Several quantitative trait loci (QTL) mapping strategies can successfully identify major-effect loci, but often have poor success detecting loci with minor effects, potentially due to the confounding effects of major loci, epistasis, and limited sample sizes. To overcome such difficulties, we used a targeted backcross mapping strategy that genetically eliminated the effect of a previously identified major QTL underlying hightemperature growth (Htg) in yeast. This strategy facilitated the mapping of three novel QTL contributing to Htg of a clinically derived yeast strain. One QTL, which is linked to the previously identified major-effect QTL, was dissected, and NCS2 was identified as the causative gene. The interaction of the NCS2 QTL with the first major-effect QTL was background dependent, revealing a complex QTL architecture spanning these two linked loci. Such complex architecture suggests that more genes than can be predicted are likely to contribute to quantitative traits. The targeted backcrossing approach overcomes the difficulties posed by sample size, genetic linkage, and epistatic effects and facilitates identification of additional alleles with smaller contributions to complex traits.

Human leukocyte antigen (HLA) genes are the most polymorphic in the human genome. They play a pivotal role in the immune response and have been implicated in numerous human pathologies, especially autoimmunity and infectious diseases. Despite their importance, however, they are rarely characterized comprehensively because of the prohibitive cost of standard technologies and the technical challenges of accurately discriminating between these highly related genes and their many allelles. Here we demonstrate a high-resolution, and cost-effective methodology to type HLA genes by sequencing, which combines the advantage of long-range amplification, the power of high-throughput sequencing platforms, and a unique genotyping algorithm. We calibrated our method for HLA-A, -B, -C, and -DRB1 genes with both reference cell lines and clinical samples and identified several previously undescribed alleles with mismatches, insertions, and deletions. We have further demonstrated the utility of this method in a clinical setting by typing five clinical samples in an Illumina MiSeq instrument with a 5-d turnaround. Overall, this technology has the capacity to deliver low-cost, high-throughput, and accurate HLA typing by multiplexing thousands of samples in a single sequencing run, which will enable comprehensive disease-association studies with large cohorts. Furthermore, this approach can also be extended to include other polymorphic genes.hematopoietic stem cell transplantation | sequence-based typing H uman leukocyte antigen (HLA) genes encode cell-surface proteins that bind and display fragments of antigens to T lymphocytes. This helps to initiate the adaptive immune response in higher vertebrates and thus is critical to the detection and identification of invading microorganisms (1). Six of the HLA genes (HLA-A, -B, -C, -DQA1, -DQB1, and -DRB1) are extremely polymorphic and constitute the most important set of markers for matching patients and donors for bone marrow transplantation (2, 3). Specific HLA alleles have been found to be associated with a number of autoimmune diseases, such as multiple sclerosis (4), narcolepsy (5), celiac disease (6), rheumatoid arthritis (7), and type I diabetes (3,8). Alleles have also been noted to be protective in infectious diseases such as HIV (9, 10), and numerous animal studies have shown that these genes are often the major contributors to disease susceptibility or resistance (11-13).HLA genes are among the most polymorphic in the human genome, and the changes in sequence affect the specificity of antigen presentation and histocompatibility in transplantation. A variety of methodologies have been developed for HLA typing at the protein and nucleic acid level. Whereas earlier HLA typing methods distinguished HLA antigens, modern methods such as sequence-based typing (SBT) determine the nucleotide sequences of HLA genes for higher resolution. However, due to cost and time constraints, HLA sequencing technologies have traditionally focused on the most polymorphic regions encoding the peptide-...

Here, we characterize the Arabidopsis thaliana embryo-defective mutant increased size exclusion limit2 (ise2). In contrast with wild-type embryos, ise2 mutants continue to traffic 10-kD fluorescent dextran in the mid-torpedo stage of development. ise2 embryos contain branched as well as simple plasmodesmata (PD) compared with wild-type embryos, which only contain simple PD. Positional cloning reveals that the ISE2 gene encodes a putative DEVH box RNA helicase that shares sequence homology with RNA helicases involved in RNA degradation pathways in other organisms. ISE2 localizes to granule-like structures in the cytoplasm. These granules increase in number when plant cells are stressed. These features are characteristic of stress granules (SGs) in mammalian cells, suggesting that ISE2 granules represent plant-specific SGs. Genetic data demonstrate that the ISE2 helicase is involved in posttranscriptional gene silencing and the determination of cell fate. These data together suggest that ISE2 function affects PD structure and function through the regulation of RNA metabolism and consequent gene expression.

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Background: Anopheles innate immunity affects Plasmodium development and is a potential target of innovative malaria control strategies. The extent and distribution of nucleotide diversity in immunity genes might provide insights into the evolutionary forces that condition pathogen-vector interactions. The discovery of polymorphisms is an essential step towards association studies of susceptibility to infection.