Performing Department
(N/A)
Non Technical Summary
Organic production systems provide natural environments that confer animal wellbeing advantages. However, antimicrobial and pesticide restrictions coupled with grazing requirements create challenges related to both internal and external parasites, some of which are also a zoonotic risk. We will collect fecal samples to determine internal parasites and record horn flies and other external parasites on approximately 3,225 organic dairy animals from multiple breeds. This data will facilitate estimation of losses due to compromised animal health, particularly for calves, and subclinical reductions in milk yield. All animals will be genotyped so that we can conduct genomic analyses and identify regions of the genome associated with parasite susceptibility. A citizen science mobile app will also be developed to allow public contribution of parasite data. We will deliver information about parasite control through a wide variety of outreach events and a web platform that will include herd-specific economic selection indexes. This effort directly addresses OREI priorities related to selection of animal breeds and genotypes adapted to organic systems and demonstration of educational tools for Cooperative Extension personnel and other professionals who advise producers on organic practices. The long-term goal of this project is to reduce economic losses from parasites and through development of genomic selection and crossbreeding programs designed specifically for organic production.
Animal Health Component
80%
Research Effort Categories
Basic
20%
Applied
80%
Developmental
0%
Goals / Objectives
The long-term goal of this project is to enhance the sustainability of organic dairy production by reducing economic losses from parasites and through development of genomic selection and crossbreeding programs designed specifically for organic production. Our supporting outreach objectives will facilitate adoption of genetics tailored organic production by engaging producers in the collection of data and development of selection indexes unique to their management system.The objectives of our project are to1. Quantify the effects endoparasite and ectoparasite load at different life stages on current and future performance.2. Determine breed, crossbreeding, and within-breed genetic effects influence parasite load.3. Develop and deliver project outreach activities to advance knowledge enhancing parasite resistance in organic dairy cattle.4. Engaging producers through an innovative and comprehensive web and mobile app-based outreach program.
Project Methods
Fecal sampling populationWe aim to collect 5,250 fecal samples during the late summer as parasite exposure is expected to increase over the course of the grazing season. Our sampling plan attempts to balance determining the repeatability of endoparasite levels across grazing seasons and life stage (calf, heifer, cow) with a sufficient sample size for genomic analysis by resampling a portion of animals from the previous year plus new cows. Calves sampled in year 1 will be sampled as heifers in year 2 and as cows in year 3. Calves and heifers that are culled or heifers that have not calved will be replaced with a cohort of the same age in subsequent years. We will aim to sample 500 new lactating cows each year with the remainder representing cows sampled the previous year. If all initially enrolled calves and heifers from year 1 are available in years 2 and 3, we would genotype 3,000 unique animals. However, we estimate that 85% of calves and heifers in years 1 and 2 will be available for sampling the subsequent year resulting in a total of approximately 3,225 unique animals.Ectoparasite evaluation Experimental herds. Herds enrolled in the fecal sampling trial will also be included in evaluation of ectoparasite infestation level using the methods for fly scoring described in the background and preliminary data. Cows and heifers will be visually scored on a scale of 0 (no flies) to 4 (heavy infestation) with pictures taken on a case (moderate to heavy infestation), control (few or no flies) basis. Flies on the side of the cow (primarily horn flies) and face flies will be evaluated separately.Animals will also be observed at least twice annually for other external parasites, including ticks, lice, mange, and ringworm. Animals will be evaluated during fly scoring while on pasture and in winter when many external parasites are more prevalent. Genotyping for other parasites will be conducted on a case, control basis and we estimated 100 case-control pairs for budgeting purposes.Public data contribution. We will develop an application for a citizen science approach where producers can submit pictures of cows with high and low levels of fly infestation. This data will be pooled with the experimental data collected to facilitate expanded genetic evaluations and is detailed more fully in our outreach plan below.Field trial. A field trial will be conducted during the third and fourth year