GOOD: Genetically optimized organic dairy

Dairy cows grazing

Jiang and Maquivar look for genetic reasons why some dairy cows are resistant to diseases

Faculty members Zhihua Jiang and Martin Maquivar have joined forces to address a key issue facing certified organic dairy farmers – how to decrease the prevalence of uterine diseases in organically managed dairy cows to improve fertility and productivity without hormones or antibiotics. The USDA/AFRI Organic Agriculture Research & Extension Initiative recently awarded them $1.5 million for their grant proposal entitled “Genomically optimized organic dairy (GOOD): genome selection against uterine diseases to improve fertility and longevity in cattle.” Dr. Jiang will blend his expertise in genetics and genomics with Dr. Maquivar’s knowledge of animal reproduction and they will engage an advisory panel of scientists, industry partners, and organic dairy producers to investigate underlying reasons for uterine diseases and determine methods that may ultimately lead to the identification of cows that are genetically resistant to metritis and endometritis, for example.

This research is important because the demand for organic dairy products in the United States continues to grow. Retail sales of fluid organic milk in 2021 were more than 2.9 billion pounds, which is a 12.7% increase from 2016 according to the U.S. Department of Agriculture Agricultural Marketing Service. In 2021, sales of organic milk exceeded $1.6 billion. Organic dairy producers are under increasing pressure to keep their cows productive and infection and disease-free.

The U.S. Department of Agriculture organic regulations (7 CFR §205) have detailed requirements for certified organic dairies regarding pasture management, feed sources, cow origin, healthcare practices, and housing conditions. Because of these regulations, organic dairy producers must overcome obstacles not necessarily encountered by their conventional counterparts. More specifically, conception rates may be impaired because artificial hormones cannot be used on organic dairies, eliminating conventional reproductive husbandry practices such as estrus or ovulation synchronization protocols. Furthermore, except in extreme cases where a cow is suffering or at risk of dying, antibiotics cannot be used to treat illness, infection, or disease.

The period from late pregnancy through early lactation is a challenging time for a cow and many factors influence milk production, health, and reproductive performance. The cow’s reproductive tract may be damaged during calving and bacteria may contaminate the uterine lumen, leading to infection and uterine disease. The risk of uterine infections is also greater if the placenta is not expelled within the first six hours after birth. Furthermore, energy requirements for late-term fetal growth and lactation are huge and confounded by the fact that cows eat less during this period. Therefore, most dairy cows enter a state of negative energy balance (NEB) in which body fat stores are mobilized to attempt to meet the high energy demands for maintenance and milk production. Alterations in a cow’s metabolic status during NEB delays uterine involution and ovulation, both of which negatively affect subsequent conception. Negative energy balance also adversely affects the cow’s immune system and makes the cow more susceptible to postpartum uterine infections such as metritis and endometritis, both of which have detrimental effects on fertility.

Metritis and clinical and subclinical endometritis are post-partum uterine diseases of lactating dairy cows commonly seen in the first seven weeks after calving that negatively affect fertility and milk yield, causing substantial economic losses on dairy farms. Persistent inflammation of the endometrial lining of the uterus causes endometritis. Clinical endometritis is characterized by purulent (pus) or mucopurulent (mucous and pus) vaginal discharge. In contrast, cows with subclinical endometritis are often not identified and treated because there are no clinical signs of the condition; however, cytological samples of the endometrium of these cows exhibit elevated numbers of polymorphonuclear neutrophils. These innate immune cells provide the first line of defense against infection and are a classical sign of inflammation.

Conventional dairy management tools to combat uterine diseases include antibiotic therapies and hormone treatments, both of which are banned on certified organic dairies. Therefore, organic dairies have implemented alternative strategies, such as an intrauterine infusion of a 50% dextrose solution, to treat clinical endometritis with varied levels of success.

In a preliminary study, Jiang and Maquivar collected endometrial samples at 7 and 21 days after calving from a small number of certified organic dairy cows with and without endometritis. They used cutting-edge technologies to profile RNA variants in the cells. They specifically focused on a mechanism known as alternative polyade-nylation or APA, which has recently gained attention as a major player in gene regulation. Polyadenylation is a biological process that occurs in a series of steps. An immature RNA is first cleaved at a specific location called a poly(A) site and then a poly(A) tail, or a long chain of adenine nucleotides, is added to produce a mature RNA. The mature RNA is ultimately encoded into a protein that contributes to traits such as disease resistance and milk production in animals. Many genes contain multiple poly(A) sites, which produce RNA variants when they use APA. Conditions such as growth or infection often alter the use of the poly(A) sites. The altered transcript or RNA variant often affects its stability in cells so that it changes the coding region of a gene, leading to production of a functionally different protein. What triggers the use of alternate poly(A) sites remains largely unknown at this time, but alterations in polyadenylation have been associated with cancer and endocrine, metabolic, and immunological diseases in humans.

Jiang and Maquivar discovered that cow’s endometrial cells also use APA in response to uterine disease. In fact, 65% of protein coding genes in the cow’s endometrial cells had two or more poly(A) sites. Many of the genes in endometrial cells of healthy cows that used APA were related to cilium organization. Cilia are microscopic hair-like projections found in large numbers on the surface of cells that produce a beating motion that propels contaminants from organs or tissues by moving fluid over the cells. It is possible that the healthy cows did not develop endometritis because the poly(A) sites triggered formation of cilia that were more effective at moving bacteria out of the uterus than their infected counterparts. Conversely, cells from cows with endometritis used APA in genes related to small proteins called cytokines that control the growth and function of cells integral to the immune system. Dysregulation of APA in these genes may be linked to development of endometritis in dairy cows.

Results from Jiang’s and Maquivar’s preliminary study are promising but do not provide convincing evidence because only a few cows were screened. Funds granted from the USDA/AFRI Organic Agriculture Research & Extension Initiative are earmarked to collect samples from 1000 certified organic dairy cows at 7 and 21 days postpartum, critical time points for diagnosis of uterine diseases. They hope to decipher the complex interactions between genes and environment and link DNA to RNA to infertility triggered by reproductive diseases in dairy cows. They will accomplish this goal by detecting DNA variants from cows that are resistant or susceptible to metritis or endometritis, profiling APA in RNA and use that information to identify signaling pathways that are related to uterine disease severity, and detecting important biomarkers that can be used to select endometritis-resistant cows and develop alternative non-antibiotic treatment protocols to optimize reproductive health in dairy cows.