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Detection-of-QTLs-with-Additive-Effects

Agricultural Sciences in China 2009, 8(9): 1039-1045

Detection of QTLs with Additive Effects, Epistatic Effects, and QTL ×Environment Interactions for Zeleny Sedimentation Value Using a Doubled Haploid Population in Cultivated Wheat

ZHAO Liang, LIU Bin, ZHANG Kun-pu, TIAN Ji-chun and DENG Zhi-ying

State Key Laboratory of Crop Biology, Group of Quality Wheat Breeding, Shandong Agricultural University, Tai’an 271018, P.R.China

Abstract

In order to understand the genetic basis for Zeleny sedimentation value (ZSV) of wheat, a doubled haploid (DH) population Huapei 3×Yumai 57 (Yumai 57 is superior to Huapei 3 for ZSV), and a linkage map consisting of 323 marker loci were used to search QTLs for ZSV. This program was based on mixed linear models and allowed simultaneous mapping of additive effect QTLs, epistatic QTLs, and QTL×environment interactions (QEs). The DH population and the parents were evaluated for ZSV in three field trials. Mapping analysis produced a total of 8 QTLs and 2 QEs for ZSV with a single QTL explaining 0.64-14.39% of phenotypic variations. Four additive QTLs, 4 pairs of epistatic QTLs, and two QEs collectively explained 46.11% of the phenotypic variation (PVE). This study provided a precise location of ZSV gene within the Xwmc 93 and GluD1 interval, which was designated as Qzsv-1D. The information obtained in this study should be useful for manipulating the QTLs for ZSV by marker assisted selection (MAS) in wheat breeding programs.

Key words: doubled haploid population, Zeleny sedimentation value, quantitative trait loci (QTLs), wheat (Triticum aestivum L.)

INTRODUCTION

The Zeleny sedimentation value (ZSV) has been proven

to be useful in wheat breeding programs for the esti-

mation of wheat eating and cooking quality (Mesdag

1964; Kne et al. 1993; Liu et al. 2003; He et al.

2004; Zhang et al. 2005; ?zberk et al. 2006; Ozturk

et al. 2008). There is a positive correlation between

sedimentation volume and gluten strength or loaf volume.

The ZSV method is often used as a screening test in

wheat breeding. Mesdag (1964) showed that the value

of ZSV is a measure for the quantity and quality of the

gluten. Because the baking value of wheat flour is largely

determined by these components, the ZSV is also con-

sidered as a useful predictor for the baking value. Liu

Received 3 December, 2008 Accepted 9 April, 2009

Correspondence TIAN Ji-chun, Professor, Tel/Fax: +86-538-8242040, E-mail: jctian9666@https://www.wendangku.net/doc/111941458.html,

et al. (2003) detected that the associations between

ZSV and DWCN’s (dry white Chinese noodle) appear-

ance and taste also fit quadratic regression model

significantly. The gluten quality-related parameter of

sedimentation value was significantly associated with

pan bread quality score (He et al. 2004). ?zberk et al.

(2006) found that the only quality analyses showing

significant correlations with market price were Zeleny

sedimentation value and hectolitre weights (kg hL-1).

Ozturk et al. (2008) reported that the cookie diameter

gave highly significant correlations with ZSV.

The advent and utilization of molecular markers has

provided powerful tools for elucidating the genetic ba-

sis of quantitatively inherited traits. However, only a

few studies have reported genetic loci that influence

ZSV in wheat (Rousset et al. 2001; Kunert et al. 2007;

1040ZHAO Liang et al.

Sun et al. 2008). Rousset et al. (2001) reported that one strong QTL for ZSV was mapped on the long arm of chromosome 1A around Glu-A1. A distally located QTL for ZSV was mapped on chromosome arm 1BS, centered on the Gli-B1/Glu-B3 region. And a major QTL for ZSV, clearly corresponding to the Glu-D1 locus, was detected on chromosome arm 1DL. Kunert et al. (2007) found four putative QTLs for ZSV. Sun et al. (2008) identified three QTLs for ZSV in a F14 RIL derived from the cross between Chuan 35050 and Shannong 483.

Additive effect QTLs were first identified and epi-static interactions among these additive effect QTLs were then estimated (Zanetti et al. 2001). However, this approach usually leaves out many QTLs that may have no additive effects but influence the trait only through epistatic interactions or QTL×environment in-teractions (QEs) (Ma et al. 2005, 2007; Rebetzke et al. 2007). Additive effect QTLs, epistatic QTLs, and QEs were detected using two-locus analyses in both the populations (Kulwal et al. 2005). Sometimes QTLs involved in such interactions contribute substantially to the total variation of a quantitative trait, and therefore should not be ignored. Further experimentation is needed to clarify whether the traits are also affected by epistatic and environment, and to dissect the genotype ×environment interaction effects at the molecular level. In this study, QTLs for ZSV were investigated based on the mixed linear model in a DH population across environments. The objective of this study was to com-prehensively characterize the genetic basis for ZSV of wheat in order to facilitate the future breeding of high-quality wheat varieties.

