Phenotypic Dairy Cattle Trait Expressions in Dependency of Social-Ecological Characteristics along Rural–Urban Gradients

Clustering of countries based on dairy productivity characteristics of Holstein cattle for breeding material selection

Background and Aim

The aim of any breeding process is to create a herd based on certain parameters that reflect an ideal animal vision. Targeted herding involves selecting the source of breeding material to be imported from another country. Therefore, there is a problem in selecting a breeding material importer to rapidly form a uterine canopy with the required properties. The purpose of this study was to evaluate a set of predictive milk productivity traits in Holstein cattle across countries.

Materials and Methods

This research was based on records of 819,358 recorded animals from 28 countries born after January 1, 2018, from open databases. We used the Euclidean metric to construct dendrograms characterizing the similarity of countries according to the complex milk productivity traits of the daughters of bulls. The Ward method was used to minimize intracluster variance when forming clusters and constructing the corresponding diagrams. Principal component analysis was used to reduce dimensionality and eliminate the effect of multicollinearity. The principal components were selected using the Kaiser-Harris criteria.

Results

A ranking of multidimensional complex milk productivity traits in different countries over the past 5 years was performed. A group of leading countries led by the USA was established according to the studied indicators, and the possible reasons for such a division into groups were described.

Conclusion

The pressure of purposeful artificial selection prevails in comparison with the pressure of natural selection concerning milk productivity traits in a certain group of countries, which allows specialists to choose suppliers when buying breeding animals and materials. The findings are based solely on data from recorded animals, which may not represent the entire breed population within each country, especially in regions where record-keeping may be inconsistent. It is expected that further studies will include regional data from large enterprises not part of Interbull, with mandatory verification and validation. An important element of such work is seen as the ability to compare the milk productivity of populations from different countries using a different scale, as well as studying the differentiation of countries by other selection traits of dairy.

Unraveling the Genomic Association for Milk Production Traits and Signatures of Selection of Cattle in a Harsh Tropical Environment

A study was designed to identify the genomic regions associated with milk production traits in a dairy cattle population reared by smallholder farmers in the harsh and challenging tropical savanna climate of Bengaluru, India. This study is a first-of-its-kind attempt to identify the selection sweeps for the dairy cattle breeds reared in such an environment. Two hundred forty lactating dairy cows reared by 68 farmers across the rural-urban transiting regions of Bengaluru were selected for this study. A genome-wide association study (GWAS) was performed to identify candidate genes for test-day milk yield, solids-not-fat (SNF), milk lactose, milk density and clinical mastitis. Furthermore, the cross-population extended haplotype homozygosity (XP-EHH) methodology was adopted to scan the dairy cattle breeds (Holstein Friesian, Jersey and Crossbred) in Bengaluru. Two SNPs, rs109340659 and rs41571523, were observed to be significantly associated with test-day milk yield. No significant SNPs were observed for the remaining production traits. The GWAS for milk lactose revealed one SNP (rs41634101) that was very close to the threshold limit, though not significant. The potential candidate genes fibrosin-like 1 (FBRSL) and calcium voltage-gated channel auxiliary subunit gamma 3 (CACN) were identified to be in close proximity to the SNP identified for test-day milk yield. These genes were observed to be associated with milk production traits based on previous reports. Furthermore, the selection signature analysis revealed a number of regions under selection for the breed-group comparisons (Crossbred-HF, Crossbred-J and HF-J). Functional analysis of these annotated genes under selection indicated pathways and mechanisms involving ubiquitination, cell signaling and immune response. These findings point towards the probable selection of dairy cows in Bengaluru for thermotolerance.

