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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.

A Novel Tiller Angle Gene, TAC3, together with TAC1 and D2 Largely Determine the Natural Variation of Tiller Angle in Rice Cultivars