Candidate gene identification and GO enrichment analysis
Panicle traits have been well-studied in crop plants and model systems and many candidate genes have been reported (Miura et al., 2010; Doust, 2007; McSteen, 2006; Vollbrecht et al., 2005). For the 18 panicle architecture QTL identified in our study, the confidence intervals ranged from 2 to 32 cM and from 0.9 to 35 Mb. We linked the QTL discovered here with known candidate genes that have been reported in previous studies (Supplemental Table S2).
Among these candidate genes, key transcription factors and hormone related genes associated with panicle development were identified in the intervals of most QTL exhibiting environmental interactions. For example, key regulators involved in GA metabolism (Pavir.3KG352627 as the homolog of GA2ox3 in 3K@38; Pavir.5KG065800 as the homolog of GA3ox2 in 5K@14.06) and CK signaling pathways (Pavir.7NG435700 as the homolog of ARR6 in 7N@54.06; Pavir.9KG213000 as the homolog of ARR1 in 9K@51.96) were found in four branching QTL x E intervals. A number of key flowering genes were also found in our panicle QTL intervals. These genes are known to be involved in the photoperiodic flowering pathway and control panicle morphology in other grasses (Shrestha et al., 2014; Tsuji et al., 2010). However, these candidate genes were not co-localized with flowering QTL that we identified, indicating the potentially complex functions of flowering time genes in the transition from vegetative to reproductive phases.
GO enrichment analysis identified 380 significant GO terms for genes within the QTL intervals for panicle traits. ‘Response to Auxin’ was one of the significantly enriched GO terms (p =0.0012). This is an exciting result as the auxin signaling pathway has been previously shown to be important in panicle meristem development and affects primary branching number in rice and other grasses (He et al., 2018; Zhang & Yuan, 2014). Several other significant terms that are relevant to our study traits include ‘response to oxidative stress’ and ‘H4/H2A histone acetyltransferase complex’ (Boycheva, Vassileva, & Iantcheva, 2014; Deng et al., 2007; Peng et al., 2018; Wu et al., 2017; Yano et al., 2019). These results point to potentially interesting candidate genes and hormone-related pathways that are likely important in panicle development.