Estimation of genetic parameters and detection of chromosomal regions affecting the major milk proteins and their post translational modifications in Danish Holstein and Danish Jersey cattle

Buitenhuis, Bart; Poulsen, Nina Aagaard; Gebreyesus, Grum; Larsen, Lotte Bach

doi:10.1186/s12863-016-0421-2

Cited by 66 publications

(80 citation statements)

References 43 publications

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“…We did not detect a QTL signal on BTA25 where the FAM20C gene is located [between 43.86 to 43.90 Mbp (BTAU 4.0)], neither for individual α S2 -CN phosphorylation isoforms nor for α S1 -and α S2 -CN PD. This is in line with results reported by Bijl et al (2014) and Buitenhuis et al (2016) and suggests that no FAM20C variants are segregating in the Dutch Holstein population or in the Danish Holstein and Danish Jersey populations. Regions associated with multiple traits were found on BTA1, 6, 11, and 14, and their effects will be discussed in detail.…”

Section: Resultssupporting

confidence: 92%

“…This resulted in lower degrees of phosphorylation of α S1 -and α S2 -CN, as shown by the negative association of the BB genotype with both α S1 -and α S2 -CN PD. Buitenhuis et al (2016) and Fang et al (2017) did not detect significant effects of β-LG genotypes on individual α S2 -CN phosphorylation isoforms, α S1 -CN PD and α S2 -CN PD, in Danish Holstein and Danish Jersey or French Montbéliarde. Differences between studies might be due to the genetic differences between studied breeds (Holstein, Montbéliarde, and Jersey), such as differences in linkage disequilibrium between β-LG genotypes and other variants that affect the traits of interest, limited sample size of Buitenhuis et al (2016) and Fang et al (2017), and the use of different analytical methods.…”

Section: Bta11mentioning

confidence: 65%

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Genome-wide association study for αS1- and αS2-casein phosphorylation in Dutch Holstein Friesian

Fang

Bovenhuis

Valenberg

et al. 2019

Journal of Dairy Science

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Phosphorylation of caseins (CN) is a crucial posttranslational modification that allows caseins to form colloid particles known as casein micelles. Both α S1and α S2 -CN show varying degrees of phosphorylation (isoforms) in cow milk and were suggested to be more relevant for stabilizing internal micellar structure than β-and κ-CN. However, little is known about the genetic background of individual α S2 -CN phosphorylation isoforms and the phosphorylation degrees of α S1 -and α S2 -CN (α S1 -CN PD and α S2 -CN PD), defined as the proportion of isoforms with higher degrees of phosphorylation in total α S1 -and α S2 -CN, respectively. We aimed to identify genomic regions associated with these traits using 50K single nucleotide polymorphisms for 1,857 Dutch Holstein Friesian cows. A total of 10 quantitative trait loci (QTL) regions were identified for all studied traits on 10 Bos taurus autosomes (BTA1, 2, 6, 9, 11, 14, 15, 18, 24, and 28). Regions associated with multiple traits were found on BTA1, 6, 11, and 14. We showed 2 QTL regions on BTA1, one affecting α S2 -CN production and the other harboring the SLC37A1 gene, which encodes a phosphorus antiporter and affects α S1 -and α S2 -CN PD. The QTL on BTA6 harbors the casein gene cluster and affects individual α S2 -CN phosphorylation isoforms. The QTL on BTA11 harbors the PAEP gene that encodes for β-lactoglobulin and affects relative concentrations of α S2 -CN-10P and α S2 -CN-11P as well as α S1 -CN PD and α S2 -CN PD. The QTL on BTA14 harbors the DGAT1 gene and affects relative concentrations of α S2 -CN-10P and α S2 -CN-11P as well as α S1 -CN PD and α S2 -CN PD. Our results suggest that effects of identified genomic regions on phosphorylation of α S1 -and α S2 -CN are related to changes in milk synthesis and phosphorus secretion in milk. The actual roles of SLC37A1, PAEP, and DGAT1 in α S1 -and α S2 -CN phosphorylation in Dutch Holstein Friesian require further investigation.

