Fine-mapping of a QTL influencing pork tenderness on porcine chromosome 2

<p>Abstract</p> <p>Background</p> <p>In a previous study, a quantitative trait locus (QTL) exhibiting large effects on both Instron shear force and taste panel tenderness was detected within the Illinois Meat Quality Pedigree (IMQP). This QTL mapped to the q arm of porcine chromosome 2 (SSC2q). Comparative analysis of SSC2q indicates that it is orthologous to a segment of human chromosome 5 (HSA5) containing a strong positional candidate gene, calpastatin (<it>CAST</it>). <it>CAST </it>polymorphisms have recently been shown to be associated with meat quality characteristics; however, the possible involvement of other genes and/or molecular variation in this region cannot be excluded, thus requiring fine-mapping of the QTL.</p> <p>Results</p> <p>Recent advances in porcine genome resources, including high-resolution radiation hybrid and bacterial artificial chromosome (BAC) physical maps, were utilized for development of novel informative markers. Marker density in the ~30-Mb region surrounding the most likely QTL position was increased by addition of eighteen new microsatellite markers, including nine publicly-available and nine novel markers. Two newly-developed markers were derived from a porcine BAC clone containing the <it>CAST </it>gene. Refinement of the QTL position was achieved through linkage and haplotype analyses. Within-family linkage analyses revealed at least two families segregating for a highly-significant QTL in strong positional agreement with <it>CAST </it>markers. A combined analysis of these two families yielded QTL intervals of 36 cM and 7 cM for Instron shear force and taste panel tenderness, respectively, while haplotype analyses suggested further refinement to a 1.8 cM interval containing <it>CAST </it>markers. The presence of additional tenderness QTL on SSC2q was also suggested.</p> <p>Conclusion</p> <p>These results reinforce <it>CAST </it>as a strong positional candidate. Further analysis of <it>CAST </it>molecular variation within the IMQP F₁boars should enhance understanding of the molecular basis of pork tenderness, and thus allow for genetic improvement of pork products. Furthermore, additional resources have been generated for the targeted investigation of other putative QTL on SSC2q, which may lead to further advancements in pork quality.</p

CCAT-prime: Science with an Ultra-widefield Submillimeter Observatory at Cerro Chajnantor

We present the detailed science case, and brief descriptions of the telescope design, site, and first light instrument plans for a new ultra-wide field submillimeter observatory, CCAT-prime, that we are constructing at a 5600 m elevation site on Cerro Chajnantor in northern Chile. Our science goals are to study star and galaxy formation from the epoch of reionization to the present, investigate the growth of structure in the Universe, improve the precision of B-mode CMB measurements, and investigate the interstellar medium and star formation in the Galaxy and nearby galaxies through spectroscopic, polarimetric, and broadband surveys at wavelengths from 200 um to 2 mm. These goals are realized with our two first light instruments, a large field-of-view (FoV) bolometer-based imager called Prime-Cam (that has both camera and an imaging spectrometer modules), and a multi-beam submillimeter heterodyne spectrometer, CHAI. CCAT-prime will have very high surface accuracy and very low system emissivity, so that combined with its wide FoV at the unsurpassed CCAT site our telescope/instrumentation combination is ideally suited to pursue this science. The CCAT-prime telescope is being designed and built by Vertex Antennentechnik GmbH. We expect to achieve first light in the spring of 2021.Comment: Presented at SPIE Millimeter, Submillimeter, and Far-Infrared Detectors and Instrumentation for Astronomy IX, June 14th, 201

An integrated RH map of porcine chromosome 10

BACKGROUND: Whole genome radiation hybrid (WG-RH) maps serve as "scaffolds" to significantly improve the orientation of small bacterial artificial chromosome (BAC) contigs, order genes within the contigs and assist assembly of a sequence-ready map for virtually any species. Here, we report the construction of a porcine: human comparative map for pig (Sus scrofa) chromosome 10 (SSC10) using the IMNpRH2(12,000-rad )porcine WG-RH panel, integrated with the IMpRH(7000-rad )WG-RH, genetic and BAC fingerprinted contig (FPC) maps. RESULTS: Map vectors from the IMNpRH2(12,000-rad )and IMpRH(7,000-rad )panels were merged to construct parallel framework (FW) maps, within which FW markers common to both panels have an identical order. This strategy reduced map discrepancies between the two panels and significantly improved map accuracy. A total of 216 markers, including 50 microsatellites (MSs), 97 genes and ESTs, and 69 BAC end sequences (BESs), were ordered within two linkage groups at two point (2 pt) LOD score of 8. One linkage group covers SSC10p with accumulated map distances of 738.2 cR(7,000 )and 1814.5 cR(12,000), respectively. The second group covers SSC10q at map distances of 1336.9 cR(7,000 )and 3353.6 cR(12,000), yielding an overall average map resolution of 16.4 kb/cR(12,000 )or 393.5 kb per marker on SSC10. This represents a ~2.5-fold increase in map resolution over the IMpRH(7,000-rad )panel. Based on 127 porcine markers that have homologous sequences in the human genome, a detailed comparative map between SSC10 and human (Homo sapiens) chromosome (HSA) 1, 9 and 10 was built. CONCLUSION: This initial comparative RH map of SSC10 refines the syntenic regions between SSC10 and HSA1, 9 and 10. It integrates the IMNpRH2(12,000-rad )and IMpRH(7,000-rad), genetic and BAC FPC maps and provides a scaffold to close potential gaps between contigs prior to genome sequencing and assembly. This map is also useful in fine mapping of QTLs on SSC10

