Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice (Zizania palustrisL.)

Abstract

Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic annual grass with significant ecological, cultural, and economic importance to the Great Lakes region of the United States and Canada. Understanding the genetic diversity of NWR is essential to conservation efforts. In this study, we assembled and genotyped a diverse collection of 789 NWR individuals using genotyping-by-sequencing and obtained 5,955 single-nucleotide polymorphisms (SNPs). Our collection consisted of samples from 12 wild NWR populations, some of which were collected temporally, a representative sampling of cultivated NWR germplasm, and a Zizania aquatica population (outgroup). Using these data, we characterized the genetic diversity, relatedness, and population structure of this broad collection of NWR genotypes. We found that wild populations of NWR clustered primarily by their lake or river of origin as well as larger clustering patterns based on watershed assignment. Contextualizing some clustering patterns with historical knowledge of ecosystem management helped to unravel some of the complexity of the population structure of wild populations. Cultivated materials were genetically distinct from wild populations, suggesting limited gene flow between the semi-domesticated crop and its wild counterparts. Estimates of linkage disequilibrium (LD) in NWR demonstrated that LD decays quickly across the genome and provided insights into the quality of the reference genome assembly of NWR. The first genome-wide scans of putative selection events in cultivated NWR were also evaluated. Overall, this study presents a large set of new SNP markers for use in NWR genetic studies as well as new insights into the gene flow, history, and complexity of wild and cultivated populations of NWR.

Northern Wild Rice (Zizania palustris L.) breeding, genetics, and conservation

“…Following the Z. palustris-Z. latifolia split, a rapid expansion of repetitive regions in the Z. palustris genome began ∼5 MYA (Haas et al, 2022), which contributed considerably to the species' large genome size in comparison with other…”

“…Two important resources that were recently developed are the assemblies and annotations of the Z. latifolia (Guo et al, 2015;Yan et al, 2022) and Z. palustris (Haas et al, 2021) genomes, which have increased our understanding of the structure and function of both genomes as well as their shared evolutionary history. Molecular marker discovery and whole-genome genotyping have also been employed recently within the genus (Haas et al, 2021(Haas et al, , 2022Millas et al, 2022;Shao et al, 2019), which has led to high resolution mapping of its genetic diversity and the development of more informed molecular breeding approaches.…”

“…While our understanding of NWR population genetics and diversity is growing, little is known about cultivated NWR germplasm. Recent studies have indicated that the UMN breeding program germplasm is highly admixed with limited population structure (Haas et al, 2022;Kahler et al, 2014), which is likely a result of the close proximity in which Crop Science cultivated populations are grown, due to space limitations. This hypothesis is supported by the clear population structure of the breeding line, "K2," which has been isolated from the rest of the program's germplasm for at least the last 20 years (Haas et al, 2022).…”

“…Recent studies have indicated that the UMN breeding program germplasm is highly admixed with limited population structure (Haas et al, 2022;Kahler et al, 2014), which is likely a result of the close proximity in which Crop Science cultivated populations are grown, due to space limitations. This hypothesis is supported by the clear population structure of the breeding line, "K2," which has been isolated from the rest of the program's germplasm for at least the last 20 years (Haas et al, 2022). In an outcrossing crop, such as NWR, it can be difficult to maintain the purity of breeding lines, as is highlighted by these findings.…”

“…This study, while small in scope, found that most pollen-mediated gene flow occurred within the first 7 m of the pollen source. Independent molecular-based studies have also found limited evidence of gene flow in wild rice (Kahler et al, 2014;Lu et al, 2005;Xu et al, 2015), with a recent study identifying clear delineations between the crop and its wild relatives (Haas et al, 2022). Xu et al (2015) has further proposed that gene flow is limited in the entire Zizania genus (Xu et al, 2015).…”