Please wait a minute...
Journal of Integrative Agriculture  2017, Vol. 16 Issue (04): 789-799    DOI: 10.1016/S2095-3119(16)61471-5
Crop Genetics · Breeding · Germplasm Resources Advanced Online Publication | Current Issue | Archive | Adv Search |
Single-nucleotide polymorphisms, mapping and association analysis of 1-FFT-A1 gene in wheat
YUE Ai-qin1, 2, LI Ang2, MAO Xin-guo2, CHANG Xiao-ping2, LI Run-zhi1, JING Rui-lian2

1 College of Agriculture, Shanxi Agricultural University, Taigu 030801, P.R.China

2 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/Key Laboratory of Crop Germplasm and Utilization, Ministry of Agriculture, Beijing 100081, P.R.China

Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
Abstract  Fructans are major nonstructural carbohydrates in wheat (Triticum aestivum L.).  Fructan 1-fructosyltransferase (1-FFT) is the key enzyme in fructan biosynthesis.  In the present study, 96 sequence variants were detected in the 1-FFT-A1 gene among 26 wheat accessions including UR208, and 15 of them result in amino acid substitutions, forming four haplotypes.  Two markers M39 and M2164 were developed based on the InDel21-39 and SNP-2164 polymorphisms to distinguish the three haplotypes in the 1-FFT-A11-FFT-A1 was located on chromosome 4A using marker M2164 and was flanked by markers Xcwm27 and 6-SFT-A1.  By association analysis using a natural wheat population consisted of 154 accessions, the results showed that the two markers were significantly associated with water-soluble carbohydrate (WSC) content in the lower internode stem and total stem at the early and middle grain filling stages, 1 000-grain weight (TGW) at different grain filling stages and peduncle length (PLE).  Comparison of the effects of three haplotypes on agronomic traits indicated that TGW, PLE and total number of spikelets per spike (TNSS) were signi?cantly influenced by haplotypes.  HapIII showed a significant positive effect on TGW, PLE and TNSS.
Keywords:  1-FFT-A1      single nucleotide polymorphism      association analysis      haplotype      marker development      wheat  
Received: 09 May 2016   Accepted:
Fund: 

This work was supported by the National Natural Science Foundation of China (31461143024), the National Major Project for Developing New Genetically Modified (GM) Crops of China (2016ZX08010005), and the Agricultural Science and Technology Innovation Program, China (ASTIP).

Corresponding Authors:  JING Rui-lian, Tel/Fax: +86-10-82105829, E-mail: jingruilian@caas.cn   
About author:  YUE Ai-qin, E-mail: yueaiqinnd@126.com.cn

Cite this article: 

YUE Ai-qin, LI Ang, MAO Xin-guo, CHANG Xiao-ping, LI Run-zhi, JING Rui-lian. 2017. Single-nucleotide polymorphisms, mapping and association analysis of 1-FFT-A1 gene in wheat. Journal of Integrative Agriculture, 16(04): 789-799.

