Identification of single nucleotide polymorphism markers for population genetic studies in Zizania palustris L.

Shao, Mingqin; Haas, Matthew; Kern, Anthony J.; Kimball, Jennifer

doi:10.1007/s12686-019-01116-9

Cited by 6 publications

(34 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In order to demonstrate the utility of the NWR reference genome for genetic studies, previously published genotyping by sequencing (GBS) data used to call SNPs without the use of the reference genome (Shao et al, 2020) were reanalyzed. The raw sequence data initially reported by Shao et al (2020) can be found at the National Center for Biotechnology Information Short Read Archive (NCBI SRA) under accession number PRJNA574141. FASTQ files were aligned to the genome using the Burrows-Wheeler Aligner (BWA-MEM) version 0.7.17 (Li, 2013) using default parameters.…”

Section: Nwr Snp Distribution and Genotyping-by-sequencing Read Depthmentioning

confidence: 99%

“…Reliable reference genomes are useful for genetic studies as they can provide insights into evolutionary events and relationships, functional genomic and linkage disequilibrium analyses, and the identification of genes responsible for traits of interest. To highlight the utility of the NWR genome, we re-examined a set of NWR SNPs reported in Shao et al (2020), and identified putative seed-shattering genes in NWR based on the well-characterized shattering genes in O. sativa (Konishi et al, 2006;Li et al, 2006;Lin et al, 2012, Zhou et al, 2012Ishii et al, 2013;Yoon et al, 2014). We then calculated the number of SNPs within 1Mb of putative shattering genes to assess GBS-derived SNP densities surrounding these genic regions.…”

Section: Leveraging the Annotated Nwr Reference Genome For Plant Imprmentioning

confidence: 99%

“…In 2020, a small GBS-driven SNP identification study was published to evaluate SNP densities at four GBS read depths for future use in genetic studies (Shao et al, 2020). Here, we present the alignment of the original GBS data (7M reads/sample) to the genome assembly along with sub-sampled sets (~3.5M, 1.75M, and 0.875M reads) to assess SNP frequency and distribution across the NWR genome ( Figure S7).…”

Section: Leveraging the Annotated Nwr Reference Genome For Plant Imprmentioning

confidence: 99%

“…Comparison of the size of these orthologs revealed that many are of similar size, however a few orthologs in NWR were almost twice the size of O. sativa genes (Table S10). Previous studies have identified that differences in gene size can be caused by increases in the amount of intergenic transposable elements (Bennetzen and Ma, 2003;Swigonova et al, 2005) as well as duplication events, where one paralog is free from selection resulting in either a loss of function or the development of novel functions within the genome (Panchy et al, 2016) To conclude these initial evaluations, we counted SNPs from Shao et al (2020) within 1 Mb upand downstream (2 Mb total window size) from the start position of each putative NWR shattering gene (Table 3). Among the 17 largest scaffolds at a read depth of 7M, the number of SNPs ranged from 54 SNPs for the sh5 candidate ZPchr0001g31104 to 489 SNPs for the OsLG1 candidate ZPchr0006g44369 (Table S10) with an average number of 254 SNPs surrounding each of the candidate regions.…”

Section: Leveraging the Annotated Nwr Reference Genome For Plant Imprmentioning

confidence: 99%

“…It is important to note that these numbers are likely over-estimates of reliable SNPs due to the limited number of samples (8) in the Shao et al (2020) dataset where assessments of minor allele frequencies were negligible. While linkage disequilibrium (LD) has yet to be evaluated in NWR, we suspect LD decays rather rapidly given the species out-crossing habit, which will require a large number of SNPs distributed along the genome to identify causal variants.…”

Section: Leveraging the Annotated Nwr Reference Genome For Plant Imprmentioning

confidence: 99%

See 4 more Smart Citations

Whole Genome Assembly and Annotation of Northern Wild Rice,Zizania palustrisL., Supports a Whole Genome Duplication in theZizaniaGenus

