Genome wide association analysis of root hair traits in rice reveals novel genomic regions controlling epidermal cell differentiation

Hanlon, Meredith T.; Vejchasarn, Phanchita; Fonta, Jenna E.; Schneider, Hannah M.; McCouch, Susan R.; Brown, Kathleen M.

doi:10.1186/s12870-022-04026-5

Table 1 Regions associated with RH traits identified through association analysis

From: Genome wide association analysis of root hair traits in rice reveals novel genomic regions controlling epidermal cell differentiation

Region	Trait	Subpop	Chr	MS-SNP position	MS-SNP -log₁₀(p)	Region size^a	GW assn^b	CW assn.^c	CW gene assn
D1	RHD	aus	1	2,035,050	4.797	158,614	p1, p4, p6	CW
D2	RHD	ALL	1	18,637,547	5.544	219,859	p4, p6, HDRA, GWLD	CW, CWG	LOC_Os01g33869
D3	RHD	ind	1	41,918,233	4.819	653,786	p1, p3, p4, p5, p6	CW
D4	RHD	ind	5	1,317,103	5.163	1,783,892	p1, p3, p4, p6	CWG	LOC_Os05g02850
D5	RHD	ALL	6	1,510,956	4.781	332,738	p1, p2, p3, p4, p5, p6, HDRA, GWLD	CW, CWG	LOC_Os06g03790
D6	RHD	ind	7	21,265,456	4.530	178,997	p3, HDRA, GWLD
D7	RHD	ALL	7	22,510,122	4.903		HDRA, GWLD	CW, CWG	LOC_Os07g37570
D7	RHD	JAPONICA	7	23,063,298	4.253	1,713,775	HDRA, GWLD	CW, CWG	LOC_Os07g38410
D7	RHD	ALL	7	23,105,291	4.239		HDRA. GWLD	CW, CWG	LOC_Os07g38460
D8	RHD	ind	8	19,789,873	6.285	137,470	p1, p3, p4, p6, HDRA, GWLD	CW, CWG	LOC_Os08g32180
D9	RHD	trj	8	24,870,099	4.266	639,351	HDRA, GWLD	CW, CWG	LOC_Os08g39350
D10	RHD	ALL	9	7,160,663	4.041	33,752	HDRA, GWLD	CW, CWG	LOC_Os09g12500
D11	RHD	ind	9	21,413,904	6.039	332,930	p1, p2, p3, p4, p6, GWLD	CW, CWG	LOC_Os09g37500
D12	RHD	ALL	10	10,332,255	6.444	1,118,756	p1, p2, p3, p4, p5, p6	CW, CWG	LOC_Os10g20510
D13	RHD	ind	12	13,749,121	6.207	352,985	p1, p2, p3, p4, p5, p6, HDRA, GWLD	CW, CWG	LOC_Os12g24140
D14	RHD	ALL	12	27,218,429	4.820	97,844	p1, p2, p3, p6	CW, CWG	LOC_Os12g43850
D14	RHD	JAPONICA	12	27,256,045	4.826		GWLD	CWG	LOC_Os12g43750
L1	RHL	ALL	5	18,292,657	5.506	173,752	p1, p2, p3, p4, p5, p6	CW, CWG
L2	RHL	ALL	6	6,127,858	4.724	188,873	HDRA, GWLD
L2	RHL	JAPONICA	6	6,127,858	4.434		HDRA, GWLD	CW
L3	RHL	ALL	8	2,480,747	5.167	258,148	p1, p2, p3, p4, p5, p6, HDRA, GWLD	CW, CWG	LOC_Os08g04990
L4	RHL	ALL	8	7,640,408	4.591	1,001,430	p6, HDRA, GWLD	CW, CWG	LOC_Os08g12790

^a Region size was determined by the method in Wang et. al (2018a) [62]
^b Genome-wide analyses include the pruned SNP sets from the RICE-RP SNPs (p1-p6), the HDRA SNP set (HDRA), and genome-wide LD blocks from the HDRA set (GWLD)
^c Chromosome-wide analysis (CW) includes all RICE-RP SNPs on the respective chromosome. Chromosome-wide gene (CWG) analysis uses the method of Hamazaki & Iwata (2020) [73] to identify associated genes

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ISSN: 1471-2229

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