Akhunov E D, Akhunova A R, Anderson O D, Anderson J A, Blak N, Clegg M T, Coleman-Derr D, Conley E J, Crossman C C, Deal K R, Dubcovsky J, Gill B S, Gu Y Q, Hadam J, Heo H, Huo N, Lazo G R, Luo M C, Ma Y Q, Matthews D E, et al. 2010. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics, 11, 702.
Andersen J R, Lübberstedt T. 2003. Functional markers in plants. Trends in Plant Science, 8, 554–560.
Asseng S, van Herwaarden A F. 2003. Analysis of the benefits to wheat yield from assimilates stored prior to grain filling in a range of environments. Plant and Soil, 256, 217–229.
Bagge M, Xia X C, Lübberstedt T. 2007. Functional markers in wheat. Current Opinion in Plant Biology, 10, 211–216.
Blacklow W M, Darbrshire B, Pheloung P. 1984. Fructans polymerized in the internodes of winter wheat as grain-filling progress. Plant Science Letters, 36, 213–218.
Chang J Z, Zhang J N, Mao X G, Li A, Jia J Z, Jing R L. 2013. Polymorphism of TaSAP1-A1 and its association with agronomic traits in wheat. Planta, 237, 1495–1508.
Edae E A, Byrne P F, Manmathan H, Haley S D, Moragues M, Lopes M S, Reynolds M P. 2013. Association mapping and nucleotide sequence variation in five drought tolerance candidate genes in spring wheat. Plant Genome, 6, 1–13.
Gao X, She M Y, Yin G X, Qiao W H, Du L P, Ye X G. 2010. Cloning and characterization of genes coding for fructan biosynthesis enzymes (FBEs) in Triticeae plants. Agricultural Science in China, 9, 313–324.
Goggin D E, Setter T L. 2004. Fructosyltransferase activity and fructan accumulation during development in wheat exposed to terminal drought. Functional Plant Biology, 31, 11–21.
Guo Z A, Song Y X, Zhou R H, Ren Z L, Jia J Z. 2009. Discovery, evaluation and distribution of haplotypes of the wheat Ppd-D1 gene. New Phytologist, 185, 841–851.
Gupta P K, Rustgi S, Kulwal P L. 2005. Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Molecular Biology, 57, 461–485.
Hu M J, Zhang H P, Cao J J, Zhu X F, Wang S X, Lu J, Chang C, Sun G L, Ma C X. 2016. Characterization of an IAA-glucose hydrolase gene TaTGW6 associated with grain weight in common wheat (Triticum aestivum L.). Molecular Breeding36, 25.
Jeong B R, Housley T L. 1992. Purification and characterization of wheat β (2,1) fructan fructan fructosyl transferase activity. Plant Physiology, 100, 199–204.
Kawakami A, Yoshida M. 2002. Molecular characterization of sucrose: Sucrose 1-fructosyltransferase and sucrose: fructan 6-fructosyltransferase associated with fructan accumulation in winter wheat during cold hardening. Bioscience Biotechnology Biochemistry, 66, 2297–2305.
Kawakami A, Yoshida M. 2005. Fructan: Fructan 1-fructosyltransferase, a key enzyme for biosynthesis of graminan oligomers in hardened wheat. Planta, 223, 90–104.
Langridge P, Fleury D. 2011. Making the most of ‘omics’ for crop breeding. Trends in Biotechnology, 29, 33–40.
Li W Y, Zhang B, Li R Z, Chang X P, Jing R L. 2015. Favorable alleles for stem water-soluble carbohydrates identified by association analysis contribute to grain weight under drought stress conditions in wheat. PLOS ONE, 10, e0119438.
Lüscher M, Erdin C, Sprenger N, Hochstrasser U, Boller T, Wiemken A. 1996. Inulin synthesis by a combination of purified fructosyltransferases from tubers of Helianthus tuberosus. FEBS Letters, 385, 39–42.
McCouch S R, Zhao K Y, Wright M, Tung C W, Ebana K, Thomson M, Reynolds A, Wang D, DeClerck G, Ali M L, McClung A, Eizenga G, Bustamante C. 2010. Development of genome-wide SNP assays for rice. Breed Science, 60, 524–535.
Müller J, Aeschbacher R A, Sprenger N, Boller T, Wiemken A. 2000. Disaccharide-mediated regulation of sucrose: fructan-6-fructosyltransferase, a key enzyme of fructan synthesis in barley leaves. Plant Physiology, 123, 265–274.
Nei M, Miller J C. 1990. A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics, 125, 873–879.
Pollock C J, Cairns A J. 1991. Fructan metabolism in grasses and cereals. Annual Review Plant Physiology and Plant Molecular Biology, 42, 77–101.
Rafalski A. 2002. Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Science, 162, 329–333.
Ritsema T, Smeekens S C M. 2003. Engineering fructan metabolism in plants. Journal of Plant Physiology, 160, 811–820.
Rozas J, Sanchez-DelBarrio J C, Messeguer X, Rozas R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496–2497.
