NEW YORK (GenomeWeb) – A research project led by the Donald Danforth Plant Science Center plans to identify the vast amount of genetic variation in sorghum in order to improve the plant for food production, particularly in sub-Saharan Africa.
In September, the Bill & Melinda Gates Foundation awarded a three-year. $6.1 million grant to the project which will also receive support from Illumina in the form of donated sequencing reagents.
The Danforth Center is leading the effort, but there are a number of other collaborators, including at the HudsonAlpha Institute for Biotechnology, NRgene, as well as researchers in India, Senegal, Ethiopia, France, and other US universities.
The project builds off of another sorghum genomics project called TERRA-REF that was launched in June 2015 with support from the US Department of Energy's Advanced Research Projects Agency-Energy. That project originally aimed to optimize breeding primarily for bioenergy.
As part of the TERRA-REF project, researchers have sequenced 400 sorghum genomes. The new project will expand on that work, sequencing 20 to 30 reference genomes as well as resequencing between 1,000 and 2,000 sorghum genomes.
"Part of the goal is to move beyond single reference genome projects," Jeremy Schmutz, co-director of the Genome Sequencing Center at HudsonAlpha, said in an interview. Similar to human genome studies, where researchers increasingly want to generate population-specific references to better capture variation, in the plant world multiple reference genomes are necessary to identify the large amount of variation that can occur even in a single species. "Sorghum is way more diverse than humans," Schmutz said.
Schmutz said that the goal is to generate around 15 to 20 reference genomes based on different sorghum varieties being grown around the world. For de novo reference genome sequencing, the researchers plan to use Pacific Biosciences' Sequel instrument, Schmutz said, since it yields long reads that are critical for assembly. The resequencing will be done on Illumina's HiSeq X Ten, in order to take advantage of the lower cost per base.
The sorghum genome is between 700 and 800 megabases in size, Schmutz said, which is larger than the rice genome but only about one quarter the size of the corn genome. It has a repeat content of around 61 percent.
For reference genome assembly, Schmutz said that the researchers are considering using 10X Genomics' technology layered on top of the PacBio sequence data. The 10X data can help orient the repetitive content. And finally, once the genome has been assembled with the PacBio base, the researchers will use Illumina sequencing for "polishing," Schmutz said.
In addition, Schmutz said, the researchers plan to incorporate RNA sequencing data from eight different tissues for each of the reference genomes, which they will use to help with annotation. "That lets us ask questions about specific areas in the germplasm that contain genes not present in other areas of the germplasm," Schmutz said. "We can move to the point where we can follow up with multilayered GWAS and we're not stuck with always comparing to one reference."
Todd Mockler of the Danforth Center said that the team would look to select diverse sorghum lines for the reference genomes. They "will be distantly related sorghum lines that are relevant for grain," he said.
For instance, added Schmutz, different countries and even villages in Africa have different lines of sorghum that have adapted through years of breeding and growing to the specific conditions there. The project provides "the opportunity to reach directly into those lines," and understand the relationship between the various phenotypes and the genotypes.
At the end of the three-year grant, the goal is to "have all these genomic resources developed and implemented into the breeding programs," Mockler said. While it is unlikely that new lines will have already been created because the breeding and planting process takes more time, the goal is to have an understanding of the genomics of sorghum, including specific variants' impacts on phenotypes. That infrastructure will enable the breeding programs to move forward at an accelerated rate, Mockler said.
The team is focusing specifically on understanding the relationship between genomics and crop yield, including drought, heat, and cold tolerance, as well as resistance to disease. For instance, said Mockler, there is a parasitic plant called Striga that affects crop plants, including sorghum, and is especially problematic in sub-Saharan Africa. Some resistance markers have been discovered in sorghum, but this project could help speed up the understanding of what enables some plants to be resistant to Striga and help with breeding resistant lines.
NRgene, an agricultural informatics and functional genomics company based in Israel, will focus on the interpretation of the genomic information and comparative genomics studies, NRgene CEO Gil Ronen said in an interview. Ronen said NRgene will look to do studies that correlate the genetic elements that are discovered through the sequencing with their phenotypes. It will also help in building the sorghum pan-genome, he said. The company has developed a tool called PanMagic that does genome-to-genome mapping to identify all classes of variations, including SNPs, copy number variations, inversions, translocations, and indels.
Aside from the end goal of developing better breeding practices for farmers growing sorghum for food, Schmutz said that the project also serves as a model for how genetic variation could be studied in other species. "This is what plant genomics should be and what we should be doing for all plants," he said.