The genetic background of bovine αs1- and αs2-casein phosphorylation

Phosphorylation of caseins (CN) is a crucial post-translational modification allowing caseins to aggregate as micelles. The formation and stability of casein micelles are important for transporting abundant minerals to the neonate and manufacturing of dairy products. Therefore, it is of great interest to explore variation in degrees of phosphorylation of caseins and study to what extent genetic and other factors contribute to this variation. This thesis aimed to investigate the genetic background of bovine milk protein composition with a focus on phosphorylation of αs1- and αs2-CN. Two studies were conducted to quantify phosphorylation levels of αs1- and αs2-CN: one in French Montbéliarde using liquid chromatography coupled with electrospray ionization mass spectrometry and the other in Dutch Holstein Friesian using capillary zone electrophoresis. In French Montbéliarde, in addition to the known isoforms αs1-CN-8P and-9P and αs2-CN-10P to -13P, three new phosphorylation isoforms were detected, namely αs2-CN-9P, αs2-CN-14P, and αs2-CN-15P. Relative concentrations of the phosphorylation isoforms varied considerably among cows. Phenotypic correlations showed that isoforms phosphorylated at higher degrees (αs1-CN-9P and αs2-CN-12P to -14P) correlated negatively with isoforms phosphorylated at lower degrees (αs1-CN-8P, αs2-CN-10P, and -11P). Furthermore, it was shown that αs1- and αs2-CN phosphorylation profiles changed across parity and lactation, and exploitable genetic variation for the phosphorylation degrees of αs1- and αs2-CN (defined as the proportion of higher-degree isoforms in αs1- and αs2-CN, respectively) exist. In Dutch Holstein Friesian, three αs2-CN isoforms, namely αs2-CN-10P to -12P, and the phosphorylation degrees of αs1- and αs2-CN were quantified. High intra-herd heritabilities were estimated for individual αs2-CN phosphorylation isoforms and the phosphorylation degrees of αs1- and αs2-CN (ranging from 0.54 to 0.89). This suggests that genetic factors contribute substantially to observed differences in αs1- and αs2-CN phosphorylation profiles. The highly positive correlation between the phosphorylation degrees of αs1- and αs2-CN (0.94) suggest that phosphorylation of αs1- and αs2-CN is related. Additionally, a total of 10 regions, distributed across Bos taurus autosomes (BTA) 1, 2, 6, 9, 11, 14, 15, 18, 24 and 28, were detected to be associated with individual αs1- and αs2-CN phosphorylation isoforms and their phosphorylation degrees. Regions on BTA1, 6, 11 and 14 were associated with multiple traits studied. Two quantitative trait loci (QTL) regions were detected on BTA1: one affecting αs2-CN production, and the other affecting αs1-CN PD and αs2-CN PD. The QTL region on BTA6 affected only individual αs2-CN isoforms. The QTL region on BTA11 and 14 affected relative concentrations of αs2-CN-10P and αs2-CN-11P, αs1-CN PD and αs2-CN PD. Results suggested that effects of identified genomic regions on αs1-CN PD and αs2-CN PD are probably due to changes in milk synthesis and phosphorus secretion in milk.</p

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype

Author Correction: Elucidating causative gene variants in hereditary Parkinson’s disease in the Global Parkinson’s Genetics Program (GP2)

Correction to: s41531-023-00526-9 npj Parkinson’s Disease, published online 27 June 2023 In this article the Global Parkinson’s Genetics Program (GP2) members names and affiliations were missing in the main author list of the Original article which are listed in the below

Defining the causes of sporadic Parkinson's disease in the global Parkinson's genetics program (GP2)

The Global Parkinson’s Genetics Program (GP2) will genotype over 150,000 participants from around the world, and integrate genetic and clinical data for use in large-scale analyses to dramatically expand our understanding of the genetic architecture of PD. This report details the workflow for cohort integration into the complex arm of GP2, and together with our outline of the monogenic hub in a companion paper, provides a generalizable blueprint for establishing large scale collaborative research consortia

