Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice

Rice

Table 2 Summary of the five genes selected from the top 10 associations in TWAS

Phenotype	Phenotype abbreviation	MSU ID	Gene Symbol	Functional description	TWAS rank	−logP	FDR adjusted P-value	Pearson’s correlation between the expression profile and the phenotype
Phenotype	Phenotype abbreviation	MSU ID	Gene Symbol	Functional description	TWAS rank	−logP	FDR adjusted P-value	All WRC (n = 57)	admixed (n = 7)	aus (n = 19)	indica (n = 21)	japonica (n = 10)
Crown root diameter	RD_C	LOC_Os03g31480	OsEXPA31	α-expansin subfamily, mediating cell wall loosening	1	5.15	0.06	−0.69	−0.38	−0.76	−0.60	−0.80
Crown root diameter	RD_C	LOC_Os08g39890	OsSPL14	Transcription activator/SPL14, a master regulator of rice plant architecture	5	4.32	0.15	0.76	0.70	0.87	0.74	0.72
The ratio of deep rooting	RDR	LOC_Os09g26999	OsDEP1	Dense and erect panicle 1, a pleiotropic gene for grain yield	5	4.08	0.28	0.54	0.39	0.20	0.68	0.21
The number of lateral root tips	NRT_L	LOC_Os08g10450	OsENT1	Equilibrative nucleoside transporter 1	6	3.88	0.37	−0.69	−0.14	−0.64	−0.47	−0.28
Crown root length	RL_C	LOC_Os12g42250	OsDEC1	Decelerator of internode elongation 1, encoding a zinc-finger transcription factor	9	3.58	0.34	−0.64	−0.43	−0.64	−0.43	−0.50