Table 2.

Summary of polymorphism and molecular diversity among 330genotypes that belongs to different categorical groups (types of rice, ecology, groups predicted based on the model-based STRUCTURE at K = 2 and K = 3, and cluster analysis).

Category	Description	Number of genotypes	Polymorphism with MAF ≥ 0.01 (%)	Average observed heterozygosity (Std)∗	Average expected heterozygosity (Std)∗∗	Average nucleotide diversity (Std)
Type of rice	Indica	172	87.9%	0.014 (0.064)	0.170 (0.143)	0.164 (0.078)
	Japonica	62	78.6%	0.015 (0.073)	0.224 (0.124)	0.186 (0.088)
	NERICA	85	90.6%	0.015 (0.065)	0.286 (0.144)	0.260 (0.123)
	ARICA	11	68.4%	0.023 (0.085)	0.255 (0.125)	0.174 (0.086)
Ecology	Irrigated lowland	88	88.3%	0.017 (0.067)	0.170 (0.144)	0.154 (0.073)
	Rainfed lowland	160	87.7%	0.013 (0.064)	0.147 (0.147)	0.144 (0.068)
	Upland	81	86.6%	0.014 (0.072)	0.175 (0.123)	0.154 (0.073)
	Lowland (Irrigated and rainfed)	248	92.0%	0.014 (0.064)	0.153 (0.143)	0.151 (0.071)
Groups based on ecology and type
	Lowland Indica	183	89.1%	0.015 (0.065)	0.163 (0.145)	0.157 (0.074)
	Lowland NERICA	65	62.8%	0.020 (0.081)	0.149 (0.144)	0.105 (0.050)
	Upland NERICA	19	37.0%	0.031 (0.118)	0.263 (0.154)	0.097 (0.047)
	Upland Japonica	63	80.1%	0.015 (0.074)	0.202 (0.121)	0.165 (0.078)
Groups based on structure at K = 2 and cluster analysis
	Group 1	82	73.0%	0.017 (0.079)	0.134 (0.136)	0.104 (0.049)
	Group 2	248	80.8%	0.015 (0.065)	0.143 (0.150)	0.135 (0.064)
Groups based on STRUCTURE at K = 3
	Group 1	82	73.0%	0.017 (0.082)	0.138 (0.139)	0.098 (0.047)
	Group 2	181	72.7%	0.016 (0.068)	0.156 (0.152)	0.138 (0.065)
	Group 3	67	52.3%	0.021 (0.085)	0.120 (0.132)	0.079 (0.038)

^∗Std, standard deviation; ^∗∗expected heterozygosity, gene diversity.