2.1 Plant Materials
Six distinct groups within the domesticated-weed-wild complex (DWWC) in
the genus Oryza , sharing a common ancestry, were sampled from Sri
Lanka for this study. These groups include inbred rice, landraces, feral
rice, weedy rice, O. rufipogon , and O. nivara .
Seeds of 42 inbred rice varieties (206 individuals; Table S3) were
collected from the Rice Research and Development Institute (RRDI) of Sri
Lanka. Seeds of 31 landraces (151 individuals) with 4-5 individuals per
variety were collected from the seed bank of the Plant Genetic Resources
Centre (PGRC) at Gannoruwa, Peradeniya, Sri Lanka (Table S2). Both
inbred and landraces (5-10 seeds of each cultivar) were planted in
equal-sized pots (9 cm diameter top, 6.3 cm diameter base, 8.7 cm depth,
and capacity: 0.37 liter) filled with sieved paddy soil and grown under
greenhouse conditions without added fertilizer. After two weeks, the
young tender leaves (3-5 leaves) from randomly selected 3-5 plants were
harvested from each cultivar and stored at -80 °C until extraction of
DNA.
The other free-living Oryza populations, including weedy, feral,
and wild rice, were sampled from various locations across Sri Lanka. To
prevent repeated samples of the same genets (clones), the distance
between sampled individuals was maintained at least 10 m apart. The
homogeneity of inbred rice makes it easy to distinguish weedy rice by
its characteristic traits, such as differences in seed and panicle
features, typically exhibiting taller stature, profuse tillering, a more
open or spreading growth habit, and weaker culms. Weedy rice plants were
collected from 20 major rice-growing areas (20 populations) in Sri Lanka
that had a recent history of heavy weed infestation, as confirmed
through personal communication with the Department of Agriculture, Sri
Lanka (see Fig. 1). One population was defined as approximately 25 weedy
rice plants randomly sampled from each field, which covered an area of
approximately one hectare. Thus, a total of 500 individual weedy rice
plants were collected across the entire geographical distribution in Sri
Lanka. The sampled rice fields infested with weedy rice were at least 30
km apart from each other. For this study, six O. nivara (183
individuals) and five O. rufipogon (132 individuals) populations
were sampled, comprising 18 to 31 individuals per population and
representing the diverse wet, dry, and intermediate zones of Sri Lanka.
Feral rice consisted of O. sativa populations that emerge
spontaneously in paddy fields abandoned for approximately 10 years.
These plants are presumed descendants of previously cultivated inbred or
landrace varieties. Unlike weedy rice, feral rice is not considered a
weed in paddy fields. In this study, we sampled seven feral rice
populations, collecting 24 individuals per population (168 individuals
in total), from abandoned paddy fields for further analysis. Green leaf
samples were collected from wild, weedy and feral rice in theMaha season from late February to March 2016. The green leaves
were collected individually in the field, placed in zip-lock bags
containing silica gel, and stored at 0-4 °C until DNA extraction.
Information on population codes, the number of individuals sampled,
locations, and GPS readings of the weedy rice populations are given in
Table S1.
Fig. 1. Geographical locations of 20 weedy rice (blue circles),
five Oryza rufipogon (green triangles), six Oryza nivara(yellow triangles) and seven feral rice (the red squares) populations
sampled in this study. Dark lines separate the climatic zones in this
study. Detailed information on these populations is provided in Table
S1.