MATERIALS AND METHODS

Materials

A population of 168 DH lines was produced from the cross between two Chinese wheat cultivars Huapei 3 (Hp3)/Yumai 57 (Ym57) and was used for the con-struction of a linkage map. The DH population and parents were kindly provided by Professor Yanhai, Henan Academy of Agricultural Sciences, Zhengzhou, China. Hp3 and Ym57 were registered by Henan Prov-ince of China in 2006 (Hai and Kang 2007) and by the state (China) in 2003 (Guo et al. 2004), respectively. The parents, planted over a large area in the Huang-Huai wheat region in China, differ in several agronomi-cally important traits as well as baking quality traits (Guo et al. 2004; Hai and Kang 2007).

The field trials were conducted in three environments, at Tai’an (36.18°N, 117.13°E), Shandong Province, China, in 2005 and 2006, and at Suzhou (31.32°N, 120.62°E), Anhui Province, China, in 2006. The ex-perimental design followed a completely randomized block design with two replications at each location. In autumn 2005, all lines and parental lines were grown in 2 m long by three-row plots (25 cm apart); in autumn 2006, the lines were grown in 2 m long by four-row plots (25 cm apart). Suzhou and Tai’an differ in cli-mate and soil conditions. In Tai’an, there were differ-ences in temperature and soil conditions between the years 2005 and 2006. During the growing season, man-agement was in accordance with the local practice. The lines were harvested individually at maturity to prevent yield loss from over-ripening. Harvested grain samples were cleaned prior to conditioning and flour milling was performed in a mill (Quadrumat Senior, Brabender, Germany) to flour extraction rates of around 70%. Prior to milling, the hard, medium hard (mixtures of hard and soft wheat) and soft wheats were tempered to around 14, 15, and 16% moisture contents, respectively.

Measurements of ZSV

Zeleny sedimentation volume was determined using AACC method 56-61A.

Construction of the genetic linkage map

A genetic linkage map of DH population with 323 markers, including 284 SSR, 37 ESTs loci, 1 ISSR loci and 1 HMW-GS loci, was constructed. This linkage map covered a total length of 2485.7 cM with an aver-age distance of 7.67 cM between adjacent markers. Thirteen markers remained unlinked. These markers formed 24 linkage groups at LOD 4.0. The chromo-somal locations and the orders of the markers in the map were in accordance with the one reported for Triti-cum aestivum L. (Somers et al. 2004). The recom-mended map distance for genome wide QTL scanning

Detection of QTLs with Additive Effects, Epistatic Effects, and QTL×Environment Interactions for Zeleny Sedimentation1041 was an interval length less than 10 cM (Doerge 2002).

Thus the map was suitable for genome-wide QTL scan-

ning in this study.

Statistical analysis

Analysis of variance (ANOVA) was carried out using

SPSS ver. 13.0 (SPSS, Chicago, USA). QTLs with

additive effects and epistatic effects as well as QEs in

the DH population were mapped by the software

QTLNetwork ver. 2.0 (Yang and Zhu 2005) based on a

mixed linear model (Wang et al. 1999). Composite in-

terval analysis was undertaken 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 permuta-

tions and a genome-wide error rate of 0.10 (suggestive)

and 0.05 (significant). The final genetic model incor-

porated significant additive effects and epistatic effects

as well as their environmental interactions.

RESULTS

Phenotypic variation for DH lines and parents

As is shown in Fig.1, ZSV of Ym57 showed higher

values than ZSV of Hp3; the means of the ZSV fell

between the two parent’s values. It expressed the ex-

istence of the large transgressive segregation. ZSV seg-

regated continuously and approximately fit normal dis-

tributions with absolute values of both skewness and

kurtosis less than 1.0, indicating that this trait was suit-

able for QTL mapping.

QTLs with additive effects and additive×

environment (AE) interactions

Four QTLs with significant additive effects were iden-

tified on chromosomes 1B, 1D, 5A, and 5D (Table 1

and Fig.2). These QTLs explained from 2.66 to

14.39% of the phenotypic variance. The Qzsv-1B had the most significant effect, accounting for 14.39% of the phenotypic variance. The Ym57 alleles at three loci, Qzsv-1B,Qzsv-1D, and Qzsv-5D, increased Fig. 1 Frequency distributions of ZSV in 168 DH lines derived from a cross of Hp3×Ym57 evaluated at three environments in the 2005 and 2006 cropping seasons. The means of trait values for the DH lines and both parents are indicated by arrows. Several statistics for the traits in the DH lines are shown on the right of each plot.

