The development of high throughput SNP genotyping technologies has improved the genetic dissection of simple and complex traits in many species including cats. The properties of feline 62,897 SNPs Illumina Infinium iSelect DNA array are described using a dataset of over 2,000 feline samples, the most extensive to date, representing 41 cat breeds, a random bred population, and four wild felid species. Accuracy and efficiency of the array’s genotypes and its utility in performing population-based analyses were evaluated. Average marker distance across the array was 37,741 Kb, and across the dataset, only 1% (625) of the markers exhibited poor genotyping and only 0.35% (221) showed Mendelian errors. Marker polymorphism varied across cat breeds and the average minor allele frequency (MAF) of all markers across domestic cats was 0.21. Population structure analysis confirmed a Western to Eastern structural continuum of cat breeds. Genome-wide linkage disequilibrium ranged from 50–1,500 Kb for domestic cats and 750 Kb for European wildcats (Felis silvestris silvestris). Array use in trait association mapping was investigated under different modes of inheritance, selection and population sizes. The efficient array design and cat genotype dataset continues to advance the understanding of cat breeds and will support monogenic health studies across feline breeds and populations.

Hereditary eye diseases of animals serve as excellent models of human ocular disorders and assist in the development of gene and drug therapies for inherited forms of blindness. Several primary hereditary eye conditions affecting various ocular tissues and having different rates of progression have been documented in domestic cats. Gene therapy for canine retinopathies has been successful, thus the cat could be a gene therapy candidate for other forms of retinal degenerations. The current study investigates a hereditary, autosomal recessive, retinal degeneration specific to Persian cats. A multi-generational pedigree segregating for this progressive retinal atrophy was genotyped using a 63 K SNP array and analyzed via genome-wide linkage and association methods. A multi-point parametric linkage analysis localized the blindness phenotype to a ~1.75 Mb region with significant LOD scores (Z ≈ 14, θ = 0.00) on cat chromosome E1. Genome-wide TDT, sib-TDT, and case–control analyses also consistently supported significant association within the same region on chromosome E1, which is homologous to human chromosome 17. Using haplotype analysis, a ~1.3 Mb region was identified as highly associated for progressive retinal atrophy in Persian cats. Several candidate genes within the region are reasonable candidates as a potential causative gene and should be considered for molecular analyses.Electronic supplementary materialThe online version of this article (doi:10.1007/s00335-014-9517-z) contains supplementary material, which is available to authorized users.

Several cat breeds are defined by morphological variation of the tail. The Japanese Bobtail is a breed that has been accepted for registration only within the past 50 years; however, the congenital kinked tail variants defining this breed were documented in the Far East centuries ago and the cats are considered 'good luck' in several Asian cultures. The recent discovery of the mutation for the tailless Manx phenotype has demonstrated that the Japanese Bobtail does not have a causative mutation in the same gene (T-Box). Here, a simple segregation analysis of cats bred from a pedigreed Japanese Bobtail demonstrated a simple autosomal dominant mode of inheritance with variable expression of the tail length and kink placement. Unexpectedly, radiological examinations of the entire vertebral column of kink-tailed cats indicated variation from the normal vertebral feline formula (C7, T13, L7, S3, Cd20-24), including cats with mostly one reduction of thoracic vertebrae (C7, T12, L7, S3), and an average of 15.8 caudal vertebrae. A few cats had variation in the number of cervical vertebrae. Several transitional vertebrae and anomalous ribs were noted. One cat had a bifid vertebra in the tail. Most cats had hemivertebrae that were usually included in the tail kink, one of which was demonstrated by gross pathology and histopathology. The abnormal vertebral formula or the placement of the kink in the tail did not coincide with morbidity or mortality.

Societal pressure to reduce enteric methane emissions from cattle continues to increase. The present study evaluated the efficacy of the commercial essential oil feed additive Agolin® Ruminant on reducing enteric gas emissions and improving milk parameters in dairy cattle. Twenty mid-lactation Holstein cows, blocked by parity and days in milk, were randomly assigned to a top dress treatment with Agolin or an un-supplemented control for a 56-day trial. Cows were group housed and individually fed twice daily. Enteric gas emissions, including methane, carbon dioxide, ammonia, and nitrous oxide, were sampled every 14 days for a 12 h period via head chambers connected to a mobile air quality laboratory. Cows supplemented with Agolin versus the control had less methane intensity (g/period/kg energy-corrected milk (ECM); p = 0.025). Ammonia was the most affected gas, with lower ammonia production (mg/period; p = 0.028), and ammonia intensity (mg/period/kg ECM; p = 0.011) in Agolin-fed versus control-fed cows. All cow performance variables, including dry matter intake, ECM, milk fat, milk protein, or feed efficiency were similar between treatments. Further research should evaluate how Agolin impacts ruminal flora, focusing on mechanistic impacts to fermentation.

