A5060257734- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Animal Genetics and Reproduction
- Reproductive Physiology in Livestock
- Milk Quality and Mastitis in Dairy Cows
- CRISPR and Genetic Engineering
- Digestive system and related health
- Genomics and Phylogenetic Studies
- Meat and Animal Product Quality
- Genomics and Chromatin Dynamics
- Wheat and Barley Genetics and Pathology
- Infant Nutrition and Health
- Effects of Environmental Stressors on Livestock
- Biopolymer Synthesis and Applications
- Molecular Biology Techniques and Applications
- Ruminant Nutrition and Digestive Physiology
- RNA regulation and disease
- Virus-based gene therapy research
- RNA Research and Splicing
- Genetics and Plant Breeding
- Viral gastroenteritis research and epidemiology
- Congenital heart defects research
- Animal health and immunology
- Immunodeficiency and Autoimmune Disorders
Livestock Improvement Corporation
2014-2024
Massey University
2024
University of Auckland
2016-2020
Abstract Lactation, hair development and homeothermy are characteristic evolutionary features that define mammals from other vertebrate species. Here we describe the discovery of two autosomal dominant mutations with antagonistic, pleiotropic effects on all three these biological processes, mediated through prolactin signalling pathway. Most conspicuously, in ( PRL) its receptor (PRLR) have an impact thermoregulation morphology phenotypes, giving prominence to this pathway outside classical...
Abstract The mammary gland is a prolific lipogenic organ, synthesising copious amounts of triglycerides for secretion into milk. fat content milk varies widely both between and within species recent independent genome-wide association studies have highlighted percentage quantitative trait locus (QTL) large effect on bovine chromosome 5. Although EPS8 MGST1 been proposed to underlie these signals, the causative status genes has not functionally confirmed. To investigate this QTL in detail, we...
Milk is composed of a complex mixture lipids, proteins, carbohydrates and various vitamins minerals as source nutrition for young mammals. The composition milk varies between individuals, with lipid in particular being highly heritable. Recent reports have highlighted region bovine chromosome 27 harbouring variants affecting fat percentage fatty acid content. We aimed to further investigate this locus two independent cattle populations, consisting Holstein-Friesian x Jersey crossbreed...
Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk most species. Bovine lactose also a key component of many human food products. However, compared to analyses other components, genetic control has been little studied. Here we present first GWAS focussed on analysis traits. Using discovery population 12,000 taurine dairy cattle, detail 27 QTL concentration yield, subsequently validate effects 26 these loci distinct 18,000 cows. We next...
Polymorphisms underlying complex traits often explain a small part (less than 1 %) of the phenotypic variance (σ2 P). This makes identification mutations underling difficult and usually only subset large-effect loci are identified. One approach to identify more is increase sample size experiments but here we propose an alternative. The aim this paper use secondary phenotypes for genetically simple during QTL discovery phase traits. We demonstrate in dairy cattle data set where were milk...
Abstract A major pleiotropic quantitative trait locus (QTL) located at ~25 Mbp on bovine chromosome 14 affects a myriad of growth and developmental traits in Bos taurus indicus breeds. These QTL have been attributed to two functional variants the bidirectional promoter PLAG1 CHCHD7 . Although is good candidate for mediating these effects, its role remains uncertain given that are also associated with expression five additional genes broader locus. In current study, we conducted (eQTL)...
Causal variants for complex traits, such as eQTL are often found in non-coding regions of the genome, where they hypothesised to influence phenotypes by regulating gene expression. Many regulatory marked histone modifications, which can be assayed chromatin immunoprecipitation followed sequencing (ChIP-seq). Sequence reads from ChIP-seq form peaks at putative regions, may reflect amount activity this region. Therefore, also associated with differences modifications excellent candidate causal...
White spotting of the coat is a characteristic trait various domestic species including cattle and other mammals. It hallmark Holstein-Friesian cattle, several previous studies have detected genetic loci with major effects for white in animals ancestry. Here, our aim was to better understand underlying molecular mechanisms spotting, by conducting largest mapping study this date.Using imputed whole-genome sequence data, we conducted genome-wide association analysis 2973 mixed-breed cows...
