AG	Anaerobic germination
bp	Basepairs
bHLH	Basic helix-loop-helix
dai	Days after imbibition
das	Days after sowing
DS	Direct seeding
DEG	Differentially expressed gene
DUF	Domain of unknown function
GEMMA	Genome-wide Efficient Mixed Model Analysis
GLM	Generalized linear model
GWAS	Genome wide association study
HISAT2	Hierarchical indexing for spliced alignment of transcripts 2
Indels	Insertions-deletions
IPP	Isopentenyl pyrophosphate
IRRI	International Rice Research Institute
IRGSP	International Rice Genome Sequencing Project
kb	Kilobasepairs
KHO	Khao Hlan On
LD	Linkage disequilibrium
LOD	Logarithm of the odds
LTP	Lipid transfer protein
Mb	Megabasepairs
MR	Ma-Zhan Red
NILs	Near isogenic lines
PAs	Proanthocyanidins
PAV	Presence-absence variant
PROLM	Prolamin
RIN	RNA integrity number
RNA-Seq	RNA Sequencing
ROS	Reactive Oxygen Species
SNP	Single Nucleotide Polymorphism
Q-Q plot	Quantile-quantile plot
QTL	Quantitative trait locus
TCA	tricarboxylic acid
TTP	Trehalose-6-phosphate phosphatase
3K RG	3000 Rice Genomes