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] Zihui Liu, Xiangjun Lai, Yijin Chen, Peng Zhao, Xiaoming Wang, Wanquan Ji, Shengbao Xu. Selection and application of four QTLs for grain protein content in modern wheat cultivars[J]. >Journal of Integrative Agriculture, 2024, 23(8): 2557-2570.
[2] Gensheng Zhang, Mudi Sun, Xinyao Ma, Wei Liu, Zhimin Du, Zhensheng Kang, Jie Zhao. Yr5-virulent races of Puccinia striiformis f. sp. tritici possess relative parasitic fitness higher than current main predominant races and potential risk[J]. >Journal of Integrative Agriculture, 2024, 23(8): 2674-2685.
[3] Myeong-Hyeon Min, Aye Aye Khaing, Sang-Ho Chu, Bhagwat Nawade, Yong-Jin Park. Exploring the genetic basis of pre-harvest sprouting in rice through a genome-wide association study-based haplotype analysis[J]. >Journal of Integrative Agriculture, 2024, 23(8): 2525-2540.
[4] Hui Fang, Xiuyi Fu, Hanqiu Ge, Mengxue Jia, Jie Ji, Yizhou Zhao, Zijian Qu, Ziqian Cui, Aixia Zhang, Yuandong Wang, Ping Li, Baohua Wang. Genetic analysis and candidate gene identification of salt tolerancerelated traits in maize[J]. >Journal of Integrative Agriculture, 2024, 23(7): 2196-2210.
[5] Wenjie Yang, Jie Yu, Yanhang Li, Bingli Jia, Longgang Jiang, Aijing Yuan, Yue Ma, Ming Huang, Hanbing Cao, Jinshan Liu, Weihong Qiu, Zhaohui Wang. Optimized NPK fertilizer recommendations based on topsoil available nutrient criteria for wheat in drylands of China[J]. >Journal of Integrative Agriculture, 2024, 23(7): 2421-2433.
[6] Peng Liu, Langlang Ma, Siyi Jian, Yao He, Guangsheng Yuan, Fei Ge, Zhong Chen, Chaoying Zou, Guangtang Pan, Thomas Lübberstedt, Yaou Shen. Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize[J]. >Journal of Integrative Agriculture, 2024, 23(7): 2178-2195.
[7] Yibo Hu, Feng Qin, Zhen Wu, Xiaoqin Wang, Xiaolong Ren, Zhikuan Jia, Zhenlin Wang, Xiaoguang Chen, Tie Cai. Heterogeneous population distribution enhances resistance to wheat lodging by optimizing the light environment[J]. >Journal of Integrative Agriculture, 2024, 23(7): 2211-2226.
[8] Bingli Jiang, Wei Gao, Yating Jiang, Shengnan Yan, Jiajia Cao, Litian Zhang, Yue Zhang, Jie Lu, Chuanxi Ma, Cheng Chang, Haiping Zhang. Identification of P-type plasma membrane H+-ATPases in common wheat and characterization of TaHA7 associated with seed dormancy and germination[J]. >Journal of Integrative Agriculture, 2024, 23(7): 2164-2177.
[9] Zhikai Cheng, Xiaobo Gu, Yadan Du, Zhihui Zhou, Wenlong Li, Xiaobo Zheng, Wenjing Cai, Tian Chang.

Spectral purification improves monitoring accuracy of the comprehensive growth evaluation index for film-mulched winter wheat [J]. >Journal of Integrative Agriculture, 2024, 23(5): 1523-1540.

[10] Yongchao Hao, Fanmei Kong, Lili Wang, Yu Zhao, Mengyao Li, Naixiu Che, Shuang Li, Min Wang, Ming Hao, Xiaocun Zhang, Yan Zhao.

Genome-wide association study of grain micronutrient concentrations in bread wheat [J]. >Journal of Integrative Agriculture, 2024, 23(5): 1468-1480.

[11] Xuan Li, Shaowen Wang, Yifan Chen, Danwen Zhang, Shanshan Yang, Jingwen Wang, Jiahua Zhang, Yun Bai, Sha Zhang.

Improved simulation of winter wheat yield in North China Plain by using PRYM-Wheat integrated dry matter distribution coefficient [J]. >Journal of Integrative Agriculture, 2024, 23(4): 1381-1392.

[12] YANG Wei-bing, ZHANG Sheng-quan, HOU Qi-ling, GAO Jian-gang, WANG Han-Xia, CHEN Xian-Chao, LIAO Xiang-zheng, ZHANG Feng-ting, ZHAO Chang-ping, QIN Zhi-lie.

Transcriptomic and metabolomic analysis provides insights into lignin biosynthesis and accumulation and differences in lodging resistance in hybrid wheat [J]. >Journal of Integrative Agriculture, 2024, 23(4): 1105-1117.

[13] Yingxia Dou, Hubing Zhao, Huimin Yang, Tao Wang, Guanfei Liu, Zhaohui Wang, Sukhdev Malhi.

The first factor affecting dryland winter wheat grain yield under various mulching measures: Spike number [J]. >Journal of Integrative Agriculture, 2024, 23(3): 836-848.

[14] Yonghui Fan, Boya Qin, Jinhao Yang, Liangliang Ma, Guoji Cui, Wei He, Yu Tang, Wenjing Zhang, Shangyu Ma, Chuanxi Ma, Zhenglai Huang.

Night warming increases wheat yield by improving pre-anthesis plant growth and post-anthesis grain starch biosynthesis [J]. >Journal of Integrative Agriculture, 2024, 23(2): 536-550.

[15] Wenqiang Wang, Xizhen Guan, Yong Gan, Guojun Liu, Chunhao Zou, Weikang Wang, Jifa Zhang, Huifei Zhang, Qunqun Hao, Fei Ni, Jiajie Wu, Lynn Epstein, Daolin Fu.

Creating large EMS populations for functional genomics and breeding in wheat [J]. >Journal of Integrative Agriculture, 2024, 23(2): 484-493.

No Suggested Reading articles found!