Developing a genome-wide selection model for genetic improvement of residual feed intake and carcass merit in a beef cattle breeding program

Residual feed intake (RFI) and carcass merit (CM) are both complex traits emerging as critical targets for beef genetic improvement.RFI and CM traits are difficult and expensive to measure and genetic improvement for these traits through traditional selection methods is not very effective.Therefore,genome-wide selection using DNA markers may be a potential alternative for genetic improvement of these traits.In this study,the efficiency of a genome-wide selection model for genetic improvement of RFI and CM was assessed.The Illumina Bovine50K bead chip was used to genotype 922 beef cattle from the Kinsella Beef Research Ranch of the University of Alberta.A Bayes model and multiple marker regression using a stepwise method were used to conduct the association test.The number of significant SNP markers for carcass weight (CWT),carcass back fat (BF),carcass rib eye area (REA),carcass grade fat (GDF),lean meat yield (LMY),and residual feed intake (RFI) were 75,54,67,57,44 and 50,respectively.Bi-variate analysis of marker scores and phenotypes for all traits were made using DMU Software.The genetic parameter for each trait was estimated.The genetic correlations of marker score and phenotype for CWT,BF,REA,GDF,LMY and RFI were 0.75,0.69,0.87,0.77,0.78,and 0.85,respectively.The average prediction accuracies of phenotypic EBV for the six traits were increased by 0.05,0.16,0.24,0.23,0.17 and 0.19,respectively.The results of this study indicated that the two-trait marker-assisted evaluation model used was a suitable alternative of genetic evaluation for these traits in beef cattle.     

Burrow plugging by prairie dogs in response to Siberian polecats

Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Siberian polecats ( Mustela eversmanni ) were placed in white-tailed prairie dog ( Cynomys leucurus ) and black-tailed prairie dog ( C. ludovicianus ) burrows to simulate a black-footed ferret ( M. nigripes ) visit. Both prairie dog species plugged burrows “visited” by polecats. White-tailed and black-tailed prairie dogs plugged 2 of 6 and 3 of 6 test burrows, respectively.        

New synonymy and new species of American bark beetles (Coleoptera: Scolytidae), Part V

Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 st1\:*{behavior:url(#ieooui) } /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} New synonymy of American Scolytidae is proposed as follows: Phloeoborus Erichson ( = Phloeotrupes Erichson), Phloeotribus Latreille ( = Eulytocerus Blandford), Scolytodes Ferrari ( = Epomadius Blandford), Carphoborus pinicolens Wood ( = Carphoborus tuberculatus Bright), Coccotrypes indicus (Eggers) ( = Dryocoetes subimpressus Eggers), Coccotrypes surinamensis Schedl ( = Coccotrypes brevipilosus Eggers), Conophthorus coniperda Schwarz ( = Conophthorus clunicus Hopkins, Conophthorus taedae Hopkins), Conophthorus ponderosae Hopkins ( = Conophthorus scopulorum Hopkins, Conophthorus contortae Hopkins, Conophthorus monticolae Hopkins, Conophthorus flexilis Hopkins, Conophthorus lambertianae Hopkins), Conophthorus resinosae Hopkins ( = Conophthorus virginianae Hopkins), Cryphalomorphus knabi (Hopkins) ( = Cryphalomorphus minutissimus Schedl), Ips grandicollis (Eichhoff) ( = Tomicus cribricollis Eichhoff), Ips perturbatus (Eichhoff) ( = Tomicus interpunctus Eichhoff), Ips tridens engelmanni Swaine ( = Ips yohoensis Swaine, Ips semirostris Hopping, Ips amiskwiensis Hopping), Leperisinus aculeatus (Say) ( = Hylesinus imperialis Eichhoff), Leperisinus californicus Swaine ( = Leperisinus hoferi Blackman), Phloeosinus serratus (LeConte) ( = Phloeosinus neotropicus Schedl), Phoeotribus championi (Blandford) ) = Eulytocerus substriatus Schedl), Pseudohylesinus sericeus (Mannerheim) ( = Pseudohylesinus yasamatsui Nobuchi), Pityophthorus boycei Swaine ( = Pityophthorus siouxensis Bright), Pityophthorus deletus LeConte ( = Pityophthorus inquietus Blackman, Pityophthorus monophyllae Blackman, Pityophthorus praelatus Bright, Pityophthorus brucki Bright), Scolytus opacus Blackman ( = Scolytus abietis Blackman), Scolytus tsugae Swaine ( = Scolytus reflexus Blackman, Scolytus wickhami Blackman), Scolytus unispinosus LeConte ( = Scolytus fiskei Blackman). The following species are named as new to science: Phloeotribus hirtus, P. ingae, P. levis, P. minor, P. nebulosus, P. simplicidens (Colombia), P. amplus, P. fici, P. squamiger, P. tetricus, P. vesculus (Venezuela), Pityophthorus discretus (Mexico).       

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis

Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis.     

An equilibrium-dependent retroviral mRNA switch regulates translational recoding

Most retroviruses require translational recoding of a viral messenger RNA stop codon to maintain a precise ratio of structural (Gag) and enzymatic (Pol) proteins during virus assembly. Pol is expressed exclusively as a Gag-Pol fusion either by ribosomal frameshifting or by read-through of the gag stop codon. Both of these mechanisms occur infrequently and only affect 5-10% of translating ribosomes, allowing the virus to maintain the critical Gag to Gag-Pol ratio. Although it is understood that the frequency of the recoding event is regulated by cis RNA motifs, no mechanistic explanation is currently available for how the critical protein ratio is maintained. Here we present the NMR structure of the murine leukaemia virus recoding signal and show that a protonation-dependent switch occurs to induce the active conformation. The equilibrium is such that at physiological pH the active, read-through permissive conformation is populated at approximately 6%: a level that correlates with in vivo protein quantities. The RNA functions by a highly sensitive, chemo-mechanical coupling tuned to ensure an optimal read-through frequency. Similar observations for a frameshifting signal indicate that this novel equilibrium-based mechanism may have a general role in translational recoding.     

Solutions for a cultivated planet

Increasing population and consumption are placing unprecedented demands on agriculture and natural resources. Today, approximately a billion people are chronically malnourished while our agricultural systems are concurrently degrading land, water, biodiversity and climate on a global scale. To meet the world's future food security and sustainability needs, food production must grow substantially while, at the same time, agriculture's environmental footprint must shrink dramatically. Here we analyse solutions to this dilemma, showing that tremendous progress could be made by halting agricultural expansion, closing 'yield gaps' on underperforming lands, increasing cropping efficiency, shifting diets and reducing waste. Together, these strategies could double food production while greatly reducing the environmental impacts of agriculture.