Description: Background: The identification of the loci and specific alleles underlying variation in quantitative traits is an important goal for evolutionary biologists and breeders. Despite major advancements in genomics technology, moving from QTL to causal alleles remains a major challenge in genetics research. Near-isogenic lines are the ideal raw material for QTL validation, refinement of QTL location and, ultimately, gene discovery. Results: In this study, a population of 75 Arabidopsis thaliana near-isogenic lines was developed from an existing recombinant inbred line (RIL) population derived from a cross between physiologically divergent accessions Kas-1 and Tsu-1. First, a novel algorithm was developed to utilize genome-wide marker data in selecting RILs fully isogenic to Kas-1 for a single chromosome. Seven such RILs were used in 2 generations of crossing to Tsu-1 to create BC1 seed. BC1 plants were genotyped with SSR markers so that lines could be selected that carried Kas-1 introgressions, resulting in a population carrying chromosomal introgressions spanning the genome. BC1 lines were genotyped with 48 genome-wide SSRs to identify lines with a targeted Kas-1 introgression and the fewest genomic introgressions elsewhere. 75 such lines were selected and genotyped at an additional 41 SNP loci and another 930 tags using 2b-RAD genotyping by sequencing. The final population carried an average of 1.35 homozygous and 2.49 heterozygous introgressions per line with average introgression sizes of 5.32 and 5.16 Mb, respectively. In a simple case study, we demonstrate the advantage of maintaining heterozygotes in our library whereby fine-mapping efforts are conducted simply by self-pollination. Crossovers in the heterozygous interval during this single selfing generation break the introgression into smaller, homozygous fragments (sub-NILs). Additionally, we utilize a homozygous NIL for validation of a QTL underlying stomatal conductance, a low heritability trait. Conclusions: The present results introduce a new and valuable resource to the Brassicaceae research community that enables rapid fine-mapping of candidate loci in parallel with QTL validation. These attributes along with dense marker coverage and genome-wide chromosomal introgressions make this population an ideal starting point for discovery of genes underlying important complex traits of agricultural and ecological significance.

Description: Nature Geoscience 8, 122 (2015). doi:10.1038/ngeo2349 Authors: Hanno Meyer, Thomas Opel, Thomas Laepple, Alexander Yu Dereviagin, Kirstin Hoffmann & Martin Werner Relative to the past 2,000 years, the Arctic region has warmed significantly over the past few decades. However, the evolution of Arctic temperatures during the rest of the Holocene is less clear. Proxy reconstructions, suggest a long-term cooling trend throughout the mid- to late Holocene, whereas climate model simulations show only minor changes or even warming. Here we present a record of the oxygen isotope composition of permafrost ice wedges from the Lena River Delta in the Siberian Arctic. The isotope values, which reflect winter season temperatures, became progressively more enriched over the past 7,000 years, reaching unprecedented levels in the past five decades. This warming trend during the mid- to late Holocene is in opposition to the cooling seen in other proxy records. However, most of these existing proxy records are biased towards summer temperatures. We argue that the opposing trends are related to the seasonally different orbital forcing over this interval. Furthermore, our reconstructed trend as well as the recent maximum are consistent with the greenhouse gas forcing and climate model simulations, thus reconciling differing estimates of Arctic and northern high-latitude temperature evolution during the Holocene.

Description: Environmental Science & Technology DOI: 10.1021/es401609n