scholarly journals Characterization of recombination features and the genetic basis in multiple cattle breeds

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Botong Shen ◽  
Jicai Jiang ◽  
Eyal Seroussi ◽  
George E. Liu ◽  
Li Ma
Keyword(s):  
Animals ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 596 ◽  
Author(s):  
Fengwei Zhang ◽  
Kaixing Qu ◽  
Ningbo Chen ◽  
Quratulain Hanif ◽  
Yutang Jia ◽  
...  

We report genome characterization of three native Chinese cattle breeds discovering ~34.3 M SNPs and ~3.8 M InDels using whole genome resequencing. On average, 10.4 M SNPs were shared amongst the three cattle breeds, whereas, 3.0 M, 4.9 M and 5.8 M were specific to LQ, WN and WS breeds, respectively. Gene ontology (GO)analysis revealed four immune response-related GO terms were over represented in all samples, while two immune signaling pathways were significantly over-represented in WS cattle. Altogether, we found immune related genes (PGLYRP2, ROMO1, FYB2, CD46, TSC1) in the three cattle breeds. Our study provides insights into the genetic basis of Chinese indicine adaptation to the tropic and subtropical environment, and provides a valuable resource for further investigations of genetic characteristics of the three breeds.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jianyu Meng ◽  
Xingjiang Chen ◽  
Changyu Zhang

Abstract Myzus persicae is a serious and widespread agricultural pest, against which, imidacloprid remains an effective control measure. However, recent reports indicate that this aphid has evolved and developed resistance to imidacloprid. This study aimed to elucidate the underlying mechanisms and genetic basis of this resistance by conducting comparative transcriptomics studies on both imidacloprid-resistant (IR) and imidacloprid-susceptible (IS) M. persicae. The comparative analysis identified 252 differentially expressed genes (DEGs) among the IR and IS M. persicae transcriptomes. These candidate genes included 160 and 92 genes that were down- and up-regulated, respectively, in the imidacloprid-resistant strain. Using functional classification in the GO and KEGG databases, 187 DEGs were assigned to 303 functional subcategories and 100 DEGs were classified into 45 pathway groups. Moreover, several genes were associated with known insecticide targets, cuticle, metabolic processes, and oxidative phosphorylation. Quantitative real-time PCR of 10 DEGs confirmed the trends observed in the RNA sequencing expression profiles. These findings provide a valuable basis for further investigation into the complicated mechanisms of imidacloprid resistance in M. persicae.


2016 ◽  
Vol 19 (11) ◽  
pp. 1454-1462 ◽  
Author(s):  
Arjun Krishnan ◽  
Ran Zhang ◽  
Victoria Yao ◽  
Chandra L Theesfeld ◽  
Aaron K Wong ◽  
...  

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S235-S235
Author(s):  
Amani Kholy ◽  
Samia A Girgis ◽  
Arwa R Elmanakhly ◽  
Mervat A F Shetta ◽  
Dalia El- Kholy ◽  
...  

Abstract Background High rates of AMR among Gram-negative bacilli (GNB) have been reported from Egypt for almost 2 decades. Surveillance and identifying the genetic basis of AMR provide important information to optimize patient care. As there is no adequate data on the genetic basis of AMR in Egypt, we aimed to identify the molecular characterization of multi-drug-resistant (MDR) Gram-negative pathogens (GNP). Methods Three major tertiary-care hospitals in Egypt participated in the “Study for Monitoring Antimicrobial Resistance Trends” (SMART) from 2014 to 2016. Consecutive GNPs were identified and their susceptibility to antimicrobials were tested. Molecular identification of ESBL, AmpC, and carbapenemase resistance genes was conducted on MDR isolates. Results We enrolled 1,070 consecutive Gram-negative isolates; only one isolate per patient according to the standard protocol of (SMART). During 2014–2015, 578 GNP were studied. Enterobacteriaceae comprised 66% of the total isolates. K. pneumoniae and E. coli were the most common (29.8% and 29.4%). K. pneumoniae and E. coli were the predominant organisms in IAI (30.5% and 30.1%, respectively) and UTI (and 38.9% and 48.6%, respectively), while Acinetobacter baumannii was the most prevalent in RTI (40.2%). ESBL producers were phenotypically detected in 53% of K. pneumoniae, and 68% of E. coli. During 2016, 495 GNP were studied. ESBL continued to be high. For E. coli and K. pneunomiea, the most active antimicrobials were amikacin (≥93%), imipenem/meropenem (≥87%) and colistin (97%). Genetic study of ertapenem-resistant isolates and 50% of isolates with ESBL phenotype revealed ESβL production in more than 90% of isolates; blaCTXM-15 was detected in 71.4% and 68.5% in K. pneumoniae and E. coli, respectively, blaTEM-OSBL in 48.5% and47.5% of K. pneumoniae and E. coli, respectively. Carbapenem resistance genes were detected in 45.4% of isolates. In K. pneumoniae, OXA-48 dominated (40.6%), followed by NDM1 (23.7%) and OXA-232 (4.5%). Conclusion Our study detected alarming rates of resistance and identified many resistance mechanisms in clinical isolates from Egyptian hospitals. These high rates highlight the importance of continuous monitoring of the resistance trend and discovering the novel resistant mechanisms of resistance, and the underscores a national antimicrobial stewardship plan in Egypt. Disclosures All authors: No reported disclosures.


