Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice

Sandhu, Nitika; Ankush, Ade Pooja; Singh, Jasneet; Raigar, Om Prakash; Bains, Sutej; Jindal, Taveena; Singh, Mohini Prabha; Sethi, Mehak; Pruthi, Gomsie; Augustine, Gaurav; Verma, Vikas Kumar; Goyal, Shivani; Kumar, Aman; Panwar, Harsh; Sihag, Manvesh Kumar; Kaur, Rupinder; Kurup, Smita; Kumar, Arvind

doi:10.1186/s12284-023-00665-w

Rice

Table 2 Detailed information on the genomic regions associated with different traits of interest identified in the different mapping populations

From: Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice

Mapping population	Trait	Chr	QTL interval (bp)	QTL span (Mb)	Left flanking marker	Peak marker (bp)	Right flanking marker	LOD	R²
F_3:4:5	%germination_4 cm	7	8906211–14769869	5.86	7:8906211	7:10322112	7:14769869	10.10	12.43
	%germination_10 cm	7	8831295–14769869	5.94	7:8831295	7:12711103	7:14769869	5.60	7.10
	Mesocotyl length_4 cm	7	8906211–15425220	6.52	7:8906211	7:11758772	7:15425220	9.90	12.19
	Mesocotyl length_10cm	7	8831295–15438381	6.61	7:8831295	7:9530368	7:15438381	7.70	9.58
	%germination_4cm	2	25640406–30681013	5.04	2:25640406	2:26193032	2:30681013	7.80	9.77
	%germination_4cm	9	8088106–8164448	0.08	9:8088106		9:8164448	6.30	7.93
	Mesocotyl length_4 cm	10	4770677–4770755	–	10:4770677	10:4770686	10:4770755	6.10	7.66
	Mesocotyl length_4 cm	11	15550458–15550470	–	11:15550458	11:15550468	11:15550470	4.70	5.95
	Root length_4cmShoot length_4cm	7	8906211–10369837	1.46	7:8906211	7:10369837	7:10369837	5.20	11.93
	Root length_10cm	3	547685–1730359	1.18	3:547685	3:777138	3:1730359	8.80	10.88
	Days to 50% floweringPlant heightGrain yield	1	25344969–34329979	8.99	1:25344969	1:28134927	1:34329979	11.80	14.41
	Days to 50% flowering	3	858902–1730359	0.87	3:858902	3:894084	3:1730359	9.30	11.51
	Days to 50% flowering	8	6986267–7377701	0.39	8:6986267	8:7232778	8:7377701	7.20	9.03
	Days to 50% flowering	9	8088106–8088106	–	–	9:8088106	–	6.20	7.82
BC₂F_2:3	%germination_4 cm	7	10923664	–	–	K_10923664	–	3.30	9.6
	%germination_10 cm	7	10131516–11112584	0.98	K_10131516	K_11112584	K_11112584	3.34	19.74
	Mesocotyl length_4 cm	7	10923664–14713452	3.79	K_10923664	K_14713452	K_14713452	8.68	11.28
	Mesocotyl length_10cm	7	10923664–14713452	0.88	K_13832487	K_14713452	K_14713452	9.00	12.80
	Shoot length_10 cm	7	10923664–14713452	3.79	K_10923664	K_14713452	K_14713452	3.30	11.20

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