QTL Mapping for chinese northern-style steamed bread specific volume

doi:10.4236/as.2011.23028

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Vol.2, No.3, 201-207 (2011)

doi:10.4236/as.2011.23028

Agricultural Scienc es

QTL mapping for Chinese northern-style steamed bread

specific volume

Peng Wu*1,2, Bin Liu*1, Tao Zhou*3, Zhuokun Li1,Haiyun Du4, Jiteng Wang5, Jichun Tian1,6

1Group of Quality Wheat Breeding of State Key Laboratory of Crop Biology of Shandong Agricultural University, Tai’an, China;

2College of Food Science and Engineering, Shandong Agricultural University, Tai’an, China;

Corresponding Aut hor: [email protected]

3College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, China;

4Tai’an Bureau of Quality and Technical Supervision, Tai’an, China;

5Rongcheng Entry-Exit Inspection and Quarantine Bureau，Rongcheng, China;

6Agronomy Department, Shandong Agricultural University, Tai’an, China;

Corresponding Aut h o r : [email protected], [email protected]

Received 25 April 2011; revised 26 June 2011; accepted 7 July 2011.

ABSTRACT

In this study, quantitative trait loci (QTLs) with

additive effects, epistatic effects for CNSB spe-

cific volume in bread wheat (Triticum aestivum

L.), were studied in cultivars Huapei 3 and Yu-

mai 57 (Triticum aestivum L.). The DH popula-

tion and the parents were planted in 2007 and

2008 in Tai’an and 2008 in Suzhou. QTL analy-

ses were performed using the software of Ici-

Mapping v2.2 based on the mixed linear model.

Five putative QTLs for CNSB specific volume

were detected on 5 chromosomes where single

QTLs explained 5.11% to 9.75% of phenotypic

variations. All of them had negative effects on

specific volume and were contributed by Yumai

57 alleles. Qsv-1B was detected in both envi-

ronment 1 and 3 with 13.88% and 4.83% pheno-

typic variations which had positive effects and

was transmitted by Huapei 3 alleles. Fourteen

pairs of QTLs with epistatic effects were de-

tected for specific volume. Seven major QTLs,

Qsv-1B/Qsv-3A, Qsv-2D/Qsv-3A, Qsv-3A/Qsv-

5B1, Qsv-1B/Qsv-6D, Qsv-2D/Qsv-4D, Qsv-4A/

Qsv-6B and Qsv-3A/Qsv-7D could account for

13.88%、20.39%、18.88%、12.31%、18.78%、11.98%,

and 17.05% of the phenotypic variation of spe-

cific volume. The information obtained in this

study will be useful for manipulating the QTLs

for CNSB specific volume proper ty by molecular

marker-assisted selecti on (MAS).

Keywords: Wheat; Doubled Haploid; Quantitative

Trait Loci; CNSB; Specific Volume

1. INTRODUCTION

Chinese steamed bread (CSB) is a staple food of the

Chinese people, especially in northern China, where it is

eaten at every meal. It has been consumed for at least

2,000 years in China, and has also been gaining in

popularity in Korea, Japan, and some Southeast Asian

countries in recent years as food culture intercommuni-

cations have rapidly developed among different coun-

tries. There are two types of steamed bread in China:

northern-style (CNSB) and southern-style (CSSB), with

differences in the ingredients and quality evaluation.

Most research has focused on CNSB, since it is by far

the most widely produced, and about 40% of Chinese

wheat consumption is used to make CNSB, particularly

in northern China [1].

CNSB quality is defined by its specific volume, ex-

ternal appearance, internal characteristics, and color.

Specific volume is an important factor in CNSB’s score,

which is the ratio of volume to weight. The greater the

value, the better leavened is the CNSB. It has significant

correlations with color, another important factor in

CNSB’s scores [2]. However, few QTL analyses have

yet been reported for those steamed bread’s specific

volume.

