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Researchers Turn to Genomics Approaches to Aid in Plant Crop Breeding

SAN DIEGO (GenomeWeb Daily News) – Researchers at the Plant and Animal Genome meeting here provided updates on crop genome sequencing, resequencing, and other projects, many of which were aimed at providing resources to breeders.

In particular, researchers focused on plants of nutritional or industrial importance and traits like carotenoid levels, oil production, and disease resistance that could enhance that could be harnessed to improve the value of those crops.

Speakers at a BGI-sponsored workshop, for instance, highlighted ongoing work with the carrot, soybean, and cassava genomes.

Using a combined BAC sequencing and whole-genome shotgun sequencing from BGI, Massimo Iorizzo, a research associate at the University of Wisconsin, and his colleagues have generated a draft carrot genome. Carrots, Iorizzo noted, have a market value reaching $6.6 billion, and are a major source of beta-carotene in the US diet.

In this approach, the BACs acted as a sort of tree onto which the shorter reads could be hung to be assembled into some 59 superscaffolds and pseudomolecules.

"We developed a high-quality draft carrot genome," Iorizzo said.

By folding in RNA-seq data, Iorizzo said that he and his colleagues predicted the carrot genome held some 32,427 predicted genes, of which about 28,800 had been annotated. By zooming into carotenoid-related genes, Iorizzo reported that they uncovered 29 annotated carotenoid genes, seven of which were previously unknown in that plant.

The carrot genome also contained hints about the plant's evolution, placing its divergence from the tomato — its most closely related cousin that has been sequenced to date — at about 53 million years ago. The tomato also appears to have undergone genome duplication and triplication events.

And while the domesticated soybean draft genome was published in early 2010 and its wild relative later that year, the University of Missouri's Babu Valliyodan is embarking on a soybean resequencing project along with his industry and government collaborators to develop better breeding tools. Soybean, he noted, is a high-impact crop that is used as both food and animal feed in the US.

As part of this endeavor, the researchers plan to sequence 1,000 Glycine max and 100 Glycine soja lines. For the first phase of the project, Valliyodan said that one cultivar would be deeply sequenced to about 150X, while another subset will be examined to about 40X depth. He expects that data to be generated by August and June of this year, respectively.

A pilot study of about 100 genomes, which underwent paired-end sequencing on the Illumina platform, has reached about 17X coverage, spanning about 97 percent of the soybean genome.

The researchers have a particular interest in oil metabolism genes in soybean. Valliyodan said that a case study of such genes has led them to identify 15 candidate genes associated with oil metabolism.

Meanwhile, Luis Augusto Becerra Lopez-Lavalle from the International Center for Tropical Agriculture in Colombia is turning to functional approaches to study traits like whitefly resistance in cassava to find markers to assist in cassava and other crop breeding. He noted that some 500 million people in Africa rely on cassava as a food source.

Using a RAD-seq approach, Lopez-Lavalle and his colleagues uncovered some 500,000 genome-wide SNP markers for more than 450 cassava accessions. From this, they noted that cassava had five subpopulations that broadly corresponded to different regions of Latin America, where the plant was domesticated. They developed a set of core SNPs that could differentiate the accession studied, setting the stage for broader marker development.

The researchers are also developing an assay to look for resistance or susceptibility to whiteflies, a pest that transmits disease among crops.

Cassava, Lopez-Lavalle pointed out, is one of the few plants with natural resistances to the bug.

"This is going to be important [beyond] cassava," he added.