Yongzhong Xing, Zhongmin Han, Kai Lu, Yong Hu, Zilong Guo, Weibo Xie, Guangwei Li, Hu Zhao, Wen Yao, Haijiao Dong, Xufeng Bai, and Lin Yang
Tiller angle is one of the most important components of the ideal plant architecture that can greatly enhance rice grain yield. Understanding the genetic basis of tiller angle and mining favorable alleles will be helpful for breeding new plant-type varieties. Here, we performed genome-wide association studies (GWAS) to identify genes controlling tiller angle using 529 diverse accessions of Oryza sativa including 295 indica and 156 japonica accessions in two environments. We identified 7 common quantitative trait loci (QTLs), including the previously reported major gene Tiller Angle Control 1 (TAC1), in the two environments, 10 and 13 unique QTLs in Hainan and Wuhan, respectively. More QTLs were identified in indica than in japonica, and three major QTLs (qTA3, qTA1b/DWARF2 (D2) and qTA9c/TAC1) were fixed in japonica but segregating in indica, which explained the wider variation observed in indica compared with that in japonica. No common QTLs were identified between the indica and japonica subpopulations. Mutant analysis for the candidate gene of qTA3 on chromosome 3 indicated a novel gene, Tiller Angle Control 3 (TAC3), encoding a conserved hypothetical protein controlling tiller angle. TAC3 is preferentially expressed in the tiller base. The ebisu dwarf (d2) mutant exhibited a decreased tiller angle, in addition to its previously described abnormal phenotype. A nucleotide diversity analysis revealed that TAC3, D2 and TAC1 have been subjected to selection during japonica domestication. A haplotype analysis identified favorable alleles of TAC3, D2 and TAC1, which may be used for breeding plants with an ideal architecture. In conclusion, there is a diverse genetic basis for tiller angle between the two subpopulations, and it is the novel gene TAC3 together with TAC1, D2, and other newly identified genes in this study that controls tiller angle in rice cultivars., Author Summary Tiller angle is the key component of plant architecture that greatly affect grain yield. However, few tiller angle-related genes that can be used for improving rice plant architecture have been isolated based on natural variation. Here, we identified 7 common tiller angle-related QTLs by a genome-wide association study, including the previously reported major gene TAC1, in two environments in the 529 diverse rice accessions and dozens of QTLs specially identified in one environment. Two QTLs were validated by mutant analysis: A novel gene TAC3, encoding a conserved hypothetical protein and preferentially expressing in the tiller base, was the candidate gene of qTA3; d2 mutant exhibited a decreased tiller angle, in addition to its previously described abnormal phenotype. A haplotype analysis identified favorable alleles of TAC3, D2 and TAC1 in indica, which may be used for breeding plants with an ideal architecture, while they were all subjected to selection and fixed in japonica. In conclusion, there is a diverse genetic basis for tiller angle between the two subpopulations, and it is the novel gene TAC3, together with TAC1 and D2 that greatly controls tiller angle in rice cultivars.