Huapei 3 is hard wheat with a higher grain protein

content and wet gluten content. Yumai 57 is soft wheat

with higher gluten index and sodium dodecyl sulfate

(SDS) sedimentation volume and is more productive

under different ecological conditions [3]. The parents

both have white seed coats. Wheat processing and end-

use characteristics, collectively known as quality traits,

are controlled by both genetics and environment. Mo-

lecular-genetic studies to elucidate this control may in-

crease the efficiency of breeding wheat for improved

quality [4]. Quantitative trait loci (QTLs) analyses of

*Peng Wu and Bin Liu, Tao Zhou contributed equally to this work.

P. Wu et al. / Agricultural Science 2 (2011) 201-207

202

quality traits have been reported using a set of 168 dou-

bled haploid (DH) lines derived from a cross of Huapei 3

× Yu mai 57.

The objectives of the study described here was to de-

tect QTLs with additive effects, epistatic effects, and

QEs for the specific volume of CNSB, which should be

useful in manipulating the QTLs for steamed-bread spe-

cific volume by the molecular marker-assisted selection

in wheat breeding programs.

2. MATERIALS AND METHODS

2.1. Plant Materials and Growth Conditions

A population of 168 DH lines, derived from a cross

between two Chinese wheat cultivars Huapei 3 (Hp3)

and Yumai 57 (Ym57), was used for the construction of

a linkage map. The DH population and parents were

kindly provided by Professor Yan Hai, Henan Academy

of Agricultural Sciences, Zhengzhou, China. Hp3 and

Ym57 were released by Henan Province in 2006 [5] and

by the State (China) in 2003 [6], respectively. The two

parents are cultivated over a large area in the Huang-

Huai Wheat Region in China, differing in several agronomi-

cally important traits as well as in baking quality traits.

The 168 DH lines and parents were planted in two

replications at each location with a completely random-

ized block design at three environments in 2007 and

2008 in Ta i’an (36.18 ˚N, 117.13˚E), Shandong Province;

in 2007 in Suzhou (31.32 ˚N, 120.62˚E), Anhui Province.

In Tai’an, there were remarkable differences in tempera-

ture and soil conditions between the years 2007 and

2008.

In autumn 2007, all lines and parental lines were

grown in 2 m long by three-row plots (25 cm apart); in

autumn 2008, the lines were grown in 2 m long by

four-row plots (25 cm apart). The soil was brown earth,

in which the av ailable N, P, and K contents in the top 20

cm were 40.2 mg/kg, 51.3 mg/kg and 70.8 mg/kg. Be-

fore planting, 27,500 kg/hectare (ha) of farmyard ma-

nure or barnyard manure (nitrogen content, 0.05% -

0.1%), 225 kg/ha of urea, 300 kg/ha of phosphorus dia-

mine fertilizer, 225 kg/ha of potassium chloride, and 15

kg/ha of zinc sulphate were added as fertilizers. In

Tai’An, the rainfalls during the growth cycles were 165

mm and 172.5 mm in 2007-2008 and 2008-2009, re-

spectively. In Suzhou, the rainfalls during the growth

cycle totaled 207.5 mm in 2008-2009.

All of crop management followed local practices.

Plots were irrigated in winter (December 1, 2007), and at

jointing (April 3, 2008), anthesis (May 7, 2008), and

grain filling (May 20, 2008). They were top-dressed with

225 kg/hectare and 75 kg/hectare urea at the jointing

(April 3, 2008) and anthesis stages (May 7, 2008) with

irrigation, respectively. The lines were harvested indi-

vidually at maturity to prevent yield loss from over-rip-

ening. Harvested grain samples from the two replicates

at each environment were mixed and cleaned prior to

conditioning. One thousand grams of grain samples from

each line at each environment were milled on a Buhler

experimental mill (model-MLU 300 m/s Buhler, Uzwil

Switzerland). Prior to milling, the hard, medium hard

(mixtures of hard and soft wheat) and soft wheats were

tempered to around 16%, 15%, and 14% moisture con-

tents for 24 hours, respectively.

