Quantitative trait loci (QTLs) for quality traits related to proteinand starch in wheat

Haiyan Sun 1, Jianhua Lu 1, Yuding Fan, Yan Zhao, Fanmei Kong, Rijun Li,Honggang Wang, Sishen Li *

National Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China

Received 2 November 2007; received in revised form 27 November 2007; accepted 6 December 2007

Abstract

Quality traits in wheat (Triticum aestivum L.) were studied by quantitative trait locus (QTL) analysis in a recombinant inbred line(RIL) population, a set of 131 lines derived from Chuan 35050 � Shannong 483 cross (ChSh). Grains from RILs were assayed for 21quality traits related to protein and starch. A total of 35 putative QTLs for 19 traits with a single QTL explaining 7.99–40.52% of phe-notypic variations were detected on 10 chromosomes, 1D, 2A, 2D, 3B, 3D, 5A, 6A, 6B, 6D, and 7B. The additive effects of 30 QTLs werepositive, contributed by Chuan 35050, the remaining 5 QTLs were negative with the additive effect contributed by Shannong 483. Forprotein traits, 15 QTLs were obtained and most of them were located on chromosomes 1D, 3B and 6D, while 20 QTLs for starch traitswere detected and most of them were located on chromosomes 3D, 6B and 7B. Only 7 QTLs for protein and starch traits were co-locatedin three regions on chromosomes 1D, 2A and 2D. These protein and starch trait QTLs showed a distinct distribution pattern in certainregions and chromosomes. Twenty-two QTLs were clustered in 6 regions of 5 chromosomes. Two QTL clusters for protein traits werelocated on chromosomes 1D and 3B, respectively, three clusters for starch traits on chromosomes 3D, 6B and 7B, and one cluster includ-ing protein and starch traits on chromosome 1D.� 2008 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science inChina Press. All rights reserved.

Keywords: Wheat; QTL; Quality trait; Protein; Starch; RIL

1. Introduction

Wheat (Triticum aestivum L., 2n = 42, AABBDD gen-ome) is an allohexaploid species with seven groups ofhomologous chromosomes. The wheat seed has a complexstructure and numerous characteristics of it can be mea-sured depending on the intended application of the wheatgrain [1]. The quality of some end-products, e.g., bread,steamed bread and noodles, are influenced considerablyby wheat quality traits determined by protein and starch.

A number of authors have reported success in teasingapart the complex genetic basis of wheat quality, including

the high molecular weight (HMW) and low molecular weight(LMW) glutenin loci [2–6], grain hardness loci (Pina-D1 andPinb-D1) [7], granule-bound starch synthase (GBSS) loci[8–10], polyphenol oxidase (PPO) loci [11,12], etc.

Most quality traits are complicated quantitative traits.Quantitative trait loci (QTLs) analysis has provided aneffective approach to dissect complicated traits into com-ponent loci to study their relative effects on a specific trait[13]. In a particular genetic background, QTL analysisallows the presence of QTLs to be identified, thereby pro-viding breeders with targets for marker-assisted varietyimprovement [14]. By using recombinant inbred lines(RILs) or double haploid (DH) lines or other populationsin combination with genetic linkage maps, a lot of QTLsfor important wheat quality traits have been detected.QTL analysis for wheat quality was focused mainly on

1002-0071/$ - see front matter � 2008 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited

and Science in China Press. All rights reserved.

doi:10.1016/j.pnsc.2007.12.013

* Corresponding author. Tel.: +86 538 8242903; fax: +86 538 8242226.E-mail address: ssli@sdau.edu.cn (S. Li).

1 These authors contributed equally to this work.

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Progress in Natural Science 18 (2008) 825–831

protein traits, e.g., grain protein content [1,15–20] anddough physical properties [1,15,16,20]. QTL analysis hasalso been used to study flour viscosity [1,9,21], bakingquality and bread scores [1,14,21–23] and noodle color[1,24,25].

The objective of this study was to identify QTLs control-ling protein and starch traits using a population of RILsderived from two Chinese winter wheat varieties and themolecular markers on the linkage map.

