Introduction
Northern Wild Rice (NWR; Zizania palustris L.) is an annual,
diploid (2n =2x =30), aquatic grass native to the Eastern
Temperate and Northern Forest ecoregions of North America1,2. Predominantly found in shallow, slow-moving
waters surrounding the Great Lakes region of North America, NWR’s
regional significance in these areas is vast and complex3–8. To begin, NWR is a natural resource that
provides food and substantial habitat for a wide range of wildlife9,10 as well as important ecosystem services such as
anchoring riparian soils and inhibiting algal blooms11. For centuries, this nutritious grain has been
hand-harvested from regional lakes and rivers by Dakota and Anishinaabe
Peoples 2,12, and ‘psin’ (Dakota) or ‘manoomin’
(Ojibwe, Anishinaabe) remains an integral component of their cultures
and lives today. The species has also become a high-value commodity crop
that includes hand-harvested grain from regional waters, and cultivated
grain from irrigated paddies, grown primarily in Minnesota (MN) and
California (CA) 13. As a part of the Oryzae tribe in the Poaceae family, Zizania species are also
considered crop wild relatives of Oryza sativa L. (white rice).
Given the many roles described above, we contend that the conservation
of NWR serves as an important intersection between our ecosystems, our
cultures and food, and our economies.
Worldwide, plant species are experiencing declines and extinction events
as a result of human activities altering natural ecosystems. For at
least the last century, NWR has been experiencing such declines in its
native habitats 14,15, and the species appears to be
slowly migrating northward 16. Recent reports have
stated that NWR is at high risk of loss, and the International Union for
Conservation of Nature has added NWR to their red list of threatened
species 17. Hydrological changes due to damming and
channelization, recreational water activity, shoreline development, and
water pollution from industrial activities have all been associated with
the decline of NWR in its natural habitats 6,15. The
species is particularly sensitive to high levels of sulfates in its
water supply and acts as an important indicator species of water quality6,18. In addition to these conservation challenges,
NWR seed is intermediately recalcitrant or desiccation intolerant, which
reduces seed longevity in storage to 1-2 years 19 and
reduces the feasibility of preservation in ex-situ seed banks.
Therefore, the genetic diversity of NWR is currently only preservedin-situ within its natural range (Porter, 2019).
Genetic diversity represents the extent of heritable variation within
and among populations of a species, and its preservation is vital for
the maintenance of long-term viability in the face of continual
environmental change 20,21. A 2008 MN Department of
Natural Resources (MN DNR) report on the health of NWR natural stands
concluded that the species’ greatest threat was an overall state-wide
decline in genetic diversity 15. Biologists and
conservationists have widely recognized the value of characterizing
genome-wide diversity within a species for use in conservation efforts22,23. However, few such studies have been conducted
for NWR, and molecular studies have heavily relied on obsolete marker
systems 5,24,25, which are laborious to produce and
often limited in number 26. The advent of low-cost
high-throughput sequencing, such as genotyping-by-sequencing (GBS),
which provides genome-wide coverage of co-dominant, single-nucleotide
polymorphism (SNP) markers, has improved the genetic diversity
characterization of extensive and complex germplasm collections27. In 2019, a study with limited sample size
demonstrated the potential for GBS to be applied to NWR28.
The cultivation of NWR in irrigated man-made paddies, similar to white
rice production, began in the 1950s to create an industry capable of
supplying a consistent source of the grain to agricultural markets. As
such, the production of cultivated NWR (cNWR) is a fairly new endeavor
and only ~60 cycles of targeted selection separate cNWR
from its wild counterparts. Breeders of cNWR have focused primarily on
adapting the species to agronomic production in paddies, and on fixing
seed-shattering resistance in the crop 2. However,
concerns regarding the potential impact of gene flow between cNWR and
natural stands of NWR have been raised given the species’ outcrossing
nature 12,29–31. The Great Lakes region is the center
of both origin and diversity of Z. palustris ; therefore, it is
important to understand the potential impact of domesticating and
cultivating cNWR in those areas. As plant breeders, we have a
responsibility to be good stewards of our natural and domesticated
plants. Thus, an understanding of how cNWR fits into local landscapes,
and particularly, to what extent gene flow is occurring among natural
stands and cNWR is essential to overall germplasm preservation.
In this study, we generated a genome-wide SNP dataset via GBS for a NWR
diversity collection to study the population structure and gene flow
within and among wild and cultivated populations. We aimed to improve
our understanding of the genetic variability within the species and
provide new information regarding the selective pressures applied to
cNWR germplasm.