Rice plant architecture is regarded as one of the major agronomical traits that influence grain yield, which is mainly determined by plant height, tiller number, tiller angle and panicle morphology. Tiller angle, mainly controlled by the asymmetric growth of tiller base, is defined as the angle between the main culm and its side tillers, and it is one of the decisive factor for achieving ideal plant architecture in rice (Wang and Li 2008, 2011). In practice, spread-out rice varieties are able to escape from some diseases but occupy too much space. By contrast, extremely compact rice varieties are less efficient in capturing light and are more susceptible to infection by pathogen attack. Thus, a suitable tiller angle is very important for rice yield (Jiang et al. 2012; Huang et al. 2016; Qu et al. 2021).
Previous studies have revealed that rice tiller angle is strongly associated with gravitropism and polar auxin transport (PAT) (Roychoudhry and Kepinski 2015; Zhang et al. 2018; Li et al. 2019). For example, LAZY1 (LA1), the first gene identified in rice, controls tiller angle and encodes a novel plant-specific protein with an unknown function. LA1 controls shoot gravitropism and tiller angle by regulating PAT, affecting the asymmetric distribution of auxin; and the la1-mutant displays enlarged tiller angle in rice (Li et al. 2007). Subsequently, several suppressors of LA1 (SOLs), such as dwarf 17 (d17), d10, d27, d14, and d3, that are involved in the strigolactones (SLs) biosynthetic or signaling pathway are able to recover the enlarged tiller angle phenotype of la1 by enhancing gravitropic response (Sang et al. 2014). Recently, it is reported that LA1-interacting protein OsBRXL4 affects its nuclear localization, and that it is essential for function of LA1 in controlling rice tiller angle. Furthermore, three rice BRXL genes (OsBRXL1, OsBRXL4, and OsBRXL5) can act redundantly in generating the rice tiller angle (Li et al. 2019). In addition, HEAT STRESS TRANSCRIPTION FACTOR 2D (HSFA2D) acts as an upstream positive regulator of LA1-meidated asymmetric distribution of auxin, thus, induces the asymmetric expression of WUSCHEL RELATED HOMEOBOX6 (WOX6) and WOX11, two transcription factors that specify tiller angle by modulating rice shoot gravitropism (Zhang et al. 2018). Other key genes/quantitative trait loci (QTLs) controlling tiller angle have also been identified and functionally characterized over the past decades, including Tiller Angle Control 1 (TAC1) (Yu et al. 2007), PROSTRATE GROWTH 1 (PROG1) (Jin et al. 2008; Tan et al. 2008). Loose Plant Architecture 1 (LPA1) (Wu et al. 2013), PLANT ARCHITECTURE AND YIELD 1 (PAY1) (Zhao et al. 2015), TILLER INCLINED GROWTH 1 (TIG1) (Zhang et al. 2019), TAC3 (Dong et al. 2016a), TAC4 (Li et al. 2021) and LA2 (Huang et al. 2021). Although these findings provide valuable information regarding tiller angle regulation, the underlying molecular mechanisms and functional relationships among them in rice is largely unknown.
Map-based cloning and association mapping have contributed to understanding of the genetic and molecular bases of many complex agronomic traits. However, conventional cloning method is extremely troublesome (Korte and Farlow 2013; Bhat et al. 2021). Fortunately, advances in next-generation sequencing (NGS) technology and bioinformatics tools, providing large-scale SNP arrays in natural groups in rice become reality (Alexandrov et al. 2015; Wang et al. 2020). Genome-wide association studies (GWAS), as a powerful method for studying the genetics of natural variation based on a linkage disequilibrium mapping approach, have widely been applied to detection of complex agronomic traits in plants (Cockram et al. 2010; Wang et al. 2016, 2020; Luján Basile et al. 2019; Okada et al. 2019; Bai et al. 2021). However, so far, only have TAC3 and DWARF2 (D2), been identified as rice tiller angle regulators by GWAS (Dong et al. 2016b). Addition attempts to identify rice tiller angle regulator using GWAS detected several genetic loci (Lu et al. 2015; Wu et al. 2019). These GWAS analyses were performed in indica and japonica varieties or indica varieties (Lu et al. 2015; Dong et al. 2016b; Wu et al. 2019), and few studies have been performed within japonica varieties that generally have smaller tiller angles than indica varieties. To understand the regulatory mechanisms of japonica rice tiller angle, more QTLs need to be identified from the japonica varieties.
The purpose of this study was to detect genetic loci significantly associated with tiller angle in japonica, based on GWAS analysis on a panel of 164 japonica varieties selected from the 3K RGP, and to explore favorable SNP alleles and reliable candidate genes that can be used to breed rice with ideal tiller angle. Taken together, our study revealed in total 11 candidate genes and provided the basis for further elucidating mechanisms underlying tiller angle in rice.