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Genomics In The Journals: Jun 7, 2012

NEW YORK (GenomeWeb News) – In Nature Genetics, three studies look at population genetics in maize, along with genetic features that have accompanied the plant's domestication and subsequent efforts to improve it.

For the first of these, an international team led by investigators in the US and China report on efforts to resequence 103 inbred maize lines as part of the Maize HapMap2 project. Analyses of these sequences — which represent 102 wild, domesticated, and improved Zea mays line as well as an Eastern gamagrass plant from a sister genus called Tripsacum — uncovered some 55 million SNPs, a slew of structural variations, and genome size differences related to so-called chromosomal knob elements in Z. mays. Despite the apparent flux in gene content and genome size within the species, though, authors of that study noted that "[t]here is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize."

Some members of the same team focused on 75 maize lines in an accompanying study that used comparative genomics and transcriptomics to explore the genetic changes associated with the plant's domestication and breeding-based improvement efforts. That group found evidence that maize domestication was accompanied by a dip in diversity, followed by the more recent restoration of diversity through introgression from wild plants. The work also points to stronger selection pressures during the initial domestication process than during the improvement efforts that followed, though both processes seem to have involved alterations in gene expression profiles.

Researchers from China Agricultural University take their own look at genetic features coinciding with maize breeding in a third Nature Genetics study. The team did shallow genome sequencing on 278 inbred maize lines with different modern breeding histories, along with deeper sequencing on four lines that had well-documented pedigrees. Together, this data helped in teasing apart some of the genetic changes that occur during the modern breeding process, including a rise in the level of rare alleles. It also highlighted stretches of the genome that seem to have been subjected to artificial selection.

A Nature Cell Biology study by Irish and German researchers reveals new components contributing to secretory pathway function in human cells. The team used more than 51,000 small, interfering RNAs to do an RNA interference-based scan of the genome in a human cell line, looking for genes whose knockdown altered the transport of a protein typically ferried from the endoplasmic reticulum to the plasma membrane by the cell's secretory system. The search led to thousands of candidate proteins. Through a series of follow-up experiments, the team not only narrowed this list down further but also began characterizing the collection of 554 proteins that seemed to influence cellular secretion.

"Previous studies on the secretory process have either been carried out with a more narrow focus on specific subsets of genes or in more simplistic organisms … where many of the proteins identified have no human equivalent," the study's first author Jeremy Simpson, a biology and environmental science researcher at University College Dublin, said in a statement.

"Now, using high content screening," he explained, "we have been able to systematically target each of the 22,000 human genes and track the journey of a specific, fluorescently-tagged protein as it travels through, and out of, over 8 million individual cells."

Using a non-invasive prenatal testing method known as Digital Analysis of Selected Regions, or DANSR, which involves sequencing specific chromosome fragments from cell-free fetal and maternal DNA found in pregnant women's plasma, members of the "Non-Invasive Chromosomal Evaluation" study found that they could accurately identify fetuses with trisomy 21 and trisomy 18 in women at at least 10 weeks gestation.

As they report in American Journal of Obstetrics & Gynecology, the researchers tested more than 3,000 women from three countries for the NICE study, which was financially supported by the San Jose-based prenatal testing company Ariosa Diagnostics and co-authored by employees of the company. Using the chromosome specific-sequencing method, the team accurately classified all 81 trisomy 21 cases — and all but one of the 38 trisomy 18 cases — as high risk. The approach produced one false-positive trisomy 21 result and two false-positive trisomy 18 identifications amongst 2,888 women carrying fetuses without these conditions.

The 2010 Deepwater Horizon oil spill altered the types of tiny eukaryotic organisms found on beaches along the Gulf of Mexico, according to a PLoS ONE study.

American researchers used Roche 454 sequencing to test sediments collected at five coastal sites in Louisiana and Alabama before oil reached the shoreline and as long as five months after the spill. They also took post-spill samples from a sixth Louisiana beach that was "persistently oiled" after the spill.

From 18S ribosomal DNA sequences in the sediment samples, the investigators determined that eukaryotic microbe communities on the beaches before oil reached the shores were diverse and comprised of a range of small worms and insects, fungi, single-celled eukaryotes, and so on. In samples taken later, though, the diversity and composition of the eukaryotic microbe communities shifted, with four of the oil-soaked beaches showing a jump in the levels of fungi known for degrading hydrocarbons.

"The development of these genomic tools provides a detailed understanding of the biological consequences of such environmental disasters," University of New Hampshire genomics researcher Kelley Thomas, the study's senior author, said in a statement, "and is the first step toward mindful approaches for mitigation and remediation of this oil spill and those we will face in the future."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

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