Genome-wide association and expression quantitative trait loci in cattle reveals common genes regulating mammalian fertility

Most genetic variants associated with fertility in mammals fall in non-coding regions of the genome and it is unclear how these variants affect fertility. Here we use genome-wide association summary statistics for Heifer puberty (pubertal or not at 600 days) from 27,707 Bos indicus, Bos taurus and crossbred cattle; multi-trait GWAS signals from 2119 indicine cattle for four fertility traits, including days to calving, age at first calving, pregnancy status, and foetus age in weeks (assessed by rectal palpation of the foetus); and expression quantitative trait locus for whole blood from 489 indicine cattle, to identify 87 putatively functional genes affecting cattle fertility. Our analysis reveals a significant overlap between the set of cattle and previously reported human fertility-related genes, impling the existence of a shared pool of genes that regulate fertility in mammals. These findings are crucial for developing approaches to improve fertility in cattle and potentially other mammals.

High frequency of delayed milk delivery to neonates in tropical beef herds

Beef-calf mortality rates across tropical and subtropical Australia are high, with sub-optimal nutrition in pregnant cows being the primary risk. The nutritional deficiencies associated with calf mortality are the same as those associated with reduced milk yields. Although the highest mortality risk occurs during neonatal life, the role of inadequate milk delivery to beef neonates is not well established. This study investigated the frequency of low milk delivery in tropically adapted neonatal calves and the time for their dams to initiate full lactation in five management groups of Brahman and Droughtmaster calving cows in the dry tropics of northern Queensland, Australia. Change in calf weight in the days following birth was the primary measure of milk uptake. Plasma globulin concentration was used to indicate colostrum uptake. Across management groups, data were available on 250 calves for regression analysis of average daily gain vs. globulin and on 78 for plotting calf growth profiles. Calves had one of two growth profiles, either with immediate high growth from birth (day one) or with high growth delayed until day three. The frequency of delayed growth calves (with inadequate milk intake to gain at least 0.5 kg by day three after birth) was on average 30% across management groups, with management groups ranging 25%-50%. The frequency of calves growing ≤0.2 kg/day to day three was 15%-37%, depending on management group. The frequency of calves growing ≤0.2 kg/day to day five was 7%-20%, depending on management group. Calf globulin explained only 25% of the variation in calf average daily gain. Our study shows that a third of tropically adapted calves may experience a three-day delay to initiation of full lactation by their dams. Although study conditions were relatively benign, any additional risks with milk delivery, such as those that occur widely in tropical and subtropical northern Australia, would place such calves at risk of dehydration and mortality. Calf plasma globulin should not be used as a standalone measure of adequacy of neonatal milk delivery, especially when comparing across herds. This study demonstrates a fundamental problem of high frequency in northern Australia. The underlying risks for delayed milk delivery should be considered in the quest for practical solutions to reduce tropically adapted beef-calf mortalities.

Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes

Cattle enterprises are one of the major livestock production systems globally and are forecasted to have stable growth in the next decade. To facilitate sustainable live weight production, optimal reproductive performance is essential. Microbial colonisation in the reproductive tract has been demonstrated as one of the factors contributing to bovine reproductive performance. Studies also implied that reproductive metagenomes are different at each stage of the estrous cycle. This study applied Oxford Nanopore Technologies’ adaptive long-read sequencing to profile the bovine reproductive microbiome collected from tropical cattle in northern Queensland, Australia. The microbiome samples were collected from cattle of different sexes, reproductive status and locations to provide a comprehensive view of the bovine reproductive microbiome in northern Australian cattle. Ascomycota, Firmicutes and Proteobacteria were abundant phyla identified in the bovine reproductive metagenomes of Australian cattle regardless of sexes, reproductive status and location. The species level taxonomical investigation suggested that gastrointestinal metagenome and the surrounding environment were potentially the origins of the bovine reproductive metagenome. Functional profiles further affirmed this implication, revealing that the reproductive metagenomes of the prepubertal and postpartum animals were dominated by microorganisms that catabolise dietary polysaccharides as an energy substrate while that of the pregnant animals had the function of harvesting energy from aromatic compounds. Bovine reproductive metagenome investigations can be employed to trace the origins of abnormal metagenomes, which is beneficial for disease prevention and control. Additionally, our results demonstrated different reproductive metagenome diversities between cattle from two different locations. The variation in diversity within one location can serve as the indicator of abnormal reproductive metagenome, but between locations inferences cannot be made. We suggest establishing localised metagenomic indices that can be used to infer abnormal reproductive metagenomes which contribute to abortion or sub-fertility.

Genetics and nutrition impacts on herd productivity in the Northern Australian beef cattle production cycle

Genetics and nutrition drive herd productivity due to significant impacts on all components of the beef cattle production cycle. In northern Australia, the beef production system is largely extensive and relies heavily on tropical cattle grazing low quality, phosphorus-deficient pastures with seasonal variations in nutritive value. The existing feedlots are predominantly grain-based; providing high-energy rations, faster turn-off and finishing of backgrounded cattle to meet market specifications. This review focusses on the beef cattle production cycle components of maternal nutrition, foetal development, bull fertility, post-natal to weaning, backgrounding, feedlotting, rumen microbes and carcass quality as influenced by genetics and nutrition. This student-driven review identified the following knowledge gaps in the published literature on northern Australian beef cattle production cycle: 1. Long-term benefits and effects of maternal supplementation to alter foetal enzymes on the performance and productivity of beef cattle; 2. Exogenous fibrolytic enzymes to increase nutrient availability from the cell wall and better utilisation of fibrous and phosphorus deficient pasture feedbase during backgrounding; 3. Supplementation with novel encapsulated calcium butyrate and probiotics to stimulate the early development of rumen papillae and enhance early weaning of calves; 4. The use of single nucleotide polymorphisms as genetic markers for the early selection of tropical beef cattle for carcass and meat eating quality traits prior to feedlotting; The review concludes by recommending future research in whole genome sequencing to target specific genes associated with meat quality characteristics in order to explore the development of breeds with superior genes more suited to the North Australian beef industry. Further research into diverse nutritional strategies of phosphorus supplementation and fortifying tropically adapted grasses with protein-rich legumes and forages for backgrounding and supplementing lot-fed beef cattle with omega-3 oil of plant origin will ensure sustainable production of beef with a healthy composition, tenderness, taste and eating quality.