Zeleny sedimentation volume (mL)

2006 in Suzhou

Zeleny sedimentation volume (mL)

2006 in Tai’an

Zeleny sedimentation volume (mL)

2005 in Tai’an

Mean: 24.39

SD: 5.45

Range: 12.00-39.00

Skewness: 0.171

Kurtosis: -0.153 25

DH lines

Ym57

Hp3

15.0020.0025.0030.0035.0040.00

DH lines

Ym57

Hp3

20.0030.0040.0050.0060.00

DH lines

Ym57

Hp3

20.0030.0040.00

Mean: 24.39

SD: 5.45

Range: 12.00-39.00

Skewness: 0.171

Kurtosis: -0.153

Mean: 24.39

SD: 5.45

Range: 12.00-39.00

Skewness: 0.171

Kurtosis: -0.153

1042ZHAO Liang et al.

Table 1 Estimated additive effects and additive ×environment (AE) interactions of QTLs for ZSV at three environments in the 2005 and 2006 cropping seasons

QTL Flanking-marker 1)Position (cM)2)

F -value P A 3)H 2 (A, %)4)

AE 1H 2 (AE 1, %)5)AE 2H 2 (AE 2, %)

AE 3H 2 (AE 3, %)

Qzsv -1B Xwmc412.2-Xcfe023.236.425.220.000-2.5214.39------Qzsv -1D Xwmc93-GluD1

61.915.910.000-1.988.93------Qzsv -5A Xbarc358.2-Xgwm18638.18.100.000 1.08 2.66------Qzsv -5D

Xcfd101-Xbarc320

60.6

12.69

0.000

-1.20

3.25

--1.04

2.44

1)Flanking marker, the interval of F peak value for QTL. The same as below.

Position, the location of F peak value for QTL in “Flanking marker”. The same as below.3)

Additive effects, a positive value indicates that the allele from Hp3 increased ZSV, a negative value indicates that the allele from Ym57 increased ZSV.4)

H 2(A, %) indicates the contribution explained by putative additive QTL.5)

H 2(AE 1, %) indicates the contribution explained by additive QTL ×environment 1 interaction. E 1, Tai’an 2005; E 2, Tai’an 2006; E 3, Suzhou 2006.

Fig. 2 A genetic linkage map of wheat showing mapping QTLs with additive effects, epistatic effects, AE, and AAE for ZSV.

1A 1B 1D 2A 3A

5A 5D 7A 7D

Locus involved in AE

Locus involved in additive effects Locus involved in epistasis

Locus involved in AAE

Detection of QTLs with Additive Effects, Epistatic Effects, and QTL ×Environment Interactions for Zeleny Sedimentation 1043

ZSV by 2.52, 1.98, and 1.20 mL, respectively, owing to additive effects. The Hp3 allele increased ZSV at the Qzsv -5A by 1.08 mL, accounting for 2.66% of the phe-notypic variance. This suggested that alleles, which increased ZSV, were dispersed within the two parents,resulting in small differences of phenotypic values be-tween the parents and transgressive segregants among the DH population. The total additive QTLs detected for ZSV accounted for 29.23% of the phenotypic variance.

One additive effect was involved in AE interactions (Table 1 and Fig.2). The Ym57 alleles at one locus,Qzsv -5D , increased the ZSV by 1.04 mL with corre-spondingly contributing 2.44% of the phenotypic variance.

QTLs with epistasis effects and epistasis ×environment (AAE) interactions

Four pairs of epistatic QTLs were identified for ZSV,and were located on chromosomes 1A, 2A, 3A, 7A and 7D (Table 2 and Fig.2). These QTLs had correspond-ing contributions ranging from 0.64 to 6.79%. One pair of epistasis, occurring between the loci Qzsv -2A /Qzsv -7A , had the largest effect, which contributed ZSV of 1.73 mL and accounted for 6.79% of the phenotypic variance. The four pairs of epistatic QTLs explained 12.11% of the phenotypic variance. All the epistatic effects were non-main-effect QTLs.

One pair of epistatic QTL was detected in AAE in-teractions for ZSV (Table 2 and Fig.2). The AAE ef-fects explained 2.33% of the phenotypic variance and this QTL, Qzsv3A.2/Qzsv7D.1, increased ZSV by 1.01mL owing to AAE effects, simultaneously the positive value means that the parent-type effect is greater than the recombinant-type effect.

