QTL‐seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation of QTLs is important for efficient crop breeding by marker‐assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. However, since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been time‐consuming and labor‐intensive. Here we report the rapid identification of plant QTLs by whole‐genome resequencing of DNAs from two populations each composed of 20–50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL‐seq as applied to plant species. We applied QTL‐seq to rice recombinant inbred lines and F₂ populations and successfully identified QTLs for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL‐seq is able to detect QTLs over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps.     

A homologue of Drosophila aurora kinase is oncogenic and amplified in human colorectal cancers.

Genetic and biochemical studies in lower eukaryotes have identified several proteins that ensure accurate segregation of chromosomes. These include the Drosophila aurora and yeast Ipl1 kinases that are required for centrosome maturation and chromosome segregation. We have identified two human homologues of these genes, termed aurora1 and aurora2, that encode cell-cycle-regulated serine/threonine kinases. Here we demonstrate that the aurora2 gene maps to chromosome 20q13, a region amplified in a variety of human cancers, including a significant number of colorectal malignancies. We propose that aurora2 may be a target of this amplicon since its DNA is amplified and its RNA overexpressed, in more than 50% of primary colorectal cancers. Furthermore, overexpression of aurora2 transforms rodent fibroblasts. These observations implicate aurora2 as a potential oncogene in many colon, breast and other solid tumors, and identify centrosome-associated proteins as novel targets for cancer therapy.     

Effect of temperature and relative humidity on the development and fecundity of Chilo partellus (Swinhoe) (Lepidoptera: Crambidae)

The spotted stemborer, Chilo partellus (Swinhoe) (Lepidoptera: Crambidae), is one of the most important insect pests attacking maize and sorghum in Ethiopia. Recent studies have indicated that the pest is spreading to new locations where it was not reported before. In the current study, laboratory investigations were carried out to determine the combined effect of different levels of relative humidity and temperature regimes on the development and fecundity of C. partellus, as these physical factors are known to play an important role in the life cycle of insects and adaptability to local climate. Developmental time, longevity, potential fecundity and realized fecundity of C. partellus were measured under controlled conditions. Three temperature regimes (22°C, 26°C and 30°C) and three relative humidity levels (40%, 60% and 80%) were tested. It was found that temperature, relative humidity (RH) and their interaction significantly affected the developmental time, adult longevity, potential fecundity and realized fecundity of the pest. Developmental time was inversely related to temperature. Mean duration of C. partellus life cycle was 70.2 days at 22°C and 80% RH, whereas it took only 26.5 days to complete its life cycle at 30°C and 40% RH. Male and female longevity were similar in most cases. The adult life span ranged between 6.9-11.1 days at 22°C and 3.1-7.2 days at 30°C for different levels of relative humidity. The most suitable conditions for C. partellus development and fecundity were 26-30°C temperatures regimes and 60-80% RH levels.     

Heavy Metal Concentration in the Urban Environment of Addis Ababa,Ethiopia

This work assesses the issue of whether the measured concentrations of heavy metals in soil, rocks, surface and ground waters in Addis Ababa can be related to anthropogenic contamination or natural weathering of rocks. Heavy metal analyses of rocks, soils, streams, springs and boreholes have been carried out to identify the presence of potentially harmful solutes. The maximum concentration of total chromium measured is 269 ppm in the northern, industry-free zone of Addis Ababa in the B ₂-horizon of soil profile (cambisol). The Ni/Cr ratio in the rocks is higher than soils, which could indicate the presence of high concentrations of Cr in soils is from weathering processes. A comparative study of different samples collected from various parts of the city indicates that the chemical composition of the hydrothermally affected volcanic rocks plays an important role in increasing heavy metal concentration in the study area. The fresh country rocks contain relatively low concentrations of heavy metals, as shown by background values. The statistical evaluation indicates that the hydrothermally altered rocks contain far higher mean heavy metal concentrations than the fresh acidic rocks (background values). Consequently, soils derived from altered rocks are enriched with respect to heavy metals. From this study it was possible to observe that the rock and soil outcrops of Addis Ababa are anomalously rich in heavy metals derived from hydrothermal activity. Therefore, heavy metal concentrations in the surrounding rocks and soils are related to geogenic sources whereas anthropogenic contribution as a cause of these concentrations is minor.     

Extrachromosomal DNA forms of copia-like transposable elements, F elements and middle repetitive DNA sequences in Drosophila melanogaster. Variation in cultured cells and embryos

Drosophila melanogaster embryos and cells in culture were screened for the presence of unintegrated covalently closed circular DNA forms that hybridize to copia-like transposable elements, the F element and uncharacterized dispersed middle repetitive DNA elements. Our results indicate that the majority of copia-like elements (including copia, 297, 412, mdg1, mdg3 and gypsy), the F elements, and 9 of 12 middle repetitive DNA elements are present as free DNA forms in cultured cells and embryos. An 18 base-pair inverted repeat has been reported to flank the long direct repeat of mdg3, implying that mdg3 is not an orthodox copia-like element; however, we have sequenced two independently isolated mdg3 clones and shown that the inverted repeat is not part of the element. The relative abundance with which free DNA forms are found varies between the cultured cells used, and between cultured cells and embryos. This variation, which can be up to 20-fold for some elements, does not correlate well with either the amount of element-specific poly(A)+ RNA present per cell or the number of element-specific sequences integrated in the genome.     

A multifaceted genomics approach allows the isolation of the rice Pia-blast resistance gene consisting of two adjacent NBS-LRR protein genes

The Oryza sativa (rice) resistance gene Pia confers resistance to the blast fungus Magnaporthe oryzae carrying the AVR-Pia avirulence gene. To clone Pia, we employed a multifaceted genomics approach. First, we selected 12 R-gene analog (RGA) genes encoding nucleotide binding site-leucine rich repeats (NBS-LRRs) proteins from a region on chromosome 11 that shows linkage to Pia. By using seven rice accessions, we examined the association between Pia phenotypes and DNA polymorphisms in the 10 genes, which revealed three genes (Os11gRGA3-Os11gRGA5) exhibiting a perfect association with the Pia phenotypes. We also screened ethyl methane sulfonate (EMS)-treated mutant lines of the rice cultivar 'Sasanishiki' harboring Pia, and isolated two mutants that lost the Pia phenotype. DNA sequencing of Os11gRGA3-Os11gRGA5 from the two mutant lines identified independent mutations of major effects in Os11gRGA4. The wild-type 'Sasanishiki' allele of Os11gRGA4 (SasRGA4) complemented Pia function in both mutants, suggesting that SasRGA4 is necessary for Pia function. However, when the rice cultivar 'Himenomochi' lacking Pia was transfected with SasRGA4, the Pia phenotype was not recovered. An additional complementation study revealed that the two NBS-LRR-type R genes, SasRGA4 and SasRGA5, that are located next to each other and oriented in the opposite direction are necessary for Pia function. A population genetics analysis of SasRGA4 and SasRGA5 suggests that the two genes are under long-term balancing selection.