“…Determining the type of loci likely to affect growth rate is less straightforward, but phytohormones, including auxin and ethylene, can trigger phytochrome-interacting factors (PIFs) (Leivar and Quail, 2011), which in turn regulate plant growth (Liu et al, 2011;Stewart et al, 2011), making phytohormone-related genes good candidates. Our literature searches implicated several phytohormone genes differentially expressed in SH vs. indica (Table 4), including five auxin related genes (LOC_Os02g57250, LOC_Os03g22270, LOC_Os03g53150, LOC_Os05g33900 and LOC_Os11g44810) (Kitomi et al, 2012;Arenhart et al, 2014;Arbelaez et al, 2017;Hoang et al, 2019), one ethylene gene (LOC_Os02g43790) (Bargsten et al, 2014;Zhang et al, 2017;Malukani et al, 2019), and one salicylic acid gene (LOC_Os11g15040) (Hsieh et al, 2018). Several other DE phytohormone genes were found assigned to the hormone metabolism MapMan bin (Table 4, Supplementary Table 15), including LOC_Os02g12890, a cytochrome P450 gene related to auxin signal transduction (Xiumei et al, 2015), LOC_Os02g47510, a gene related to abscisic acid (Wang et al, 2015;Borah et al, 2017) and ethylene related genes (LOC_Os05g28740, LOC_Os05g05680, LOC_Os10g39140 and LOC_Os03g08500) (Sudo et al, 2008;Galland et al, 2014;Yang et al, 2015;González-Schain et al, 2019).…”