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Author: search.filters.author.Couldrey CStart date: 2020

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    Structural and epistatic regulatory variants cause hallmark white spotting in cattle
    (American Association for the Advancement of Science, 2025-11-14) Jivanji S; Wilkinson E; Tang L; Tiplady KM; Yeates A; Harland C; Gray C; Couldrey C; Worth G; Gamache I; Desjardins J; Tabares JAA; Yamanaka N; McNaughton L; Brennan L; Cloutier M-P; Cowan M; Ellison R; Fransen T; Monehan T; Spelman RJ; Snell RG; Charlier C; Yamanaka Y; Garrick D; Mort R; Littlejohn MD
    Despite being one of the most iconic and immediately recognizable traits in domestic cattle, the variants underpinning the white-spotted coat pattern of Holstein-Friesian and related breeds remain uncharacterized. Here, we report two variants modulating these effects, comprising intronic and long-distance-acting regulatory variants of the MITF and KIT genes. We confirm causality through "Holsteinized" mouse models edited for these alleles and show that these variants are likely responsible for spotting traits in other bovine breeds. These effects include epistatic impacts on other bovine coat patterns, such as fine-scale speckling, "black socks," and reversal of the otherwise dominant, "white-face" trait characteristic of Hereford cattle.
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    Identification of candidate novel production variants on the Bos taurus chromosome X
    (Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association, 2023-11) Trebes H; Wang Y; Reynolds E; Tiplady K; Harland C; Lopdell T; Johnson T; Davis S; Harris B; Spelman R; Couldrey C
    Chromosome X is often excluded from bovine genetic studies due to complications caused by the sex specific nature of the chromosome. As chromosome X is the second largest cattle chromosome and makes up approximately 6% of the female genome, finding ways to include chromosome X in dairy genetic studies is important. Using female animals and treating chromosome X as an autosome, we performed X chromosome inclusive genome-wide association studies in the selective breeding environment of the New Zealand dairy industry, aiming to identify chromosome X variants associated with milk production traits. We report on the findings of these genome-wide association studies and their potential effect within the dairy industry. We identify missense mutations in the MOSPD1 and CCDC160 genes that are associated with decreased milk volume and protein production and increased fat production. Both of these mutations are exonic SNP that are more prevalent in the Jersey breed than in Holstein-Friesians. Of the 2 candidates proposed it is likely that only one is causal, though we have not been able to identify which is more likely.
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    Non-additive QTL mapping of lactation traits in 124,000 cattle reveals novel recessive loci
    (BioMed Central Ltd, 2022-12) Reynolds EGM; Lopdell T; Wang Y; Tiplady KM; Harland CS; Johnson TJJ; Neeley C; Carnie K; Sherlock RG; Couldrey C; Davis SR; Harris BL; Spelman RJ; Garrick DJ; Littlejohn MD
    BACKGROUND: Deleterious recessive conditions have been primarily studied in the context of Mendelian diseases. Recently, several deleterious recessive mutations with large effects were discovered via non-additive genome-wide association studies (GWAS) of quantitative growth and developmental traits in cattle, which showed that quantitative traits can be used as proxies of genetic disorders when such traits are indicative of whole-animal health status. We reasoned that lactation traits in cattle might also reflect genetic disorders, given the increased energy demands of lactation and the substantial stresses imposed on the animal. In this study, we screened more than 124,000 cows for recessive effects based on lactation traits. RESULTS: We discovered five novel quantitative trait loci (QTL) that are associated with large recessive impacts on three milk yield traits, with these loci presenting missense variants in the DOCK8, IL4R, KIAA0556, and SLC25A4 genes or premature stop variants in the ITGAL, LRCH4, and RBM34 genes, as candidate causal mutations. For two milk composition traits, we identified several previously reported additive QTL that display small dominance effects. By contrasting results from milk yield and milk composition phenotypes, we note differing genetic architectures. Compared to milk composition phenotypes, milk yield phenotypes had lower heritabilities and were associated with fewer additive QTL but had a higher non-additive genetic variance and were associated with a higher proportion of loci exhibiting dominance. CONCLUSIONS: We identified large-effect recessive QTL which are segregating at surprisingly high frequencies in cattle. We speculate that the differences in genetic architecture between milk yield and milk composition phenotypes derive from underlying dissimilarities in the cellular and molecular representation of these traits, with yield phenotypes acting as a better proxy of underlying biological disorders through presentation of a larger number of major recessive impacts.