Genome-Wide Association Studies Reveal the Genetic Basis of Fertility Restoration of CMS-WA and CMS-HL in xian/indica and aus Accessions of Rice (Oryza sativa L.)

Rice

Table 1 Genome-wide significant associations for pollen fertility, BSS and NSS of the F₁ population with the background of CMS-WA in year 2013 and 2014 using the linear mixed model

Trait	Chr.	2013					2014					Known loci
Trait	Chr.	Position	P-LMM	Allele¹⁾	MAF²⁾	PVE (%)³⁾	Position	P-LMM	Allele	MAF	PVE (%)	Known loci
Pollen fertility	1						5,631,778	2.97E-08	A/T	0.168	19.01	Rf3
	9						10,301,051	8.11E-08	G/A	0.361	2.90
	10	18,809,352	5.42E-12	C/T	0.359	37.67	18,803,763	2.33E-20	C/T	0.350	48.46	Rf4
BSS	4	113,551	6.54E-10	A/G	0.241	16.90
	4						962,149	1.36E-08	A/C	0.172	15.89
	6	11,935,371	1.18E-08	T/A	0.061	11.91
	6						28,616,342	2.37E-07	G/A	0.495	2.93
	8	6,798,111	4.27E-08	C/T	0.078	25.48
	9						10,218,016	3.38E-08	G/A	0.358	4.45
	10	18,826,378	3.50E-13	T/G	0.176	33.54	18,803,939	2.02E-14	C/T	0.182	19.37	Rf4
	12						23,866,969	9.55E-09	T/C	0.325	20.10
NSS	4	54,458	3.07E-08	A/C	0.326	12.51
NSS	10	18,807,815	4.20E-10	C/G	0.413	41.52	18,803,939	2.02E-16	C/T	0.182	19.05	Rf4