Richard Spelman

Linkage Disequilibrium and Persistence of Phase in Holstein–Friesian, Jersey and Angus Cattle

When a genetic marker and a quantitative trait locus (QTL) are in linkage disequilibrium (LD) in one population, they may not be in LD in another population or their LD phase may be reversed. The objectives of this study were to compare the extent of LD and the persistence of LD phase across multiple cattle populations. LD measures r and r2 were calculated for syntenic marker pairs using genomewide single-nucleotide polymorphisms (SNP) that were genotyped in Dutch and Australian Holstein–Friesian (HF) bulls, Australian Angus cattle, and New Zealand Friesian and Jersey cows. Average r2 was ∼0.35, 0.25, 0.22, 0.14, and 0.06 at marker distances 10, 20, 40, 100, and 1000 kb, respectively, which indicates that genomic selection within cattle breeds with r2 ≥ 0.20 between adjacent markers would require ∼50,000 SNPs. The correlation of r values between populations for the same marker pairs was close to 1 for pairs of very close markers (<10 kb) and decreased with increasing marker distance and the extent of divergence between the populations. To find markers that are in LD with QTL across diverged breeds, such as HF, Jersey, and Angus, would require ∼300,000 markers.

Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature

We report mapping of a quantitative trait locus (QTL) with a major effect on bovine stature to a ∼780-kb interval using a Hidden Markov Model–based approach that simultaneously exploits linkage and linkage disequilibrium. We re-sequenced the interval in six sires with known QTL genotype and identified 13 clustered candidate quantitative trait nucleotides (QTNs) out of >9,572 discovered variants. We eliminated five candidate QTNs by studying the phenotypic effect of a recombinant haplotype identified in a breed diversity panel. We show that the QTL influences fetal expression of seven of the nine genes mapping to the ∼780-kb interval. We further show that two of the eight candidate QTNs, mapping to the PLAG1-CHCHD7 intergenic region, influence bidirectional promoter strength and affect binding of nuclear factors. By performing expression QTL analyses, we identified a splice site variant in CHCHD7 and exploited this naturally occurring null allele to exclude CHCHD7 as single causative gene.

Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers

Feed makes up a large proportion of variable costs in dairying. For this reason, selection for traits associated with feed conversion efficiency should lead to greater profitability of dairying. Residual feed intake (RFI) is the difference between actual and predicted feed intakes and is a useful selection criterion for greater feed efficiency. However, measuring individual feed intakes on a large scale is prohibitively expensive. A panel of DNA markers explaining genetic variation in this trait would enable cost-effective genomic selection for this trait. With the aim of enabling genomic selection for RFI, we used data from almost 2,000 heifers measured for growth rate and feed intake in Australia (AU) and New Zealand (NZ) genotyped for 625,000 single nucleotide polymorphism (SNP) markers. Substantial variation in RFI and 250-d body weight (BW250) was demonstrated. Heritabilities of RFI and BW250 estimated using genomic relationships among the heifers were 0.22 and 0.28 in AU heifers and 0.38 and 0.44 in NZ heifers, respectively. Genomic breeding values for RFI and BW250 were derived using genomic BLUP and 2 bayesian methods (BayesA, BayesMulti). The accuracies of genomic breeding values for RFI were evaluated using cross-validation. When 624,930 SNP were used to derive the prediction equation, the accuracies averaged 0.37 and 0.31 for RFI in AU and NZ validation data sets, respectively, and 0.40 and 0.25 for BW250 in AU and NZ, respectively. The greatest advantage of using the full 624,930 SNP over a reduced panel of 36,673 SNP (the widely used BovineSNP50 array) was when the reference population included only animals from either the AU or the NZ experiment. Finally, the bayesian methods were also used for quantitative trait loci detection. On chromosome 14 at around 25 Mb, several SNP closest to PLAG1 (a gene believed to affect stature in humans and cattle) had an effect on BW250 in both AU and NZ populations. In addition, 8 SNP with large effects on RFI were located on chromosome 14 at around 35.7 Mb. These SNP may be associated with the gene NCOA2, which has a role in controlling energy metabolism.