Author(s):  
Nicolas Dupré ◽  
Jean-Pierre Bouchard ◽  
Bernard Brais ◽  
Guy A. Rouleau

ABSTRACT:Historical events have shaped the various regional gene pools of the French-Canadian (FC) population, leading to increased prevalence of some rare diseases. The first studies of these founder effects were performed in large part by astute clinicians such as André Barbeau. In collaboration with others, he contributed greatly to the delineation of phenotypic subtypes of these conditions. As such, the following neurogenetic disorders were first identified in patients of FC origin: AOA2, ARSACS, HSAN2, RAB, and HMSN/ACC. We have summarized our current knowledge of the main hereditary ataxias, spastic parapareses and neuropathies that are particular to the FC population. The initial genetic characterization of the more common and homogeneous of these diseases has been largely completed. We predict that the regional populations of Canada will allow the identification of new rare forms of hereditary ataxias, spastic parapareses and neuropathies, and contribute to the unravelling of the genetic basis of these entities.


1955 ◽  
Vol 6 (6) ◽  
pp. 833 ◽  
Author(s):  
FW Dry

The recessive N gene, nr, is demonstrated by monogenic ratios. For the most part nr/nr characters are intermediate between those of N/N and N/+. About a sixth of nr/nr lambs have no shoulder patch, and in certain fibre type details, and in hairiness, nr/nr animals tend to be intermediate between the two dominant-N genotypes. On the other hand, all nr/nr ewes have been hornless; a few have had horn-lumps, one scum By contrast, about one N/+ ewe in 10 grows horns. All the nr/nr rams reared to 1 year, except one with scurs, have grown horns. Carrier (+/nr) sheep have birthcoats which we do not know how to distinguish from those of ordinary Romneys, though there is evidence that one dose of nr increases halo-abundance on the back slightly. A few +/nr lambs have been grade VI. Just a few +/nr sheep have fleeces as hairy as the average N/+. A quarter or more of the +/nr rams have had horns, mostly small, at 4 months, and nearly all the others have had scurs. The genes N and nr are not allelic, but may be linked. Because the sheep has 26 pairs of autosomes free assortment seems more probable. In general the characterization of sheep deemed N/+.+/nr is intermediate between that of N/N.+/+ and N/+.+/+. The noticeable difference between N/+.+/nr and +/+ nr/nr is the more powerful growth of horns in the double heterozygotes. An analysis of breeding results from N/+.+/nr sheep indicates that the great majority of N/+.nr/nr animals of both sexes have the horn and halocoverage characters of homozygous dominant-N's. In N/+.+/nr, some ewes have horns, and the shoulder patch is absent about as often as in nr/nr. The frequencies of these characters in N/+.+/nr are applied in showing that the genetic basis of horns in ewes, and the genetic basis of full halo-coverage, in heterozygotes of the dominant-N stock are different; and that it is not the gene nr which makes horns grow in the dominant-N heterozygous ewes; and one piece of evidence suggests that it is not the nr gene that determines absence of shoulder patch in the birthcoats of the dominant-N stock. It is concluded that if the dominant-N stock is not completely free from nr, that gene has only the same sort of frequency as in the Romney breed. Matings made as +/+.nr/nr X +/+.+/+, the latter no-halo ewes, from flocks outside the College, or if bred at the College unrelated to any N-type sheep, have given a small proportion of N-grade lambs. It now appears that at least most of these lambs, called 'dominoes', have received one dose of a dominant gene for N-grade, probably the gene N, from the no-halo parent. One no-halo ewe from an outside source had an N-grade son, proved nr/nr, by a domino ram, the dam thus being shown to carry the gene nr.


Gene ◽  
2013 ◽  
Vol 519 (1) ◽  
pp. 150-158 ◽  
Author(s):  
Guillermo Giovambattista ◽  
Shin-nosuke Takeshima ◽  
Maria Veronica Ripoli ◽  
Yuki Matsumoto ◽  
Luz Angela Alvarez Franco ◽  
...  

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