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Acta Agron Sin ›› 2016, Vol. 42 ›› Issue (06): 820-831.doi: 10.3724/SP.J.1006.2016.00820


Mapping QTLs For Wheat Panicle Traits with High Density SNP Genetic Map

LIU Kai,DENG Zhi-Ying,LI Qing-Fang,ZHANG Ying,SUN Cai-Ling,TIAN Ji-Chun*,CHEN Jian-Sheng*   

  1. Group of Wheat Quality Breeding, College of Agronomy, Shandong Agricultural University / State Key Laboratory of Crop Biology, Tai’an 271018,China
  • Received:2015-11-09 Revised:2016-03-14 Online:2016-06-12 Published:2016-03-21
  • Contact: 陈建省, E-mail: jshch@sdau.edu.cn, Tel: 0538-8249236; 田纪春, E-mail: jctian@sdau.edu.cn E-mail:liukaiyouxiang@163.com
  • Supported by:

    This study was supported by the Natural Science Foundation of Shandong Province, China (2015ZRB01179 and ZR2013CM004) and the Project of Germplasm Resource Enhancement in Shandong Province.


Panicle traits of wheat are closely correlated between each other,of them grain number per spike and 1000-grain weight are important components of grain yield. In this study,we mapped quantitative trait loci (QTLs) associated with wheatspike traits using a recombinant inbred line (RIL) population (173 lines of F8:9) derived from a cross of Shannong 01-35×Gaocheng 9411.The phenotypic data were collected in five environments and the high density genetic map was constructedusing90k SNP array,DArT technology and traditional molecular markers. In a combination analysis of five environments, many additive QTLs were detected includingseven for 1000-grain weight,eight for spike length,threefor grain number per spike, five for fertile spikelet number per spike, three for sterile spikelet number per spike,four for spikelet number per spike, and six for spike density.Some QTLs showed high rates of phenotypic variation explained (PVE). For example, the PVE of QTLs for 1000-grain weight on 1B, 4B, 5B and 6A ranged from 6.00% to 36.30%,with the favorable alleles from the large-grain parent Shannong 01-35; the PVE of QTLs for spike length ranged from 14.34% to 25.44%, and thatfor sterile spikelet number per spike from 8.70% to 37.70%. In addition to additive loci,32 pairs of epistatic QTLs were detected, which explained 0.05–1.05% of the phenotypic variations. The marker interval between EX_C101685 and RAC875_C27536 on chromosome 4B showed pleiotropic effectsin 1000-grain weight, spike length, grain number per spike, fertile spike number, sterile spikelet number, and spikelet number per spike, with the PVE ranging from 5.40% to 37.70%. There stable main QTLs were detected in multiple environments. Besides, markerinterval between wPt-0959 and TaGw2-CAPS on 6Ahad a locus controllingboth 1000-grain weight and spikelet number per spike. These results are valuable in developing molecular markers, fine mapping and cloning genes for spike traits in wheat.