A high density linkage map of the bovine genome

BackgroundRecent technological advances have made it possible to efficiently genotype large numbers of single nucleotide polymorphisms (SNPs) in livestock species, allowing the production of high-density linkage maps. Such maps can be used for quality control of other SNPs and for fine mapping of quantitative trait loci (QTL) via linkage disequilibrium (LD).ResultsA high-density bovine linkage map was constructed using three types of markers. The genotypic information was obtained from 294 microsatellites, three milk protein haplotypes and 6769 SNPs. The map was constructed by combining genetic (linkage) and physical information in an iterative mapping process. Markers were mapped to 3,155 unique positions; the 6,924 autosomal markers were mapped to 3,078 unique positions and the 123 non-pseudoautosomal and 19 pseudoautosomal sex chromosome markers were mapped to 62 and 15 unique positions, respectively. The linkage map had a total length of 3,249 cM. For the autosomes the average genetic distance between adjacent markers was 0.449 cM, the genetic distance between unique map positions was 1.01 cM and the average genetic distance (cM) per Mb was 1.25.ConclusionThere is a high concordance between the order of the SNPs in our linkage map and their physical positions on the most recent bovine genome sequence assembly (Btau 4.0). The linkage maps provide support for fine mapping projects and LD studies in bovine populations. Additionally, the linkage map may help to resolve positions of unassigned portions of the bovine genome.

Mutation in Bovine β-Carotene Oxygenase 2 Affects Milk Color

β-Carotene biochemistry is a fundamental process in mammalian biology. Aberrations either through malnutrition or potentially through genetic variation may lead to vitamin A deficiency, which is a substantial public health burden. In addition, understanding the genetic regulation of this process may enable bovine improvement. While many bovine QTL have been reported, few of the causative genes and mutations have been identified. We discovered a QTL for milk β-carotene and subsequently identified a premature stop codon in bovine β-carotene oxygenase 2 (BCO2), which also affects serum β-carotene content. The BCO2 enzyme is thereby identified as a key regulator of β-carotene metabolism.

Genetic variation in PLAG1 associates with early life body weight and peripubertal weight and growth in Bos taurus

Variation at the pleiomorphic adenoma gene 1 (PLAG1) locus has recently been implicated in the regulation of stature and weight in Bos taurus. Using a population of 942 outbred Holstein-Friesian dairy calves, we report confirmation of this effect, demonstrating strong association of early life body weight with PLAG1 genotype. Peripubertal body weight and growth rate were also significantly associated with PLAG1 genotype. Growth rate per kilogram of body weight, daily feed intake, gross feed efficiency and residual feed intake were not significantly associated with PLAG1 genotype. This study supports the status of PLAG1 as a key regulator of mammalian growth. Further, the data indicate the utility of PLAG1 polymorphisms for the selection of animals to achieve enhanced weight gain or conversely to aid the selection of animals with lower mature body weight and thus lower maintenance energy requirements.

Effects of reduced frequency of milk removal on gene expression in the bovine mammary gland

Regulation of milk synthesis and secretion is controlled mostly through local (intramammary) mechanisms. To gain insight into the molecular pathways comprising this response, an analysis of mammary gene expression was conducted in 12 lactating cows shifted from twice daily to once daily milking. Tissues were sampled by biopsy from adjacent mammary quarters of these animals during the two milking frequencies, allowing changes in gene expression to be assessed within each animal. Using bovine-specific, oligonucleotide arrays representing 21,495 unique transcripts, a range of differentially expressed genes were found as a result of less frequent milk removal, constituting transcripts and pathways related to apoptotic signaling (NF-kappaB, JUN, ATF3, IGFBP5, TNFSF12A) mechanical stress and epithelial tight junction synthesis (CYR61, CTGF, THBS1, CLDN4, CLDN8), and downregulated milk synthesis (LALBA, B4GALT1, UGP2, CSN2, GPAM, LPL). Quantitative real-time PCR was used to assess the expression of 13 genes in the study, and all 13 of these were correlated (P < 0.05) with values derived from array analysis. It can be concluded that the physiological changes that occur in the bovine mammary gland as a result of reduced milk removal frequency likely comprise the earliest stages of the involution response and that mechano-signal transduction cascades associated with udder distension may play a role in triggering these events.

