Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

Pan, Zhaoyuan; Tan, Bin; Cao, Guiyuan; Zheng, Rongqi; Liu, Meng; Zeng, Ruizhen; Wang, Shaokui; Zhu, Haitao; Ye, Heng; Zhao, Guangmiao; Cao, Wei; Liu, Guifu; Zhang, Guiquan; Zhou, Yuliang

doi:10.1186/s12284-021-00544-2

Rice

Table 1 Summary of the SSSLs detected with putative LTG QTLs in four field environments

From: Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

SSSL code	Donor code	Chr	Substituted segment^a	Length (cM)	Putative QTL	a*	R² (%)*	Cropping season^b	Detected season^c
S1	W14	1	RM246–RM297-RM212–RM315	16.7	qLTG1	− 0.18 ± 0.02	28.6 ± 7.0	abcd	ab
S2	W14	1	RM5–RM237-RM212–RM315	34.2	qLTG1	− 0.17 ± 0.10	29.4 ± 11.8	abcd	acd
S3	W09	2	RM106–RM263-RM530–RM240	30.2	qLTG2	0.10 ± 0.04	20.0 ± 4.5	abcd	bd
S4	W08	2	PSM122–RM263-RM166–RM213	54.5	qLTG2	0.11 ± 0.06	18.9 ± 10.9	abcd	bc
S5	W06	3	RM175–RM489-PSM428–PSM429	16.1	qLTG3a	0.16 ± 0.02	33.0 ± 1.0	acd	cd
S6	W06	3	RM231–RM489-RM218–RM563	28.7	qLTG3a	0.16 ± 0.01	29.8 ± 7.8	acd	acd
S7	W06	3	RM489–RM545-RM218–RM563	21.9	qLTG3a	0.18 ± 0.01	36.2 ± 5.4	acd	cd
S8	W17	3	PSM127–RM426-RM168–RM186	16.4	qLTG3b	− 0.10 ± 0.01	19.2 ± 5.8	abcd	ad
S9	W06	4	RM119–RM273-RM252–RM241	12.9	qLTG4	− 0.14 ± 0.01	25.8 ± 7.0	acd	ad
S10	W06	4	PSM194–RM273-RM252–RM241	16.2	qLTG4	− 0.16 ± 0.08	26.9 ± 6.6	acd	ad
S11	W06	4	PSM358–PSM196-RM252–RM241	47.0	qLTG4	− 0.20 ± 0.13	32.9 ± 13.8	acd	ad
S12	W11	5	RM480–RM31-PSM386–End	8.4	qLTG5	0.15 ± 0.02	28.0 ± 1.5	abcd	bcd
S13	W01	5	PSM384–RM178-RM334–End	22.4	qLTG5	0.14 ± 0.01	28.7 ± 2.2	bcd	cd
S14	W27	6	End–RM508-RM217–RM253	16.6	qLTG6	0.06 ± 0.01	8.9 ± 0.5	acd	ac
S15	W23	6	End–RM508-RM121–RM136	44.9	qLTG6	0.15 ± 0.02	29.9 ± 9.9	abcd	bd
S16	W06	7	RM481–PSM142–PSM143	10.0	qLTG7a	− 0.22 ± 0.09	39.4 ± 3.7	acd	ad
S17	W05	7	PSM142–RM2-RM10–PSM353	45.4	qLTG7b	− 0.24 ± 0.08	39.9 ± 8.9	abcd	abc
S18	W06	8	PSM155–RM547–PSM393	6.5	qLTG8a	0.15 ± 0.02	26.9 ± 4.4	abcd	bc
S19	W06	8	RM284–RM556-RM210–RM80	9.1	qLTG8b	0.17 ± 0.03	33.6 ± 1.3	abcd	cd
S20	W06	8	PSM394–RM515-OSR7–RM447	36.4	qLTG8b	0.15 ± 0.01	28.3 ± 2.4	abcd	bcd
S21	W27	9	RM105–RM434-RM410–RM257	17.1	qLTG9	− 0.21 ± 0.01	34.2 ± 6.0	abcd	ac
S22	W06	11	PSM409–PSM412–PSM414	28.8	qLTG11a	0.16 ± 0.01	32.2 ± 4.3	abcd	bd
S23	W06	11	PSM174–PSM175-RM536–PSM415	40.2	qLTG11a	0.15 ± 0.03	30.3 ± 9.8	abcd	cd
S24	W17	11	RM21–PSM365-PSM417–PSM460	15.4	qLTG11b	− 0.19 ± 0.07	34.1 ± 9.7	acd	acd

*a = average additive effect of the QTL in different detected seasons; R² (%) = average additive effect contribution (%) of the QTL in different detected seasons
^aThe single lines in the middle of markers indicate substituted segments while the double lines on the border of markers indicate segments recombination might appear. SSR markers labeled "RM" were selected from public resources, and those labeled "PSM" were developed in our laboratory
^b^,cThe letters a, c represent early cropping seasons in 2015 and 2016, and b, d represent late cropping seasons in 2015 and 2016, respectively. Detected seasons mean the time when putative QTLs were detected on the SSSLs

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