Tag: Genomics

Brassicaceae is one of the largest angiosperm families and provides many opportunities for studies of evolution. Of course, its most famous species, Arabidopsis thaliana is an important resource, but Brassicaceae also includes the very interesting Brassica crops (cabbage, turnip) that demonstrate the…

Evolution starts with molecular variation and phenotypic diversity, upon which selection acts. Flood and Hancock review the approaches used to detect adaptive evolution. The top down approach starts with the phenotype and works to identify its genomic basis; examples are quantitative trait locus (QTL)…

A considerable knowledge gap remains between the plant genome and the plant metabolome. To address this, Schläpfer et al. have developed a computational pipeline to identify metabolic enzymes, pathways, and gene clusters. Although metabolic genes are known to cluster in bacteria and fungi, until recently…

The classic art of plant breeding involves carefully examining a genetically segregating population for traits of interest. Increasingly, high-throughput, automated phenotyping systems are being used; for example, robots can carry plants to imaging chambers for data collection. However, growth-chamber…

There are many accessions of Arabidopsis thaliana beyond the ecotypes predominantly used in research laboratories.  In this article, The 1001 Genomes Consortium describe a resource based on whole-genome sequencing of 1,135 A. thaliana genomes from Europe, North Africa, and North America.  This data…

Landraces are native varieties that have been selected for adaptation to their native environment, and as such they provide a wealth of largely unexplored genetic potential. Romero Navarro et al. used a new approach called F-one association mapping (FOAM) in combination with genome-wide association strategy…

There is much to be learned from comparing plant genomes, but as Rensing writes, currently available genomic data are skewed heavily towards angiosperms. He argues that a richer understanding of plant evolution depends upon gaining insights into the non-seed plants, including ferns, mosses and liverworts,…

Fultz and Slotkin explore the question of how transposable element (TE) silencing is initiated. As they describe, there are two recognized mechanisms, one based on TE identity (meaning that it can be silenced through siRNAs initiated from a related TE, and in which de novo silencing can occur in the…