2. Materials and methods

2.1. Plant materials and experimental design

The population for QTL analysis was 131 RILs derivedfrom Chuan 35050 � Shannong 483 (ChSh population, F14

in 2006). Chuan 35050 was a variety with higher strengthquality in west-southern winter wheat region of China,and Shannong 483 was a variety with ordinary strengthquality in Huang-huai winter wheat region. Shannong483 was derived from ‘‘Ai-Meng-Niu”, a well-known germ-plasm and backbone parent used in wheat breading inChina and cultivated by Shandong Agricultural Universityin 1980. From ‘‘Ai-Meng-Niu” more than 16 cultivars havebeen developed that had been planted over 30 million ha inChina till 2000.

The 131 RILs and their parents were planted in twoenvironments, Tai’an (Huang-huai winter wheat region)and Yantai (northern winter wheat region), China in2001, with two replications. A plot of six rows with 2 mlong and 26.7 cm apart was planted with 70 seeds in eachrow. During the growth period, the rainfalls in Tai’anand Yantai were 200–290 mm and 220–310 mm, respec-tively, and accumulative temperatures were about2200 �C and 2000 �C, respectively. The soil type of thetwo experimental fields was all loamy soil, and the grainyield of the wheat was about 7500 kg/ha.

2.2. Quality analysis

A composite grain sample was made for each line of theShCh population by pooling half of the harvested grainfrom Tai’an and Yantai. Grain protein content (GPC)was determined by NIR method according to AACC39-10. Grain glutenin macropolymer content (GMPC) wasestimated by Weegels et al.’s method [26]. Samples weremilled on a Brabender Quadrumat Junior Laboratory Mill(C.W. Brabender Instrument Company, NJ, USA) as indi-cated in AACC26-21. Flour wet gluten content (WGC) anddry gluten content (DGC) were measured by followingNational Standards of China (GB/714607-93 and GB/714606-93), respectively. Zeleny sedimentation volume(ZSV) was determined using AACC56-61 method. Flourwater absorption (FWA), dough development time(DDT), dough stability time (DST), mixing tolerance index(MTI) and breakdown time (BDT) were measured using afarinorgraph (Brabender, Germany) according to

AACC54-21. Flour paste viscosity was estimated using aRapid Visco Analyser (RVA, Newport Scientific, Austra-lia) following manufacturer’s instruction. Falling number(FN) and swelling power (SP) were determined asdescribed in AACC56-81 and Ref. [27], respectively. Amy-lose (ALC) and amylopectin content (APC) were measuredby IK-I2 method [28].

2.3. QTL analysis

The linkage map of the ShCh population which we pre-viously established [29] and the information on markers ofthis map were used in QTL analysis. This map included 381loci on all the wheat chromosomes, comprising of 167 SSR,94 EST-SSR, 76 ISSR, 26 SRAP, 15 TRAP and 3 Glu loci,and covering 3636.7 cM with the average distance of14.8 cM between the two markers. The HMW-GS (highmolecular weight glutenin subunit) of the parents (Chuan35050 and Shannong 483) was (1, 7+9, 5+10) and (N,7+8, 2+12), respectively, so the differences at Glu-A1,Glu-B1 and Glu-D1 loci were 1, N; 7+8, 7+9 and 5+10,2+12, respectively.

The QTLMaper 2.0 based on the mixed-model [30] wasused to conduct QTL mapping. Walking speed chosen forall QTLs was 1.0 cM. Additive effects of detected QTLswere estimated by Bayesian test. A QTL was claimed tobe significant at a LOD peak value 2.5.

3. Results

3.1. Phenotypic variation for RILs and parents

For all the 21 quality traits we analyzed, most traits dif-fered obviously between the two parents, Chuan 35050and Shannong 483 (Table 1). Chuan 35050 had a highernumerical value for most protein traits, GPC, GMPC,WGC, DGC, ZSV, DDT, DST and BDT, but a lower valuefor MTI, when compared with those of Shannong 483. Forstarch traits, Chuan 35050 also had a higher value for almostall the tested traits. The RIL population had a wide rangeand considerable variation for most traits, especially forfarinorgraph parameters and viscosity (Table 1). The trans-gressive inheritance was found for all the traits except forDGC, and continuous distributions were common. Thelowest variation was FWA with CV of 2.31%. The variationsof the other traits were high with CV from 5.5% of PET to46.18% of DST. Therefore, this population was suitablefor detecting QTLs for all the traits except for FWA.