Key words: Common wheat, 90k array, QTL mapping, Panicle, SNP

[1] 郑德波, 杨小红, 李建生, 严建兵, 张士龙, 贺正华, 黄益勤. 基于SNP标记的玉米株高及穗位高QTL定位. 作物学报, 2013, 39: 549-556
Zheng D B, Yang X H, Li J S, Yan J B, Zhang S L, He Z H, Huang Y Q. QTL identification for plant height and ear height based on SNP mapping in maize (Zea mays L.). ActaAgron Sin,2013, 39: 549–556(in Chinese with English abstract)
[2] 关强, 张月学, 徐香玲, 孙德全, 林红, 潘丽艳, 马延华. DNA 分子标记的研究进展及几种新型分子标记技术. 黑龙江农业科学, 2008, (1): 102–104
Guan Q, Zhang Y X, Xu X L, Sun D Q, Li S Y, Lin H, Pan L Y, Ma Y H. Development of DNA molecular marker and several new types of molecular markers. Heilongjiang AgricSci, 2008, (1): 102–104 (in Chinese with English abstract)
[3] Zou Y P, Ge S. A novel molecular marker-SNPs and its application. Biodiversity Sci, 2003, 11: 370–382
[4] Paterson A H, Lander E S, Hewitt J D, Peterson S, Lincoln S E, Tanks ley S D. Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature, 1988, 335: 721–726
[5] Huang X Q, Kempf H, Canal M W, Roder M S. Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and a synthetic wheat (TriticumaestivumL.). TheorAppl Genet, 2004, 109: 933–943
[6] Ma Z Q, Zhao D M, Zhang C Q, Zhang Z Z, Xue S L, Lin F, Kong Z X, Tian D G, Luo Q Y. Molecular genetic analysis of five spike-related traits in wheat using RIL and immortalized F2 populations. MolGenet Genomics, 2007, 277: 31–42
[7] Deng S, Wu X, Wu Y, Zhou R., Wang H, Jia J, Liu S. Characterization and precise mapping of a QTL increasing spike number with pleiotropic effects in wheat. TheorAppl Genet, 2011, 122: 281–289
[8] Cui F, Zhao C H, Ding A M, Li J, Wang L, Li X F, Bao Y G, Li J M, Wang H G. Construction of an integrative linkage map and QTL mapping of grain yield-related traits using three related wheat RIL populations. TheorAppl Genet, 2014, 127: 659–675
[9] Cui F, Ding A M, Li J, Zhao C H, Wang L, Wang XQ, Qi X L, Li X F, Li G Y, Gao J R, Wang H G. QTL detection of seven spike-related traits and their genetic correlations in wheat using two related RIL populations. Euphytica, 2012, 186: 177–192
[10] Jia H, Wan H, Yang S, Zhang Z, Kong Z, Xue S, Zhang L, Ma Z. Genetic dissection of yield-related traits in a recombinant inbred line population created using a key breeding parent in China’s wheat breeding. TheorAppl Genet, 2013, 126: 2123–2139
[11] Huang X Q, Cloutier S, Lycar L, Radovanovic N, Humphreys D G, Noll J S, Somers D J, Brown P D. Molecular detection of QTLs for agronomic and quality traits in a doubled haploid population derived from two Canadian wheat (TriticumaestivumL.). TheorAppl Genet, 2006, 113: 753–766
[12] 丁安明, 李君, 崔法, 赵春华, 马航运, 王洪刚. 利用小麦关联RIL群体定位产量相关性状QTL. 作物学报, 2011, 37: 1511–1524
Ding A M, Li J, Cui F, Zhao C H, Ma H Y, Wang H G. QTL mapping for yield related traits using two associated RIL populations of wheat. ActaAgron Sin, 2011, 37: 1511–1524 (in Chinese with English abstract)
[13] 王瑞霞, 张秀英, 伍玲, 王瑞, 海林, 游光霞, 闫长生, 肖世和. 不同生态环境下冬小麦籽粒大小相关性状的QTL分析. 中国农业科学, 2009, 42: 398–407
Wang R X, Zhang X Y, Wu L, Wang R, Hai L, You G X, Yan C S, Xiao S H. QTL analysis of grain size and related traits in winter wheat under different ecological environments. SciAgric Sin, 2009, 42: 398–407 (in Chinese with English abstract)
[14] 姚琴, 周荣华, 潘昱名, 傅体华, 贾继增. 小麦品种偃展1号与品系早穗30重组自交系群体遗传连锁图谱构建及重要农艺性状的QTL分析. 中国农业科学, 2010, 43: 4130–4139
Yao Q, Zhou R H, Pan Y M, Fu T H, Jia J Z. Construction of genetic linkage map and QTL analysis of agronomic important traits based on a RIL population derived from common wheat variety Yanzhan 1 and Zaosui 30. SciAgric Sin, 2010, 43: 4130–4139 (in Chinese with English abstract)
[15] Börner A, Schumann E, Fürste A, Cöster H, Leithold B, Röder M S, Weber W E. Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (TriticumaestivumL.). TheorAppl Genet, 2002, 105: 921–936
[16] Sourdille P, Tixier MH, Charmet G, Gay G, Cadalen T, BernardS, Bernard M. Location of genes involved in ear compactness in wheat (Triticumaestivum) by means of molecular markers. Mol Breed, 2000, 6: 247–255
[17] 张坤普, 徐宪斌, 田纪春. 小麦籽粒产量及穗部相关性状的QTL定位. 作物学报, 2009, 35: 270–278
Zhang K P, Xu X B, Tian J C. QTL mapping for grain yield and spike related traits in common wheat. ActaAgron Sin, 2009, 35: 270–278 (in Chinese with English abstract)
[18] 吴秋红, 陈娇娇, 陈永兴, 周升辉, 张德云, 王国鑫, 王振忠, 王立新, 袁成国, 尤明山, 刘志勇. 燕大1817/北农6 号重组自交系群体穗部性状的QTL定位. 作物学报, 2015, 41: 349–358
