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

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dc.citation.issue1
dc.citation.volume53
dc.contributor.authorTiplady KM
dc.contributor.authorLopdell TJ
dc.contributor.authorReynolds E
dc.contributor.authorSherlock RG
dc.contributor.authorKeehan M
dc.contributor.authorJohnson TJJ
dc.contributor.authorPryce JE
dc.contributor.authorDavis SR
dc.contributor.authorSpelman RJ
dc.contributor.authorHarris BL
dc.contributor.authorGarrick DJ
dc.contributor.authorLittlejohn MD
dc.coverage.spatialFrance
dc.date.accessioned2024-04-16T23:02:46Z
dc.date.accessioned2024-07-25T06:36:03Z
dc.date.available2021-07-20
dc.date.available2024-04-16T23:02:46Z
dc.date.available2024-07-25T06:36:03Z
dc.date.issued2021-07-20
dc.description.abstractBACKGROUND: 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. While 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. Using imputed whole-genome sequence for 38,085 mixed-breed New Zealand dairy cattle, we conducted GWAS on 895 individual FT-MIR wavenumber phenotypes, and assessed the value of these direct phenotypes for identifying candidate causal genes and variants, and improving our understanding of the physico-chemical properties of milk. RESULTS: Separate GWAS conducted for each of 895 individual FT-MIR wavenumber phenotypes, identified 450 1-Mbp genomic regions with significant FT-MIR wavenumber QTL, compared to 246 1-Mbp genomic regions with QTL identified for FT-MIR predicted milk composition traits. Use of mammary RNA-seq data and gene annotation information identified 38 co-localized and co-segregating expression QTL (eQTL), and 31 protein-sequence mutations for FT-MIR wavenumber phenotypes, the latter including a null mutation in the ABO gene that has a potential role in changing milk oligosaccharide profiles. For the candidate causative genes implicated in these analyses, we examined the strength of association between relevant loci and each wavenumber across the mid-infrared spectrum. This revealed shared association patterns for groups of genomically-distant loci, highlighting clusters of loci linked through their biological roles in lactation and their presumed impacts on the chemical composition of milk. CONCLUSIONS: This study demonstrates the utility of FT-MIR wavenumber phenotypes for improving our understanding of milk composition, presenting a larger number of QTL and putative causative genes and variants than found from FT-MIR predicted composition traits. Examining patterns of significance across the mid-infrared spectrum for loci of interest further highlighted commonalities of association, which likely reflects the physico-chemical properties of milk constituents.
dc.description.confidentialfalse
dc.format.pagination62-
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/34284721
dc.identifier.citationTiplady KM, Lopdell TJ, Reynolds E, Sherlock RG, Keehan M, Johnson TJ, Pryce JE, Davis SR, Spelman RJ, Harris BL, Garrick DJ, Littlejohn MD. (2021). Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle.. Genet Sel Evol. 53. 1. (pp. 62-).
dc.identifier.doi10.1186/s12711-021-00648-9
dc.identifier.eissn1297-9686
dc.identifier.elements-typejournal-article
dc.identifier.issn0999-193X
dc.identifier.numberARTN 62
dc.identifier.pii10.1186/s12711-021-00648-9
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/70517
dc.languageeng
dc.publisherBioMed Central Ltd
dc.publisher.urihttps://gsejournal.biomedcentral.com/articles/10.1186/s12711-021-00648-9
dc.relation.isPartOfGenet Sel Evol
dc.rights(c) The author/sen
dc.rights.licenseCC BY 4.0en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectAnimals
dc.subjectCattle
dc.subjectGenome-Wide Association Study
dc.subjectHybridization, Genetic
dc.subjectMilk
dc.subjectOligosaccharides
dc.subjectQuantitative Trait Loci
dc.subjectSpectroscopy, Fourier Transform Infrared
dc.titleSequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle
dc.typeJournal article
pubs.elements-id447411
pubs.organisational-groupOther
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