Selective Sweeps in Cattle Genomes in Response to the Influence of Urbanization and Environmental Contamination

A genomic study was conducted to identify the effects of urbanization and environmental contaminants with heavy metals on selection footprints in dairy cattle populations reared in the megacity of Bengaluru, South India. Dairy cattle reared along the rural-urban interface of Bengaluru with/without access to roughage from public lakeshores were selected. The genotyped animals were subjected to the cross-population-extended haplotype homozygosity (XP-EHH) methodology to infer selection sweeps caused by urbanization (rural, mixed, and urban) and environmental contamination with cadmium and lead. We postulated that social-ecological challenges contribute to mechanisms of natural selection. A number of selection sweeps were identified when comparing the genomes of cattle located in rural, mixed, or urban regions. The largest effects were identified on BTA21, displaying pronounced peaks for selection sweeps for all three urbanization levels (urban_vs_rural, urban_vs_mixed and rural_vs_mixed). Selection sweeps are located in chromosomal segments in close proximity to the genes lrand rab interactor 3 (RIN3), solute carrier family 24 member 4 (SLC24A4), tetraspanin 3 (TSPAN3), and proline-serine-threonine phosphatase interacting protein 1 (PSTPIP1). Functional enrichment analyses of the selection sweeps for all three comparisons revealed a number of gene ontology (GO) and KEGG terms, which were associated with reproduction, metabolism, and cell signaling-related functional mechanisms. Likewise, a number of the chromosomal segments under selection were observed when creating cattle groups according to cadmium and lead contaminations. Stronger and more intense positive selection sweeps were observed for the cadmium contaminated group, i.e., signals of selection on BTA 16 and BTA19 in close proximity to genes regulating the somatotropic axis (growth factor receptor bound protein 2 (GRB2) and cell ion exchange (chloride voltage-gated channel 6 (CLCN6)). A few novel, so far uncharacterized genes, mostly with effects on immune physiology, were identified. The lead contaminated group revealed sweeps which were annotated with genes involved in carcass traits (TNNC2, SLC12A5, and GABRA4), milk yield (HTR1D, SLCO3A1, TEK, and OPCML), reproduction (GABRA4), hypoxia/stress response (OPRD1 and KDR), cell adhesion (PCDHGC3), inflammatory response (ADORA2A), and immune defense mechanism (ALCAM). Thus, the findings from this study provide a deeper insight into the genomic regions under selection under the effects of urbanization and environmental contamination.

Urbanisation threats to dairy cattle health: Insights from Greater Bengaluru, India

Complex urbanisation dynamics, on the one hand, create a high demand for animal products, and on the other hand put enormous pressure on arable land with negative consequences for animal feed production. To explore the impact of accelerated urbanisation on dairy cattle health in urban farming systems, 151 farmers from different parts of the Greater Bengaluru metropolitan area in India were individually interviewed on aspects addressing cattle management and cattle health. In addition, 97 samples of forages from the shores of 10 different lakes, and vegetable leftovers used in cattle feeding were collected for nutritional analysis. Along with the use of cultivated forages, crop residues, and concentrate feed, 47% and 77% of the farmers occasionally or frequently used lake fodder and food leftovers, respectively. Nutritionally, lake fodder corresponded to high-quality pasture vegetation, but 43% of the samples contained toxic heavy metals such as arsenic, cadmium, chromium, and lead above official critical threshold levels. Therefore, lake fodder may affect cows' health if consumed regularly; however, heavy metal concentrations varied between lakes (P < 0.05), but not between fodder types (P > 0.05). Although 60% of the interviewed farmers believed that their cows were in good health, logit model applications revealed that insufficient drinking water supply and the use of lake fodder negatively impacted cattle health (P < 0.05). While it remains unknown if regular feeding of lake fodder results in heavy metal accumulation in animal products, farmers and farm advisors must address this and other urbanization-related challenges to protect cattle health.

