Table 1
Principle Component Analysis (PCA) revealed three distinct clusters with
a slight overlap of individuals from different groups (Fig. 2). The wild
species, O. rufipogon formed a separate cluster (Cluster I)
scattered along with the PCA plot, indicating higher levels of genetic
diversity. Oryza nivara cluster (Cluster II) was well
differentiated from other Oryza types, but a considerable portion
of landraces, feral and weedy individuals overlapped. The large cluster
(Cluster III) reflects the close genetic relationship among inbred
cultivars, landraces, feral and weedy types. The feral populations were
grouped with inbred rice varieties as they are currently undergoing the
process of de-domestication (Ellstrand et al., 2010). A
considerable number of feral individuals were grouped with the wildO. nivara , potentially a high level of reverse introgression from
the wild species. Many inbred rice cultivars overlapped with the feral
and landraces. In contrast, weedy rice displayed a diffused distribution
in the PCA scatter plot, reflecting a close genetic relationship with
inbred cultivars, feral rice, and O. nivara . Most of the weedy
rice showed a close evolutionary relationship with the inbred and
landraces and few displayed close genetic similarities to O.
nivara .
Fig. 2. Scatter plot of the first and second principal
components (PC) based on the variation of 33 SSR loci for 1340
individuals of 20 weedy rice populations, five O. rufipogonpopulations, six O. nivara populations, 42 inbred rice varieties,
seven feral rice populations and 31 landraces from Sri Lanka showing the
considerable overlap of genotypes in different Oryza types at 33
SSR loci.
The STRUCTURE analysis of DWWC demonstrated a distinct ∆K peak at K=2
levels (Fig. S1), indicating that wild Oryza was differentiated
from other Oryza groups. Within the analysis, two populations of
weedy rice (W4 and W6) and three populations of feral rice (F1, F2, and
F5) were classified as out-groups (Fig. 3) in relation to their
respective Oryza groups, leading to the formation of two separate
groups for both weedy and feral rice. This observation can likely be
attributed to the adaptation of O. nivara to the rice ecosystems,
a process driven by persistent habitat disturbances, continued selective
pressures, or hybridization events between cultivated (inbred and
landraces) plants and their reproductively compatible wild counterparts
(Cao et al ., 2006). Consequently, K=2 was determined to be the
most biologically realistic population number. Further, ∆K peaks at K=9
and K=5 (Fig. S1) were considered for further examination of population
models. The K=9 model is highly intricate, suggesting that the physical
classification of Oryza groups presents a challenge due to the
genetic relationships among populations and individuals based on
prevailing patterns of genetic admixture. However, the K=5 model is
generally consistent with the Principal Component Analysis (PCA) results
(Figs. 3 and 4).
The two wild Oryza species, O. nivara and O.
rufipogon , differentiated from others. Moreover, these two wild species
exhibited genetic differences from one another, i.e. some populations
showing admixture, while most individuals can be reliably assigned to a
specific population. The O. rufipogon group comprised a most
distinct group with a more heterogeneous genetic background. Two weedy
and three feral populations were highly admixed with the wild O.
nivara . Widely cultivated types, inbred rice varieties, and landraces
shared a common ancestry and were evident as largely close groups to
weedy rice with the admixture nature. However, some individuals of
landraces were admixed with the wild Oryza and weedy rice. The
evolution of the weedy type reflects the complex process of genetic
incorporation from the crop (inbred or landraces), non-cultivated wildOryza . This illustrates the multi-way genetic transfer to the
evolution of weedy types. The STRUCTURE results suggest that there is a
complex integration of multi-way gene flow among all members of the DWWC
in the rice ecosystem in Sri Lanka. However, when examining K values
ranging from 5 to 10, it becomes clear that there is an admixed genetic
background for individuals in some populations/cultivars. While most
individuals could be assigned to a single population or cultivar, the
occurrence of further groupings is uncommon (Fig. 3).
Fig. 3. STRUCTURE graph showing genotype clustering of 20 weedy
rice populations, five O. rufipogon populations, six O.
nivara populations, 42 inbred rice varieties, seven feral rice
population and 31 landraces by model‐based population assignment at K
from 2 to 10. Each vertical bar represents an individual, with its
assignment probability to genetic clusters represented by different
colors. Codes for the weedy rice, O. rufipogon , O. nivaraand feral rice populations are presented in Table S1.
Fig. S1
The UPGMA tree shows similar results, with all Oryza types
genetically structured into two well-separated major groups (O.
rufipogon and all other Oryza types) and further divided into
respective populations and cultivars (Fig. 4). The O. rufipogongroup forms a separate cluster (Cluster I). Besides, the large cluster
was further divided into two sub-clusters (Cluster II and Cluster III).
Moreover, all O. nivara , three feral rice (F1, F2, and F5) and
two weedy (W4 and W6) rice populations, and a few landraces formed a
distinct cluster (Cluster III), as shown in the PCA. The large cluster
(Cluster III) consisted of inbred varieties, landraces, unmanaged
abandoned feral populations, and weedy rice. Most weedy rice populations
were grouped with landraces, however, W2 and W3 populations displayed
closer relationships with landraces. Furthermore, W1 was distinct from
the weedy rice cluster, while the rest of the populations were
subdivided into two clusters. Feral rice populations were grouped into a
large cluster, but they were also clustered with the inbred rice group.
Inbred rice varieties and landraces showed complex clustering patterns
due to the relatively high genetic distances among their respective
cultivars.
Fig. 4. The UPGMA cladogram is based on Nei (1972) genetic
distance. Dendrogram (UPGMA) was constructed based on polymorphisms of
33 SSR loci in six Oryza types (20 weedy rice populations, fiveO. rufipogon populations, six O. nivara populations, 42
inbred rice varieties, seven feral rice populations, and 31 landraces),
using Nei’s unbiased genetic distance (Nei, 1972). The bar represents
genetic distance, with the same color sharing the same source of
collection. Population or varieties/cultivars codes for the sixOryza types of populations are presented in Table S1.
The AMOVA analysis revealed a significant portion of the total genetic
diversity present within populations (56%) and among populations
(28%), while relatively low (16%) genetic differentiation was observed
among Oryza types (Table S7; P <0.01). In
specific Oryza types, the total variation was partitioned into
among populations/cultivars and within
populations/cultivars. A notably
larger variation was observed within populations compared to among
populations (Table S7).