4.1 Genetic diversity and population structure of DWWC
Genetic diversity (H E) in O. rufipogon andO. nivara populations revealed by SSR markers in the present
study was relatively higher than those of previously reported,
signifying a comparable degree of genetic diversity within the broader
South Asian region (Banaticla-Hilario et al., 2013; Kurodaet al., 2007; Pusadee et al., 2013; Samal et al.,2018; Sandamal et al., 2018; Zhou et al., 2003). Among the
similar studies, the Chinese O. rufipogon population showed anH E value of 0.413 (Zhou et al., 2013),
while in Vientiane Plain of Laos, the H E values
for O. rufipogon ranged from 0.37 to 0.77 and for O.
nivara ranged from 0 to 0.64 (Kuroda et al., 2007). In the Asia
Pacific region, reported H E values were 0.39 for
Nepal O. nivara , 0.67 for Southeast Asian O. nivara , and
0.70 for Southeast Asian O. rufipogon (Banaticla‐Hilario et
al., 2013). In the Indian peninsula, H E values
of 0.63 for O. rufipogon and 0.64 for O. nivara were
reported (Singh et al., 2018). Previous studies revealed thatO. rufipogon and O. nivara have significant but low
divergence, implying ongoing speciation processes with potential gene
flow between them (Liu et al ., 2015; Pusadee et al ., 2016;
Zheng and Ge, 2010; Sandamal et al ., 2018). In the present study,
the presence of admixtures in the studied wild populations (Fig. 3), and
high genetic diversity along with the PC1 in PCA results supported this
hypothesis. Furthermore, O. rufipogon showed high
within-population variation (63%) and lower among-population variation
(37%), while O. nivara exhibits 48% within-population and 47%
among-population variation. In Sri Lanka, O. rufipogon showed
lower population differentiation compared to O. nivara (Table
S7), potentially due to limited gene flow among O. rufipogonpopulations in the wet and intermediate zones.
The present study revealed a moderately high overall genetic diversity
(H E= 0.566) in weedy rice populations collected
across Sri Lanka, with higher within-population genetic variance (79%)
than among-population variance (21%). This suggests the consistently
high genetic diversity within weedy populations that can be attributed
to the introgression from other DWWC types to weedy lineages. STRUCTURE
analysis (Fig. 3) indicated a high admixture of some weedy rice
individuals with wild Oryza , suggesting bidirectional gene flow
between weedy and wild Oryzas . Unlike previous studies (Heet al ., 2014), our research included a large number of
individuals (1340) from various locations in Sri Lanka, potentially
explaining the detection of the grouping of weedy populations withO. nivara . The high admixture may result from wild rice adapting
to cultivated rice habitats due to ongoing selection and habitat
disturbances (De Wet and Harlan, 1975; Vaughan et al ., 2001).
Similar studies carried out worldwide have reported low to high genetic
diversity in weedy rice populations (Han et al ., 2020; Caoet al ., 2006; Yu et al ., 2005, Neik et al ., 2019;
Gealy et al ., 2003; Song et al ., 2014; Prathepha, 2011),
suggesting that genetic diversity in weedy rice is variable and
influenced by regional and local factors. Our study makes a significant
contribution to genetic studies by reporting the genetic structure of
South Asian weedy rice populations at a larger scale, highlighting the
high genetic diversity and admixture in the DWWC in Sri Lanka.
In Sri Lanka, rice is grown across diverse physical environments with
varying altitudes, soils, and hydrological regimes. The rice-growing
altitudes range from 0 to 900 m above sea level, with temperatures
ranging from 30 °C (± 5 °C) at sea level to about 15 °C at higher
elevations (Dhanapala, 2007). The country has a long history of
cultivating rice, with numerous endemic cultivars, wild species, and
landraces, predominantly long-duration cultivars and photoperiod
sensitive (Weerakoon et al ., 2011). The development of inbred
varieties occurred through artificial hybridization at the Rice Research
and Development Institute (RRDI) of Sri Lanka, some of which utilize
superior individuals and exotic germplasm imported from Indonesia
utilized for developing high-yielding cultivars (Dhanapala, 2020). This
led to moderately high genetic diversity in Sri Lankan inbred rice
compared to other rice types examined. Landraces and feral populations
also displayed high levels of genetic diversity. The genetic
differentiation among cultivated Oryza types (inbred and
landraces), inbred and feral rice, and landraces and feral rice was
considerably low (Table S5), indicating a close genetic relationship
among rice types. Our findings revealed the dynamic nature of
domesticated, wild, and weedy components in the Sri Lankan rice
ecosystem, with high admixture and recurrent gene flow observed among
different Oryza types. The presence of shared private alleles
among all DWWC rice groups confirms the high admixture nature of these
populations (Fig. S2). This highlights the significant contribution of
introgression and multi-way gene flow in shaping the genetic diversity
of the DWWC in Sri Lanka.