Haas

Kono

Macchietto

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural, and agricultural significance, specifically in the Great Lakes region of the United States. Using long- and short-range sequencing, Hi-C scaffolding, and RNA-seq data from eight tissues, we generated an annotated whole genome de novo assembly of NWR. The assembly is 1.29 Gb, highly repetitive (~76.0%), and contains 46,421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole genome duplication prior to the Zizania-Oryza speciation event have both led to an increase in genome size of NWR in comparison with O. sativa and Z. latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed conservation of large syntenic blocks with Oryza sativa L., which were used to identify putative seed shattering genes. Estimates of divergence times revealed the Zizania genus diverged from Oryza ~26-30 million years ago (MYA), while NWR and Zizania latifolia diverged from one another ~6-8 MYA. Comparative genomics confirmed evidence of a whole genome duplication in the Zizania genus and provided support that the event was prior to the NWR-Z. latifolia speciation event. This high-quality genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.

show abstract

Section: Nwr Snp Distribution and Genotyping-by-sequencing Read Depthmentioning

confidence: 99%

Section: Leveraging the Annotated Nwr Reference Genome For Plant Imprmentioning

confidence: 99%

Section: Leveraging the Annotated Nwr Reference Genome For Plant Imprmentioning

confidence: 99%

Section: Leveraging the Annotated Nwr Reference Genome For Plant Imprmentioning

confidence: 99%

Section: Leveraging the Annotated Nwr Reference Genome For Plant Imprmentioning

confidence: 99%

See 3 more Smart Citations

Whole Genome Assembly and Annotation of Northern Wild Rice,Zizania palustrisL., Supports a Whole Genome Duplication in theZizaniaGenus

Haas

Kono

Macchietto

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

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

et al. 2023

Self Cite

View full text Add to dashboard Cite

Cultivated Northern Wild Rice (NWR; Zizania palustris L.) is a high‐value, small commodity crop grown in irrigated paddies, primarily in Minnesota and California. Domestication of the species began ∼60 years ago as demand for the nutritional grain outpaced hand‐harvesting efforts from lakes and rivers in the Great Lakes region of the United States and Canada. Cultivated NWR cultivars are open‐pollinated and highly heterogeneous and have primarily been bred for seed retention, yield, and seed size. As a lowland crop, NWR's life cycle, particularly its unique seed physiology, poses challenges to breeding efforts, limiting selection cycles per year, and requiring annual grow‐outs of all germplasm. Recent efforts have increased the genomic resources available to NWR researchers, including a reference genome assembly and methodology optimization for genotyping‐by‐sequencing technologies. The species’ close phylogenetic relationship with white rice (Oryza sativa) also provides a unique opportunity to utilize comparative genomic approaches to identify genes conferring agronomic traits of interest in NWR, particularly domestication traits such as seed retention. Z. palustris is an enigmatic species with regional ecological, cultural, and agricultural significance in the Great Lakes. As NWR is grown in both the centers of origin and diversity, it is important for NWR plant breeders to be good stewards of our domesticated plants and include a diversity of stakeholders in our decision‐making processes. In this work, we have aimed to unpack some of the disputes regarding the breeding of cultivated NWR and the science behind our work. Additionally, we have discussed conservation efforts for natural stands of NWR which will help preserve the many ecosystem, nutritional, spiritual, and economic services provided by this important species.

show abstract

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

Haas

McGilp

Shao

et al. 2022

Preprint

View full text Add to dashboard Cite

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.

show abstract

Identification of single nucleotide polymorphism markers for population genetic studies in Zizania palustris L.

Cited by 6 publications

References 29 publications

Whole Genome Assembly and Annotation of Northern Wild Rice,Zizania palustrisL., Supports a Whole Genome Duplication in theZizaniaGenus

Whole Genome Assembly and Annotation of Northern Wild Rice,Zizania palustrisL., Supports a Whole Genome Duplication in theZizaniaGenus

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

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

Contact Info

Product

Resources

About