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This Week in PLOS: Nov 26, 2018

In PLOS Genetics, researchers from Australia and Canada report on findings from a genome sequencing — and population re-sequencing — study of Chardonnay wine plant clones. After using single-molecule, real-time long read sequencing to put together a 490 million base genome assembly for Chardonnay, the team identified nearly 29,700 predicted protein-coding genes with the help of RNA sequence data. It went on to sequence 15 more Chardonnay clones, uncovering more than 1,620 genetic markers that could be used to differentiate between them. And by mapping sequences from the Pinot noir and Gouais breeds to the new genome, the authors saw signs of inbreeding in the predicted Chardonnay parent plants. 

A team from the US, Spain, and Italy reporting in PLOS One describes a consensus high-density genetic map for the peach tree, assembled by integrating — and adding to — existing linkage maps for multiple peach cultivars. By bringing together five genetic linkage maps and array-based genotype profiles for 65 hybrid peach plants, the researchers came up with a consensus map that contained 2,975 SNPs and 116 simple sequence repeats, along with a morphological marker linked to peach ripening time. "This consensus genetic linkage map represents the most comprehensive peach map available to date," they write, "and could serve as a new reference map for peach."

Researchers from Spain's National Institute for Agricultural and Food Research and Technology and elsewhere present an analysis of trait-related candidate and causal gene diversity in European pig breeds for another PLOS One paper. Using multiple blood samples per breed, the team considered dozens of variants at 33 candidate genes linked to pig traits ranging from coat color or meat quality to reproduction or disease resistance in 20 pig breeds. Along with the potential utility of the resulting SNP segregation catalogue, the study's authors say, the candidate genes identified in the analysis may serve as the basis for future population analyses in the European pig breeds.