Table 3.

Analysis of molecular variance (AMOVA) for the extraction of molecular variation of 330 genotypes based on 15,020 polymorphic SNPs.

Category	Source of variation	d.f.	Sum of squares	Variance components	Percentage of variation
Groups based on STRUCTURE at K = 2 and cluster analysis	Among populations	1	742,206.2	3,007.2	76.0
	Within populations	658	626,670.4	952.4	24.0
	Total	659	1,368,876.6	3,959.6	100.0
Groups based on STRUCTURE at K = 3	Among populations	2	796,434.7	2,025.8	69.9
	Within populations	657	572,441.8	871.3	30.1
	Total	659	1,368,876.5	2,897.1	100.0
Lowland and upland ecologies	Among populations	1	621,554.3	2,516.9	68.9
	Within populations	658	747,322.3	1,135.7	31.1
	Total	659	1,368,876.6	3,652.6	100.0
Indica lowland, NERICA lowland, and upland	Among populations	2	649,553.4	1,657.0	60.2
	Within populations	657	719,323.2	1,094.9	39.8
	Total	659	1,368,876.6	2,751.9	100.0
Indica lowland, NERICA lowland, NERICA upland, and Japonica upland	Among populations	3	65,534.9	1,609.3	59.7
	Within populations	656	713,534.7	1,087.7	40.3
	Total	659	779,069.6	2,697.0	100.0
Irrigated lowland, rainfed lowland, and upland ecologies	Among populations	2	629,557.5	1,512.5	57.6
	Within populations	651	725,858.2	1,114.9	42.4
	Total	653	1,355,415.7	2,627.4	100.0
Indica, Japonica, NERICA, and ARICA	Among populations	3	422,336.3	1,011.8	41.2
	Within populations	656	946,540.3	1,442.9	58.8
	Total	659	1,368,876.6	2,454.7	100.0
NERICA and ARICA	Among populations	1	7,747.8	151.3	7.5
	Within populations	188	350,241.7	1,862.9	92.5
	Total	189	357,989.5	2,014.2	100.0