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International Team Sequences Apple Genome

By Andrea Anderson

NEW YORK (GenomeWeb News) – A group of researchers from Italy, the US, France, New Zealand, and Belgium reported in the early, online edition of Nature Genetics yesterday that they have sequenced a draft version of the domesticated apple genome — a feat that's expected to lead to a better understanding of the biology of apples and related plants as well as improved apple varieties.

"A practical goal of sequencing the complex heterozygous apple genome is to accelerate the breeding of this economically important perennial crop species," co-lead author Riccardo Velasco, a researcher with the Instituto Agrario San Michele, and his co-authors wrote. "Many genes related to disease resistance, aroma and taste, plant development, and reaction to the environment have been identified and mapped to chromosomes."

The team used a combination of Sanger and high-throughput sequencing to tackle the genome of the Golden Delicious variety of domesticated apple, Malus x domestica. Based on the genome sequence and comparisons with related plants, the team concluded that domesticated apple most closely resembles a wild plant from central Asia called Malus sieversii and is descended from an ancestral plant that underwent genome duplication within the past 50 million years or so.

Domesticated apple belongs to Rosaceae, the same family as cherry, strawberry, and rose plants. But apples and other members of a sub-tribe called Pyreae have far more chromosomes than the rest of the Rosaceae family: 17 compared with the seven to nine chromosomes found in other Rosaceae plants.

Using a combination of Sanger and Roche 454 GS FLX Titanium sequencing, Velasco and his colleagues generated sequence covering about 81 percent of the heterozygous Golden Delicious apple genome to 16.9 times coverage.

The team's analyses indicate that the apple genome, estimated at about 742.3 million bases, contains some 57,386 genes, 178 microRNAs, 4,021 transcription factor coding sequences, and nearly 32,000 open reading frames resulting from transposable elements.
Among the groups of genes that have been expanded in the apple genome is a sub-clade of genes coding for transcription factors in the MADS-box group — previously implicated in fruit and flower-related processes.

Unlike other Rosaceae family plants, members of the Pyreae tribe, such as apples and pears, develop fruit — known as the pome — from a part of their flowers called the receptacle rather than from their ovaries, Velasco told GenomeWeb Daily News.

"Pome fruit is derived by enlargement of the receptacle, which is the region below the whorl of sepals in the apple flower," he and his co-authors noted. "MADS-box genes may regulate pome development, as they determine the eventual fate of floral tissues in all plant species analyzed so far."

Gene families coding for metabolic proteins seem to be expanded in the genome, the team reported, including 71 genes related to the metabolism of sorbitol, which helps ferry carbohydrates that are produced during photosynthesis through plants.

The apple's large gene repertoire seems to partly reflect the heterozygous genome composition as well as genome duplication, the researchers explained.

Based on their analysis of the apple genome, they concluded that this duplication likely occurred 50 million or more years ago and involved plants from the same species or lineage, referred to as an autopolyploidization, rather than through a so-called allopolyploidization involving ancestral plants from more than one lineage.

"It was already known that apple was supposed to be a full tetraploid," Velasco said. "From the results we have, it's most likely an autopolyploidization of a previous species which should have had nine chromosomes."

While apples now have 17 rather than 18 chromosomes, he explained, chromosome 15 is nearly twice the size of the others, suggesting it may represent two ancestral chromosomes.

Meanwhile, the team's comparisons between genes in wild and domestic apple plants, including other domestic apple varieties, combined with information in the newly sequenced genome, indicate that domesticated apple is most closely related to a plant called M. sieversii, native to an area near present day Kazakhstan and China.

Next, the team hopes to tease apart functional roles of genes and gene families that seem to influence traits such as fruit production or disease resistance and begin applying such insights — for instance, through marker-assisted breeding efforts to help "find out the best combination possible to obtain new, high quality varieties," Velasco explained.

"To identify all the genes that are contained [in the apple genome] and classify them is the first step," he said. "But breeding institutions clearly are interested in economically interesting genes or gene families."

Similar approaches could potentially be applied to help develop apple varieties with pathogen self-resistance as well, Velasco added, since the wild plant M. sieversii isn't affected by some diseases and pests that can damage domesticated apple crops.

"The wild, closest relative [to domesticated apple] is so resistant to any kind of illness of apple, which is very promising for obtaining high quality, self-resistant new apple," Velasco noted.

Members of the team are currently re-sequencing other apple varieties to not only learn more about genes linked to specific traits, but also to unravel phylogenetic relationships between these varieties in cases where they're not already known.

And, Velasco explained, comparing the apple genome with sequences from related crop plants such as peach and strawberry may be another avenue for uncovering the genes behind economically important traits.

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