Multi-ancestry genome-wide association meta-analysis of Parkinson?s disease

Although over 90 independent risk variants have been identified for Parkinson’s disease using genome-wide association studies, most studies have been performed in just one population at a time. Here we performed a large-scale multi-ancestry meta-analysis of Parkinson’s disease with 49,049 cases, 18,785 proxy cases and 2,458,063 controls including individuals of European, East Asian, Latin American and African ancestry. In a meta-analysis, we identified 78 independent genome-wide significant loci, including 12 potentially novel loci (MTF2, PIK3CA, ADD1, SYBU, IRS2, USP8, PIGL, FASN, MYLK2, USP25, EP300 and PPP6R2) and fine-mapped 6 putative causal variants at 6 known PD loci. By combining our results with publicly available eQTL data, we identified 25 putative risk genes in these novel loci whose expression is associated with PD risk. This work lays the groundwork for future efforts aimed at identifying PD loci in non-European populations

Bases génétiques de la phosphorylation des caséines bovines αs1 et αs2

Phosphorylation of caseins (CN) is a crucial post-translational modification allowing caseins to aggregate as micelles. The formation and stability of casein micelles are important for transporting abundant minerals to the neonate and manufacturing of dairy products. Therefore, it is of great interest to explore variation in degrees of phosphorylation of caseins and study to what extent genetic and other factors contribute to this variation. This thesis aimed to investigate the genetic background of bovine milk protein composition with a focus on phosphorylation of αs1- and αs2-CN. Thus, two studies were conducted to quantify phosphorylation levels of αs1- and αs2-CN: one in French Montbéliarde (FM) using liquid chromatography coupled with electrospray ionization mass spectrometry and the other in Dutch Holstein Friesian (DHF) using capillary zone electrophoresis. In FM, in addition to the known isoforms αs1-CN-8P and-9P and αs2-CN-10P to -13P, three new phosphorylation isoforms were detected, namely αs2-CN-9P, αs2-CN-14P, and αs2-CN-15P. Relative concentrations of the phosphorylation isoforms varied considerably among cows. Phenotypic correlations showed that isoforms phosphorylated at higher degrees (αs1-CN-9P and αs2-CN-12P to -14P) correlated negatively with isoforms phosphorylated at lower degrees (αs1-CN-8P, αs2-CN-10P, and -11P). Furthermore, it was shown that αs1- and αs2-CN phosphorylation profiles changed across parity and lactation, and exploitable genetic variation for the phosphorylation degrees of αs1- and αs2-CN (defined as the proportion of higher-degree isoforms in αs1- and αs2-CN, respectively) exists in FM. In DHF, three αs2-CN isoforms, namely αs2-CN-10P to -12P, and the phosphorylation degrees of αs1- and αs2-CN were quantified. High intra-herd heritabilities were estimated for individual αs2-CN phosphorylation isoforms and the phosphorylation degrees of αs1- and αs2-CN (ranging from 0.54 to 0.89). This suggests that genetic factors contribute substantially to observed differences in αs1- and αs2-CN phosphorylation profiles. The correlation between the phosphorylation degrees of αs1- and αs2-CN was 0.94. Additionally, a total of 10 regions, distributed across Bos taurus autosomes (BTA) 1, 2, 6, 9, 11, 14, 15, 18, 24 and 28, were detected to be associated with individual αs1- and αs2-CN phosphorylation isoforms and their phosphorylation degrees in DHF. Regions on BTA1, 6, 11 and 14 were associated with multiple traits studied. Two quantitative trait loci (QTL) regions were detected on BTA1: one affecting αs2-CN production, and the other affecting αs1-CN PD and αs2-CN PD. The QTL region on BTA6 affected only individual αs2-CN isoforms. The QTL region on BTA11 and 14 affected relative concentrations of αs2-CN-10P and αs2-CN-11P, αs1-CN PD and αs2-CN PD. Results suggested that effects of identified genomic regions on αs1-CN PD and αs2-CN PD are probably due to changes in milk synthesis and phosphorus secretion in milk. Finally, differences among studies due to factors such as analytical methods, trait definitions, and breed on genetic parameters and correlations are discussed using the two dataset from this thesis. It is concluded that differences in heritability estimates for αs1-CN-8P and -9P, αs2-CN-10P, -11P and -12P, and αs1-CN PD between FM and DHF were mainly due to genetic differences