The present invention discloses a rice whole
genome SNP
chip and an application thereof. A method for preparing the
chip comprises: (1) obtaining a
first class of probes on a
chip, wherein sequencing is performed to obtain a parental
genome sequence, resequencing data of other rice varieties in a public
database are combined, a Nipponbare
genome is adopted as a reference sequence, a MAQ
software is adopted to match and analyze all the
sequencing data, and finally a SNP marker is screened; (2) obtaining a second class of probes on the chip, wherein a rice function
gene is obtained from the public
database, sequence difference reflecting
gene function is searched, and a SNP /
INDEL probe is designed according to the sequence difference; (3) adopting an infinium chip
manufacturing technology to produce a SNP chip; and (4) testing accuracy and application efficiency of the chip. The chip of the present invention can be applicable for rice
germplasm resource molecule marker
fingerprint analysis, seed authenticity detection, filial generation
genotyping, and other related researches.