Dairy cattle provide a major benefit to the world through upcycling human inedible feedstuffs into milk and associated dairy products. However, as beneficial as this process has become, it is not without potential negatives. Dairy cattle are a source of greenhouse gases through enteric and waste fermentation as well as excreting nitrogen emissions through their feces and urine. However, these negative impacts vary widely due to how and what these animals are fed. In addition, there are many promising opportunities for further reducing emissions through feed and waste additives. The present review aims to further expand on where the industry is today and the potential avenues for improvement. This area of research is still not complete and additional information is required to further improve our dairy systems impact on sustainable animal products.

The objective of the present study was to mitigate ammonia (NH3), greenhouse gases (GHGs), and other air pollutants from lactating dairy cattle waste using different freestall management techniques. For the present study, cows were housed in an environmental chamber from which waste was removed by either flushing or scraping at two different frequencies. The four treatments used were (1) flushing three times a day (F3), (2) flushing six times a day (F6), (3) scraping three times a day (S3), and (4) scraping six times a day (S6). Flushing freestall lanes to remove manure while cows are out of the barn during milking is an industry standard in California. Gas emissions were measured with a mobile agricultural air quality lab connected to the environmental chamber. Ammonia and hydrogen sulfide (H2S) emissions were decreased (p < 0.001 and p < 0.05) in the flushing vs. scraping treatments, respectively. Scraping increased NH3 emissions by 175 and 152% for S3 and S6, respectively vs. F3. Ethanol (EtOH) emissions were increased (p < 0.001) when the frequency of either scraping or flushing was increased from 3 to 6 times but were similar between scraping and flushing treatments. Methane emissions for the F3 vs. other treatments, were decreased (p < 0.001). Removal of dairy manure by scraping has the potential to increase gaseous emissions such as NH3 and GHGs.

Animal manure is a source of greenhouse gas (GHG) emissions and other pollutants and nuisances such as ammonia and odors. There are several technologies to reduce emissions on animal farms including manure additives; however, few have been proven effective and easy to apply to dairy lagoon systems. The present research aimed at testing the ability of the commercial additive “SOP LAGOON” to reduce emissions of GHGs (i.e., carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O)), as well as ammonia (NH3) and odors from lagoon stored liquid manure. Emissions of GHGs, NH3 and odors were measured in the laboratory from barrels filled with 65 L of manure treated with SOP LAGOON or left untreated as a control. Manure was collected from a commercial dairy that is located in Solano County, California. Emissions of GHGs and NH3 were continuously measured for one week using flux chambers placed on top of the barrels and connected to a mobile air emissions laboratory. The effects of the untreated control, versus the two respective treatment additive doses of 30.8 and 61.6 g/m3 of manure were compared to each other. The low dose was selected based on the manufacturer recommendation and the high dose was selected by doubling the low dose. Results showed that SOP LAGOON applied at the high dose (61.6 g of SOP LAGOON per m3 of manure) versus the control greatly reduced (p < 0.05) emissions of CO2, CH4, N2O and NH3 by 14.7%, 22.7%, 45.4% and 45.9%, respectively. Furthermore, the high dose of SOP LAGOON treated samples versus the control samples showed less odor intensity (p < 0.05). There was no significant effect of the low dose of SOP LAGOON on the emissions of different gases. The HIGH dose of SOP LAGOON might decrease the number of methanogens and hydrolytic microorganisms and their excreted enzymes during manure storage. Further studies are needed to investigate the mechanism of emission reduction using SOP LAGOON.

Feed additives have received increasing attention as a viable means to reduce enteric emissions from ruminants, which contribute to total anthropogenic methane (CH4) emissions. The aim of this study was to investigate the efficacy of the commercial feed additive SOP STAR COW (SOP) to reduce enteric emissions from dairy cows and to assess potential impacts on milk production. Twenty cows were blocked by parity and days in milk and randomly assigned to one of two treatment groups (n = 10): supplemented with 8 g/day SOP STAR COW, and an unsupplemented control group. Enteric emissions were measured in individual head chambers over a 12-h period, every 14 days for six weeks. SOP-treated cows over time showed a reduction in CH4 of 20.4% from day 14 to day 42 (p = 0.014), while protein % of the milk was increased (+4.9% from day 0 to day 14 (p = 0.036) and +6.5% from day 0 to day 42 (p = 0.002)). However, kg of milk protein remained similar within the SOP-treated cows over the trial period. The control and SOP-treated cows showed similar results for kg of milk fat and kg of milk protein produced per day. No differences in enteric emissions or milk parameters were detected between the control and SOP-treated cows on respective test days.