Ruuska S A, Rebetzke G J, van Herwaarden A F, Richards R A, Fettell N A, Tabe L, Jenkins C L D. 2006. Genotypic variation in water-soluble carbohydrate accumulation in wheat. Functional Plant Biology, 33, 799–809.
Schnyder H. 1993. The role of carbohydrate storage and redistribution in the source-sink relations of wheat and barley during grain filling: a review. New Phytologist, 123, 233–245.
Sharp P J, Kreis M, Shewry P R, Gale M D. 1988. Location of β-amylase sequences in wheat and its relatives. Theoretical and Applied Genetics, 75, 286–290.
Song Y X. 2005. QTL analysis of the wheat earing period and other agronomic characters. Ph D thesis, Sichuan Agricultural University, China. (in Chinese)
Su J Y, Zheng Q, Li H W, Li B, Jing R L, Tong Y P, Li Z S. 2009. Detection of QTLs for phosphorus use efficiency in relation to agronomic performance of wheat grown under phosphorus sufficient and limited conditions. Plant Science, 176, 824–836.
Su Z Q, Hao C Y, Wang L F, Dong Y N. 2011. Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 122, 211–223.
Suárez-González E M, López M G, Délano-Frier J P, Gómez-Leyva J F. 2014. Expression of the 1-SST and 1-FFT genes and consequent fructan accumulation in Agave tequilana, and A. inaequidens, is differentially induced by diverse (a)biotic-stress related elicitors. Journal of Plant Physiology, 171, 359–372.
Vijn I, Smeekens S. 1999. Fructan: more than a reserve carbohydrate? Plant Physiology, 120, 351–360.
Wang Z H, Liu X L, Li R Z, Chang X P, Jing R L. 2011. Development of near-infrared reflectance spectroscopy models for quantitative determination of water-soluble carbohydrate content in wheat stem and glume. Analytical Letters, 44, 2478–2490.
Xue G P, McIntyre C L, Jenkins C L D, Glassop D, van Herwaarden A F, Shorter R. 2008. Molecular dissection of variation in carbohydrate metabolism related to water soluble carbohydrate accumulation in stems of wheat (Triticum aestivum L.). Plant Physiology, 146, 441–454.
Yang D L, Jing R L, Chang X P, Li W. 2007. Identification of quantitative trait loci and environmental interactions for accumulation and remobilization of water-soluble carbohydrates in wheat (Triticum aestivum L.) stems. Genetics, 176, 571–584.
Yue A Q, Li A, Mao X G, Chang X P, Li R Z, Jia J Z, Jing R L. 2011. Single nucleotide polymorphism and mapping of 6-SFT-A gene responsible for fructan biosynthesis in common wheat. Scientia Agricultura Sinica, 44, 2216–2214. (in Chinese)
Yue A Q, Li A, Mao X G, Chang X P, Liu Y P, Li R Z, Jia J Z, Jing R L. 2016. Sequence polymorphism and cumulative effect with 6-SFT-A2 of fructan biosynthesis gene 6-SFT-D in wheat. Acta Agronomica Sinica, 42, 11–18. (in Chinese)
Yue A Q, Li A, Mao X G, Li R Z, Jing R L. 2015. Identification and development of a functional marker from 6-SFT-A2 associated with grain weight in wheat. Molecular Breeding, 35, 63.
Zhang B, Li W Y, Chang X P, Li R Z, Jing R L. 2014. Effects of favorable alleles for water-soluble carbohydrates at grain filling on grain weight under drought and heat stresses in wheat. PLOS ONE, 9, e102917.
Zhang H Y, Mao X G, Zhang J N, Chang X P, Jing R L. 2013. Single-nucleotide polymorphisms and association analysis of drought resistance gene TaSnRK2.8 in common wheat. Plant Physiology and Biochemistry, 70, 174–181.
Zhang J J, Xu Y J W, Dell B, Vergauwen R, Biddulph B, Khan N, Luo H, Appels R, Ende W V D A. 2015. Wheat 1-FEH w3 variant underlies enzyme activity for stem WSC remobilization to grain under drought. New Phytologist, 205, 293–305.
Zhang J N, Hao C Y, Ren Q, Chang X P, Liu G R, Jing R L. 2011. Association mapping of dynamic developmental plant height in common wheat. Planta, 234, 891–902.
Zhang Y J, Liu J D, Xia X C, He Z H. 2014. TaGS-D1, an ortholog of rice OsGS3, is associated with grain weight and grain length in common wheat. Molecular Breeding, 34, 1097–1107.
[1] Tiantian Chen, Lei Li, Dan Liu, Yubing Tian, Lingli Li, Jianqi Zeng, Awais Rasheed, Shuanghe Cao, Xianchun Xia, Zhonghu He, Jindong Liu, Yong Zhang. Genome wide linkage mapping for black point resistance in a recombinant inbred line population of Zhongmai 578 and Jimai 22[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3311-3321.
