In this study , a pair of degenerate PCR primer was designed base on the known LMW-GS genes , with which 4 district sequences were obtained from a weak gluten variety of wheat , Chuannong 16 , designated as LMWCN16-1 , LMWCN16-2 , LMWCN16-3 , and LMWCN16-4 , respectively . The total lengths of the 4 genes were 902 , 915 , 909 and 927 bp ,respectively . All these genes were predicted to be located at Glu-D3 locus and amount of DNA variations were found , including 97 nucleotide substitutions and several insertions and deletions (indels) . Sequence analysis indicated that the pairwise identities between the 4 genes were from 81.9% to 95.6% . LMWCN16-2 and LMWCN16-3 were more close related , while LMWCN16-4 was distinguished from LMWCN16-2 and LMWCN16-3 by a longer repetitive domain and the different position of the seventh cysteines involved in inter-molecular disulphide bond . These differences might result in different effects on the formation of the glutenin polymer and consequently the wheat quality . LMWCN16-1 is a putative pseudogene due to the five inframe stop codons and the frame shifting mutation in its C-terminal domain . The function loss of LMWCN16-1 might weaken the proportion of Glu-D3 in the total LMW-GS and bring negative influence on wheat quality .