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This Week in PNAS: Jun 28, 2016

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.

In the early, online edition of the Proceedings of the National Academy of Sciences this week, researchers from Mexico and the US explore the genetic and physical effects that genomic selection has had on Holstein dairy cattle in the US over the past seven years. Using several models, the team considered selection differentials over time in cows, bulls, and their parents (sires and dams), focusing on traits such as milk yield, fat yield, productive lifespan, daughter pregnancy rate, and somatic cell score, a means of measuring infection and udder health. Results of the analyses suggest genomic selection had relatively rapid effects on traits with lower heritability, such as fertility, udder health, and lifespan. Overall, the study's author say, their findings "clearly demonstrate the positive impact of genomic selection in US dairy cattle, even though this technology has only been in use for a short time." GenomeWeb has more on this here

A team from Japan, the US, Finland, and the UK takes a crack at untangling the reproductive relevance of evolutionarily conserved and testes-enriched genes in mice for another paper slated to appear in PNAS this week. Using a CRISPR/Cas9 genome engineering and resources available through the Knockout Mouse Project, the researchers tracked the fertility effects in mice missing testes-enriched genes that are conserved in humans. In the process, they found 54 such genes that were dispensable for fertility. "[O]ur results suggest that one should determine whether a gene of interest is essential for male fertility in vivo before spending significant effort to analyze the molecular function of the gene in vitro," the team writes.

Finally, Spanish, German, and Dutch researchers report on efforts to assemble an Arabidopsis thaliana genome using a combination of short reads, long reads, and linkage data. The approach produced 117 million bases of sequence assembled on five chromosome-length sequences, the team reports. And its comparison with the fully assembled Arabidopsis reference genome uncovered 564 transpositions, 47 inversions, and hundreds of genes specific to one assembly or the other, as well as more than 4 million bases of non-reference sequence, largely in the form of sequence duplications.