Wu Q H, Chen J J, Chen Y X, Zhou S H, Zhang D Y, Wang G X, Wang Z Z, Wang L X, Yuan C G, You M S, Liu Z Y. Mapping quantitative trait loci related to spike traits using a RILs population of Yanda 1817 × Beinong 6 in wheat (TriticumaestivumL.). ActaAgron Sin,2015, 41: 349–358 (in Chinese with English abstract)
[19] 宋彦霞, 景蕊莲, 霍纳新, 任正隆, 贾继增. 普通小麦(Triticumaestivum L.)不同作图群体抽穗期QTL分析. 中国农业科学, 2006, 39: 2186–2193
Song Y X, Jing R L, Huo N X, Ren Z L, Jia J Z. Detection of QTL for heading in common wheat (Triticumaestivum L.) Using Different Populations. SciAgric Sin, 2006, 39: 2186–2193 (in Chinese with English abstract)
[20] 李文才, 李涛, 赵逢涛, 李兴峰, 王洪刚. 小麦D基因组产量性状QTL定位. 华北农学报, 2005, 20(1): 23–26
Li W C, Li T, Zhao F T, Li X F, Wang H G. QTL of wheat yield traits in D genome. ActaAgricBoreali-Sin,2005, 20(1): 23–26 (in Chinese with English abstract)
[21] Patil R M, Tamhankar S A, Oak M D. Mapping of QTL for agronomic traits and kernel charactersin durum wheat (Triticum durum Desf.). Euphytica, 2013, 190: 117–129
[22] Sears E R. The aneuploids of common wheat. Univ Miss Res Bull, 1954, 572: 1–58
[23] Rao M V P. Mapping of the sphaerococcum gene “S” on chromosome 3D of wheat. Cereal Res Commun,1977, 5: 15–17
[24] Kato K, Miura H, Sawada S. QTL mapping of genes controlling ear emergence time and plant height on chromosome 5A of wheat. TheorAppl Genet, 1999, 98: 472–477
[25] Paillard S, Schnurbusch T, Winzeler M, Messmer M, Sourdille P, Abderhalden O, Keller B, Schachermayr G. An integrative genetic linkage map of winter wheat (TriticumaestivumL.).TheorAppl Genet, 2003, 107: 1235–1242
[26] Johnson E B, Nalam V J, Zemetra R S, Riera-Lizarazu O. Mapping the compactum locus in wheat (TriticumaestivumL.) and its relationship to other spike morphology genes of the Triticeae. Euphytica, 2008, 163: 193–201
[27] Ma Z Q, Zhao D M, Zhang C Q, Zhang Z Z, Xue S L, Lin F, Kong Z X, Tian D G, Luo Q Y. Molecular genetic analysis of five spike-related traits in wheat using RIL and immortalized F2 populations. Mol Genet Genomics, 2007, 277: 31–42
[28] Wang J S, Liu W H, Wang H, Li L H, Wu J, Yang X M, Li X Q, Gao A N. QTL mapping of yield-related traits in the wheat germplasm 3228. Euphytica, 2011, 177: 277-292
[29] Kearsey M J, Pooni H S. The Genetical Analysis of Quantitative Traits. Garland Science(Publishers) Ltd.,Chapman and Hall, London, 2004. pp 65–66
[30] 陈建省,陈广风, 李青芳, 张晗, 师翠兰, 孙彩铃, 邓志英, 刘凯, 谷植群, 田纪春. 利用基因芯片技术进行小麦遗传图谱构建及粒重QTL分析. 中国农业科学, 2014, 47: 4769–4779
Chen J S,Chen G F, Li Q F, Zhang H, Shi C L, Sun C L, Deng Z Y, Liu K, Gu Z Q, Tian J C. Construction of genetic map using genotyping chips and QTL analysis of grain weight. SciAgric Sin,2014, 47: 4769–4779 (in Chinese with English abstract)
[31] 唐立群, 肖层林, 王伟平. SNP分子标记的研究及其应用进展. 中国农学通报, 2012, 28(12): 154–158
Tang L Q, Xiao C L, Wang W P. Research and application progress of SNP markers. Chin AgricSci Bull,2012, 28(12): 154–158 (in Chinese with English abstract)
[32] 卢翔, 张锦鹏, 王化俊, 杨欣明, 李秀全, 李立会. 小麦–冰草衍生后代3558-2穗部相关性状的遗传分析和QTL定位. 植物遗传资源学报, 2011, 12: 86–91
Lu X, Zhang J P, Wang H J. Genetic Analysis and QTL mapping of wheat spike traits in a derivative line 3558-2 from wheat × Agropyroncristatum offspring. J Plant Genet Resour,2011, 12: 86–91 (in Chinese with English abstract)
[33] Cavanagh C R, Chao S, Wang S, Huang B E, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira G L, Akhunova A. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl AcadSci USA, 2013, 110: 8057–8062
[34] Shah M M, Gill K S, Baenziger P S, Yen Y, Kaeppler S M, Ariyarathne H M. Molecular mapping of loci for agronomic traits on chromosome 3A of bread wheat. Crop Sci, 1999, 39: 1728–1732
[35] Li Q F, Zhang Y, Liu T T, Wang F F, Liu K, Chen J S, Tian J C. Genetic analysis of kernel weight and kernel size in wheat (TriticumaestivumL.) using unconditional and conditional QTL mapping. Mol Breed, 2015, 35: 194
[36] Jantasuriyarat C, Vales M I, Waston C J W, Riera-Lizarazu O. Identification and mapping of genetic loci affecting the free-threshing habit and spike compactness in wheat (Triticumaestivum L.).TheorAppl Genet, 2004, 108: 261–273
[37] 王瑾, 廖祥政, 杨学举, 周荣华, 贾继增. 人工合成小麦Am3大穗多粒QTL的发掘与利用. 植物遗传资源学报, 2008, 9: 277–282
Wang J, Liao X Z, Yang X J, Zhou R H, Jia J Z. Mapping of large-spike and much-kernel QTL by using a synthetic wheat Am3 as donor. J Plant Genet Resour, 2008, 9: 277–282 (in Chinese with English abstract)
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