3.2. Analysis of QTLs for quality traits

Mapping analysis produced a total of 35 putative QTLsfor 19 traits with a single QTL explaining 7.99–40.52% ofphenotypic variations (Table 2 and Fig. 1). The 35 QTLswere distributed on 10 chromosomes, 1D, 2A, 2D, 3B, 3D,5A, 6A, 6B, 6D and 7B. The additive effects of 30 QTLs werepositive with the additive coming from Chuan 35050; the

826 H. Sun et al. / Progress in Natural Science 18 (2008) 825–831

remaining 5 QTLs were negative with the additive effectscontributed by Shannong 483. Twenty-two QTLs were clus-tered (P3 QTLs) in 6 regions on 5 chromosomes, 1D, 3B,3D, 6B and 7B (Fig. 1 and Table 2).

For protein traits, 15 QTLs for 9 traits were detected onchromosomes 1D, 2A, 2D, 3B, 5A, 6A and 6D. ElevenQTLs (73.3%) were located mainly on chromosomes 1D,3B and 6D. The numbers of QTLs for GPC, DGC, ZSVand DDT were 3, 2, 3 and 2, respectively, and one QTLwas identified for GMPC, WGC, DST, MTI and BDT.The additive effects mainly came from the parent Chuan35050 (11 QTLs, 73%). Thirteen QTLs (86.7%) explainedmore than 10% of phenotypic variations, with the most of40.52% from QBdt.sdau-1D and 37.63% from QDdt.sdau-

1D. So the QBdt.sdau-1D and QDdt.sdau-1D may be majorgene loci for protein traits. For a single trait, the contribu-tions ranged from 15.27% of MTI to 50.63% of DDT(Table 2).

Twenty QTLs for 10 starch traits were localized on chro-mosomes 1D, 2A, 2D, 3B, 3D, 6A, 6B and 7B. ThirteenQTLs (65%) were located on chromosomes 3D, 6B and7B. The numbers of QTLs for PV, TV, FV, BD, PET andALC traits were 3, 2, 3, 3, 3 and 2, respectively. One QTLwas detected for each trait of ST, PAT, FN and SP. Theadditive effects all came from the parent Chuan 35050except for QFv.sdau-1D. The contributions from 17 QTLs(85%) were more than 10%, and the contributions of a sin-gle trait ranged from 17.9% of FN to 52.87% of PET.Among the 10 traits, 6 contributed (60%) about 50%(Table 2).

4. Discussion

Previous studies have identified QTLs for qualitytraits on almost all the 21 wheat chromosomes. Thesestudies were mainly related to protein traits and bread-making quality [1,15–23]. For flour viscosity, the QTLanalysis was mainly on Wx gene [1,9,21]. In this study,a total of 35 putative QTLs with a single QTL explaining7.99–40.52% of phenotypic variations were detected on10 chromosomes using the RIL population (ChSh). Forprotein traits, 15 QTLs were obtained and mostwere located on chromosomes 1D, 3B and 6D, while20 QTLs for starch traits were detected and most werelocated on chromosomes 3D, 6B and 7B. The proteinand starch traits trended to distribute on distinctchromosomes.

It is difficult to compare the position of QTL from thisstudy with that of the previous studies in detail becausedifferent maps and the markers on the maps were used.In this study, four QTLs were mapped around Glu-D1

locus on chromosome 1D which is consistent with theresults from others [15,20]. In fact, the Glu-D1 in ChShpopulation was the gene that codes HMW subunits 2+12and 5+10, both affect greatly the protein quality [2–6].Moreover, as Kunert et al. [31] reported that there is a sed-imentation volume QTL around the locus Xgwm642 onchromosome 1D, we also mapped a QTL of ZSV aroundXgwm642.

