The invention relates to the field of
plant gene positioning technology, and particularly to a method for positioning a rice complex trait
gene. The method comprises the steps of constructing an F2 group by means of two rice parents with remarkable target trait difference, dividing the F2 group into more than 3 or 3 subgroups according to a
phenotype, selecting more than 30 or 30 single strains with the same
phenotype in each subgroup, extracting
DNA for constructing a plurality of mixing pools and performing re-sequencing, through comparing the sequencing reads of each mixing
pool with a
reference genome sequence, detecting SNP by means of
software GATK, calculating the SNP-index and deltaSNP-index value of the corresponding site by means of an SNP-
index method, drawing the distribution map of the deltaSNP-index, using the area which corresponds with a substantial associated deltaSNP-index as a candidate area, using the area which corresponds with the interaction of different deltaSNP-indexes at the same physical positions as a final candidate area, and predicting the
candidate gene according to a
gene annotation website, a sequencing depth and the deltaSNP-index value. The methodhas advantages of low cost, short time consumption and high efficiency. A plurality of candidate genes can be positioned. A candidate area with the
target gene can be quickly shortened. The number oftarget genes which are closely linked can be accurately predicted.