Fig. S1. Development of allele-specific marker.A, Gene structure of OsBadh2 showing the polymorphic 8-bp deletion and three SNPs in the XWX17 allele compared to the sequences of Nipponbare (NPB) and GM4 alleles. B, Schematic diagram showing the development of the allele-specific (Mfgr) for fgr. C and D, Verification of AS-PCR marker for grain fragrance in 30 rice accessions by electrophoresis on 3% agarose gels. M, Marker; Lanes 1 to 30 indicate Nipponbare, R9311, GM4, Shuhui 527, Yuejingsimiao 2, Yuewangsimiao, Yueqisimiao, Teqing, IR64, R900, Huazhan, Jinsui 128, Huanghuazhan, Daohuaxiang 2, Xiangyaxiangzhen, Yueyou 9113, Nongxiang 18, Dalixiang, Tianyouhuazhan, Jigeng 88, Dongdao 2, Xiangwanxian 13, Xiangwanxian 17, Nongxiang 24, Nongxiang 32, Taoyouxiangzhan, Xiangwanxian 12, Yuzhenxiang, Y Liangyou 1 and R1128, respectively.

Fig. S2. Breeding strategy for developing rice inbred lines with high grain quality, yield and rice blast resistance. CS, Changsha; SY, Sanya; MAS, Marker-assisted selection; XWX17, Xiangwanxian 17.

Fig. S3. Comparisons of agronomic traits in three inbred lines against recurrent parent Xiangwanxian 17 (XWX17).* and ** represent significant differences at the 0.05 and 0.01 levels, respectively.

Fig. 1. Integrating marker-assisted selection with traditional breeding experience to breed novel fragrant rice variety, Nongxiang 42, with high eating and cooking quality and broad-spectrum rice blast resistance.A, Genotyping three desired alleles in Xiangwanxian 17 (XWX17), Gumei 4 (GM4) and three developed inbred lines. B, Comparison of rice grain appearance between XWX17 and Nongxiang 42. C, Leaf blast disease resistance comparison in CO39, Nongxiang 42, XWX17 and GM4. D and E, Field performance of Nongxiang 42 and XWX17, respectively. F, Graphical genotyping of the genetic background of Nongxiang 42 using 48 simple sequence repeat markers. Chr, Chromosome.