Estimation of genetic parameters and detection of quantitative trait loci for minerals in Danish Holstein and Danish Jersey milk

Buitenhuis, Bart; Poulsen, Nina Aagaard; Larsen, Lotte Bach; Sehested, Jakob

doi:10.1186/s12863-015-0209-9

Cited by 38 publications

(54 citation statements)

References 31 publications

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“…The same authors found these wavelengths phenotypically associated with FT-IR-predicted Fat% (2,518 cm −1 ) and lactose percentage (2,587 cm −1 ); however, the same wavelengths were not associated with FTIR-predicted Prot%. In the study by Wang and Bovenhuis (2018), wavenumbers 2,518 and 2,587 cm −1 were associated with several SNP in a sub-region of chromosome 1 of the bovine genome where a QTL for the concentration of phosphorus in milk has been reported (SLC37A1, Buitenhuis et al, 2015;Kemper et al, 2016).…”

Section: Discussionmentioning

confidence: 98%

A landscape of the heritability of Fourier-transform infrared spectral wavelengths of milk samples by parity and lactation stage in Holstein cows

Rovere

Campos

Tempelman

et al. 2019

Journal of Dairy Science

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Fourier-transform near-and mid-infrared (FTIR) milk spectral data are routinely collected in many countries worldwide. Establishing an optimal strategy to use spectral data in genetic evaluations requires knowledge of the heritabilities of individual FTIR wavelength absorbances. Previous FTIR heritability estimates have been based on relatively small sample sizes and have not considered the possibility that heritability may vary across parities and stages of the lactation. We used data from ~370,000 test-day records of Canadian Holstein cows to produce a landscape of the heritability of FTIR spectra, 1,060 wavelengths in the near-and mid-infrared spectrum (5,011-925 cm −1 ), by parity and month of the lactation (mo 1 to 3 and mo 1 to 6, respectively). The 2 regions of the spectrum associated with absorption of electromagnetic energy by water molecules were estimated to have very high phenotypic variances, very low heritabilities, and very low proportion of variance explained by herd-year-season (HYS) subclasses. The near-or short-wavelength infrared (SWIR: 5,066-3,672 cm −1 ) region was also characterized by low heritability estimates, whereas the estimated proportion of the variance explained by HYS was high. The midwavelength infrared region (MWIR: 3,000-2,500 cm −1 ) and the transition between mid and long-wavelength infrared region (MWIR-LWIR: 1,500-925 cm −1 ) harbor several waves characterized by moderately high (≥0.4) heritabilities. Most of the high-heritability regions contained wavelengths that are reported to be associated with important milk metabolites and components.Interestingly, these 2 same regions tended to show more variability in heritabilities between parity and lactation stage. Second parity showed heritability patterns that were distinctly different from those of the first and third parities, whereas the first 2 mo of the lactation had clearly distinct heritability patterns compared with mo 3 to 6.

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Section: Discussionmentioning

confidence: 98%

A landscape of the heritability of Fourier-transform infrared spectral wavelengths of milk samples by parity and lactation stage in Holstein cows

Rovere

Campos

Tempelman

et al. 2019

Journal of Dairy Science

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“…One may question whether observing such differences between datasets indicated group specific allele effects, or simply group differences in terms of statistical power due to a difference in allele frequency. This question often arises when GWAS is applied separately to genetic groups, as in maize [16,56] or dairy cattle [57,58], and is very difficult to answer except for obvious configurations such as associations at SNPs segregating only in one group.…”

Section: Accounting For Genetic Groups In Gwasmentioning

confidence: 99%

Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering

et al. 2020

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When handling a structured population in association mapping, group-specific allele effects may be observed at quantitative trait loci (QTLs) for several reasons: (i) a different linkage disequilibrium (LD) between SNPs and QTLs across groups, (ii) group-specific genetic mutations in QTL regions, and/or (iii) epistatic interactions between QTLs and other loci that have differentiated allele frequencies between groups. We present here a new genomewide association (GWAS) approach to identify QTLs exhibiting such group-specific allele effects. We developed genetic materials including admixed progeny from different genetic groups with known genome-wide ancestries (local admixture). A dedicated statistical methodology was developed to analyze pure and admixed individuals jointly, allowing one to disentangle the factors causing the heterogeneity of allele effects across groups. This approach was applied to maize by developing an inbred "Flint-Dent" panel including admixed individuals that was evaluated for flowering time. Several associations were detected revealing a wide range of configurations of allele effects, both at known flowering QTLs (Vgt1, Vgt2 and Vgt3) and new loci. We found several QTLs whose effect depended on the group ancestry of alleles while others interacted with the genetic background. Our GWAS approach provides useful information on the stability of QTL effects across genetic groups and can be applied to a wide range of species. Author summaryIdentification of genomic regions involved in genetic architecture of traits has become commonplace in quantitative genetics studies. Genetic structure is a common feature in human, animal and plant species and most current methods target genomic regions whose effects on traits are conserved between genetic groups. However, a heterogeneity of allele effects may be observed due to different factors: a group-specific correlation between PLOS GENETICS PLOS Genetics | https://doi.org/10.the alleles of the tagged marker and those of the causal variant, a group-specific mutation at the causal variant or an epistatic interaction between the causal variant and the genetic background. We propose a new method adapted to structured populations including admixed individuals, which aims to identify these genomic regions and to unravel the previous factors. The method was applied to a maize inbred diversity panel including lines from the dent and the flint genetic groups, as well as admixed lines, evaluated for flowering time. Several genomic regions were detected with various configurations of allele effects, with evidence of epistatic interactions between some of the loci and the genetic background. PLOS GENETICSDisentangling group specific QTL allele effects from genetic background epistasis in GWAS PLOS Genetics | https://doi.org/10.