Rurbanity: a concept for the interdisciplinary study of rural-urban transformation

Along with climate change, population growth, and overexploitation of natural resources, urbanisation is among the major global challenges of our time. It is a nexus where many of the world's grand challenges intersect, and thus key to sustainable development. The widespread understanding of urbanisation as a successive and unidirectional transformation of landscapes and societies from a rural to an urban state is increasingly questioned. Examples from around the globe show that 'the rural' and 'the urban' are not only highly interdependent, but actually coexist and often merge in the same space or livelihood strategy. Our concept of rurbanity provides an integrated theoretical framework which overcomes the rural-urban divide and can be operationalised for empirical research. Rurbanity is the next stringent step following the gradual widening of previous concepts from urban-centred approaches through the emphasis on urban peripheries to attempts of abolishing any distinction of a rural environment and acknowledging the highly dynamic nature of globalising urbanisation. Building on complex systems theory and assemblage thinking, our concept explores complementary aspects of the distinct epistemic worldviews dominating the natural and social sciences. Within this theoretical frame, we derive four analytical dimensions as entry points for empirical research: Endowments and Place, Flows and Connectivity, Institutions and Behaviour, and Lifestyles and Livelihoods. Two examples illustrate how these dimensions apply, interact, and together lead to a comprehensive, insightful understanding of rurban phenomena. Such understanding can be an effective starting point for assessing potential contributions of rurbanity to long-term global sustainability.

Effects of Heat Stress across the Rural-Urban Interface on Phenotypic Trait Expressions of Dairy Cattle in a Tropical Savanna Region

Among all livestock systems in tropical regions, the dairy sector is facing huge challenges to sustain productivity under the rapidly changing climatic conditions. To date, there is a lack of knowledge on the combined effects of climate, season, and farm location on trait responses in different cattle breeds. Consequently, this study presents a novel approach to assess the impact of several climatic and geographical factors on production traits, energy efficiency indicators, and hygiene traits in dairy cattle reared across the rural–urban interface in the tropical savanna region of Bengaluru, a rising megacity in southern India. In total, 96 cattle were selected across Bengaluru’s rural–urban interface, reflecting a broad variety of social-ecological systems. The traits considered included test day milk yield (MY), body condition score (BCS), body weight (BW), hock assessment score (HAS), udder hygiene score (UHS), and upper leg hygiene score (ULHS). Apart from cow-related factors such as breed, lactation stage, lactation number, and milking frequency, the environmental classification variables of season, farm location (as expressed by survey stratification index, SSI), and temperature humidity index (THI) significantly affected most of the traits, with indication for breed-by-environment interactions. In particular, season significantly influenced production and hygiene traits. Furthermore, an evident breed variation was observed in the seasonal influence on BW, wherein exotic cows had a higher BW than crossbreds during the summer season. The distinct trend of SSI in its influence on most of the traits indicates that cows housed in urban areas had better trait expression than those in rural areas, thereby revealing a predominant role of management. The THI had a significant effect on MY, BCS, and HAS, and THI = 75 was identified as heat stress threshold. The results indicate the importance of considering ecological, social, and climatic factors simultaneously in order to improve primary and functional breed-specific traits of dairy cattle reared in challenging environments.

Impacts of COVID-19 on Small-Scale Dairy Enterprises in an Indian Megacity—Insights from Greater Bengaluru

Natural calamities and pandemics massively affect small-scale entrepreneurs. In this paper, we aim to assess how the COVID-19 pandemic affected small dairy farms in the megacity of Bengaluru, India, where they supply a high share of the milk demand. In 2020 a total of 129 farms were visited before the first lockdown (January to March) and interviewed again after the lockdown had been loosened (August to September). Questions addressed feed supply to dairy cows, milk yield and marketing, and coping strategies for lockdown impacts. Results showed that the share of farmers not feeding concentrates increased from 1% before lockdown to 7% afterward (p < 0.05), and those not offering dry forages increased from 20% to 33% (p < 0.05) due to increasing forage prices. Milk yield dropped in all surveyed farms from 3905 L before to 2861 L after lockdown (p < 0.05) due to the sale of 30% of lactating cows across the farms. Enabling farmers to better cope with shocks through feed storage and by processing their surplus milk into durable products should be prioritised by supporting institutions such as dairy cooperatives. Alternatively, insurance schemes can capacitate farmers to maintain a fresh milk supply to urban consumers in the wake of global challenges.

