Whole-genome meta-analysis coupled with haplotype analysis reveal new genes and functional haplotypes conferring pre-harvest sprouting in rice

Aloryi, Kelvin Dodzi; Okpala, Nnaemeka Emmanuel; Amenyogbe, Mawuli Korsi; Bimpong, Daniel; Karikari, Benjamin; Guo, Hong; Bello, Semiu Folaniyi; Akaba, Selorm; Yeboah, Akwasi; Ahmed, Abdul Razak; Ngegba, Patrick Maada; Kamara, Nabieu; Anyanwu, Juliet Nkiruku; Essandoh, Danielle Ama; Qiu, Xianjin; Tian, Xiaohai; Wang, Guoli; An, Tianyue

doi:10.1186/s12870-025-06551-5

Table 1 List of QTL mapping studies used in the meta-analysis

From: Whole-genome meta-analysis coupled with haplotype analysis reveal new genes and functional haplotypes conferring pre-harvest sprouting in rice

Parents	Pop types^a	Pop	Marker type^b	No. of markers	Traits^c	Ref
Nipponbare (Japonica) × Kasalath (indica)	BC	98	RFLPs	245	SD	Lin et al. 1998 [50]
Pei-kuh × O. rufipogon	RIL	125	SSRs	147	SD	Cai and Miroshima, 2000 [51]
Pei-kuh × O. rufipogon	RIL	125	RFLPs	147	SD	Cai and Miroshima, 2000 [51]
Nipponbare (Japonica) × Kasalath (indica)	BC	98	RFLPs	127	LTG	Miura et al. 2001 [52]
IR64 (Indica) × Asominori (Japonica)	RIL	71	RFLPs	289	PHS	Dong et al. 2003 [53]
Hayamasari (Japonica) × Italica Livorno (Japonica)	BC	122	RFLP, SSRs	285	LTG	Fujino et al. 2004 [54]
EM93-1 X EM93-1 (indica-type Breeding line) × SS18-2 (indica wild-type weedy rice)	BC	156	SSRs	161	SD	Gu et al. 2004 [55]
ZYQ8 (indica) × JX17 (Japonica)	DH	127	RFLPs, SSRs	160	SD	Guo et al. 2004 [56]
SS18-2 (weedy Rice) × EM93-1 (Cultivated rice)	BC	156	SSRs	175	SD	Gu et al. 2005 [57]
IR50 (indica) × Tatsumimochi (Japonica) × Miyukimochi (Japonica) 3-way Breeding	F₂	166	SSRs	108	SD	Wan et al. 2005 [58]
Nanjing35 (Japonica) × N22 (indica) and USSR (Japonica) × N22 (Indica)	BC, F₂	398	SSRs	381	SD	Wan et al. 2006 [59]
Zhenshan 97B (indica) × AAV002863 (Japonica)	DH	198	SSRs	140	LTG	Chen et al. 2006 [60]
USSR5 (Japonica) × N22 (Indica)	F₂	148	SSRs	122	LTG	Jiang et al. 2006 [61]
Hayamasari × Italica Livorno	BC	256	SSRs, SNPs, Indels	6	LTG	Fujino et al. 2008 [62]
K81 × G46B	F₂	164	SSRs	45	PHS	Gao et al. 2008 [63]
IR64 (Indica) × Asominori (Japonica)	RIL	72	RFLPs, SSRs	200	GR, GI, MGT	Ji et al. 2009 [64]
Nipponbare × Koshihikari (Japonica)	BC	79	SSRs, SNPs	NA	PHS	Hori et al. 2010 [65]
Nipponbare (Japonica) × Kasalath (Indica)	BC	28	FNPs, SNPs, Indels	NA	SD	Sugimoto et al. 2010 [13]
SS18-2 × EM93-1	BC	327	SSRs	NA	SD	Ye et al. 2010 [66]
SL506 × Koshihikari	F2	87	SSRs	NA	SD	Marzougui et al. 2011 [67]
ZS97 × MH63 (Hybrid Shanyou 63)	RIL	240	SSRs, RFLPs	43	SD	Li et al. 2011 [68]
N22 (Indica) × Nanjing35 (Japonica)	BC	122	SSRs	192	SD	Xie et al. 2011 [69]
s Bengal × PSRR-1; Cypresss × PSRR-1	RIL	372	SSRs	212	SD	Subudhi et al. 2012 [70]
USSR5 (Japonica) × N22 (Indica)	RIL	181	SSRs	176	LTG	Li et al. 2013 [71]
Nipponbare × Kasalath	BC	98	RFLPs	245	SD	Sasaki et al. 2013 [72]
Jiucaiqing (Japonica) × IR26 (Indica)	RIL	150	SSRs	135	SD	Wang et al. 2014 [73]
Tong88-7 × Millyang23	RIL	160	SSRs, STSs	NA	LTG	Lee et al. 2015 [74]
EM93-1 (Indica) × SS18-2 (weedy rice)	F2	2,592	SSRs	7	SD	Ye et al. 2015 [75]
Owarihatamochi (Japonica) × Koshihikari (Japonica)	BC	44	SNPs	NA	SD	Mizuno et al. 2018 [76]
Odae (Japonica) × Unbong40 (Japonica)	RIL	160	KASPs, CAPS, SNPs	288	PHS	Cheon et al. 2020 [77]
Jinsang x Gopum	F2	88	SNPs	441	PHS	Jang et al. 2020 [78]
Hwayeong × Wandoaengmi6	RIL	186	SNPs	1024	PHS	Lee et al. 2023 [79]

^aBC: backcross population, F₂: second filial generation population, RIL: recombinant inbred lines. ^bSSR: simple sequence repeat, SNP: single nucleotide polymorphisms, STS: sequence-tagged sites, RFLP: restriction fragment length polymorphism, KASP: Kompetitive Allele-specifc PCR, CAPS: Cleaved Amplified Polymorphic Sequences, FNPs: Functional Nucleotide Polymorphisms, Indels: Insertion Deletion^cSD: seed dormancy, GI: germination index, LTG: low-temperature germination, GR: germination rate, PHS: pre-harvest sprouting

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