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: Modeling sub-canopy elevation is an important step in the processing of waveform lidar data to measure three dimensional forest structure. Here, we present a methodology based on high resolution discrete-return lidar (DRL) to correct the ground elevation derived from large-footprint Laser Vegetation Imaging Sensor (LVIS) and to improve measurement of forest structure. We use data acquired over Barro Colorado Island, Panama by LVIS large-footprint lidar (LFL) in 1998 and DRL in 2009. The study found an average vertical difference of 28.7 cm between 98,040 LVIS last-return points and the discrete-return lidar ground surface across the island. The majority (82.3%) of all LVIS points matched discrete return elevations to 2 m or less. Using a multi-step process, the LVIS last-return data is filtered using an iterative approach, expanding window filter to identify outlier points which are not part of the ground surface, as well as applying vertical corrections based on terrain slope within the individual LVIS footprints. The results of the experiment demonstrate that LFL ground surfaces can be effectively filtered using methods adapted from discrete-return lidar point filtering, reducing the average vertical error by 15 cm and reducing the variance in LVIS last-return data by 70 cm. The filters also reduced the largest vertical estimations caused by sensor saturation in the upper reaches of the forest canopy by 14.35 m, which improve forest canopy structure measurement by increasing accuracy in the sub-canopy digital elevation model.