Mining rice new germplasm containing S5n gene by functional molecular marker and sequencing

Inter-subspecific hybrids between indica and japonica varieties yield strong biological heterosis, but it is difficult to utilize the hybrids directly in commercial production due to sterility of F₁. A special gene S₅ⁿ may overcome the hybrids sterility, which is caused by the interaction between S₅ loci. Recently, S₅ⁿ had been cloned, and it was revealed containing a large DNA deletion sequence that made the gene nonfunctional, compared to S₅ⁱ or S₅^j. We designed a pair of primers flanking the deletion sequence of S₅ⁿ, and then applied to distinguish the varieties with S₅ⁿ or non-S₅ⁿ, convincing result suggested that the primers could be served as functional molecular marker to efficiently identify the new germplasm with S₅ⁿ. Using the functional marker, we surveyed 197 varieties from China National Micro-core Rice Collection, and found ten of which represented S₅ⁿ including following varieties: Haobuka, S₅ⁿ- bangqishiluo, Mubanggu, Xiaohonggu, Mowanggu’neiza, Laozaogu, Fanhaopi, Feie’nuo2, Baoxie-7B, Teqingxuanhui. Among them, two varieties Sanbangqishiluo and Laozaogu was previously reported to contain S₅ⁿ gene. Further sequence analysis on the DNA sequence covering both sides of deletion in S₅ⁿ of the 10 varieties confirmed that the detected sequences in above varieties was identical with those of varieties containing S₅ⁿ, such as 02428 and Linglun. These results suggested that the gene in S₅ lo- cus of the ten varieties was also nonfunctional and it proved the presence of S₅ⁿ gene.