粳稻品系Y98149是从离子束诱变的后代中获得的显性半矮秆突变体，与野生型Y98148是一对株高近等基因系。将已经获得的3个与水稻显性半矮秆基因紧密连锁的RAPD标记分别克隆、测序，根据测序结果设计了3对特异性PCR引物，成功地将RAPD标记S1041525、S1076549和S1272403转化成更稳定的SCAR标记SCS1041498、SCS1076510和SCS1272388。通过Y98148×Y98149的F2代分离群体的分析，这3个SCAR标记与显性半矮秆基因的遗传距离分别为12.6 cM、7.5 cM和16.3 cM, 且位于基因的同一侧。序列同源性比较表明，标记S1272403为单拷贝，其核苷酸序列与水稻第7染色体上两个BAC克隆B1249D05(AP006451)和OJ1212-C12(AP005604)同源性为99%，B1249D05与OJ1212-C12有23 kb的重叠区域，标记S1272403位于这个重叠区域，据此初步将显性半矮秆基因定位，为进一步精确定位和图位克隆奠定了基础。
Utilization of dwarf and semi-dwarf genes was one of the greatest achievements in rice breeding in 20th century. Through ion beam mutagenesis, a new rice semi-dwarf mutant Y98149 was obtained. The plant height of Y98149 was controlled by a pair of dominant genes, not affected by cytoplasm. This dominant semi-dwarf gene could be used to resolve the problem of the dwarf gene deficient in rice dwarf breeding and the heterobeltiosis of F1 in plant height in the utilization of inter-subspecific heterosis. Y98148 and Y98149 are near-isogenic lines(NILs) of dominant semi-dwarf gene. A RAPD analysis was made between NILs with arbitrary 10-mer oligonucleotide primers and three polymorphic RAPD bands were obtained. The three special RAPD bands were recovered ,purified and inserted in pUCm-T vector, and then transferred into E.coli. JM109. Positive colonies were identified for sequencing(Fig.1). According to the obtained sequences, 18–24-mer specific primers were designed as SCAR primers, and the SCAR-PCR reaction conditions were optimized. Consequently, RAPD markers S1041525, S1076549 and S1272403 were successfully converted into SCAR markers SCS1041498, SCS1076510 and SCS1272388, most optimal annealing temperature were 61℃,58℃ and 62℃,respectively. F2 progeny with 384 individuals of Y98148×Y98149 was analyzed to map SCAR markers in relationship to this gene. The result indicated that the genetic distances of SCS1041498, SCS1076510 and SCS1272388 to the gene were 12.6 cM, 7.5 cM and 16.3 cM, respectively. The blast result indicated nucleotide sequence of marker S1272403 was 99% identical with the BAC clones B1249D05（AP006451）and OJ1212_C12（AP005604）on chromosome 7 and was a single copy in rice genomic DNA. B1249D05 and OJ1212_C12 had a overlap of 23 kb, which marker S1272403 lay in. So this new semi-dwarf gene was considered to be located on chromosome 7 preliminarily. The markers are useful to marker-assisted selection for the breeding and tagging it with positional cloning.
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