New research reveals previously hidden features of plant genomes

Date:
August 10, 2020
Source:
University of Saskatchewan
Summary:
An international team has decoded the full genome for the black
mustard plant -- research that will advance breeding of oilseed
mustard crops and provides a foundation for improved breeding of
wheat, canola and lentils.



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


==========================================================================
The team, co-led by P2IRC researchers Andrew Sharpe and Isobel Parkin,
used a new genome sequencing technology (Nanopore) that results in very
long "reads" of DNA and RNA sequences, providing information for crop
breeding that was previously not available. The results are published
today in Nature Plants.

"This work provides a new model for building other genome assemblies
for crops such as wheat, canola and lentils. Essentially, it's a recipe
for generating a genome sequence that works for any crop," said Sharpe, director of P2IRC.

"We now know that we can get the same quality of genomic data and level
of information about genetic variation for these important national
and international crops. This means we can make breeding more efficient
because we can more easily select genes for specific desired traits."
Sharpe said his team is already using this software platform in the Omics
and Precision Agriculture Lab (OPAL) at the USask Global Institute for
Food Security (GIFS) to sequence larger and more complex crop genomes.

Black mustard (Brassica nigra), commonly used in seed form as a cooking
spice, is grown on the Indian sub-continent and is closely related to
mustard and canola crops grown in Canada. The research provides a clearer, "higher resolution" view of the plant's genes and gives researchers
and breeders a more defined view of which genes are responsible for
which traits.



==========================================================================
The resulting gene assembly for black mustard also helps explain how the
black mustard genome differs from those of its close crop relatives --
such as cabbage, turnip and canola.

The team also uncovered the first direct evidence of functional
centromeres, structures on chromosomes essential for plant fertility,
and detected other previously hard to identify regions of the genome. This knowledge provides a foundation for improving crop production.

Parkin, a USask adjunct professor and P2IRC member, said the use of
long-read sequence data has enabled unprecedented access to previously
hidden features of plant genomes.

"This provides not only insights into how crops evolve but enables the identification of novel structural variation -- now known to play an
important role in the control of many key agronomic traits," said Parkin,
also the lead research scientist with AAFC Saskatoon Research Centre.

They also found in the sequence multiple copies of certain genes that
express specific traits. This could mean that certain traits, such as
fungal resistance, could be expressed more strongly through several genes.

Other USask members of the team include GIFS researcher Zahra-Katy Navabi
and bioinformatics specialist Chu Shin Koh. Other team members include
Sampath Perumal, a post-doctoral fellow with Parkin, as well as others
from the University of Ottawa, Thompson River University, the National
Research Council, and researchers from the United Kingdom and China.

"The genome assembly for black mustard that we have developed is a
great example of how new Nanopore sequencing technology quickly reveals important genome biology," Sharpe said, noting that this advanced
sequencing technology and capability is available to public and private
plant breeding organizations through the OPAL at GIFS.


========================================================================== Story Source: Materials provided by University_of_Saskatchewan. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Perumal, S., Koh, C.S., Jin, L. et al. A high-contiguity Brassica
nigra
genome localizes active centromeres and defines the ancestral
Brassica genome. Nat. Plants, 2020 DOI: 10.1038/s41477-020-0735-y ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/08/200810115522.htm

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