2.2. Steamed Bread Preparation

CNSB was prepared according to the Chinese stan-

dard SB/T10139-93 App endix A [7]. Th e milled sample,

100 g of flour, was mixed with the yeast solution (1g dry

yeast dispersed in 48 ml 38˚C water). Dough was fer-

mented for 60 min in a fermentation cabinet (38˚C, 85%

rh) after 3 min mixing. The fermented dough was di-

vided into two pieces and each shaped by hand for 3 min

into a round dough piece with a smooth surface. Then

the breads were steamed for 20 min in a steam chamber

(>100˚C) after resting in the air for 15 min. Then the

steamed breads were cooled in the air for 40 min.

2.3. Specific Volume Measurements of

CNSB Samples

Steamed bread was placed in a covered bamboo con-

tainer at room temperature immediately after steaming.

Then the steamed breads were cooled in the air for 40

min. Samples were measured using an electric balance

for weight and a substitution method with rapeseed for

volume. All scores were taken three times per sample.

The mean values of CNSB specific volume in each en-

vironment were used for statistical analyses.

All determinations were made at least three times, and

were expressed on a 14% - 16% moisture basis.

2.4. DNA Marker Assay and Construction of

the Genetic Map

A genetic linkage map of DH population with 323

markers, including 284 SSR loci, 37 EST loci, 1 inter-

simple sequence repeat (ISSR) locus, and 1 HMW-GS

locus was constructed. This linkage map covered a total

length of 2,485.7 cm with an average distance of 7.67

cm between adjacent markers. Thirteen markers re-

mained unlinked. These linked markers formed 24 link-

age groups at LOD 4.0. The genomic locations of

marker loci/linkage groups were determined based on

the wheat consensus map. Thirty loci (7.03%) were

mapped on different chromosomal locations compared

with the map published by Somers et al. [8]. The rec-

ommended map distance for genome wide QTL scan-

ning was an interval length less than 10 cm [9]. In this

P. Wu et al. / Agricultural Science 2 (2011) 201-207

203203

study, the interval length was 7.67 cm, so the map was

deemed suitable for genome-wide QTL scanning.

The genetic map was constructed with MAPMAKER/

Exp version 3.0b [10]. First, the ‘group’ command was

used to divide the markers in the sequence into linkage

groups at a LOD of 4.0. Then, the ‘compare’ command

was used to compute the maximum likelihood map for

each specified order of markers, and to report the orders

sorted by the likelihoods of their maps. The ‘try’ and

‘ripple’ commands were used to add markers to frame-

work maps and to check the final marker order. Unlinked

groups were oriented and placed for the same chromo-

some based on the microsatellite consen sus map [8]. Th e

Kosambi mapping function [11] was used to convert

recombination fractions into cm as map distances. The

linkage map was finally drawn using the software Map-

chart, versi on 2.1 [12].

2.5. Statistical Analysis

Analysis of variance (ANOVA) was carried out using

the SPSS version 13.0 (SPSS, Chicago, USA) program.

QTLs with additive effects and epistatic effects as well

as QEs in the DH population were mapped by the soft-

ware QTLNetwork, version 2.0 [13], based on the mixed

linear model [14]. Composite interval analysis was un-

dertaken using forward-backward stepwise, multiple

linear regression with a probability into and out of the

model of 0.05 and window size set at 10 cm. Significant

thresholds for QTL detection were calculated for each

data set using 1000 permutations and a genome-wide

error rate of 0.10 (suggestive) and 0.05 (significant). The

final genetic model incorporated significant additive

effects and epistatic effects as well as their environ-

mental interactions.

Each QTL was named for steamed bread’s specific

volume by the first two letters with the relevant chro-

mosomal number such as “Qsv”. If there were more than

one QTL on a chromosome, the serial number was added

after the chromosomal number, separated by a hyphen.

The positions of these QTLs were indicated by the

marker interval bracketing the concerned QTL with the

estimated distance (cm) from the left marker.

