Nanopore genome sequencing technology
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Nanopore Genome Sequencing Technology Reveals Hidden Plant Traits

The full genome for the black mustard plant has been decoded by an international team of researchers at the Agriculture and Agri-Food Canada (AAFC) and Plant Phenotyping and Imaging Research Centre (P2IRC) at the University of Saskatchewan (USask). The research will advance the breeding of oilseed mustard crops and provide a foundation for improved breeding of canola, lentils, and wheat.

A new genome sequencing technology (Nanopore) was used by researchers led by Isobel Parkin and Andrew Sharpe to obtain very long “reads” of DNA and RNA sequences, providing previously unknown information for crop breeding. The journal Nature Plants published the results.

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The research offers a new model for building genome assemblies for crops like lentils, canola, and wheat. Sharpe, director of P2IRC, said its a new recipe for building the genome sequence of any crop. The researchers now know that the same quality of genomic data and genetic variation can be obtained for these crops. They can more easily select genes for specific desired traits and make breeding more efficient.

To sequence larger and more complex crop genomes, Sharpe and his team are using the software platform in the Omics and Precision Agriculture Lab (OPAL) at the USask Global Institute for Food Security (GIFS).

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Black mustard (Brassica nigra) commonly grown in the Indian sub-continent is much similar to the canola crops and mustard grown in Canada and is usually used in seed form as a cooking spice. A “higher resolution,” clearer view of plant genes is provided by the research, offering breeders and researchers a more defined view of which genes are responsible for which traits. The results also explain how the block mustard is different from its close relatives like turnip, canola, and cabbage.

The team also uncovered structures on chromosomes essential for plant fertility, the first direct evidence of functional centromeres, and the hard to identify regions of the genome.

Unprecedented access to previously hidden features of plant genomes has been enabled by the use of long-read sequence data, said Parkin, a USask adjunct professor, and P2IRC member. Parkin, also the lead research scientist with AAFC Saskatoon Research Centre, said the research enables the identification of novel structural variation as well as provide insights into how crops evolve.

Multiple copies of certain genes that express specific traits were also found in the sequence. This means that several genes could strongly express certain traits like fungal resistance.

The genome assembly developed by researchers for the black mustard is a great example of how important genome biology can be quickly revealed using Nanopore sequencing technology. Public and private plant breeding organizations can make use of this advanced sequencing technology through GIFS and OPAL.

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