Genome-wide association study of salt tolerance at the seed germination stage in rice

BMC Plant Biology

Table 3 Summary of loci significantly associated with stress susceptibility indices of seed germination-related traits

Trait^a	Chr.^b	Number of significant signals^c	Lead SNP position (bp)^d	P value	Gene harbored lead SNP	Panel^e	Allele^f	Mean SSI		Known QTL/Trait
Trait^a	Chr.^b	Number of significant signals^c	Lead SNP position (bp)^d	P value	Gene harbored lead SNP	Panel^e	Allele^f	Major	Minor	Known QTL/Trait
MGT	1	3	15,450,039	6.22E-10	LOC_Os01g27710-LOC_Os01g27720	Whole	G/A	1.09	2.92	RM1-R886 [31]/Na⁺ uptake; K⁺ concentration; Na⁺: K⁺ ratio
MGT	1	1	17,736,489	9.93E-09	LOC_Os01g32330	Whole	C/T	1.23	2.57	RM1-R886 [31]/Na⁺ uptake; K⁺ concentration; Na⁺: K⁺ ratio
VI	2	7	666,962	1.15E-09	LOC_Os02g02190	Whole, non-Indica	A/G	0.98	0.31
MGT	4	1	16,501,431	2.32E-08	LOC_Os04g27950-LOC_Os04g27960	Indica	C/T	1.57	1.47
MGT	5	2	29,704,394	5.10E-09	LOC_Os05g51770	Whole	T/C	1.35	1.32	qRGR-5 [43] /relative germination rate with ABA; qGR5–1 [44] /Germination rate
VI	6	1	23,605,165	2.93E-09	LOC_Os06g39756-LOC_Os06g39750	non-Indica	G/A	1.08	0.27	RG716 [45]/Salinity tolerance
VI	9	2	2,214,950	9.71E-10	LOC_Os09g04210	non-Indica	A/T	0.94	0.52
VI	10	1	10,723,028	3.54E-10	LOC_Os10g21100-LOC_Os10g21110	Whole	G/A	1.02	0.36
VI	11	1	27,305,217	4.64E-09	LOC_Os11g45110-LOC_Os11g45120	non-Indica	T/C	1.01	0.37	RM206 [46]/Relative shoot elongation under submergence
MGT	12	2	5,000,802	2.88E-08	LOC_Os12g09510-LOC_Os12g09520	Whole	A/C	1.16	3.93	qCTS12 [47]/Seedling cold tolerance; rv12–2 [48]/Root volume at seedling stage
VI	12	1	14,215,505	2.41E-08	LOC_Os12g24780	Indica	C/T	1.06	0.92	qtl12.1 [49] /Drought resistance

^a Traits for which significant signals were associated with stress susceptibility index of that trait. MGT, mean germination time; VI, vigor index
^b Chromosome number
^c Number of significant association signals detected in region
^d Representative SNP position on rice genome assembly MSU version 7.0
^e Panel containing significant GWAS sites
^f Major allele/minor allele

ISSN: 1471-2229