1 Introduction
The evolution of crop species may extend beyond the control of a
breeder. Perhaps the most dynamic opportunities for spontaneous
evolution are in regions rich with reproductively compatible plants in
both managed and unmanaged populations. For example, managed populations
may consist of both landraces and inbred rice varieties, while unmanaged
populations may include both wild rice and weedy rice, descended from
the crop or wild species from which the crop has evolved. According to
Molina et al. (2011), the rice crop has been domesticated from
wild Oryza species, specifically O. rufipogon Griff. in
Asia and O. barthii A. Shiv. in Africa. It is ecologically
logical for the epicenters of rice cultivation to have weedy types that
are admixtures of the wild relatives, off-types of the selected and
cultivated strains, and various outcrosses (Pusadee et al., 2013;
Veltman et al., 2019) as they co-exist in adjoining habitats. In
such regions, gene flow between cultivated plants, wild relatives, and
their weedy descendants present would generate a variation on which
artificial and natural selections could act. Such
”domesticated-weed-wild complexes” (hereafter, DWWC) are poised to be
genetically rich meta-populations of evolutionary experimentation. While
it is easy to tentatively identify such potential complexes by the
occurrence of visually apparent hybrids, it is much more difficult to
measure whether the gene flow plays a role in the evolution of
co-occurring reproductive-compatible relatives (Pusadee et al.,2013; Song et al., 2014). Therefore, the apparent hybrids might
be aberrant individuals, or if they are true hybrids, they might be
sterile evolutionary dead ends. Genetic analysis is necessary to
document whether and how gene exchange occurs (Ellstrand, 2003; Linderet al ., 1998; Leak-Garcia et al ., 2012). Using a panel of
638 domesticated and wild rice genomes, Wang et al . (2017)
examined the genetic ancestry of wild rice and demonstrated that most
modern wild rice types are heavily admixed with domesticated rice due to
gene flow from both pollen and seeds. This suggests that what has been
thought of as wild rice may actually be different stages of feralized
domesticated rice. Further, the Southeast Asian wild-like weedy rice may
have originated from weedy descendants of coexisting cultivars (Sudoet al ., 2021; Neik et al ., 2019).
Most genetic studies of DWWC have focused on one-way introgression of
crop alleles into wild or weedy populations (Ellstrand, 2003), whereas
only a few studies have examined multi-way gene flow among all members
of the DWWC to evaluate whether it is an integrated ”complex”. The
island nation of Sri Lanka is an ideal system to study the multilateral
gene flow of a DWWC due to its geographical isolation from the rest of
South Asia, and its highly diverse topography and climate. The DWWC on
the island involves six evolutionarily distinct groups in theOryza genus, including landraces, inbred rice varieties, two wild
species, feral populations, and weedy rice. Landraces (traditional rice
accessions) have grown for more than two and a half millennia across the
island (Weerakoon et al., 2011) and inbred rice varieties
cultivated since the 1960s (Dhanapala, 2020). Reproductively compatible
free-living wild relatives of the rice include two wild species, the
annual O. nivara and the perennial O. rufipogon .
Self-sustaining feral populations that have emerged from cultivated
fields abandoned (approximately ten years prior) represent an additional
category of free-living lineages (Qiu et al., 2020).
Nevertheless, their inclusion as part of the DWWC has not yet been
recognized. The latter thus presents an unusual opportunity as it
represents the early portion of the evolutionary trajectory to
de-domestication (Ellstrand et al., 2010). The sixth category is
one of the world’s worst rice weeds, weedy rice (Oryza spp.).
Unlike feral populations, which are sustained without human
intervention, weedy rice is typically restricted to cultivated rice
fields, making it a significant threat to sustainable rice production in
Sri Lanka (Ratnasekera, 2015). Given the six categories, there are
thirty potential pathways for gene flow among the Sri LankanOryza types if all of them participate in the DWWC.
Therefore, our study aimed to use SSR loci to characterize the
populations of the entire array of Sri Lankan Oryza categories
and address the following research questions: (1) What is the influence
of the genetic background of DWWC components and their participation in
an integrated complex on the population? (2) To what extent does
multi-way gene flow exist among all members of the DWWC? (3) What role
has the DWWC played in the origin and evolution of weedy rice in Sri
Lanka?