Genome Scan of Rice Landrace Populations Collected Across Time Revealed Climate Changes’ Selective Footprints in the Genes Network Regulating Flowering Time

Ahmadi, Nourollah; Barry, Mamadou Billo; Frouin, Julien; de Navascués, Miguel; Toure, Mamadou Aminata

doi:10.1186/s12284-023-00633-4

Rice

Table 2 Enrichment in gene ontology terms related to reproductive biological processes, of the chromosomic segments bearing the 24 independent loci most likely under section

From: Genome Scan of Rice Landrace Populations Collected Across Time Revealed Climate Changes’ Selective Footprints in the Genes Network Regulating Flowering Time

Identity of GO term	Description of the biological process	Agri-GO					Panther-GO
		AN in Ref (24,075)	AN in input (1240)		Fold Enrichment	q value	N in Ref (43,658)	N in input (1464)		Fold Enrichment	q value
		AN in Ref (24,075)	Obs	Exp	Fold Enrichment	q value	N in Ref (43,658)	Obs	Exp	Fold Enrichment	q value
GO:0000003	Reproduction	133	65	6.85	9.49	1.20E−33	587	37	19.68	1.88	3.37E−02
GO:0048608	Reproductive structure development	668	66	26.24	2.51	2.50E−02	–	–	–	–	–
GO:0003006	Reproductive developmental process	668	66	26.24	2.51	2.50E−02	–	–	–	–	–
GO:0009908	Flower development	662	64	26.01	2.46	3.40E−02	–	–	–	–	–
GO:0022414	Reproductive process	114	65	5.87	11.07	1.10E−36	585	37	19.62	1.89	3.38E−02
GO:0009314	Response to radiation	38	31	1.96	15.84	1.80E−20	–	–	–	–	–
GO:0009416	Response to light stimulus	38	31	1.96	15.84	1.80E−20	–	–	–	–	–
GO:0009856	Pollination	114	20	5.87	3.41	3.10E−04	143	18	4.8	3.75	7.96E−04
GO:0009875	Pollen-pistil interaction	–	–	–	–	–	114	14	3.82	3.66	7.94E−03
GO:0048544	Recognition of pollen	–	–	–	–	–	110	14	3.69	3.8	5.86E−03
GO:0050896	Response to stimulus	1026	221	52.84	4.18	3.50E−63	3646	216	122.26	1.77	1.72E−12
GO:0007165	Signal transduction	240	46	12.36	3.72	1.10E−10	1074	60	36.01	1.67	1.86E−02
GO:0009605	Response to external stimulus	25	18	1.29	13.98	5.40E−11	–	–	–	–	–
GO:0023052	Signalling	447	72	23.02	3.13	2.00E−13	1089	60	36.52	1.64	2.51E–02
GO:0009791	Post–embryonic development	2033	167	79.87	2.09	2.50E−02	–	–	–	–	–
GO:0006950	Response to stress	873	164	44.96	3.65	3.80E−39	2109	135	70.72	1.91	3.11E−09
GO:0051716	Cellular response to stimulus	132	55	6.80	8.09	1.10E−25	1874	92	62.84	1.46	3.35E−02
GO:0050789	Regulation of biological process	2027	159	104.40	1.52	1.10E−05	4214	206	141.31	1.46	2.85E−05

AN, and N Number of annotated genes in the O. sativa (ref) and in the input genes list, using MSU7.0 or RAP-DB as reference, respectively. Obs observed; Exp expected

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