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“…Milk mineral (Ca, Se, K, Mg, P, and Zn) concentrations in the Dutch milk samples were determined by inductively coupled plasma-atomic emission spectrometry (ICP-AES; Vista Axial, Varian, Australia) on whole milk as described by van Hulzen et al (2009). For the Danish milk samples, milk minerals (Ca, Se, K, Mg, P, and Zn) were extracted from skim milk by acid sonication and identified using inductively coupled plasma mass spectrometry (ICP-MS) as described by Buitenhuis et al (2015).…”

Section: Mineral Contentsmentioning

confidence: 99%

Effects of the diacylglycerol o-acyltransferase 1 (DGAT1) K232A polymorphism on fatty acid, protein, and mineral composition of dairy cattle milk

Bovenhuis

Visker

Poulsen

et al. 2016

Journal of Dairy Science

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Several studies have described associations between the diacylglycerol o-acyltransferase 1 (DGAT1) K232A polymorphism and routinely collected milk production traits but not much is known about effects of the DGAT1 polymorphism on detailed milk composition. The aim of this study was to estimate effects of the DGAT1 polymorphism on milk fatty acid, protein, and mineral composition. We looked for effects that were significant and consistent in Danish Holstein Friesian (HF), Danish Jersey, and Dutch HF as these are likely to be true effects of the DGAT1 K232A polymorphism rather than being effects of linked loci. For fatty acid composition, significant and consistent effects of the DGAT1 polymorphism were detected on C14:0, C16:0, C15:0, C16:1, C18:1 cis-9, conjugated linoleic acid (CLA) cis-9,trans-11, C18:2 cis-9,cis-12, and C18:3 cis-9,cis-12,cis-15 content (percent by weight, wt/wt %). For C16:0, C16:1, and C18:1 cis-9, the DGAT1 polymorphism explained more than 10% of the phenotypic variation. Significant effects on milk protein composition in Dutch HF could not be confirmed in Danish Jersey or Danish HF. For mineral content, significant and consistent effects of the DGAT1 polymorphism on calcium, phosphorus, and zinc were detected. In the Dutch HF population, the contribution of the DGAT1 K232A polymorphism to phenotypic variance was 12.0% for calcium, 8.3% for phosphorus, and 6.1% for zinc. Different from effects on fatty acid composition, effects of the DGAT1 polymorphism on yields of long-chain fatty acids C18:1 cis-9, CLA cis-9,trans-11, C18:2 cis-9,cis-12, and C18:3 cis-9,cis-12,cis-15 were not significant. This indicates that effects of DGAT1 on these fatty acids are indirect, not direct, effects: DGAT1 affects de novo synthesis of fatty acids and, consequently, the contribution of the long-chain fatty acids to total fat is decreased. In addition, effects of the DGAT1 polymorphism on yields of Ca, P, and Zn were not significant, which indicates that effects on these minerals are the result of indirect rather than direct effects of DGAT1: effects on calcium, phosphorus, and zinc content can be explained by effects of DGAT1 on milk volume. The reported effects of the DGAT1 polymorphism on fatty acid and mineral composition of milk are substantial and therefore relevant for milk quality.

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Estimation of genetic parameters and detection of quantitative trait loci for minerals in Danish Holstein and Danish Jersey milk

Cited by 38 publications

References 31 publications

A landscape of the heritability of Fourier-transform infrared spectral wavelengths of milk samples by parity and lactation stage in Holstein cows

A landscape of the heritability of Fourier-transform infrared spectral wavelengths of milk samples by parity and lactation stage in Holstein cows

Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering

Effects of the diacylglycerol o-acyltransferase 1 (DGAT1) K232A polymorphism on fatty acid, protein, and mineral composition of dairy cattle milk

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