The co-locations of QTLs and QTL clusters for differ-ent traits have been found in the previous studies

Table 1Phenotypes for 21 quality traits of recombinant inbred lines (RILs) and their parents

Traits Parents RIL population

Chuan 35050 Shannong 483 Average Min Max SD CV (%)

Protein traits

Grain protein content (%) 11.71 11.15 12.96 10.04 14.65 0.79 6.10GMP content (%) 6.16 5.14 5.53 3.30 7.40 0.81 14.59Wet gluten content (%) 34.00 25.30 35.50 24.20 44.10 3.37 9.51Dry gluten content (%) 11.20 8.30 11.30 8.40 13.70 0.91 8.06Zeleny sedimentation volume (ml) 36.00 28.00 31.00 18.00 46.00 4.58 14.70Flour water absorption (%) 63.20 60.90 61.47 58.00 66.80 1.42 2.31Dough development time (min) 6.00 3.40 4.22 1.90 11.50 1.47 34.79Dough stability time (min) 8.00 2.30 4.09 1.00 10.90 1.89 46.18Mixing tolerance index (F.U.) 36.00 114.00 72.64 22.00 214.00 30.65 42.19Breakdown time (min) 10.50 4.50 6.62 2.30 15.10 2.36 35.70

Starch traits

Peak viscosity (RVU) 198.83 100.08 173.59 79.75 243.50 35.39 20.39Trough viscosity (RVU) 120.67 47.25 111.99 26.91 184.75 35.40 31.61Final viscosity (RVU) 223.67 101.08 203.25 63.58 288.08 49.49 24.35Breakdown (RVU) 78.17 52.83 61.60 46.00 79.33 6.55 10.65Setback (RVU) 103.00 53.83 91.26 36.67 121.17 15.32 16.78Peak time (min) 6.13 5.40 6.07 5.00 6.66 0.33 5.50Pasting temperature (�C) 68.20 68.55 69.84 65.85 87.30 5.62 8.05Falling number (sec) 471.50 247.00 400.41 213.00 620.50 78.46 19.59Swelling power (g.g�1) 9.97 6.81 9.93 4.68 12.97 1.42 14.34Amylose content (%) – 15.42 16.18 12.26 24.94 2.09 12.91Amylopectin content (%) – 45.28 47.24 32.29 56.05 3.48 7.37

H. Sun et al. / Progress in Natural Science 18 (2008) 825–831 827

[1,15,16,18,20,23]. We also found a high frequency of co-locations of QTLs and 6 QTL clusters in this study. TwoQTL clusters for protein traits were located on chromo-somes 1D and 3B. The cluster on 1D was in the regionof Xwmc336b–Xgwm642-Glu-D1-Xsrap19–Xsrap29b andthe LOD peak values were found to be near the locusGlu-D1. This cluster included four QTLs, QZsv.sdau-

1D.2, QDdt.sdau-1D, QDst.sdau-1D and QBdt.sdau-1D,with high contributions of 15.48–40.52%. The effectsfrom Chuan 35050 were positive for all the four QTLs,indicating a positive correlation of these QTLs whichwas also verified by the analysis of simple correlationcoefficients (Table 3). The cluster on 3B included threeQTLs of ZSV, GPC and GMPC with the LOD peak val-ues at Xwmc418 locus. The relationship of the threeQTLs was also positive and accorded with simple corre-lation coefficients (Table 3).

For starch traits, three QTL clusters were located onchromosomes 3D, 6B and 7B. The cluster on 3D was clo-sely linked with Xwmc529 and Xsrap8 loci and involvedfour QTLs for PV, TV, FV and PET with high contribu-tions of 24.02–31.36%. Five QTLs for PV, TV, FV, STand PET were in the cluster region of Xgwm644–Xgwm193–Xgwm608b of chromosome 6B. The range ofcontributions was from 16.88% to 22.18%. The clusteron 7B was between the loci Xubc857c and Xswes94,which had three QTLs for PV, PET and SP withlower contributions (9.22–21.95%). All QTLs within theabove three clusters showed a positive relationship.and accorded with simple correlation coefficients (Table4).

