Table 2.

QTLs identified for the two cold-tolerance traits by GWAS in the geng (GJ) and xian (XI) subgroups.

Population	Trait a	QTL	Chr.	QTL Region (Mb)	Lead SNP	p-Value	Cloned Gene
GJ	SR	qSR2.1g	2	19.64–19.94	19,785,654	4.94 × 10−6
XI	SR	qSR1.1x	1	3.45–3.75	3,604,713	4.19 × 10−7	OsPLDα1 [29]
		qSR1.2x	1	20.23–21.03	20,231,449	1.39 × 10−7
		qSR4.1x	4	3.63–4.80	3,855,187	3.33 × 10−10
		qSR5.1x	5	5.71–6.01	5,861,711	1.21 × 10−6
		qSR11.1x	11	23.79–25.42	25,393,345	8.00 × 10−9
		qSR12.1x	12	5.71–7.25	5,754,489	6.05 × 10−11
XI	SCT	qSCT1.1x	1	3.45–3.75	3,604,730	1.34 × 10−7	OsPLDα1 [29]
		qSCT1.2x	1	21.88–22.18	22,038,470	9.39 × 10−7
		qSCT4.1x	4	3.50–3.80	3,653,716	1.19 × 10−7
		qSCT8.1x	8	1.42–1.72	1,578,048	5.94 × 10−7
		qSCT11.1x	11	24.03–24.33	25,393,345	3.17 × 10−7
		qSCT12.1x	12	5.71–7.33	5,754,489	4.48 × 10−7

^a SR—survival rate, SCT—leaf score of cold tolerance.