Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice

Table 1 Summary of QTL studies utilized for meta-QTL analysis

Parents	Population type^a	Population size	No. of markers	Marker type^b	Traits^c	References
IR64/KHAIYAN//IR64	BC₂	150	155	SSR	AG	[92]
IR64/Khao Hlan	BC₂	398	136	SSR	AG	[22]
IR64 x Nanhi	F₂	300	234	SNP	AG	[93]
IR64 x Kharsu80A	F₂	190	384	SNP	AG	[11]
BJ1 x NSIC Rc222	BC₂	205	102	SSR	AG	[19]
FR13A x IR42	RIL	103	232	SSR, SNP, STS	SUB	[18]
IR42 x FR13A	RIL	103	232	SNP, SSR, STS	AG	[18]
Kinmaze (japonica) x DV85 (indica)	RIL	81	137	RFLP	AG	[94]
USSR5 x N22	F₂	148	121	SSR	LTG, AG	[95]
Tai Nguyen x Anda.	F₂	285	1405	SNP	AG	[96]
Kinmaze (japonica)/DV85 (indica)	RIL	81	137	RFLP, SSR	AG	[97]
Indra x AC 39,416 A	RIL	184	104	SSR	AG	[21]
Swarna Sub1 x AC39416A	F₂	188	83	SSR	AG	[20]
IR72 x Madabaru	F₂	466	115	SSR	SUB	[98]
IR42 x Ma-Zhan Red	F₂	175	118	SSR	AG	[99]
Habiganj x Patnai23	F₂	192	85	RFLP, SSR	LEI	[100]

^aBC: backcross population, F₂: second filial generation population, RIL: recombinant inbred lines. ^bSSR: simple sequence repeat, SNP: single nucleotide polymorphism, STS: sequence-tagged sites, RFLP: restriction fragment length polymorphism. ^cAG: anaerobic germination, SUB: submergence, LTG: low-temperature germination, LEI: lowest elongated internode

ISSN: 1471-2164