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 In Del21-39 and SNP-2164 polymorphisms to distinguish the three haplotypes in the 1-FFT-A1. 1-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,1000-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 significantly influenced by haplotypes. HapIII showed a significant positive effect on TGW,PLE and TNSS. Fructan 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- 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 In Del21-39 and SNP-2164 polymorphisms to distinguish the three haplotypes in the 1-FFT- A1. 1-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, 1000-grain weight (TGW) at different grain filling stages and peduncle length (PLE). Comparison of the effects o f three haplotypes on agronomic traits indicated that TGW, PLE and total number of spikelets per spike (TNSS) were pre-observed by haplotypes. HapIII showed a significant positive effect on TGW, PLE and TNSS.