Maintaining Food Value of Wild Rice (Zizania palustris L.) Using Comparative Genomics

Kahler, A. L.; Kern, Anthony J.; Porter, R. A.; Phillips, Ronald L.

doi:10.1007/978-94-007-7575-6_9

Cited by 12 publications

(27 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…NWR is also a monoecious outcrosser with severe inbreeding depression, increasing the difficulty of genetic mapping studies and requiring the maintenance of effective population sizes for the survival of the species in natural settings. Currently, genomic resources in the species are limited to studies using a small number of molecular markers, including isozymes (Lu et al., 2005), restriction fragment length polymorphisms (Kennard et al., 2002; Kennard et al., 1999), simple sequence repeats (Kahler et al., 2014) and single‐nucleotide polymorphisms (SNPs) (Shao et al., 2020). The alignment of molecular markers to a reference genome can more readily provide researchers with the ability to investigate the functional relationships between genes and traits of interest, important physiological mechanisms and the architecture of genetic diversity within the species.…”

Section: Introductionmentioning

confidence: 99%

Whole‐genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole‐genome duplication in the Zizania genus

Haas

Kono²,

Macchietto³

et al. 2021

The Plant Journal

View full text Add to dashboard Cite

Zizania palustris L. (northern wild rice, NWR) 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 USA. Using flow cytometry, we first estimated the NWR genome size to be 1.8 Gb. 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 was 1.29 Gb in length, highly repetitive (approx. 76.0%) and contained 46 421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole-genome duplication (WGD) after the Zizania-Oryza speciation event have both led to an increase in the genome size of NWR in comparison with Oryza sativa L. and Zizania latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed the conservation of large syntenic blocks between NWR and O. sativa, which were used to identify putative seed-shattering genes. Estimates of divergence times revealed that the Zizania genus diverged from Oryza approximately 26-30 million years ago (26-30 MYA), whereas NWR and Z. latifolia diverged from one another approximately 6-8 MYA. Comparative genomics confirmed evidence of a WGD in the Zizania genus and provided support that the event occurred prior to the NWR-Z. latifolia speciation event. This 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: Introductionmentioning

confidence: 99%

Whole‐genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole‐genome duplication in the Zizania genus

Haas

Kono²,

Macchietto³

et al. 2021

The Plant Journal

View full text Add to dashboard Cite

show abstract

“…While mechanisms to reduce the abscission layer have evolved in different species at different times, the convergent evolution of the non-shattering trait is often the result of independent mutations at orthologous loci in response to strong artificial selection (Doebley, 2006;Purugganan and Fuller, 2009;Lenser and Theißen, 2013;Olsen and Wendel, 2013;Tranbarger et al, 2017). This convergence of shattering resistance mechanisms within the grass family has afforded researchers the ability to utilize comparative genomic approaches to identify candidate genes within new species of interest (Van Deynze et al, 1998;Nalam et al, 2006;Kahler et al, 2014;Fu et al, 2019). Initial genetic studies suggest the genetic control of non-shattering in NWR is recessive, putatively controlled by two to three genes, and likely orthologous with several O. sativa shattering-related genes (Elliott and Perlinger, 1977;Kennard et al, 2000;Kennard et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

“…NWR is also a monoecious outcrosser with severe inbreeding depression, increasing the difficulty of genetic mapping studies, and requiring the maintenance of effective population sizes for the species survival in natural settings. Currently, genomic resources in the species are limited to studies using a small number of molecular marker studies including isozymes (Lu et al ., 2005), restriction fragment length polymorphisms (RFLP) (Kennard et al ., 1999; Kennard et al ., 2002), simple sequence repeats (SSR) (Kahler et al ., 2014), and single nucleotide polymorphisms (SNP) (Shao et al ., 2020). Alignment of molecular markers to a reference genome can more readily provide researchers the ability to investigate the functional relationships between genes and traits of interest, important physiological mechanisms, and the architecture of genetic diversity within the species.…”

Section: Introductionmentioning

confidence: 99%

“…As a part of the Oryzeae tribe, members of the Zizania genus are considered crop wild relatives of O. sativa (Porter, 2019), and techniques including hybridization (Liu et al ., 1999; Shan et al ., 2005; Yang et al ., 2012), protoplast fusion (Liu et al ., 1999), and gene introduction (Abedinia et al ., 2000), have been utilized to introgress favorable traits from these species into O. sativa . Early comparative mapping studies in NWR revealed significant collinearity with O. sativa (Kennard et al ., 2000; Kahler et al ., 2014) as well as duplications in the copy number of two O. sativa Adh genes (Hass et al ., 2003). Duplication events have been hypothesized in NWR given the species has three additional chromosomes, in comparison to O. sativa , which appear to be duplicates of O. sativa chromosomes 1, 4, and 9 (Kennard et al ., 2000).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

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

“…NWR is a monoecious, cross‐pollinated plant and relatively resistant to self‐pollination. Inbreeding depression has commonly been observed in breeding programmes (Grombacher et al, 1996; Kennard, Phillips, Porter, Grombacher, & Phillips, ; Kennard, Phillips, & Porter, ; Kahler, Kern, Porter, & Phillips, ; Porter, ). The species inflorescence consist of a single panicle per stem (main or tiller) with pistillate spikelets or female florets located above the staminate spikelets.…”

Section: Introductionmentioning

confidence: 99%

Phenological stages of cultivated northern wild rice according to the BBCH scale

Duquette

Kimball

2020

Annals of Applied Biology

View full text Add to dashboard Cite

Cultivated northern wild rice (NWR), Zizania palustris L., is an aquatic grass native to North America that is grown in paddies and harvested for its grain. Domestication of the species began in Minnesota in the early 1950s to provide a stable source of the grain for food processors and to utilise marginal agricultural land. The University of Minnesota has been conducting breeding research on NWR since the 1960s. However, a detailed description of the species phenological stages has not been documented, which would help to standardise results across studies, aid in building accurate crop models, and improve the efficacy of time-sensitive crop management practices. We present here a phenological scale of cultivated NWR based on the widely adopted Biologische Bundesantalt, Bundessortenamt and Chemische Industrie (BBCH) scale, a system for a uniform coding of phenologically similar stages in plant species ' (Bleiholder et al., Gesunde Pflanzen, 1989, 41, 381-384; Meier et al., Nachrichtenblatt des Deutschen Pflanzenschutzdienstes (Braunschweig), 1993, 45(2), 37-41). Data were collected in lab, greenhouse, and field settings at the North Central Research and Outreach Center at the University of Minnesota in Grand Rapids, MN. Ten principal and secondary phenological stages are described using the two-digit BBCH coding system. The description and coding of the scale covers the principal periods from seed storage to seed harvest. K E Y W O R D SBBCH scale, northern wild rice, phenological stages, phenology, Zizania palustris

show abstract

Maintaining Food Value of Wild Rice (Zizania palustris L.) Using Comparative Genomics

Cited by 12 publications

References 22 publications

Whole‐genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole‐genome duplication in the Zizania genus

Whole‐genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole‐genome duplication in the Zizania genus

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

Phenological stages of cultivated northern wild rice according to the BBCH scale

Contact Info

Product

Resources

About