Table 1.

Survey of RPAN gene presence frequency of rice histone deacetylases.

Locus ID (MSU)	Locus ID (RAP)	Gene name	Gene presence frequency
			JAP%	IND%	AUS%	ARO%	ADM%
LOC_Os01g40400	Os01g0586400	HDA701	–	–	–	–	–
LOC_Os06g38470	Os06g0583400	HDA702/OsHDAC1	99.8	99.7	99.5	100	100
LOC_Os02g12350	Os02g0214900	HDA703/OsHDAC3	95.8	28.1	69.7	82.2	52.8
LOC_Os07g06980	Os07g0164100	HDA704	100	100	100	99.0	100
LOC_Os08g25570	Os08g0344100	HDA705	100	99.9	100	100	100
LOC_Os06g37420	Os06g0571100	HDA706/OsHDAC6	98.9	99.3	99.5	99.0	98.4
LOC_Os01g12310	–	HDA707	–	–	–	–	–
LOC_Os11g09370	Os11g0200000	HDA709	99.1	97.8	98.6	99.0	98.4
LOC_Os02g12380	Os02g0215200	HDA710/OsHDAC2	98.8	1.0	0.9	37.6	49.6
LOC_Os04g33480	Os04g0409600	HDA711	98.1	98.2	95.5	97.0	98.4
LOC_Os05g36920	Os05g0440250	HDA712	99.9	99.9	100.0	99.0	100.0
LOC_Os07g41090	Os07g0602200	HDA713	99.9	99.9	100.0	99.0	99.2
LOC_Os12g08220	Os12g0182700	HDA714/OsHDAC10	100	99.9	99.5	100	100
LOC_Os05g36930	Os05g0440300	HDA716	100	99.8	100	100	100
LOC_Os05g51830	Os05g0597100	HDT701	100	99.9	100	100	100
LOC_Os01g68104	Os01g0909100	HDT702	100	100	100	99.0	100
LOC_Os04g20270	Os04g0271000	SRT701/OsSRT1	100	99.9	99.1	99.0	100
LOC_Os12g07950	Os12g0179800	SRT702/OsSir2b	100	99.8	100	100	100

Gene Presence Frequency taken from RPAN (http://cgm.sjtu.edu.cn/3kricedb/index.php). JAP, japonica; IND, indica; AUS, aus/boro group, which is more closely related to indica; ARO, aromatic basmatic/sadri group, which is more closely related to japonica; ADM, admixed, intermediate types. The bold values highlighted genes which have significant differential polymorphisms between japonica-related and indica-related accessions.