Utilisation of marker assisted selection in a commercial dairy cow population

Abstract Genetic and economic benefits of marker assisted selection (MAS) to a commercial dairy cow population were evaluated by calculating selection advance resulting from four pathways of selection. In addition to background polygenic effects, a single additive quantitative trait loci (QTL) was segregating. Three sizes of QTL were assessed; 0.5, 1.0 and 2.0 genetic standard deviations ( σ G ) (difference between homozygotes), at each of four starting QTL frequencies; 0.01, 0.10, 0.35 and 0.75 over a thirty year time horizon. No recombination existed between QTL and a marker. Two MAS strategies were evaluated by comparison to a breeding scheme that had no genotypic knowledge of the QTL, over a thirty year time horizon. Economic benefits were calculated from the returns of extra milk produced (accounting for increased feed costs) less identification costs of the QTL and subsequent genotyping costs. In both strategies increase in QTL frequency was not immediate and thus returns were received in the later years of the analysis. The MAS strategy that utilised knowledge of QTL genotype for bull dams and bull sires had superior genetic gain at all QTL sizes and frequencies. However, it was only profitable for a 1.0 σ G QTL at 0.1 and 0.35 frequencies, and a 2.0 σ G QTL at all except the highest frequency (0.75). Long-term genetic loss was observed. The second MAS strategy of progeny testing only homozygous and heterozygous QTL bulls required a QTL of size 1.0 σ G at frequencies of 0.1 or 0.35 or a 2.0 σ G QTL at frequencies of 0.01, 0.1 and 0.35 to be more profitable than the current breeding scheme. The choice of MAS strategy should depend on QTL size and frequency.

Multiple-marker mapping of wood density loci in an outbred pedigree of radiata pine

Abstract The objective of this study was to determine the genetic location and effects of genomic regions controlling wood density at three stages, i.e., rings corresponding to ages 1–5 (WD1_5), rings corresponding to ages 6–10 (WD6_10), and outer wood density (WD14) in a full-sib pedigree (850.055×850.096) of Pinus radiata. The number of offspring measured at these three stages were 80, 93 and 93, respectively. Only a single linkage group of the parent 850.55 was considered for mapping quantitative trait loci (QTLs). A multiple-marker least-squares approach was employed for mapping QTLs for each of the three traits, using a single-QTL model. Logistic regression was used for multiple-trait QTL mapping. Critical values for test-statistic were calculated empirically by ’shuffling’ the data. A putative QTL with large effect on WD1_5 appears to be segregating at the 73 cM position (experimentwise P<0.01). The width of the 95% bootstrap confidence interval for this putative QTL was 40 cM (i.e. 56–96 cM). The effect of this QTL on the expression of wood density at later stages was diminished. From multiple-trait analysis, two marker locations (at 66 cM and 91 cM) were found to be significantly associated (experimentwise P <0.05) with the expression of wood density at different ages. These results are encouraging for the application of marker information to early selection in order to increase juvenile wood density, although the putative QTLs detected in this study need to be verified in an independent population.

Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle

Lactation, hair development and homeothermy are characteristic evolutionary features that define mammals from other vertebrate species. Here we describe the discovery of two autosomal dominant mutations with antagonistic, pleiotropic effects on all three of these biological processes, mediated through the prolactin signalling pathway. Most conspicuously, mutations in prolactin (PRL) and its receptor (PRLR) have an impact on thermoregulation and hair morphology phenotypes, giving prominence to this pathway outside of its classical roles in lactation.