A high utility integrated map of the pig genome

International audienc

Nucleo-cytoplasmic transport of proteins and RNA in plants

Merkle T. Nucleo-cytoplasmic transport of proteins and RNA in plants. Plant Cell Reports. 2011;30(2):153-176.Transport of macromolecules between the nucleus and the cytoplasm is an essential necessity in eukaryotic cells, since the nuclear envelope separates transcription from translation. In the past few years, an increasing number of components of the plant nuclear transport machinery have been characterised. This progress, although far from being completed, confirmed that the general characteristics of nuclear transport are conserved between plants and other organisms. However, plant-specific components were also identified. Interestingly, several mutants in genes encoding components of the plant nuclear transport machinery were investigated, revealing differential sensitivity of plant-specific pathways to impaired nuclear transport. These findings attracted attention towards plant-specific cargoes that are transported over the nuclear envelope, unravelling connections between nuclear transport and components of signalling and developmental pathways. The current state of research in plants is summarised in comparison to yeast and vertebrate systems, and special emphasis is given to plant nuclear transport mutants

QTL Mapping and Molecular Dissection of Meat Quality Traits in Swine

134 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2007.Improvement of meat quality is important for consumer satisfaction. As many pork quality traits cannot be assessed in the live animal, selection for these traits must rely upon genetic determinants known as quantitative trait loci (QTL). To facilitate fine-mapping of swine QTL, a &sim;1 Mb-resolution human-pig comparative map, composed of 2,274 markers in 34 linkage groups, was constructed using the radiation hybrid method. Comparative analyses revealed 51 conserved synteny groups, including 173 conserved segments, and overall comparative coverage greater than 90%. This map was used, together with porcine linkage and bacterial artificial chromosome (BAC) physical maps, to fine-map a QTL affecting pork tenderness that was detected, on the q arm of porcine chromosome 2 (SSC2q), within the Illinois Meat Quality Pedigree (IMQP). Nine novel microsatellite markers within the &sim;30-Mb region surrounding the most likely QTL position, including one within the candidate gene calpastatin (CAST), were developed. These markers, along with nine publicly-available markers, were used to perform linkage and haplotype analyses within the IMQP. Within-family linkage analyses revealed at least two families segregating for a highly-significant QTL in strong positional agreement with CAST. A combined analysis of these two families yielded QTL intervals of 36 cM and 7 cM for Instron shear force and taste panel tenderness, respectively, while haplotype analyses suggested further refinement to a 1.8 cM interval containing CAST. To identify allelic variation that may influence pork tenderness, the complete genomic sequence of porcine CAST was determined. Nearly 77.6% of this gene was then re-sequenced from each of six IMQP F1 boars. Based on heterozygosity, 393 of 896 discovered polymorphisms appeared concordant with previous QTL data. The location of this variation within the CAST gene suggests that a causative mutation is likely to be regulatory. Functional characterization of CAST variation should enhance understanding of the molecular basis of pork tenderness, and thus allow for genetic improvement of pork products. The effectiveness of CAST polymorphisms for marker-assisted selection (MAS) of pork tenderness can now be assessed. Furthermore, genomic resources developed in this study may be used to investigate many other porcine QTL, including additional tenderness QTL suggested on SSC2q.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD

Fine-mapping of a QTL influencing pork tenderness on porcine chromosome 2-2

<p><b>Copyright information:</b></p><p>Taken from "Fine-mapping of a QTL influencing pork tenderness on porcine chromosome 2"</p><p>http://www.biomedcentral.com/1471-2156/8/69</p><p>BMC Genetics 2007;8():69-69.</p><p>Published online 12 Oct 2007</p><p>PMCID:PMC2213680.</p><p></p>ated by allele size and ordered relative to the linkage map. Marker names and map positions, in cM, are indicated above the respective alleles. Individual boar IDs, as well as the breed of origin (B = Berkshire, D = Duroc), are indicated to the left of each segment. Black boxes indicate haplotypes shared by both individuals (108120, 207061) that appear to be segregating for QTL at the position as well as a putative secondary position near marker SW1879. Duroc alleles shaded in dark gray are also shared with non-segregating boars, and only those alleles shaded in black are unique to individuals with coincident QTL positions. Berkshire alleles shaded in light gray indicate shared alleles in the chromosomal region of interest