3. RESULTS AND DIS CUSSION

3.1. Statistical Analysis of the Phenotypic

Assessments

The DH population had a wide range and considerable

variation for CNSB specific volume traits. Mean values

for CNSB specific volume traits for the DH population

and the parents in three environments are shown in Ta-

ble 1. The mean of CNSB specific volume was between

that of Hp3 and Ym57, which expressed the existence of

the large transgressive segregation, whereas the phenol-

typic variations among the DH lines were obvious.

Transgressive segregants were observed in all the envi-

ronments, with some lines higher or lower than the par-

ents. The specific volume traits among the DH popula-

tion segregated continuously, and followed a normal

distribution (Figure 1), and both absolute values of

skewness and kurtosis were less than 1.0 (Ta b le 1 ), in-

dicating its polygenic inheritance and suitability of the

data for QTL analysis [15].

Mean, SE, Max, Min, SD, Skew, and Kurt are the av-

erage, standard error, maximum, minimum, standard

deviation, skewness, and kurtosis of all observations for

the DH population in the three environments.

3.2. QTL Analyses

Five additive QTLs and fourteen pairs of epistatic ef-

fects were identified for specific volume of CNSB in

three years (Tables 2 and 3) by using the software of

QTLNet-work version 2.0 [13] and IciMapping v2.2

[16], based on the mixed linear model.

Seven QTLs (Qsv-1B/Qsv-3A Xbarc119-Xgwm18/

Xbarc321-Xswes107, Qsv-2D/Qsv-3A Xcfd53-Xwmc18/

Xbarc321-Xswes107, Qsv-3A/Qsv-5B1 Xwmc264-

Xcfa2193/Xgwm213-Xswes861.2, Qsv-1B/Qsv-6D

Xbarc061-Xwmc766/Xswes679.1-Xcfa2129, Qsv-2D/

Table 1. Phenotypic performance of wheat CNSB specific

volume in three environm e n t s .

Parents DH population

huapei3yumai57Mean Max. Min. SDSkew.Kurt.

specific volume1.892.091.98 2.28 1.66 0.110.20.06

Table 2. Estimated additive (A) of QTLs for steamed bread specific volume in the three environments.

Trait Chrom Site (cM) LeftMarker RightMarkerAdditive effectsLOD Contributions (%)

specific volume 1 Qsv-6A 68 Xwmc553 Xgwm732 –0.06 2.31 9.37

specific volume 2 Qsv-7B2 13 Xwmc273.1 Xcfd22.1 –0.06 3.12 7.38

specific volume 2 Qsv-7D 75 Xbarc352 Xgwm295 –0.05 2.461 6.84

specific volume 3 Qsv-1A 54 Xcfd59 Xwmc402.2–0.04 2.191 5.11

specific volume 3 Qsv-3D 94 Xbarc071 Xgwm114 –0.06 3.711 9.75

1 2007 Tai’An, 2 2008 Tai’An, 3 2007 Suzhou.

P. Wu et al. / Agricultural Science 2 (2011) 201-207

204

Figure 1. Frequency distribution of steamed bread specific volume related traits

in 168 doubled haploid lines derived from the cross of Huapei 3 × Yumai 57

evaluated at 3 environments.

Table 3. Estimated epistasis (AA) of QTLs for steamed bread specific volume in the three environments.

QTL Site (cm)QTLSite(cm)Epistatic effects Contributions

Trait 1 1 (cm)Flanking marker 2 2 (cm)Flanking marker LOD (%)

specific volume 1 Qsv-1B 34 Xbarc119-Xgwm18Qsv-3A26 Xbarc321-Xswes1070.07 3.13 13.88

specific volume 1 Qsv-2D 26 Xcfd53-Xwmc18 Qsv-3A16 Xbarc321-Xswes1070.08 4.08 20.39

specific volume 1 Qsv-3A 140 Xwmc264-Xcfa2193Qsv-5B142 Xgwm213-Xswes861.2–0.08 3.58 18.88

specific volume 1 Qsv-6D 0 Xwmc412.1-Xcfd49Qsv-7A86 Xwmc530-Xcfa21230.05 3.39 8.58