A cluster including QTLs for protein and starch traitswas on chromosome 1D with peak LOD aroundXwmc432a locus. The effects of three QTLs for ZSV,

Table 2Additive effects of QTLs for quality traits

Traits QTL Maker intervala Sitesb (cM) LOD Additive effect c Phenotypic variation (%) General contribution (%)

Protein traits

GPC QGpc.sdau-3B Xwmc418–Xubc834a 0 4.31 0.26 13.34 43.21QGpc.sdau-5A Xsrap27–Xwmc524 27 3.17 �0.33 21.23QGpc.sdau-6A Xswes123a–Xswes123b 0 3.55 �0.21 8.64

GMPC QGmpc.sdau-3B Xwmc418–Xubc834a 0 3.02 0.23 12.65 29.08WGC QWgc.sdau-6D Xswes426b–Xubc807d 4 2.73 1.38 16.43DGC QDgc.sdau-2D Xissr23a–Xwmc181b 0 2.56 �0.28 7.99 23.54

QDgc.sdau-6D Xswes426b–Xubc807d 3 2.89 0.39 15.55ZSV QZsv.sdau-1D.1 Xwmc432a–Xwmc336c 0 5.98 �1.68 16.48 42.26

QZsv.sdau-1D.2 Glu-D1-Xsrap19 2 4.83 1.63 15.48QZsv.sdau-3B Xwmc418–Xubc834a 0 3.98 1.33 10.30

DDT QDdt.sdau-1D Glu-D1-Xsrap19 4 12.74 0.90 37.63 50.63QDdt.sdau-2A Xwmc181b–Xubc840c 0 5.65 0.53 13.00

DST QDst.sdau-1D Glu-D1-Xsrap19 4 5.12 0.85 21.22 21.22MTI QMti.sdau-1D Xwmc432a–Xwmc336c 6 3.42 9.92 15.27 15.27BDT QBdt.sdau-1D Xgwm642-Glu-D1 8 6.41 1.66 40.52 40.52

Starch traits

PV QPv.sdau-3D Xwmc529–Xsrap8 1 4.64 20.36 27.27 52.64QPv.sdau-6B Xgwm644–Xgwm193 7 6.38 15.52 15.83QPv.sdau-7B Xubc857c–Xswes94 7 3.65 12.04 9.54

TV QTv.sdau-3D Xwmc529–Xsrap8 1 4.73 22.67 31.36 50.55QTv.sdau-6B Xgwm193–Xgwm608b 0 6.78 17.55 18.94

FV QFv.sdau-1D Xwmc432a–Xwmc336c 1 3.64 �16.18 8.31 49.67QFv.sdau-3D Xwmc529–Xsrap8 0 4.45 27.78 24.48QFv.sdau-6B Xgwm644–Xgwm193 6 5.88 23.06 16.88

BD QBd.sdau-1D Xswes652–Xgwm458 2 4.48 2.53 12.63 52.01QBd.sdau-2D Xubc859a–Xswes624e 1 8.32 3.16 19.62QBd.sdau-3B Xubc823a–Xissr25a 26 7.65 3.17 19.76

ST QSt.sdau-6B Xgwm193–Xgwm608b 0 5.85 6.06 22.18 22.18PET QPet.sdau-3D Xwmc529–Xsrap8 1 4.19 0.17 24.02 52.87

QPet.sdau-6B Xgwm644–Xgwm193 6 7.29 0.16 19.63QPet.sdau-7B Xubc857c–Xswes94 2 3.72 0.11 9.22

PAT QPat.sdau-6A Xwmc163–Xswes119b 8 4.25 3.20 29.92 29.92FN QFn.sdau-6B Xgwm132b–Xwmc487 2 3.53 31.14 17.90 17.90SP QSp.sdau-7B Xubc857c–Xswes94 1 5.32 0.59 21.95 21.95ALC QAlc.sdau-2A Xubc840c–Xsrap29a 0 3.90 0.76 12.57 25.86

QAlc.sdau-2D Xissr23a–Xwmc181b 1 4.26 0.78 13.29

For abbreviations of the traits, refer to Table 1.a The interval of LOD peak value for QTL.b The distance of LOD peak value for QTL after the first marker in ‘‘marker interval”.c Positive means that the additive effects came from Chuan 35050, while negative from Shannong 483.

