Assembly of multiple varieties of maize to assist the efficient breeding of more productive varieties, gene editing, and the discovery of key agronomical traits
Ness Ziona, Israel – 1 August 2018 – The de novo genome assembly of diverse lines of maize gives researchers unique insights into the diversity and evolution of the species. In the latest publication of Nature Genetics this week, maize researchers and NRGene have generated a reference assembly, annotated, and described the maize inbred line W22.
This work gives the research community unprecedented access and accuracy to a genome that has been utilized extensively by maize geneticists for many years to study gene action. The W22 genome has been host to functional genomics tools including Mutator and Ac/Ds transposable element mutant collections. With this highly accurate and high-quality assembly, researchers can further accelerate their functional analyses and better understand how genomic variation affects biological processes in this economically important crop.
With the addition of this publication, NRGene, the leading provider of genomic big data analysis, has delivered to the public seven full maize genome sequences of the nine genomes available.
Many of the maize genomes assembled by NRGene have already been published in first-tier scientific journals (See references 1-5.) and are available in the maize genome database (MaizeGDB). The availability of multiple, high quality, full genomes is crucial for maize, since the genomic diversity between varieties in maize is enormous, reaching up to a 45% difference in genomic sequence between two varieties.
“Having access to multiple maize denovo genome assemblies is critical to enable studies of all types of genetic and epigenetic variation,” said Dr. Nathan Springer, Professor at University of Minnesota. “The high-quality assembly of the W22 genome developed with NRGene’s analytics is providing insights into the diversity of transposon organization within the maize genome and how this influences epigenetics and gene expression.”
Researchers are already using this vital genetic resource to speed up genetic research and breeding toward maximizing maize productivity in diverse geographies and market segments.
NRGene’s assemblies correctly positioned structural variations of the maize genome.
“Utilizing NRGene’s assembly, we were able to identify a presence/absence variation for an important insect resistance gene,” stated Dr. Georg Jander, investigator at Boyce Thompson Institute at Cornell University.
“NRGene has incorporated multiple assemblies to enable us to describe more diversity in our lines that could be detected by previous methods,” said Dr. Chris-Carolin Schön of Munich University, Germany. “They’ve really accelerated our research.”
Maize is grown in broad temperate and tropical climates. Altogether, maize is among the three largest cultivated crops with 2.607 million tons produced in 2017 (FAOSTAT), making it a vital income resource to many millions of farmers around the globe. Maize grains’ multiple uses include food, feed, processed food, starch, oil, ethanol, and many more. Maize seed sales are close to 40% of total global seed sales, making it the leading revenue generator for many seed companies.
DeNovoMAGICTM can assemble virtually any genome de novo. The unique assembly engine completes even the most challenging assembly within days of obtaining the raw sequence data, with outstanding results. DeNovoMAGIC has been successfully deployed by the world’s leading seed companies and academic institutions and has successfully assembled genomes of many plants and animals to the highest standards.
“We are proud to enable researchers around the world to view and review the broad genetic diversity in maize with multiple, reference-grade, full genome sequences,” says Dr. Gil Ronen, CEO of NRGene. “Moreover, we are releasing to the public the first full pan-genome of maize, formerly used only by commercial companies. The pan-genome is created by all-to-all comparisons of the latest versions of all available maize genomes. This pan-genome view enables researchers and breeders, for the first time, to use all genomes’ data in parallel, rather than using a single reference genome.”
PanMAGICTM delivers complete species diversity. PanMAGIC compares all-to-all full genomes to get the best view of local differences such as SNPs, InDels, Gene PAV, CNV as well as structural variations of all kinds. Existing historical data can easily be incorporated into the results.
NRGene is a genomic big data company delivering cutting-edge software and algorithms to reveal the complexity and diversity of humans, plants and animals for supporting the most advanced medical research and sophisticated breeding programs. NRGene tools have already been employed by some of the leading seed companies worldwide as well as the most influential research teams in academia. www.nrgene.com. Follow us: Twitter, LinkedIn, and Facebook.
Links to Scientific Papers:
- The maize CML247 genome: Lu et al. 2015
- The maize PH207 genome: Hirsch et al. 2016
- The maize MO17 and PI566673 genome: Yang et al. 2017
- The maize W22 genome: Springer et al. 2018
- The maize EP1 and F7 genomes: Schoen et al. 2017
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