Gastrointestinal nematode and Eimeria spp. infections in dairy cattle along a rural-urban gradient

Endoparasite infections can lead to considerable economic losses in dairy cattle due to decreases in milk yield and quality. Environmental and host-related factors contribute to endoparasite infection intensity and probability. Moreover, advancing urbanization influences parasite infection dynamics in livestock due to close human-animal cohabitation and changes in animal housing conditions. The aim of the present study was to investigate social-ecological effects on gastrointestinal nematode (GIN) and Eimeria spp. infections in dairy cattle along a rural-urban gradient in the emerging Indian megacity Bangalore. In this regard, 726 faecal samples from 441 dairy cattle of different ages and physiological stages were collected from 101 farms and examined at three visits between June 2017 and April 2018. Based on a survey stratification index (SSI) comprising built-up density and distance to the city center, we assigned the farms to urban, mixed and rural areas. GIN eggs were identified in the faeces of 243 cattle (33.5%; 95% confidence interval [CI]: 30.1-36.9%), and Eimeria spp. oocysts in the faeces of 151 cattle (20.8%; 95% CI: 17.9-23.7%). Co-infection rates of GIN and Eimeria spp. were 8.5 to 12.2% higher in rural compared to urban and mixed areas. The SSI effect significantly influenced Eimeria spp. infection probability and oocyst per gram of faeces (OpG; P < 0.001) with an infection probability and OpG higher than 26% and 40% for cattle kept in rural areas compared to cattle from urban areas. However, the SSI effect was not significant for the infection probability of GIN and for GIN eggs per gram of faeces (EpG). Infection probabilities and EpG/OpG were significantly higher in calves and heifers compared to lactating and dry cows. Moreover, we estimated significantly lower OpG values in summer compared to the other seasons. No differences were estimated for GIN and Eimeria spp. infection probabilities and EpG/OpG with regard to pasture access and breed. The variations in endoparasite infection intensity and probability observed along the rural-urban gradient of Bangalore reflect the variability in dairy husbandry systems governed by the social-ecological context.

Dairy production in an urbanizing environment-Typology and linkages in the megacity of Bengaluru, India

Urbanization is a main driver of agricultural transition in the Global South but how it shapes trends of intensification or extensification is not yet well understood. The Indian megacity of Bengaluru combines rapid urbanization with a high demand for dairy products, which is partly supplied by urban and peri-urban dairy producers. To study the impacts of urbanization on dairy production and to identify key features of dairy production systems across Bengaluru's rural-urban interface, 337 dairy producers were surveyed on the socio-economic profile of their household, their dairy herd and management, resources availability and, in- and output markets. A two-step cluster analysis identified four spatially explicit dairy production systems based on urbanization level of their neighborhood, reliance on self-cultivated forages, pasture use, cattle in- and outflow and share of specialized dairy genotypes. The most extensive dairy production system, common to the whole rural-urban interface, utilized publicly available feed resources and pasture grounds rather than to cultivate forages. In rural areas, two semi-intensive and one intensive dairy production systems relying on self-cultivation of forage with or without pasture further distinguished themselves by their herd and breeding management. In rural areas, the village's dairy cooperative, which also provided access to inputs such as exotic genotype through artificial insemination, concentrate feeds and health care, was often the only marketing channel available to dairy producers, irrespective of the dairy production system to which they belonged. In urban areas, milk was mostly sold through direct marketing or a middleman. Despite rapidly progressing urbanization and a population of 10 million, Bengaluru's dairy sector still relies on small-scale family dairy farms. Shifts in resources availability, such as land and labor, are potential drivers of market-oriented intensification but also extensification of dairy production in an urbanizing environment.