Genetic analysis of milk citrate predicted by milk mid-infrared spectra of Holstein cows in early lactation.

Milk citrate is regarded as an early biomarker of negative energy balance in dairy cows during early lactation and serves as a suitable candidate phenotype for genomic selection due to its wide availability across a large number of cows through milk mid-infrared spectra prediction. However, its genetic background is not well known. Therefore, the objectives of this study were to (1) analyze the genetic parameters of milk citrate; (2) identify genomic regions associated with milk citrate; and (3) analyze the functional annotation of candidate genes and quantitative trait loci (QTL) related to milk citrate in Walloon Holstein cows. In total, 134,517 test-day milk-citrate phenotypes (mmol/L) collected within the first 50 d in milk on 52,198 Holstein cows were used. These milk-citrate phenotypes, predicted by milk mid-infrared spectra, were divided into 3 traits according to the first (citrate1), second (citrate2), and third to fifth parity (citrate3+). Genomic information for 566,170 SNPs was available for 4,479 animals. A multiple-trait repeatability model was used to estimate genetic parameters. A single-step GWAS was used to identify candidate genes for citrate and post-GWAS analysis was done to investigate the relationship and function of the identified candidate genes. The heritabilities estimated for citrate1, citrate2, and citrate3+ were 0.40, 0.37, and 0.35, respectively. The genetic correlations among the 3 traits ranged from 0.98 to 0.99. The genomic correlations among the 3 traits were also close to 1.00 across the genomic regions (1 Mb) in the whole genome, which means that citrate can be considered as a single trait in the first 5 parities. In total, 603 significant SNPs located on 3 genomic regions (chromosome 7, 68.569-68.575 Mb; chromosome 14, 0.15-1.90 Mb; and chromosome 20, 54.00-64.28 Mb), were identified to be associated with milk citrate. We identified 89 candidate genes including GPT, ANKH, PPP1R16A, and 32 QTL reported in the literature related to the identified significant SNPs. These identified QTL were mainly reported associated with milk fatty acids and metabolic diseases in dairy cows. This study suggests that milk citrate in Holstein cows is highly heritable and has the potential to be used as an early proxy for the negative energy balance of Holstein cows in a breeding objective.

Assessing the relative importance of health and conformation traits in the cavalier king Charles spaniel.

BACKGROUND: The selection of a future breeding dog is a complicated task, in which disease characteristics and different traits have to be combined and weighed against one another. Truncation selection, that is the exclusion of affected animals, may be very inefficient when selecting on a large number of traits, and may result in a reduction of the genetic diversity in a population or breed. Selection could be facilitated by the use of a selection index that combines multiple traits or breeding values into one score. This however requires a consideration of their relative value according to their economic weight, which is difficult to express in monetary units for health traits. The use of a choice experiment to derive non-market values might be a solution to this problem. This is a pilot study to assess the potential use of choice experiments to ascertain the public preference and relative importance attached to health- and conformation traits in the selection of a Cavalier King Charles spaniel. The focus was on two prevalent disorders, mitral valve disease and syringomyelia, and on several important conformation traits such as muzzle length and eye shape. Based on available prior information, a Bayesian D-optimal design approach was used to develop a choice experiment and the resulting choice sets. RESULTS: Every participant (breeder or owner) in the choice experiment was presented with a total of 17 choice sets, in which at most four traits could vary to reduce the cognitive burden. A total of 114 respondents participated in the choice experiment and results showed that respondents (breeders/owners) current attitudes were directed towards health (syringomyelia and mitral valve disease), followed by eye shape and level of inbreeding. CONCLUSIONS: This approach identifies the value breeders and owners attach to certain traits in the breeding objective. The resulting relative weights, represented as the logworths obtained from the choice experiment, could be an alternative to economic weights. They could be implemented as a weight when breeding values are available, but more study on this topic will be necessary. A challenge in this approach is to scale up the experiment with additional traits. Moreover, for other traits, the genetic parameters and correlations should be known first, in order to include them in the health selection index as well.

Twelve years of chiari-like malformation and syringomyelia scanning in Cavalier King Charles Spaniels in the Netherlands: Towards a more precise phenotype.

Chiari-like malformation (CM), syringomyelia (SM) and middle ear effusion (also called PSOM) are three conditions that frequently occur in Cavalier King Charles Spaniels (CKCS). Both CM and SM are currently screened in the Netherlands prior to breeding and are graded according to the British Veterinary Association's Kennel Club (BVA/KC) scheme. This study evaluated the prevalence and estimated genetic parameter of CM, SM and middle ear effusion from 12 years of screening results. For SM, the classical method using the BVA/KC scheme, was compared with exact measuring of the central canal dilation. For CM, the BVA/KC scheme was compared with a more detailed scheme. Next to this the presence of microchip artifacts was assessed. 1249 screening of 1020 dogs were re-evaluated. Results indicated the presence of CM in all dogs, suggesting it has become a breed-specific characteristic. And although different grades of CM were observed, the condition did not deteriorate over time. SM was present in 39% of the dogs and a clear age effect was demonstrated, with SM increasing with age. This emphasizes the importance of screening at appropriate age, since SM can worsen with increasing age. One alternative is to promote repeated measures. The presence of middle ear effusion in this study was 19%-21% for dogs younger than 3 years, and 32%-38% for dogs older than 3 years. In as much as 60%, microchip artifacts were noticed, leading to the recommendation to place microchips in another location in breeds that are susceptible to developing SM. Finally, this study estimated the heritability of CM in this population, due to the lack of phenotypic variance, to be very low at 0.02-0.03. The heritability for SM central canal dilatation to be 0.30, compared to 0.13 for the classical BVA/KC method, using a model including the age effect and the combined effect of veterinary clinic and year of the evaluation. Genetic correlations were rather small, ranging from 0.16-0.33. As a conclusion, screening for SM and CM in the entire population should be maintained, and a selection scheme against SM should be based on estimated breeding values for the exact measurement of the central canal dilatation.

Genomics of a revived breed: Case study of the Belgian campine cattle.

Through centuries of both natural and artificial selection, a variety of local cattle populations arose with highly specific phenotypes. However, the intensification and expansion of scale in animal production systems led to the predominance of a few highly productive cattle breeds. The loss of local populations is often considered irreversible and with them specific qualities and rare variants could be lost as well. Over these last years, the interest in these local breeds has increased again leading to increasing efforts to conserve these breeds or even revive lost populations, e.g. through the use of crosses with similar breeds. However, the remaining populations are expected to contain crossbred individuals resulting from introgressions. They are likely to carry exogenous genes that affect the breed's authenticity on a genomic level. Using the revived Campine breed as a case study, 289 individuals registered as purebreds were genotyped on the Illumina BovineSNP50. In addition, genomic information on the Illumina BovineHD and Illumina BovineSNP50 of ten breeds was available to assess the current population structure, genetic diversity, and introgression with phenotypically similar and/or historically related breeds. Introgression with Holstein and beef cattle genotypes was limited to only a few farms. While the current population shows a substantial amount of within-breed variation, the majority of genotypes can be separated from other breeds in the study, supporting the re-establishment of the Campine breed. The majority of the population is genetically close to the Deep Red (NL), Improved Red (NL) and Eastern Belgium Red and White (BE) cattle, breeds known for their historical ties to the Campine breed. This would support an open herdbook policy, thereby increasing the population size and consequently providing a more secure future for the breed.