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Nature Papers Include TOPMed Analysis; Study of Ancient, Modern Common Bean Seeds

Members of the international Trans-Omics for Precision Medicine (TOPMed) program report the sequencing and analysis of 53,831 diverse human genomes in this week's Nature. TOPMed was founded to use whole-genome sequencing and other omics data to better understand risk factors for heart, lung, blood, and sleep disorders. From the first samples sequenced, the researchers report detecting more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome, of which 97 percent have frequencies of less than 1 percent and 46 percent are singletons that are present in only one individual. "These rare variants provide insights into mutational processes and recent human evolutionary history," the TOPMed team writes. The group also presents newly available resources including a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through the Database of Genotypes and Phenotypes.

In a study of ancient and modern seeds of the common bean from the southern Andes a team led by scientists from the University of Ferrara uncovers new details about the selection strategies used by early farmers in the region. The researchers used whole-genome shotgun sequencing and other techniques to gather data on 30 common bean seeds, dated between 2,500 and 600 years ago and obtained from various archeological sites in Argentina, which they compared to modern genomic data. They used the data to analyze the temporal dynamics of genetic variation and selection during the domestication process of the common bean and found that most domestic traits were selected for before 2,500 years ago, with little to no loss of whole-genome heterozygosity. Additionally, single seeds from modern cultivars showed reduced variation when compared with highly variable ancient seeds, indicating that intensive selection within cultivars in the past few centuries "probably partitioned ancestral variation within different genetically homogenous cultivars." Overall, the study's authors conclude that selection strategies from the past few centuries, versus earlier times, more intensively reduced genetic variation within cultivars and produced improvements by focusing on a few plants carrying traits of interest.