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Peach GWAS Leads to Loci Linked to Fruit Traits

NEW YORK (GenomeWeb) – A genome-wide association study has identified sites in the peach genome that influence traits important to its growth and value as a commercial fruit crop.

Chinese researchers brought together genome sequences for representatives from more than 100 peach accessions for a genome-wide association study focused on a dozen traits, uncovering loci linked to several qualitative features including fruit shape, texture, color, or hairiness. Their findings appeared online today in Nature Communications.

While some of the sites identified in the GWAS fell near parts of the peach genome that have been implicated in such traits through prior linkage studies, the team noted that the new analysis refined and clarified these associations.

"The present findings help clarify the genetic basis for major agronomic traits in peach, potentially allowing for more efficient breeding," senior author Lirong Wang, a biology and genetic improvement researcher at the Chinese Academy of Agricultural Sciences, and co-authors wrote. "Future GWAS analysis, in conjunction with deep sequencing, can be expected to further examine the genetic basis for agronomic traits in peach given [its] high resolution despite the low level of [linkage disequilibrium]."

Using Illumina GAII instruments, the researchers re-sequenced 45 peach accessions, adding to the 10 wild and 74 cultivated accessions that members of the same team re-sequenced for a peach population, evolution, and domestication study that was published in Genome Biology in 2014.

Across the full collection of 129 wild accessions, landraces, ancient varieties, or modern varieties sequenced to an average of just over four-fold coverage, they narrowed in on nearly 4.1 million high-quality SNPs that separated the peach accessions into two broad clusters that were analyzed as distinct sub-populations for the subsequent GWAS.

Using several different analytical models, the researchers searched for variants that were over-represented in peach representatives with 12 different agronomic traits — a search that led to variants with apparent ties to 10 traits such as fruit flesh texture and lack of acidity. Fruit shape, for example, was associated with a variant in the PpCAD1, a gene that also appeared to have more pronounced expression early on in flat peaches and later on in the development of round fruit.

On the other hand, the variants that cropped up for some other fruit traits, such as fruit hairiness or flesh coloring did not quite fit with findings reported from past reverse genetic studies. The team proposed that these discrepancies might reflect roles for transposable element sequences in some peach traits.