NEW YORK (GenomeWeb News) – Researchers reported today that they have completed an improved draft version of the corn genome and are already applying information in the genome to learn more about the plant's biology.
A paper describing the maize sequencing project appears online today in Science, along with several companion papers addressing everything from maize genetic diversity to hybrid vigor. In addition, a collection of papers in PLoS Genetics — and individual papers in the Proceedings of the National Academy of Science and Plant Physiology — are providing additional details and analyses related to the project.
"Having the complete genome in hand will make it easier to breed new varieties of corn that produce higher yields or are more tolerant to extreme heat, drought, or other conditions," University Genome Sequencing Center Co-director Richard Wilson, senior author on the genome sequencing paper, said in statement.
The collaboration had two levels, Wilson told GenomeWeb Daily News. He and his colleagues at Washington University's Genome Sequencing Center — along with collaborators at the Cold Spring Harbor Laboratory, University of Arizona, and Iowa State University — were part of the main genome sequencing consortium.
Meanwhile, as data from the sequencing arm of the project was deposited into a public database, members of the broader maize genetic community applied the data to answer their own research questions.
Wilson and his team sequenced the 2.3 billion base genome of a corn variety called B73, developed at Iowa State University in the early 1970s, mainly using Sanger sequencing.
While they initially attempted to use a clone-by-clone approach, Wilson explained, the researchers soon realized that the method probably wouldn't yield high quality sequence given the highly repetitive nature of the maize genome. Instead, they fell back on "a tried and true BAC-by-BAC approach," using bacterial artificial chromosome and fosmid clones.
After shotgun sequencing the clones to four to six times coverage, the researchers cobbled together a reference genome, making automated and manual sequence improvements as they went.
Since finishing a rough draft of the genome early last year, the team has been closing gaps, refining the sequence data, and fine-tuning maize gene models, Wilson said.
Their analysis indicates that the ten maize chromosomes house about 32,540 protein-coding genes and 150 miRNA genes. The team's subsequent transcription sequencing experiments suggest around 91 percent of the protein-coding genes identified are expressed in maize tissues.
Maize also appears to share 8,494 gene families with rice, sorghum, and Arabidopsis.
Not surprisingly, given what was known about the genome before the sequencing project, the researchers also found a slew of repeat sequences and transposons in maize: nearly 85 percent of the genome is comprised of transposable elements.
With the improved maize draft genome in hand, Wilson's group and others are focusing on its applications for everything from basic biology to agriculture and biofuel research. For instance, Wilson said, the genome contains information that will be useful for understanding specific corn traits as well as doing marker-assisted breeding.
"Just as cytogenetic and genetic maps revolutionized research and crop improvement over the last century, the B73 maize reference sequence promises to advance basic research and to facilitate efforts to meet the world's growing needs for food, feed, energy, and industrial feed stocks in an era of global climate change," the researchers concluded.
In a companion paper in Science, Cornell University and US Department of Agriculture researcher Edward Buckler led a team of researchers who reported that they have developed the first maize haplotype map, using 3.3 million SNPs, insertions, and deletions detected through selective re-sequencing of 27 inbred maize lines.
Results of that study suggest maize haplotypes are widely divergent, with between ten and 30 fold differences in recombination rate. The researchers also turned up almost 150 regions in the maize genome that have relatively low diversity — patterns that they suspect are due in part to selective sweeps involved in processes such as domestication and/or geographic differentiation.
Meanwhile, another paper explored the genetic basis for heterosis (commonly called hybrid vigor), the ability of hybrid maize lines to perform better than their parental lines.
By comparing transcripts and analyzing expression quantitative trait loci from hybrid lines developed by crossing B73 with the maize hybrid Mo17, senior author Patrick Schnable, an agronomy researcher at Iowa State University, and his colleagues were able to pinpoint roughly 4,000 expression quantitative trait loci. Their results indicate that many of these eQTLs are paternally inherited alleles that influence the expression of other genes.
"[P]aternally linked genes are capable of sculpting the transcriptome," Schnable said in a statement. "That knowledge will modify our approaches to crop improvement."
Finally, in a brief appearing online in Science, Mexican researchers reported that they have sequenced the genome of the Mexican popcorn strain, Palomero toluqueno. When they compared this genome with the B73 reference sequence, they found that the Palomero genome is 22 percent smaller — and contains about 20 percent less repetitive DNA — than the reference strain. Their results also suggest that the Palomero genome has been influenced, at least in part, by environmental factors such as the metal content in soils where it's grown.
A package of papers in PLoS Genetics is addressing everything from corn centromere and genome structure to transposons and maize microRNAs.
In a perspectives article in Science, French National Institute for Agricultural Research (INRA) researcher Catherine Feuillet and Kellye Eversole, with the Bethesda-based company Eversole Associates, noted that "[t]hese and companion studies represent a milestone in genetics and plant biology, as well as the crowning achievement of a group of corn growers and scientists who envisioned changing the world of agriculture."
Feuillet and Eversole also touted maize as a model for other crop plants, offering insights into the effects of domestication, hybrid vigor, and transposon activity on plant genomes.
Data from the maize genome is available online at www.maizegenome.org.