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.