specific volume 2 Qsv-1A 48 Xwmc550-Xbarc269Qsv-3A174 Xcfa2170-Xbarc51 0.06 3.41 7.83

specific volume 2 Qsv-1B 76 Xbarc061-Xwmc766Qsv-6D144 Xswes679.1-Xcfa21290.08 3.14 12.31

specific volume 2 Qsv-2D 130 Xbarc129.2-Xcfd50Qsv-4D28 Xwmc331-Xgwm1940.1 3.15 18.78

specific volume 2 Qsv-4A 2 Xwmc718-Xwmc262Qsv-6B26 Xbarc247-Xbarc1129–0.09 3.03 11.98

specific volume 2 Qsv-6A 84 Xcfe179.2-Xcfe179.1Qsv-6B8 Xcfa2187-Xgwm219–0.07 3.84 8.54

specific volume 3 Qsv-1A 86 Xgwm498-Xcwem6.2Qsv-5A30 Xswes45-Xbarc180 –0.05 7.48 7.37

specific volume 3 Qsv-1B 38 Xcwem9-Xbarc120.3Qsv-6D108 Xgwm133.2-Xswes861.10.07 3.42 4.83

specific volume 3 Qsv-3A 0 Xbarc310-Xbarc321Qsv-7D78 Xbarc352-Xgwm295–0.08 15.89 17.05

specific volume 3 Qsv-3D 0 Xcfd34-Xbarc376Qsv-7A90 Xwmc530-Xcfa2123–0.04 5.18 5.14

specific volume 3 Qsv-5B2 2 Xbarc36-Xbarc140Qsv-7A22 Xgwm60-Xbarc070 –0.05 7.56 9.39

1 2007 Tai’An, 2 2008 Tai’An, 3 2007 Su zhou

Qsv-4D Xbarc129.2-Xcfd50/Xwmc331-Xgwm, Qsv-4A/

Qsv-6B Xwmc718-Xwmc262/Xbarc247-Xbarc1129 and

Qsv-3A/Qsv-7D Xbarc310-Xbarc321/Xbarc352-Xgwm295)

explained the phenotypic variance respectively for

13.88%, 20.39%, 18.88%, 12.31%, 18.78%, 11.98%, and

17.05% (Table 3). All of them were major QTLs and

could be used in the molecular marker-assisted selection

(MAS) in wheat breeding programs.

The QTL Qsv-1B was detected both in environment-1

and environment-3, which explained the phenotypic

variance of 13.88% and 4.83%.

Five additive QTLs were detected for specific volume

on five chromosomes 6A, 7B2, 7D, 1A and 3D (Figure

2). They explained phenotypic variance from 5. 11% to

9.75%. All of the five QTLs had negative effects on spe-

cific volume and were contributed by Yumai 57 alleles

that have the higher specific volume. The total additive

QTL detected for specific volume accounted for

38.454% of the phenotypic variance.

Fourteen pairs of epistatic effects were identified for

specific volume and located on chromosomes 1B-3A,

2D-3A, 3A -5B1, 6D-7A, 1A-3A, 1 B-6D, 2D -4D, 4A- 6B,

6A-6B, 1A-5A, 1B-6D, 3A-7D, 3D-7A and 5B2-7A

(Figure 3). They explained the phenotypic variance

ranging from 4.83% to 20.39%. Qsa1B/ Qsa3D-2 and

Qsa2A/Qsa3A had negative effects of –0.1525 and

–0.1516. The general contribution of three pairs of

epistatic QTLs was 164.95%.

QTLs for the specific volume of wheat products have

een reported briefly by some authors. The study of b

P. Wu et al. / Agricultural Science 2 (2011) 201-207

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Figure 2. Positions of additive QTLs conferring steamed bread specific volume in 168 doubled

haploid lines derived from the cross of Huapei 3 × Yumai 57 evaluated in the three environ-

ments.

QTLs for the volume of bread of the RIL population

derived from two India wheat cultivars “HI 977” and

“HD 2329” as parents, shows that the most influenced

QTLs are located on chromosomes 6B and 6D, while

other QTLs are located on chromosomes 1B, 1D, 2A, 3A,

5B, and 5D [17]. This was similar to our conclusions.