828 H. Sun et al. / Progress in Natural Science 18 (2008) 825–831

MTI and FV were negative, positive, and negative,respectively. In addition, three regions with the co-loca-tions of QTLs were detected, which were between DDTand ALC on chromosome 2A, DGC and ALC on 2D,WGC and DGC on 6D.

In all 35 QTLs, only 7 QTLs (20%) for protein andstarch traits were co-located in three regions of three chro-mosomes, 1D, 2A and 2D, which indicated that the QTLsfor protein and starch traits might be distributed on dis-tinct regions of chromosomes.

Fig. 1. Locations of 35 QTLs for quality traits based on RILs derived from the cross Chuan 35050 � Shannong 483. QTLs are indicated on the left side ofeach chromosome, and the names of markers on the right side. The intervals of QTLs were LOD P 2.0 with LOD peak values higher than 2.5. Asterisks(*) indicate that the loci were located on chromosomes using Chinese Spring nulli-tetrasomic lines [29].

H. Sun et al. / Progress in Natural Science 18 (2008) 825–831 829

5. Conclusions

(1) A total of 35 putative QTLs for 19 traits with asingle QTL explaining 7.99–40.52% of phenotypicvariations were detected on 10 chromosomes, 1D,2A, 2D, 3B, 3D, 5A, 6A, 6B, 6D and 7B. Theadditive effects of 30 QTLs were positive that was

contributed by Chuan 35050, the remaining 5 QTLswere negative with additive effects contributed byShannong 483.

(2) For protein traits, we obtained 15 QTLs and most(73.3%) of them were located on chromosomes 1D,3B and 6D, while we detected 20 QTLs for starchtraits and most (65%) of them on chromosomes 3D,6B and 7B. Only 7 QTLs (20%) for protein and starch

Fig. 1 (continued)

Table 3Simple correlation coefficients (r) between protein traits

Traits GPC WGC DGC GMPC ZSV DDT DST MTI

WGC 0.795**

DGC 0.832** 0.955**

GMPC 0.615** 0.380** 0.359**

ZSV 0.443** 0.228** 0.241** 0.556**

DDT 0.085 80.252** �0.162 0.263** 0.450**

DST 0.041 �0.243** �0.173 0.247** 0.509** 0.881**

MTI �0.108 0.092 0.101 �0.299** �0.538** �0.583** �0.777**

B8DT 0.095 �0.226** �0.155 0.273** 0.509** 0.922** 0.977** �0.767**

For abbreviations of the traits, refer to Table 1.** p < 0.01.

Table 4Simple correlation coefficients (r) between starch traits

Traits PV TV FV BD ST PET PAT FN SP

TV 0.982**

FV 0.978** 0.990**

BD 0.095 �0.097 �0.062ST 0.889** 0.883** 0.941** 0.027PET 0.946** 0.968** 0.951** �0.119 0.832**

PAT 0.220* 0.252** 0.191* �0.168 0.031 0.299**

FN 0.742** 0.762** 0.795** �0.107 0.806** 0.704** �0.107SP 0.771** 0.762** 0.755** 0.047 0.677** 0.771** 0.278** 0.525**

ALC 0.002 0.057 0.050 �0.288** 0.028 0.044 0.259** �0.047 �0.004

For abbreviations of the traits, refer to Table 1.* p < 0.05.

** p < 0.01.

830 H. Sun et al. / Progress in Natural Science 18 (2008) 825–831

traits were co-located in three regions on chromo-somes 1D, 2A and 2D. The protein and starch traitQTLs showed a distinct distribution pattern onchromosomes.

(3) Twenty-two QTLs were clustered in 6 regions on 5chromosomes. Two QTL clusters for protein traitswere localized on chromosomes 1D and 3B, threeclusters for starch traits on chromosomes 3D, 6Band 7B, and one cluster including QTLs for proteinand starch traits on chromosome 1D.

Acknowledgments

This work was supported by National Key TechniqueProgram for Regulation of Agricultural Structure (GrantNo. 06-02-04B) and National Natural Science Foundationof China (Grant No. 3057155).

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