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Section: Resultssupporting

confidence: 92%

Section: Bta11mentioning

confidence: 65%

Genome-wide association study for αS1- and αS2-casein phosphorylation in Dutch Holstein Friesian

Fang

Bovenhuis

Valenberg

et al. 2019

Journal of Dairy Science

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“…There were eleven sites shared between Holstein and Nordic Red Cattle, two sites between Holstein and Jersey, and one site between Nordic Red Cattle and Jersey. Among these sites were gene variants, such as ABCA12 (Chr2:103,682,772-103,684,297 in Holstein & Jersey) associated with growth and development, 55 , 56 TTC1 (Chr7:73,725,513-73,725,918 in Holstein & Nordic Red Cattle) with cold tolerance, 57 VWA3B (Chr11:3,521,329-3,522,551 in Holstein & Nordic Red Cattle) with milk glycosylated kappa-casein percentage, 58 and were intergenic variants, such as Chr15:41,393,393-41,393,780 (in Jersey and Nordic Red Cattle) and Chr20:26,812,159-26,812,834 (in Holstein and Jersey) overlap QTL associated with calving traits, 59 , 60 Chr20:45,816,245-45,820,519 (in Holstein & Nordic Red Cattle) with meat and carcass trait, 61 and Chr23:49,778,653-49,782,567 (in Holstein and Nordic Red Cattle) with body weight 62 . We also identified a highly differentiated fertility associated gene DST/BPAG1 63 , 64 (Chr23:3,486,232-3,486,603) in Nordic Red Cattle.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle

et al. 2017

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Large genomic deletions are potential candidate for loss-of-function, which could be lethal as homozygote. Analysing whole genome data of 175 cattle, we report 8,480 large deletions (199 bp–773 KB) with an overall false discovery rate of 8.8%; 82% of which are novel compared with deletions in the dbVar database. Breakpoint sequence analyses revealed that majority (24 of 29 tested) of the deletions contain microhomology/homology at breakpoint, and therefore, most likely generated by microhomology-mediated end joining. We observed higher differentiation among breeds for deletions in some genic-regions, such as ABCA12, TTC1, VWA3B, TSHR, DST/BPAG1, and CD1D. The genes overlapping deletions are on average evolutionarily less conserved compared with known mouse lethal genes (P-value = 2.3 × 10−6). We report 167 natural gene knockouts in cattle that are apparently nonessential as live homozygote individuals are observed. These genes are functionally enriched for immunoglobulin domains, olfactory receptors, and MHC classes (FDR = 2.06 × 10−22, 2.06 × 10−22, 7.01 × 10−6, respectively). We also demonstrate that deletions are enriched for health and fertility related quantitative trait loci (2-and 1.5-fold enrichment, Fisher’s P-value = 8.91 × 10−10 and 7.4 × 10−11, respectively). Finally, we identified and confirmed the breakpoint of a ∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8), causing stillbirth in Nordic Red Cattle.

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“…Firstly, one selective sweep study in a German Holstein population revealed an extended range of LD in haplotypes that contain the casein cluster [53]. Secondly, GWA study on casein traits in a Danish Holstein population identified a broad GWAS peak (BTA6:60-100 Mb) that contains the casein cluster [54]. The broad GWAS peak also indicate high LD in this regions, that matched with the findings from Qanbari et al [53] Another explanation for the high MAF of CNVR 547 might be the direct selection on the variant itself.…”

Section: Interesting Cnvrmentioning

confidence: 99%

Functional and population genetic features of copy number variations in two dairy cattle populations

et al. 2020

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Background: Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features.Results: We discovered 14,272 autosomal CNVs, which were aggregated into 1755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (MAF ≥ 0.05). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes, which are related to starch digestion and body size, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF ≥ 0.05) showed slightly higher LD (r 2 =~0.1 at 10 kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD (r 2 =~0.5 at 10 kb distance). Conclusions:Our analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17, which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers.

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Estimation of genetic parameters and detection of chromosomal regions affecting the major milk proteins and their post translational modifications in Danish Holstein and Danish Jersey cattle

Cited by 66 publications

References 43 publications

Genome-wide association study for αS1- and αS2-casein phosphorylation in Dutch Holstein Friesian

Genome-wide association study for αS1- and αS2-casein phosphorylation in Dutch Holstein Friesian

Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle

Functional and population genetic features of copy number variations in two dairy cattle populations

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