of the trial at WCROC to demonstrate the effects of selection for horn fly infestation level on fly distribution levels. Genomic PTA for horn fly infestation (described below in genomic analysis section) and breed differences will be used to generate groups of 25 heifers each. One group will include 20 high and 5 low susceptibility heifers, whereas the second group will have the reverse (20 low and 5 high susceptibility). With this design, we aim to address the extent to which the average number of flies per heifer is different between groups versus how numbers of flies are distributed between high and low susceptibility animals within the group. This will help demonstrate the extent to which genetic and breed selection can be used to manage fly infestation levels.Growth and performanceGrowth. Calves enrolled in the study in year 1 will be weighed at birth and then monthly for 3 months after birth. Blood samples will be collected at 48 to 72 hours after birth to determine serum total protein levels using a Brix refractometer. The animals will be weighed again in year 2 (approximately 1 year of age) and year 3 (during first lactation). Heifers will be weighed upon enrollment in the trial during year 1 again in first lactation in year 2.Performance. Herds will be selected that are enrolled in a DHI testing program to determine milk yield, fat and protein yield and concentration, somatic cell count, fertility, and culling. Additionally, we will determine digestive efficiency on a case control basis. Fecal neutral detergent fiber (NDF) and indigestible NDF (iNDF) will be determined as described in our previous work for 50 lactating cows with a high endoparasite load to determine potentially degradable NDF (pdNDF). These will be matched to 50 control cows based on herd, age, breed, and stage of lactation. We will use the same sample for pdNDF determination as used to determine parasite levels. Fecal and feed NDF and iNDF can be used to derive total tract dry matter digestibility and NDF digestibility. However, diet NDF and iNDF are constants in digestibility formulas assuming cows are fed the same diet and the nutrient intake of cows while on pasture can be uncertain depending on fluctuations in pasture quality and intake of pasture. Therefore, pdNDF will be our measure of digestibility for simplicity.Fecal collection. Samples will be collected by inserting a gloved hand in the rectum of cows and heifers and extracting a handful of feces to avoid environmental contamination. For sample collection from calves, we will manually stimulate defecation into a sterile container by inserting a gloved finger into the anus because hand insertion is not feasible due to the size of the rectum.Endoparasite quantification. Parasitic eggs will be separated from feces using the Wisconsin sugar float method. Using our previous procedures, we will microscopically determine fecal egg counts of protozoal oocysts and helminth nematodes, cestodes, and trematodes to the family or genus level. Subsequently, qPCR will determine the relative differences among genus and species for 500 case-control pairs. We elect to use a case-control approach to provide a manageable workload while validating microscopic fecal egg counts. A two-trait analysis with visual and qPCR scores will be conducted as we have previously described for visual and counts of fly levels.We will release nuclear material from the oocytes using a freeze-thaw method to facilitate DNA extraction with ethanol precipitation. The primary GIN genera we will quantify via qPCR include Cooperia, Haemonchus, Trichostrongylus, Nematodirus, Ostertagia and Strongyloides. We will use a multi-plex qPCR approach with primers designed to amplify unique ITS2 rDNA sequences. qPCR will also be used to quantify Cryptosporidium spp. with particular focus on Cryptosporidium parvum and Eimeria sp). The qPCR procedure can only be used to determine the relative proportions of each species as opposed to absolute proportions because there is no internal independent standard reference gene. Relative abundance will then be multiplied by the total fecal egg count to derive quantities of individual parasites.Genotyping: Hair samples will be collected from all animals to facilitate genotyping. Samples will be genotyped for ~42K SNPs at a commercial lab and forwarded to the Council on Dairy Cattle breeding for imputation to the ~79K genotypes used in national genomic analyses and to receive genomic PTA (gPTA) for traits included in the national genetic evaluation system (yield, fertility, survival, type traits, RFI, etc.); imputation will be done with high accuracy since we are working with AI sired cows. By partnering with some farms with whom we have already worked and collected data, we will be able to leverage previously collected family genotypes to expand the accuracy of genomic evaluations for the current study; many of the cows that were previously genotyped will be dams of those cows that will be sampled in the current study (estimated to be ~400).