Core microbiota at root niches of host genotypes
To identify the core microbiota within a niche of host genotype, we first established a Rank-Abundance curve of the detected ASVs for each sample. First, the highest relative abundance value of all the ASVs was recorded as RAmax, and the ASV with relative abundance > RAmax*0.9 was considered to be one dominant ASV (dASV). The dASVs appearing in all the five soils and four replicates were used as the core ASVs of the niche (Fig. S6). In the rhizosphere, there were 2 core ASVs shared by all the three host genotypes in the basal zone (Fig. 4a), both of which belonged to unclassified Micrococcaceae, with higher relative abundance than most of the other niches (Fig. 4b). In the endosphere, three core ASVs, annotated as unclassified Burkholderiaceae,Rhizobacter , and Methylotenera (Fig. 4b) appeared in both apical and basal segments of the EF genotype (Fig. 4a). The endosphere in the apical zone of LF2 genotype harboured the largest number of core ASVs, but these ASVs did not appear in other niches (Fig. 4a).