As far as the specific volume of steamed bread in

China, only Fan’s study has been reported, which de-

tected the QTLs for the specific volume on 6B

Xgwm193-Xgwm608b [18]. That was not consistent

with our results. A number of factors contributed to the

difference as follows, different population and experi-

mental conditions, different QTL analyses methods, and

no allele variation for corresponding traits in parents.

The five QTLs with additive effects for the specific

volume of CNSB had negative effects and were contrib-

uted by Yu mai 5 7 alleles in our study.

No additive effects were detected in most of the QTLs

(86%) for the specific volume of CNSB with epistatic

effects. Two QTLs (Qsv-1A-Qsv-5A with 7.37% contri-

butions and Qsv-3A-Qsv-7D with 17.05% contriburions)

were involved in additive effects in the detected 14 pairs

of epistatic QTLs. This indicates that several loci in-

volved in epistatic interactions may not have significant

effects for CNSB specific volume alone, and may affect

the trait expression by epistatic interactions. These re-

sults suggest that some of the additive QTLs may be

detected with effects confounded by epistatic effects, if

the epistatic effects were ignored in QTL mapping.

Qsv-1B was detected for CNSB specific volume in

our study in environment-1 and environment-3 account-

ing for 13.88% and 4.83% of the phenotypic variations

which had positive effects and were contributed by

Huapei 3 alleles. Thus, breeders must take into account

such complexity and examine the effects of individual

loci in the targeted genetic background, in order to ob-

tain the expected phenotypes of the genes of interest [19].

The present investigation might be the first report of

epistatic QTLs associated with CNSB specific volume

using molecular markers. The results indicate that epis-

tasis was an important genetic basis for CNSB specific

volume variations.

4. CONCLUSIONS

In summary, a total of five putative QTLs and four-

teen pairs of QTLs with epistatic effects were detected

for specific volume in 168 DH lines derived from a cross

Huapei 3 × Yumai 57. Five putative QTLs for CNSB

specific volume were detected on 5 chromosomes, where

single QTLs explained 5.11% to 9.75% of phenotypic

variations. All of them had negative effects on specific

volume and were contributed by Yumai 57 alleles.

Qsv-1B was detected in both environment 1 and 3 with

13.88% and 4.83% phenotypic variations, which had

positive effects and was transmitted by Huapei 3 alleles.

Fourteen pairs of QTLs with epistatic effects were de-

tected for specific volume. Seven major QTLs, Qsv-1B/

Qsv-3A, Qsv-2D/Qsv-3A, Qsv-3A/Qsv-5B1, Qsv-1B/

Qsv-6D, Qsv-2 D/Qsv-4D, Qsv-4A/Qsv-6B an d Qsv-3A/

Qsv-7D could account for 13.88%, 20.39%, 18.88%,

P. Wu et al. / Agricultural Science 2 (2011) 201-207

206

Figure 3. Positions of estimated epistasis QTLs conferring steamed bread specific volume in 168

doubled haploid lines derived from the cross of Huapei 3 × Yumai 57 evaluated in the three envi-

ronments.

P. Wu et al. / Agricultural Science 2 (2011) 201-207

207207

12.31%, 18.78%, 11.98% and 17.05% of the phenotypic

variation of specific volume. The information obtained

in this study will be useful for manipulating the QTLs

for CNSB specific volume property by molecular

marker-assisted selection (MAS).

5. ACKNOWLEDGEMENTS

The authors thank gratefully Dr. C.E.（Chuck）Walker (Kansas State

University) for his editorial suggestions and careful reading of the

manuscript. The DH population and parents were kindly provided by

Professor Yan Hai, Henan Academy of Agricultural Sciences, Zheng-

zhou, China. Fin ancial support was provided by the 973 program of

the National Nature Science Foundation of China (2009CB118301),

and the National Natural Science Foundation of China (No. 30971764)

from the Ministry of Science and Technology of the People’s Republic

of China.

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