## 3 Results
### Principal Component Analysis (PCA) of Endophytic Bacteria in Pea Embryos  
Principal component analysis (PCA) was carried out on endophytic bacterial samples from the embryos of all six pea cultivar groups, including DGPS, FGPS, SPS, SCPS, SEPS, and SHPS. PCA is an unsupervised learning algorithm used to essentially cluster unlabeled bacterial microbiome data through dimensionality reduction, which ends up with principal components that explain as much variation as possible [68]. Principal components 1, 2, and 3 (PC1, PC2, and PC3) contributed 51.9%, 29.7%, and 6.5% of the total variation, respectively (Figure 5). S18P07.2 in the fresh grain pea sample (FGPS) group, as well as S18P11.2 and S18P10.1 in the snow pea sample (SPS) group, showed relatively long distances and low similarities to all the other samples in the PCA map (Figure 5). Except for these two outliers, all bacterial collections, especially those from SEPS, exhibited short distances, good sample parallelism, and similar components and community structures (Figure 5). Most samples aggregated in both PC1 and PC2 (Figure 5), indicating that there is no significant structural difference in endophytic bacterial communities from pea embryos of different cultivars/accessions. In conclusion, the PCA results implicate that most endophytic bacteria from all six pea embryo cultivar groups can all be clustered together with relatively short distances (Figure 5).  
Figure 4: The dilution curves of bacterial diversity indexes in pea embryos.  
Linear Discriminant Analysis (LDA) Coupled with Effect Size Measurement (LEfSe) Analysis of Endophytic Bacteria in Pen Embryos  
Linear discriminant analysis (LDA) coupled with effect size measurement (LEfSe) analysis was carried out to analyze endophytic bacterial difference in pea embryos. LefSe is used for high-dimensional identification and characterization of two or more significant groups in bacterial microbiome data [69,70]. LefSe scores represent the effective sizes of abundant species and indicate species enriched in the groups. Relatively abundant endophytic bacterial species (LDA score > 3, which is more stringent than the default LDA score threshold of 2) were identified from all six cultivar groups of DGPS (_Bifidobacterium_, _Bifidobacteriales_, _Bifidobacteriaceae_, and _Blutia_), FGPS (_Prevotella_7_, _Eubacterium_coprostandigenes_group_, _Entonomplasmatales_, _Entonomplasmatales_Increta_Sedis_, _Candidatus_Hepatoplasma_, _Spirochaetae_, _Spirochaetaceae_, _Spirochaetales_, _Spirochaetes_, and _Treponema_2_), SPS (_Geodermaphilaceae_), SCPS (_Marvinbryanti_), SEPS (_Ruminococcus_2_, _Incretae_Sedis_, and _Peptoclostridium_), and SHPS (_Peptostretocytococcaceae_, _Romboutsia_, _Flaviolbacter_, _Ruminococcaceae_UCG_013_, _Deferribacteraceae_, _Deferribacetres_, _uncultured_bacterium_, _Deferribacterales_, _Mucispirillum_, _Btri41_, _Flammeovirgaceae_, _Ambiguous_taxa_, _Phaselicystidaee_, _Phaselicystis_, _Candidatus_Nitrosoarchaeum_limutia_SFB1_, and _SAR324_clade_Marine_group_B_) (Figure 6).  
Figure 5: Principal component analysis (PCA) of endophytic bacteria in all six pea embryo cultivar groups. DGPS: dry grain pea samples; FGPS: fresh grain pea samples; SPS; snow pea samples; SCPS: sweet crispy pea samples; SEPS: pea tip (seedling of pea) samples; SHPS: pea sprout (shoot of pea) samples.