Conference review: bovine genomics from academia to industry

Henderson, David C.; Thomas, M. G.; Da, Yang

doi:10.1002/cfg.467

Cited by 8 publications

(7 citation statements)

References 22 publications

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“…Sex prediction using only chrY SNP is logically simpler to use, but not all commercial SNP chips contain chrY SNP. Sex prediction only using the heterozygosity rates of chrX SNP can be more challenging as care must be taken to avoid using PAR SNP and highly inbred females such, as L1 Dominette 01449 (Henderson et al, 2005 ), can look like males if not enough SNP are used. Also sex-selected semen (often female selected) can have odd results as the low chrY content can result in no chrY genotpyes due to low signal intensity caused by the low number of chrY containing semen cells.…”

Section: Icbf Parentage and Qc Pipelinesmentioning

confidence: 99%

SNP Data Quality Control in a National Beef and Dairy Cattle System and Highly Accurate SNP Based Parentage Verification and Identification

McClure

McCarthy

Flynn³

et al. 2018

Front. Genet.

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A major use of genetic data is parentage verification and identification as inaccurate pedigrees negatively affect genetic gain. Since 2012 the international standard for single nucleotide polymorphism (SNP) verification in Bos taurus cattle has been the ISAG SNP panels. While these ISAG panels provide an increased level of parentage accuracy over microsatellite markers (MS), they can validate the wrong parent at ≤1% misconcordance rate levels, indicating that more SNP are needed if a more accurate pedigree is required. With rapidly increasing numbers of cattle being genotyped in Ireland that represent 61 B. taurus breeds from a wide range of farm types: beef/dairy, AI/pedigree/commercial, purebred/crossbred, and large to small herd size the Irish Cattle Breeding Federation (ICBF) analyzed different SNP densities to determine that at a minimum ≥500 SNP are needed to consistently predict only one set of parents at a ≤1% misconcordance rate. For parentage validation and prediction ICBF uses 800 SNP (ICBF800) selected based on SNP clustering quality, ISAG200 inclusion, call rate (CR), and minor allele frequency (MAF) in the Irish cattle population. Large datasets require sample and SNP quality control (QC). Most publications only deal with SNP QC via CR, MAF, parent-progeny conflicts, and Hardy-Weinberg deviation, but not sample QC. We report here parentage, SNP QC, and a genomic sample QC pipelines to deal with the unique challenges of >1 million genotypes from a national herd such as SNP genotype errors from mis-tagging of animals, lab errors, farm errors, and multiple other issues that can arise. We divide the pipeline into two parts: a Genotype QC and an Animal QC pipeline. The Genotype QC identifies samples with low call rate, missing or mixed genotype classes (no BB genotype or ABTG alleles present), and low genotype frequencies. The Animal QC handles situations where the genotype might not belong to the listed individual by identifying: >1 non-matching genotypes per animal, SNP duplicates, sex and breed prediction mismatches, parentage and progeny validation results, and other situations. The Animal QC pipeline make use of ICBF800 SNP set where appropriate to identify errors in a computationally efficient yet still highly accurate method.

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Section: Icbf Parentage and Qc Pipelinesmentioning

confidence: 99%

SNP Data Quality Control in a National Beef and Dairy Cattle System and Highly Accurate SNP Based Parentage Verification and Identification

McClure

McCarthy

Flynn³

et al. 2018

Front. Genet.

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“…A variety of bioinformatic tools are available for data-mining depending on the question being asked (Hanai et al, 2006). Many experts indicated that bioinformatics and computational biology approaches will be major areas of emphasis in the next few years in both research and practical usage even for livestock (Henderson et al, 2005).…”

Section: 'Genomics': Definition History Potential Benefits and Limimentioning

confidence: 99%

“…Cattle genomics and application to beef quality Henderson et al (2005) predict that there are three challenges currently facing the beef industry with the use of genetic markers in genetic selection: (i) the adequate collection of DNA marker information by breed associations, (ii) quality control mechanisms for use and interpretation of DNA marker information, and (iii) increased expertise to use genetic markers discovered by the scientific communities. Furthermore, the improvement of the efficiency of markerassisted selection does require the characterisation of regulatory sequences of gene expression, the development of methods to rapidly screen genomes of multiple individuals, a better understanding of gene functions and interactions, and more emphasis on complex traits with low heritabilities.…”

Section: Bovine Genome Sequencing and Applications For Breedingmentioning

confidence: 99%

“…Gene expression profiling has been used to document changes in gene expression for example following infection by pathological organisms (Meade et al, 2006), during the metabolic changes imposed by lactation in dairy cows (Loor et al, 2005), in cloned bovine embryos Somers et al, 2006) and in various other models (reviewed by Henderson et al, 2005 and.…”

Section: Applications Of Functional Genomicsmentioning

confidence: 99%

“…This allowed the identification of up to 110 genes differentially expressed from 110 days post-conception to 15 months of age after birth. Among these genes, 33% have Table 4 Some examples of current initiatives in bovine genomics research applied to beef quality (extracted, adapted and updated from Henderson et al (2005) France http://www.inra.fr/agenae/ Analyse of genes determining physiological functions of four species (bovine, pig, poultry and trout). Specific projects concern bovine muscle characteristics and beef quality: MUGENE (integrated biology of beef quality including genetic markers, transcriptomics and proteomics) and QUALVIGENE (genetic markers of beef quality) Beef CRC (Cooperative Research Centre for Beef Quality)…”

Section: Comparison Of Gene Expression Between Muscle Typesmentioning

confidence: 99%

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Recent advances in cattle functional genomics and their application to beef quality

Hocquette

Lehnert

Barendse

et al. 2007

Animal

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The advent of high-throughput DNA sequencing techniques, array technology and protein analysis has increased the efficiency of research in bovine muscle physiology, with the ultimate objective of improving beef quality either by breeding or rearing factors. For genetic purposes, polymorphisms in some key genes have been reported for their association with beef quality traits. The sequencing of the bovine genome has dramatically increased the number of available gene polymorphisms. The association of these new polymorphisms with the variability in beef quality (e.g. tenderness, marbling) for different breeds in different rearing systems will be a very important issue. For rearing purposes, global gene expression profiling at the mRNA or protein level has already shown that previously unsuspected genes may be associated either with muscle development or growth, and may lead to the development of new molecular indicators of tenderness or marbling. Some of these genes are specifically regulated by genetic and nutritional factors or differ between different beef cuts. In recognition of the potential economic benefits of genomics, public institutions in association with the beef industry are developing livestock genomics projects around the world. From the scientific, technical and economical points of view, genomics is thus reshaping research on beef quality.

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Electrospray Ionization

Gross¹

2017

Mass Spectrometry

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Conference review: bovine genomics from academia to industry

Cited by 8 publications

References 22 publications

SNP Data Quality Control in a National Beef and Dairy Cattle System and Highly Accurate SNP Based Parentage Verification and Identification

SNP Data Quality Control in a National Beef and Dairy Cattle System and Highly Accurate SNP Based Parentage Verification and Identification

Recent advances in cattle functional genomics and their application to beef quality

Electrospray Ionization

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