was detected
for 3 KW environments as well as for average KW
in a 26-cM region on 5BL close to the centromere.
Single-marker analysis or interval mapping ap-
proaches have so far not reported any KW QTLs
on 5B, but Breseghello and Sorrells (2006) re-
ported KW loci by association mapping on 5B.
The consistent QTLs detected by CIM were also
observed by MCIM analysis, which led to their
added confirmation.
To gauge the approximate location of the con-
sistent QTLs identified for TKW, KL, and KW in
the wheat genome, the closest marker for each
QTL was searched in the wheat physical map
(Sourdille et al. 2004). Based on the deletion bin
positions of the physically mapped SSRs, Xbarc13
and Xbarc55 linked to QTkw.ncl-2B.1 were in the
deletion bin 2BS1-0.53-0.75. Similarly, Xgwm382
associated with QKl.ncl-2D.1 was detected in
2DL9-0.76-1.00, while Xgwm371, the closest
marker for QTkw.ncl-5B.2 and QKw.ncl-5B.1,
was detected in 5BL1-0.55-0.75. However,
Xgwm213 associated with both QTkw.ncl-5B.2
and QKw.ncl-5B.1, and Xbarc74 linked to
QKw.ncl-5B.1 were located in the neighbouring
deletion bin 5BL6-0.29-0.55. More markers need
to be mapped in the region of consistent QTLs to
detect smaller support intervals, while the chro-
mosomal bin positions of the closely linked mark-
ers should be confirmed experimentally, using
deletion lines of wheat, to determine the physical
location of these QTLs.
Some differential and overlapping QTLs for
kernel characters were also detected in this study.
TKW, KL, and KW indicated high heritability,
which was consistent with earlier reports on TKW
(Campbell et al. 1999; Huang et al. 2006; Kumar
et al. 2006; Wang et al. 2009), KL and KW (Camp-
bell et al. 1999). Rank correlation between the
pairs of environments (data not shown) for each
trait was positive and significant except between
KW2003Lud and KW2007Pun (ñ = 0.076). In
view of these observations, the detection of con-
sistent QTLs was not unexpected. However,
ANOVA indicated significant environmental ef-
fects on the traits, thereby suggesting the presence
of differential loci with minor effects that might be
detected in individual environments. In the present
study, 5 QTLs for TKW and KL each and 6 QTLs
for KW were detected in single environments,
428 P. Ramya et al.
while QTkw.ncl-2D.1 and QKw.ncl-2D.2 were de-
tected in 2 environments each, and QTkw.ncl-1A.1
and QTkw.ncl-2D.2 were detected in 3 environ-
ments each. A 19-cM region on 1A in the
short-arm centromere region between markers
Xwmc24 and Xgwm357 harboured peaks for
TKW2000Lud, TKW2007Lud, and TKW200
6Pun. This region was also reported to be associ-
ated with a QTL for TKW by Kumar et al. (2006)
in the same population, with field trials conducted
in wheat-growing regions in North India. In an
earlier study, Campbell et al. (1999) reported a
QTL on 1A as controlling kernel weight by using
RFLP markers by single-marker analysis. Hence
the QTLs mentioned in those studies may in fact
be the same as QTkw.ncl-1A.1. Since the chromo-
somal region on 1A harbouring QTkw.ncl-1A.1
was also detected for multiple TKW environments
by MCIM, it could be considered as an important
QTL for TKW in addition to QTkw.ncl-2B.1 and
QTkw.ncl-5B.2.
Positive and significant correlations were ob-
served among TKW, KL and KW, which sug-
gested that selection for heavier kernels might lead
to indirect selection for larger seeds. In earlier
studies, Dholakia et al. (2003) and Breseghello
and Sorrels (2007) reported positive correlations
among kernel weight, KL, and KW. Those studies
also reported individual markers associated with
multiple correlated kernel size and shape traits.
Similarly, in this study, CIM indicated QTLs for
different correlated traits with partial or complete
overlap in the associated marker intervals. In addi-
tion to this, both MCIM and joint MCIM detected
QTLs for TKW2003Lud and KW2003Lud on
chromosomes 2B, 2D, and 5B, and for all the
3 traits for Pune in 2005 on 4B. This suggested the
presence of underlying pleiotropic loci. Similarly,
when average TKW, KL, and KW values across
environments were used for the same analysis,
TKW and KW showed common QTL regions on
chromosomes 2B and 5B. Fine mapping of such
common or overlapping QTL regions is needed to
ascertain whether these regions harbour distinct
QTLs with pleiotropic effects or closely linked
QTLs governing individual traits.
Conclusions
In view of the QTL analysis for kernel characters
providing a base for their marker-assisted selec-
tion during breeding for wheat quality, our study
provides information on significant and consistent
QTLs detected in diverse agro-climatic regions. A
well-saturated framework linkage map with a
wider coverage of the genome might reveal addi-
tional QTLs for TKW, KL, and KW. Neverthe-
less, the genomic regions identified in the current
study can be targeted for further studies in genetic
dissection of wheat kernel quality traits, and their
validation might yield informative markers for
marker-assisted selection during breeding for
wheat quality.
Acknowledgements. We thank the Department of
Biotechnology, India, for financial assistance for the
project. The field trials at Pune were conducted at the
Agharkar Research Institute (ARI), Pune, so we are
grateful to Dr. V. S. Rao, former Director, ARI, for
the facility provided and help extended. We also
thank the Leibniz Institute of Plant Genetics and
Crop Plant Research as well as TraitGenetics, Ger-
many, for 21 gwm primers, and Prof. MD Gale for
psp primers. Ms. Richa Rai and Ms. Preeti Moudgal
provided help in phenotypic evaluations, Dr.
Bhushan Dholakia in fieldwork, and Mr. Manje
Gowda in data analysis. PR acknowledges the Coun-
cil of Scientific and Industrial Research, India, for
the Junior Research Fellowship.
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