DISCUSSION

Epistatic effects and QTL ×environment interactions were important genetic basis for ZSV in wheat

Epistasis, as an important genetic basis for complex traits, has been well demonstrated in recent QTL map-ping studies (Cao et al . 2001; Fan et al . 2005; Ma et al .2005, 2007). Ma et al . (2005) provided a strong evi-dence for the presence of epistatic effects on dough rheological properties in a wheat DH population. In the present study, four pairs of QTLs with epistatic ef-fects were detected for ZSV in three environments (Table 2 and Fig.2). The four pairs of epistatic QTLs explained 12.11% of the phenotypic variance.

ZSV was predominantly influenced by the effects of genotype (Zhang et al . 2004, 2005), and in the present study, only one AE interaction and one AAE interaction were found. It is suggested that QTL ×environment interactions just play a minor role, but QTL ×environment interactions should not be ignored.

ZSV and subunits of high molecular weight glutenins

Subunits of high molecular weight glutenins strongly influence wheat bread making quality. This study pro-vided a precise location of ZSV gene within the Xwmc 93 and GluD1 interval, which was designated Qzsv -1D and was located in the central region of a 2 cM interval.Also Rousset et al . (2001) detected a major QTL for sedimentation volume on 1DL, clearly corresponding to the Glu -D1 locus. Kunert et al . (2007) found that the SSR marker Xgwm642 on 1DL identified a QTL

Table 2 Estimated epistatic effects and epistasis ×environment (AAE) interactions of QTLs for ZSV at three environments in the 2005 and 2006 cropping seasons

Position Position H 2

H 2

(cM)(cM)(AA, %)2)(AAE 1, %)3)

(AAE 2, %)

(AAE 3, %)

Qzsv -1A Xwmc278-Xbarc120.156.3Qzsv -3A.1Xbarc1177-Xbarc276.2196.3-0.94 1.99------Qzsv -2A Xgwm636-Xcfe6729.1Qzsv -7A Xbarc259-Xwmc59653.7-1.73 6.79------Qzsv -3A.2Xcfa2193-Xgwm155152.7Qzsv -7D.1Xcfd175-Xwmc14181.5-1.09 2.69 1.01 2.33----Qzsv -3A.2

Xcfa2193-Xgwm155

152.7

Qzsv -7D.2

Xgdm67-Xwmc634

161.5

-0.53

0.64

The epistatic effect. A positive value means that the parent-type effect is greater than the recombinant-type effect, and the negative value means that the parent-type effect is less than the recombinant-type effect.

2)H 2 (AA, %) indicates the contribution explained by putative epistatic QTL.

3)H 2 (AAE 1, %) indicates the contribution explained by epistatic QTL ×environment 1 interaction. E 1, Tai’an 2005; E 2, Tai’an 2006; E 3

, Suzhou 2006.QTL Flanking-marker QTL Flanking-marker

AA 1)

AAE 1AAE 2

AAE 3

1044ZHAO Liang et al. for ZSV. The position indicates an influence of the

Glu-D1 locus. And a major QTL, clearly correspond-

ing to the Glu-D1 locus, was detected on chromosome

arm 1DL. Correlation coefficient between Glu-1 score

and sedimentation values was significant (r=0.553).

There were significant correlations between sedimen-

tation values and Glu-lAa,Glu-1Ac,Glu-Ba, and Glu-

1Bc

alleles, respectively (Kne et al. 1993). The

sedimentation values showed statistically significant

associations with the status of the Glu-A1 locus

(Witkowski et al. 2008).

In this study, the Qzsv-1D increased ZSV by 1.98

mL, correspondingly contributing 8.93% of the pheno-

typic variance. Barro et al. (2003) found that HMW-

GS 1Ax1 increased the sedimentation value. In contrast,

HMW-GS 1Dx5 drastically decreased in sedimentation

value.

In summary, four additive QTLs, four pairs of epi-

static QTLs, and two QEs were detected for ZSV in

168 DH lines derived from a cross Hp3×Ym57. One

major QTL,Qzsv-1B, was closely linked to Xwmc412.20.2

cM and could account for 14.39% of the phenotypic

variation without any influence from the environment.

Therefore, the Qzsv-1B could be used in MAS in wheat

breeding programs. The results showed that both ad-

ditive and epistatic effects were important as a genetic

basis for ZSV, and were also sometimes subject to en-

vironmental modifications.

Acknowledgements

This work was supported by the National Basic Re-

search Program of China (2009CB118301), the National

High-Tech Research and Development (863) Program

of China (2006AA100101 and 2006AA10Z1E9), and

the Doctor Foundation of Shandong Agricultural

University, China (23023). Thanks Prof. Chuck Walker,

University of Kansas State University, USA, for his

kindly constructive advice on the language editing of

the manuscript.

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(Edited by ZHANG Yi-min)