[2] Dili Lai, Md. Nurul Huda, Yawen Xiao, Tanzim Jahan, Wei Li, Yuqi He, Kaixuan Zhang, Jianping Cheng, Jingjun Ruan, Meiliang Zhou. Evolutionary and expression analysis of sugar transporters from Tartary buckwheat revealed the potential function of FtERD23 in drought stress[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3334-3350.
[3] Zimeng Liang, Juan Li, Jingyi Feng, Zhiyuan Li, Vinay Nangia, Fei Mo, Yang Liu. Brassinosteroids improve the redox state of wheat florets under low-nitrogen stress and alleviate degeneration[J]. >Journal of Integrative Agriculture, 2025, 24(8): 2920-2939.
[4] Qing Li, Zhuangzhuang Sun, Zihan Jing, Xiao Wang, Chuan Zhong, Wenliang Wan, Maguje Masa Malko, Linfeng Xu, Zhaofeng Li, Qin Zhou, Jian Cai, Yingxin Zhong, Mei Huang, Dong Jiang. Time-course transcriptomic information reveals the mechanisms of improved drought tolerance by drought priming in wheat[J]. >Journal of Integrative Agriculture, 2025, 24(8): 2902-2919.
[5] Liulong Li, Zhiqiang Mao, Pei Wang, Jian Cai, Qin Zhou, Yingxin Zhong, Dong Jiang, Xiao Wang. Drought priming enhances wheat grain starch and protein quality under drought stress during grain filling[J]. >Journal of Integrative Agriculture, 2025, 24(8): 2888-2901.
[6] Xinhu Guo, Jinpeng Chu, Yifan Hua, Yuanjie Dong, Feina Zheng, Mingrong He, Xinglong Dai. Long-term integrated agronomic optimization maximizes soil quality and synergistically improves wheat yield and nitrogen use efficiency[J]. >Journal of Integrative Agriculture, 2025, 24(8): 2940-2953.
[7] Jinpeng Li, Siqi Wang, Zhongwei Li, Kaiyi Xing, Xuefeng Tao, Zhimin Wang, Yinghua Zhang, Chunsheng Yao, Jincai Li. Effects of micro-sprinkler irrigation and topsoil compaction on winter wheat grain yield and water use efficiency in the Huaibei Plain, China[J]. >Journal of Integrative Agriculture, 2025, 24(8): 2974-2988.
[8] Baohua Liu, Ganqiong Li, Yongen Zhang, Ling Zhang, Dianjun Lu, Peng Yan, Shanchao Yue, Gerrit Hoogenboom, Qingfeng Meng, Xinping Chen. Optimizing management strategies to enhance wheat productivity in the North China Plain under climate change[J]. >Journal of Integrative Agriculture, 2025, 24(8): 2989-3003.
[9] Ziqiang Che, Shuting Bie, Rongrong Wang, Yilin Ma, Yaoyuan Zhang, Fangfang He, Guiying Jiang. Mild deficit irrigation delays flag leaf senescence and increases yield in drip-irrigated spring wheat by regulating endogenous hormones[J]. >Journal of Integrative Agriculture, 2025, 24(8): 2954-2973.
[10] Xianhong Zhang, Zhiling Wang, Danmei Gao, Yaping Duan, Xin Li, Xingang Zhou. Wheat cover crop accelerates the decomposition of cucumber root litter by altering the soil microbial community[J]. >Journal of Integrative Agriculture, 2025, 24(7): 2857-2868.
[11] Zhongwei Tian, Yanyu Yin, Bowen Li, Kaitai Zhong, Xiaoxue Liu, Dong Jiang, Weixing Cao, Tingbo Dai. Optimizing planting density and nitrogen application to mitigate yield loss and improve grain quality of late-sown wheat under rice–wheat rotation[J]. >Journal of Integrative Agriculture, 2025, 24(7): 2558-2574.
[12] Wei Liu, Xueling Huang, Meng Ju, Mudi Sun, Zhimin Du, Zhensheng Kang, Jie Zhao. Molecular evidence of the west-to-east dispersal of Puccinia striiformis f. sp. tritici in central Shaanxi and the migration of the inoculum from Gansu[J]. >Journal of Integrative Agriculture, 2025, 24(6): 2251-2265.
[13] Abdoul Kader Mounkaila Hamani, Sunusi Amin Abubakar, Yuanyuan Fu, Djifa Fidele Kpalari, Guangshuai Wang, Aiwang Duan, Yang Gao, Xiaotang Ju. The coupled effects of various irrigation schedules and split nitrogen fertilization modes on post-anthesis grain weight variation, yield, and grain quality of drip-irrigated winter wheat (Triticum aestivum L.) in the North China Plain[J]. >Journal of Integrative Agriculture, 2025, 24(6): 2123-2137.
[14] Mingmei Wu, Rui Dong, Yan Zhang, Haojie Liao, Tian Tian, Dandan Xu, Youjun Zhang, Zhaojiang Guo, Shaoli Wang.
Overexpression of TuABCC4 is associated with abamectin resistance in Tetranychus urticae Koch
[J]. >Journal of Integrative Agriculture, 2025, 24(6): 2299-2310.
[15] Rumeng Wang, Jinsong Luo, Jian Zeng, Yingying Xiong, Tianchu Shu, Dawei He, Zhongsong Liu, Zhenhua Zhang. BjuB05.GS1.4 promotes nitrogen assimilation and participates in the domestication of shoot nitrogen use efficiency in Brassica juncea[J]. >Journal of Integrative Agriculture, 2025, 24(5): 1800-1812.
No Suggested Reading articles found!