Identification and characterization of copy number variations in cattle

Copy number variations (CNVs) are an important source of genetic changes. They are defined as a gain or loss of genomic region ranging from 50 bp to several megabases. CNVs have been shown to be associated with many diseases and some phenotypic traits in several species, including cattle. We used Pindel, Delly, BreakDancer, and CNVnator to identify CNVs using whole-genome sequencing data of 200 animals from eight French dairy and beef cattle breeds. We selected only deletions and duplications predicted by at least two tools and present in at least two animals. We identified a total of 29,132 autosomal deletions and duplications which cover between 31 to 34% (784 to 865 Mb) of the autosomal genome, with an average of 6,000 events per animal. Among these deletions and duplications, 27,690 were present in at least two animals. Out of theses, 26,417 events were deletions, 674 were duplications and 599 regions were both (deletion and duplication within the same region). We defined a CNV as deletion and duplication in the same region, and we termed this region as CNV-Region (CNVR). The size of CNVRs ranged from 100 bp to 9.3 Mb with a median of 1.3 kb and a mean of 45 kb. From the identified deletions and duplications, 8,283 overlapped with 9,733 annotated genes including 290 CNVRs overlapping with 974 annotated genes, including some genes known to be implicated in some traits of economic importance. Our study provides an extensive view of the CNVRs in French dairy and beef breeds. CNVRs with an effect on some commercially interesting phenotypes could be used to improve genetic selection of these eight French breeds

Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

Background: In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability.[br/] Results: In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data.[br/] Conclusions: To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection

Study of the genetic determinism of muscular development

National audienc

WFIKKN1 and WFIKKN2: “Companion” proteins regulating TGFB activity

The WFIKKN (WAP, Follistatin/kazal, Immunoglobulin, Kunitz and Netrin domain-containing) protein family is composed of two multidomain proteins: WFIKKN1 and WFIKKN2. They were formed by domain shuffling and are likely present in deuterostoms. The WFIKKN (also called GASP) proteins are well known for their function in muscle and skeletal tissues, namely, inhibition of certain members of the transforming growth factor beta (TGFB) superfamily such as myostatin (MSTN) and growth and differentiation factor 11 (GDF11). However, the role of the WFIKKN proteins in other tissues is still poorly understood in spite of evidence suggesting possible action in the inner ear, brain and reproduction. Further, several recent studies based on next generation technologies revealed differential expression of WFIKKN1 and WFIKKN2 in various tissues suggesting that their function is not limited to MSTN and GDF11 inhibition in musculoskeletal tissue. In this review, we summarize current knowledge about the WFIKKN proteins and propose that they are “companion” proteins for various growth factors by providing localized and sustained presentation of TGFB proteins to their respective receptors, thus regulating the balance between the activation of Smad and non-Smad pathways by TGFB

A new otogelin ENU mouse model for autosomal-recessive nonsyndromic moderate hearing impairment

International audienceApproximately 10 % of the population worldwide suffers from hearing loss (HL) and about 60 % of persons with early onset HL have hereditary hearing loss due to genetic mutations. Highly efficient mutagenesis in mice with the chemical mutagen, ethylnitrosourea (ENU), associated with relevant phenotypic tools represents a powerful approach in producing mouse models for hearing impairment. A benefit of this strategy is to generate alleles to form a series revealing the full spectrum of gene function in vivo. It can also mimic the range of human mutations and polymorphisms for HL. In the course of a genome ENU mutagenesis program, we selected a new mouse model for hearing defect based on a dysmorphological screen. We identified by gene mapping the mutation responsible for this phenotype and characterized it at the histological level of the inner ear and evaluated the vestibule by following the recommendations of the standard operating procedures, IMPReSS. We have identified and characterized a new recessive allele of the otogelin gene, Otogvbd/vbd, due to a homozygous one base pair substitution at the splice donor site of intron 29. This mutation leads to a frame-shift and a premature stop codon. We observed a decrease in the amount of sensory cells in the maculae of Otogvbd/vbd mice as well as an apparent drastically decreased density to almost absence of the otoconial membrane. Compared to Otogtm1Prs and twister, the two other existing otogelin alleles, the detailed analysis of Otogvbd/vbd revealed that these mice share some common behavioural characteristics either with Otogtm1Prs or twister whereas the fine vestibular phenotype and the hearing defect are different. Our results emphasize the importance of detecting and characterizing a new allele of a gene in order to get comprehensive information about the gene function

Morphometric analysis of muscle cross sections using multicolor immunofluorescence imaging

Morphometric analysis of muscle cross sections using multicolor immunofluorescence imaging . International Conference on Biomedical Engineering (ICBE 2018

Endogenous two- and three-photon fluorescence of a biological substance with a picosecond ultrawide band laser source

International audienc