Abstract Background Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition other novel traits from samples. While there have been many genome-wide association studies (GWAS) conducted on FT-MIR predicted traits, few GWAS individual wavenumbers. Using imputed whole-genome sequence 38,085 mixed-breed New Zealand dairy cattle, we 895 wavenumber phenotypes, assessed the value of these direct phenotypes identifying...
Fourier-transform mid-infrared (FT-MIR) spectroscopy is a high-throughput and inexpensive methodology used to evaluate concentrations of fat protein in dairy cattle milk samples. The objective this study was compare the genetic characteristics FT-MIR predicted fatty acids individual proteins with those that had been measured directly using gas liquid chromatography methods. data based on 2,005 samples collected from 706 Holstein-Friesian × Jersey animals were managed seasonal, pasture-based...
Over many years, artificial selection has substantially improved milk production by cows. However, the genes that underlie quantitative trait loci (QTL) remain relatively poorly characterised. Here, we investigate a previously reported QTL located at CSF2RB locus on chromosome 5, for several phenotypes, to better understand its underlying genetic and molecular causes. Using population of 29,350 taurine dairy cows, conducted association analyses yield composition traits, identified highly...
Abstract Background The DGAT1 gene encodes an enzyme responsible for catalysing the terminal reaction in mammary triglyceride synthesis, and underpins a well-known pleiotropic quantitative trait locus (QTL) with large influence on milk composition phenotypes. Since first described over 15 years ago, protein-coding variant K232A has been assumed as causative underlying these effects, following in-vitro studies that demonstrated differing levels of synthesis between two protein isoforms....
We report the generation of an organism-wide catalog 976,813 cis -acting regulatory elements for bovine detected by assay transposase accessible chromatin using sequencing (ATAC-seq). regroup these in 16 components nonnegative matrix factorization. Correlation between genome-wide density peaks and transcription start sites, correlation peak accessibility expression neighboring genes, enrichment factor binding motifs support their potential. Using a previously established 12,736,643 variants,...
Abstract Background Deleterious recessive conditions have been primarily studied in the context of Mendelian diseases. Recently, several deleterious mutations with large effects were discovered via non-additive genome-wide association studies (GWAS) quantitative growth and developmental traits cattle, which showed that can be used as proxies genetic disorders when such are indicative whole-animal health status. We reasoned lactation cattle might also reflect disorders, given increased energy...
Abstract In vitro investigation of bovine lactation processes is limited by a lack physiologically representative cell models. This deficiency most evident through the minimal or absent expression lactation-specific genes in cultured mammary tissues. Primary epithelial cells (pbMECs) extracted from lactating tissue and grown culture initially express milk protein transcripts at relatively levels. However, drops dramatically after only three four passages, which greatly reduces utility...
Milk samples from 10,641 dairy cattle were screened by a mass spectrometry method for extreme concentrations of the A or B isoforms whey protein, β-lactoglobulin (BLG), to identify causative genetic variation driving changes in BLG concentration.A cohort cows, single sire family, was identified that produced milk containing low concentration protein isoform. genome-wide association study (GWAS) isoform AB heterozygous detected group highly significant nucleotide polymorphisms (SNPs) within...
Abstract Background Bovine lactoferrin (Lf) is an iron absorbing whey protein with antibacterial, antiviral, and antifungal activity. Lactoferrin economically valuable has extremely variable concentration in milk, partly driven by environmental influences such as milking frequency, involution, or mastitis. A significant genetic influence also been previously observed to regulate content milk. Here, we conducted mapping of conjunction RNA-seq, ChIP-seq, ATAC-seq data pinpoint candidate...
Genome sequence variants affecting complex traits (quantitative trait loci, QTL) are enriched in functional regions of the genome, such as those marked by certain histone modifications. These believed to influence gene expression. However, due linkage disequilibrium among nearby variants, pinpointing precise location QTL is challenging. We aimed identify allele-specific binding (ASB) (asbQTL) that cause variation level modification, measured height peaks assayed ChIP-seq (chromatin...
Detection of CNVs (copy number variants) and ROH (runs homozygosity) from SNP (single nucleotide polymorphism) genotyping data is often required in genomic studies. The post-analysis CNV generally involves many steps, potentially across multiple computing platforms, which requires the researchers to be familiar with different tools. In order get around this problem improve research efficiency, we present an R package that integrates summarization, annotation, map conversion, comparison...