Development of a Next-Generation NIL Library in Arabidopsis Thaliana for Dissecting Complex Traits

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.NSF DEB-1022196, DEB-0618302, DEB-0618347, IOS-09221457Integrative Biolog

Pockets of Proterozoic hydrocarbons and implications for the Archaean

Precambrian biomarkers convey invaluable information about the early evolution of life, ancient ecosystems, redox conditions, climate and depositional environment and prospective petroleum systems. They are however thermally unstable, easily obliterated by contamination and thus extremely difficult to find. This is particularly true if conditions favourable for biomarker preservation had to prevail for more than 2.5 billion years – the prerequisite for finding Archaean biomarkers. Many organic geochemists abandoned this hope after original discoveries of Archaean biomarkers proved to be of younger origin [1,2] but our study of ca. 550-825 Ma old sediments from the Centralian Superbasin now shows that biomarkers can be preserved in distinctive pockets in seemingly barren areas, even if sections are metamorphosed in parts. Most Centralian sections seem empty. Yet, eventually we identified intervals with preserved biomarkers in three drill cores. A detailed investigation of 825 Ma sediments in drill core Mt Charlotte-1 revealed maturity variations that are most likely due to hydrothermal influence and in turn control the hydrocarbon preservation. Sediments might appear metamorphosed after localized, subtle alteration by hydrothermal fluids but protected intervals can still contain biomarkers. The same might be true for Archaean sediments and we might still find those protected intervals with indigenous biomarkers that allow us to glimpse the early life on earth

Indonesian Throughflow drove Australian climate form humid Pliocene to arid Pleistocene

Late Miocene to mid-Pleistocene sedimentary proxy records reveal that northwest Australia underwent an abrupt transition from dry to humid climate conditions at 5.5 million years (Ma), likely receiving year-round rainfall, but after ~3.3 Ma, climate shifted toward an increasingly seasonal precipitation regime. The progressive constriction of the Indonesian Throughflow likely decreased continental humidity and transferred control of northwest Australian climate from the Pacific to the Indian Ocean, leading to drier conditions punctuated by monsoonal precipitation. The northwest dust pathway and fully established seasonal and orbitally controlled precipitation were in place by ~2.4 Ma, well after the intensification of Northern Hemisphere glaciation. The transition from humid to arid conditions was driven by changes in Pacific and Indian Ocean circulation and regional atmospheric moisture transport, influenced by the emerging Maritime Continent. We conclude that the Maritime Continent is the switchboard modulating teleconnections between tropical and high-latitude climate systems.published_or_final_versio

Diagenetic evolution of lower Jurassic platform carbonates flanking the Tazoult salt wall (Central High Atlas, Morocco)

Platform carbonates diagenesis in salt basins could be complex due to potential alterations of fluids related and non‐related to diapirism. This paper presents the diagenetic history of the Hettangian to Pliensbachian platform carbonates from the Tazoult salt wall area (central High Atlas, Morocco). Low structural relief and outcrop conditions allowed to define the entire diagenetic evolution occurred in the High Atlas diapiric basins since early stages of the diapiric activity up to their tectonic inversion. Precipitation of dolomite and calcite from both warmed marine‐derived and meteoric fluids characterised diagenetic stages during Pliensbachian, when the carbonate platforms were exposed and karstified. Burial diagenesis occurred from Toarcian to Middle Jurassic, due to changes of salt‐induced dynamic related to increase in siliciclastic input, fast diapir rise and rapid burial of Pliensbachian platforms. During this stage, the diapir acted as a physical barrier for fluid circulation between the core and the flanking sediments. In the carbonates and breccias flanking the structures, dolomite and calcite precipitated from basinal brines, whereas carbonate slivers located in the core of the structure, were affected by the circulation of Mn‐rich fluids. The final diagenetic event is characterised by the income of meteoric fluids into the system during uplift caused by Alpine orogeny. These results highlight the relevant influence of diapirism on the diagenetic modifications in salt‐related basins in terms of diagenetic events and involved fluids

Whiting–related sediment export along the Middle Miocene carbonate ramp of Great Bahama Bank.

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