水稻显性半矮秆基因的SCAR标记及初步定位

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。

SCAR Markers and Preliminary Gene Mapping of a Dominant Semi-dwarf Mutant in Rice

Utilization of dwarf and semi-dwarf genes was one of the greatest achievements in rice breeding in 20^th 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.