9 Works

Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

Kathryn Tiplady, Thomas Lopdell, Edwardo Reynolds, Richard Sherlock, Michael Keehan, Thomas Johnson, Jennie Pryce, Stephen Davis, Richard Spelman, Bevin Harris, Dorian Garrick & Mathew Littlejohn
Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition and other novel traits from milk samples. Whilst there have been many genome-wide association studies (GWAS) conducted on FT-MIR predicted traits, there have been few GWAS for individual FT-MIR wavenumbers. Here we examine associations between genomic regions and individual FT-MIR wavenumber phenotypes within a population of 38,085 mixed-breed New Zealand dairy cattle with imputed whole-genome sequence. GWAS were conducted for each...

Data from: Multiple QTL underlie milk phenotypes at the CSF2RB locus

Thomas J. Lopdell, Kathryn Tiplady, Christine Couldrey, Thomas J. J. Johnson, Michael Keehan, Stephen R. Davis, Bevin L. Harris, Richard J. Spelman, Russell G. Snell & Mathew D. Littlejohn
Background: Over many years, artificial selection has substantially improved milk production by cows. However, the genes that underlie milk production quantitative trait loci (QTL) remain relatively poorly characterised. Here, we investigate a previously reported QTL located at the CSF2RB locus on chromosome 5, for several milk production phenotypes, to better understand its underlying genetic and molecular causes. Results: Using a population of 29,350 taurine dairy cows, we conducted association analyses for milk yield and composition...

Data from: Sequence-based association analysis reveals an MGST1 eQTL with pleiotropic effects on bovine milk composition

Mathew D. Littlejohn, Kathryn Tiplady, Tania A. Fink, Klaus Lehnert, Thomas Lopdell, Thomas Johnson, Christine Couldrey, Michael D. Keehan, Richard G. Sherlock, Chad Harland, Andrew Scott, Russell G. Snell, Stephen R. Davis & Richard J. Spelman
GWAS_pop_dataChromosome 5 Illumina BovineHD genotypes and phenotypes for the milk fat percentage GWAS population.RNAseq_pop_imputed_seq_dataChromsome 5 imputed sequence and gene expression data used for eQTL mappingRNAseq_pop_imputed_seq_data_with_gap_varsChromsome 5 imputed sequence and gene expression data used for eQTL mapping - with reference gap variantsLarge_pop_imputed_seqChromsome 5 imputed sequence and phenotype data used for milk composition association mappingRNAseq_pop_del_haplotypeGene expression (phenotypes), pedigree, and diplotype (haplotype pair) data for analysis of the CNV-proxy haplotypeZipped library of Supplementary files 1-12A zipped collection of...

Data from: Functional confirmation of PLAG1 as the candidate causative gene underlying major pleiotropic effects on body weight and milk characteristics

Tania Fink, Kathryn Tiplady, Thomas Lopdell, Thomas Johnson, Russell G. Snell, Richard J. Spelman, Stephen R. Davis & Mathew D. Littlejohn
A major pleiotropic quantitative trait locus (QTL) located at ~25Mbp on bovine chromosome 14 affects a myriad of growth and developmental traits in Bos taurus and indicus breeds. These QTL have been attributed to two functional variants in the bidirectional promoter of PLAG1 and CHCHD7, and although PLAG1 is a good candidate for mediating these effects, its role remains uncertain given these variants are also associated with expression of five additional genes at the broader...

Data from: DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content

Thomas J. Lopdell, Kathryn Tiplady, Maksim Struchalin, Thomas J.J. Johnson, Michael Keehan, Ric Sherlock, Christine Couldrey, Stephen R. Davis, Russell G. Snell, Richard J. Spelman & Mathew D. Littlejohn
Lactose provides an easily-digested energy source for neonate mammals, and is the primary carbohydrate in milk. Lactose is also a key component of many human food products, though compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we present the first GWAS of milk lactose concentration and yield, investigated in a population of 12,000 taurine dairy cattle. We detail 27 QTL spanning these traits, and subsequently validate...

Data from: Non-additive association analysis using proxy phenotypes identifies novel cattle sydromes

Edwardo Reynolds & Mathew Littlejohn
Mammalian species carry ~100 loss-of-function variants per individual, where ~1-5 of these impact essential genes and cause embryonic lethality or severe disease when homozygous. The functions of the remainder are more difficult to resolve, though are assumed to impact fitness in less manifest ways. Here, we present data behind one of the largest sequence-resolution screens of cattle to date, targeting discovery and validation of non-additive effects in 130,725 animals. We highlight six novel recessive loci...

A new mechanism for a familiar mutation – bovine DGAT1 K232A modulates gene expression through multi-junction exon splice enhancement

Thomas Lopdell, Tania Fink, Kathryn Tiplady, Renee Handley, Thomas Johnson, Richard Spelman, Stephen Davis, Russell Snell & Mathew Littlejohn
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 a large influence on milk composition phenotypes. Since first described over 15 years ago, a protein-coding variant K232A has been assumed as the causative variant underlying these effects, following in-vitro studies that demonstrated differing levels of triglyceride synthesis between the two protein isoforms. In the current study, we used...

Data from: Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle

Matthew D. Littlejohn, Kristen M. Henty, Tiplady Kathryn, Thomas Johnson, Chad Harland, Thomas Lopdell, Richard G. Sherlock, Wanbo Li, Steven D. Lukefahr, Bruce C. Shanks, Dorian J. Garrick, Russel G. Snell, Richard J. Spelman & Stephen R. Davis
WGS Variants from 556 NZ Dairy Animals Chr23:30627379-40627379rtg_3.3.1_556_animal_Chr23:30627379-40627379_for_dryad.vcf.gzExome Variants in Multiple Breeds Chr20:34783594-42331973GATK-10MB-Window-Exomes.vcf.gzHairy syndrome genotypes and phenotypesGenotypes and phenotype used for genome-wide analysis of the hairy syndrome, Plink binary format (.bim .bed .fam)gen_phen_data_for_paper.zipHairy bull progeny TaqMan resultsHairy_bull_progeny_TaqMan_results.txtphysiological phenotypesphysiological_phenos.zipDFAM association results for 628,279 SNPDFAM_assoc_results.zipPhased genotypes and phenotypes for 82 Senepol crossbreedsphased_gen_phen_data_slick.zip

Genome-wide association analysis reveals QTL and candidate mutations involved in white spotting in cattle

Swati Jivanji, Gemma Worth, Thomas J. Lopdell, Anna Yeates, Christine Couldrey, Edwardo Reynolds, Kathryn Tiplady, Lorna McNaughton, Thomas J.J. Johnson, Stephen R Davis, Bevin Harris, Richard Spelman, Russell G Snell, Dorian Garrick & Mathew D. Littlejohn
Background White spotting of the coat is a characteristic trait of various domestic species including cattle and other mammals. It is a hallmark of Holstein-Friesian cattle, and several previous studies have detected genetic loci with major effects for white spotting in animals with Holstein-Friesian ancestry. Here, our aim was to better understand the underlying genetic and molecular mechanisms of white spotting, by conducting the largest mapping study for this trait in cattle, to date. Results...

Registration Year

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Resource Types

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  • Livestock Improvement Corporation
  • University of Auckland
  • Massey University
  • University of Liège
  • Lincoln University
  • Texas A&M University
  • La Trobe University
  • Hospital Universitário da Universidade de São Paulo
  • Iowa State University