between breeds. As for αs2-CN PD, it was defined differently in FM and DHF due to analytical methods used. It is shown that both trait definitions successfully quantified the proportion of isoforms with higher degrees of phosphorylation because of similar estimated correlations using both definitions on the FM dataset. Additionally, it is hypothesized that a two-casein-kinase system is involved in the phosphorylation of αs1- and αs2-CN based on results in this thesis.La phosphorylation des caséines (CN) est une modification post-traductionnelle qui permet l’aggrégation des caséines sous formes de micelles. La stabilité de ces structures est essentielle pour transporter les minéraux au nouveau-né et fabriquer des produits laitiers. Il est par conséquent fondamental d'explorer la variation du degré de phosphorylation (PD) des CN, et d'étudier dans quelle mesure les facteurs génétiques contribuent à cette variation. Cette thèse visait à étudier le contexte génétique de la composition des protéines du lait de vache, en mettant l'accent sur la phosphorylation des CN αs1 et αs2. Deux études ont été menées pour analyser leur niveau de phosphorylation : la première en race Montbéliarde française (FM), en utilisant la chromatographie liquide couplée à la spectrométrie de masse à ionisation par électro-nébulisation et l'autre en race Holstein Friesian néerlandaise (DHF), en utilisant l’électrophorèse capillaire de zone. En race FM, en plus des isoformes connues : αs1-CN-8P et -9P, de αs2-CN-10P à -13P, trois nouvelles isoformes ont été détectées (αs2-CN-9P, αs2-CN-14P et αs2-CN-15P). Les concentrations relatives de ces isoformes variaient considérablement entre vaches. Les corrélations phénotypiques ont montré que les isoformes phosphorylées aux degrés les plus élevés (αs1-CN-9P, de αs2-CN-12P à -14P) étaient corrélées négativement avec les isoformes phosphorylées à des degrés inférieurs (αs1-CN-8P, αs2-CN-10P et -11P). En outre, les profils de phosphorylation des CN αs1 et αs2 changent avec la parité et le stade de lactation, et il est possible d’exploiter en FM la variation génétique du PD de ces caséines (définie comme la proportion d'isoformes ayant les taux de phosphorylation les plus élevés). En DHF, nous avons quantifié 3 isoformes d’αs2-CN, à savoir αs2-CN-10P, -11P, et -12P et les PD des CN αs1 et αs2. Des héritabilités intra-troupeau élevées ont été estimées pour les isoformes de phosphorylation d'αs2-CN et les PD des CN αs1 et αs2 (comprise entre 0,54 et 0,89). Ceci suggère que des facteurs génétiques contribuent substantiellement aux différences observées dans les profils de phosphorylation de ces CN. La correlation entre les degrés de phosphorylation de αs1-CN et d’αs2-CN était de 0,94. Nous avons montré que 10 régions, réparties sur les autosomes BTA1, 2, 6, 9, 11, 14, 15, 18, 24 et 28, sont associées aux isoformes de phosphorylation des CN αs1 et αs2 et leurs PD en DHF. Les régions sur BTA1, 6, 11 et 14 étaient associées à plusieurs caractères étudiés. Deux régions quantitative trait loci (QTL) ont été détectées sur BTA1 : l'une affectant la production d'αs2-CN et l'autre le PD des deux CN. La région QTL localisée sur BTA6 affectait uniquement les isoformes d'αs2-CN. Les régions QTL situées sur BTA11 et BTA14 influencent les concentrations relatives en αs2-CN-10P et -11P, et les PD des CN αs1 et αs2. Ces résultats suggèrent que les effets des régions génomiques identifiées impactant les PD sont probablement dus à des modifications de biosynthèse des constituants du lait et à la sécrétion de phosphore dans le lait. Enfin, les différences observées sur les paramètres génétiques estimés et les corrélations, sont discutées sur la base de l'ensemble des données issues des deux études décrites dans cette thèse. En conclusion, les différences observées sur les estimations d'héritabilité entre FM et DHF semblent principalement dues à des composantes génétiques. Quant au PD de l'αs2-CN, il a été défini différemment en FM et en DHF, en raison des méthodes analytiques. Il a été possible de quantifier avec succès la proportion d'isoformes présentant des degrés de phosphorylation élevés, en raison de la similitude dans les corrélations estimées avec les deux définitions aux données de FM. Finalement, sur la base des résultats présentés dans cette thèse, nous avons émis l'hypothèse qu'un système comportant deux caséines-kinases puisse être impliqué dans la phosphorylation des CN αs1 et αs2

Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle

Background Little is known about the genetic architecture of economically important traits in Brown Swiss cattle because only few genome-wide association studies (GWAS) have been carried out in this breed. Moreover, most GWAS have been performed for single traits, thus not providing detailed insights into potentially existing pleiotropic effects of trait-associated loci. Results To compile a comprehensive catalogue of large-effect quantitative trait loci (QTL) segregating in Brown Swiss cattle, we carried out association tests between partially imputed genotypes at 598,016 SNPs and daughter-derived phenotypes for more than 50 economically important traits, including milk production, growth and carcass quality, body conformation, reproduction and calving traits in 4578 artificial insemination bulls from two cohorts of Brown Swiss cattle (Austrian-German and Swiss populations). Across-cohort multi-trait meta-analyses of the results from the single-trait GWAS revealed 25 quantitative trait loci (QTL; P < 8.36 × 10− 8) for economically relevant traits on 17 Bos taurus autosomes (BTA). Evidence of pleiotropy was detected at five QTL located on BTA5, 6, 17, 21 and 25. Of these, two QTL at BTA6:90,486,780 and BTA25:1,455,150 affect a diverse range of economically important traits, including traits related to body conformation, calving, longevity and milking speed. Furthermore, the QTL at BTA6:90,486,780 seems to be a target of ongoing selection as evidenced by an integrated haplotype score of 2.49 and significant changes in allele frequency over the past 25 years, whereas either no or only weak evidence of selection was detected at all other QTL. Conclusions Our findings provide a comprehensive overview of QTL segregating in Brown Swiss cattle. Detected QTL explain between 2 and 10% of the variation in the estimated breeding values and thus may be considered as the most important QTL segregating in the Brown Swiss cattle breed. Multi-trait association testing boosts the power to detect pleiotropic QTL and assesses the full spectrum of phenotypes that are affected by trait-associated variants

Novel functional sequences uncovered through a bovine multiassembly graph

Many genomic analyses start by aligning sequencing reads to a linear reference genome. However, linear reference genomes are imperfect, lacking millions of bases of unknown relevance and are unable to reflect the genetic diversity of populations. This makes reference-guided methods susceptible to reference-allele bias. To overcome such limitations, we build a pangenome from six reference-quality assemblies from taurine and indicine cattle as well as yak. The pangenome contains an additional 70,329,827 bases compared to the Bos taurus reference genome. Our multiassembly approach reveals 30 and 10.1 million bases private to yak and indicine cattle, respectively, and between 3.3 and 4.4 million bases unique to each taurine assembly. Utilizing transcriptomes from 56 cattle, we show that these nonreference sequences encode transcripts that hitherto remained undetected from the B. taurus reference genome. We uncover genes, primarily encoding proteins contributing to immune response and pathogen-mediated immunomodulation, differentially expressed between Mycobacterium bovis-infected and noninfected cattle that are also undetectable in the B. taurus reference genome. Using whole-genome sequencing data of cattle from five breeds, we show that reads which were previously misaligned against the Bos taurus reference genome now align accurately to the pangenome sequences. This enables us to discover 83,250 polymorphic sites that segregate within and between breeds of cattle and capture genetic differentiation across breeds. Our work makes a so-far unused source of variation amenable to genetic investigations and provides methods and a framework for establishing and exploiting a more diverse reference genome.ISSN:0027-8424ISSN:1091-649