Body weight (BW) at different ages are of increasing importance in dairy cattle breeding schemes, because of their strong correlation with energy efficiency traits, and their impact on cow health, longevity and farm economy. In total, 15,921 dairy cattle from 56 large-scale test-herds with BW records were genotyped for 45,613 single nucleotide polymorphisms (SNPs). This dataset was used for genome-wide association studies (GWAS), in order to localize potential candidate genes for direct and maternal genetic effects on BW recorded at birth (BW0), at 2 to 3 months of age (BW23), and at 13 to 14 months of age (BW1314). The first 20 principal components (PC) of the genomic relationship matrix ( $${\mathbf{G}}$$ ) grouped the genotyped cattle into three clusters. In the statistical models used for GWAS, correction for population structure was done by including polygenic effects with various genetic similarity matrices, such as the pedigree-based relationship matrix ( $${\mathbf{A}}$$ ), the $${\mathbf{G}}$$ -matrix, the reduced $${\mathbf{G}}$$ -matrix LOCO (i.e. exclusion of the chromosome on which the candidate SNP is located), and LOCO plus chromosome-wide PC. Inflation factors for direct genetic effects using $${\mathbf{A}}$$ and LOCO were larger than 1.17. For $${\mathbf{G}}$$ and LOCO plus chromosome-wide PC, inflation factors were very close to 1.0. According to Bonferroni correction, ten, two and seven significant SNPs were detected for the direct genetic effect on BW0, BW23, and BW1314, respectively. Seventy-six candidate genes contributed to direct genetic effects on BW with four involved in growth and developmental processes: FGF6, FGF23, TNNT3, and OMD. For maternal genetic effects on BW0, only three significant SNPs (according to Bonferroni correction), and four potential candidate genes, were identified. The most significant SNP on chromosome 19 explained only 0.14% of the maternal de-regressed proof variance for BW0. For correction of population structure in GWAS, we suggest a statistical model that considers LOCO plus chromosome-wide PC. Regarding direct genetic effects, several SNPs had a significant effect on BW at different ages, and only two SNPs on chromosome 5 had a significant effect on all three BW traits. Thus, different potential candidate genes regulate BW at different ages. Maternal genetic effects followed an infinitesimal model.

Contents of milk fatty acids (FA) display remarkable alterations along climatic gradients. Detecting candidate genes underlying such alterations might be beneficial for the exploration of climate sensitivity in dairy cattle. Consequently, we aimed on the definition of FA heat stress indicators, considering FA breeding values in response to temperature-humidity index (THI) alterations. Indicators were used in GWAS, in ongoing gene annotations and for the estimation of chromosome-wide variance components. The phenotypic data set consisted of 39,600 test-day milk FA records from 5,757 first-lactation Holstein dairy cows kept in 16 large-scale German cooperator herds. The FA traits were C18:0, polyunsaturated fatty acids (PUFA), saturated fatty acids (SFA), and unsaturated fatty acids (UFA). After genotype quality control, 40,523 SNP markers from 3,266 cows and 930 sires were considered. Meteorological data from the weather station in closest herd distance were used for the calculation of maximum hourly daily THI, which were allocated to 10 different THI classes. The same FA from 3 stages of lactation were considered as different, but genetically correlated traits. Consequently, a 3-trait reaction norm model was used to estimate genetic parameters and breeding values for FA along THI classes, considering either pedigree (A) or genomic (G) relationship matrices. De-regressed proofs and genomic estimated breeding values at the intermediate THI class 5 and at the extreme THI class 10 were used as pseudophenotypes in ongoing genomic analyses for thermoneutral (TNC) and heat stress conditions (HSC), respectively. The differences in de-regressed proofs and in genomic estimated breeding values from both THI classes were pseudophenotypes for heat stress response (HSR). Genetic correlations between the same FA under TNC and HSC were smallest in the first lactation stage and ranged from 0.20 for PUFA to 0.87 for SFA when modeling with the A matrix, and from 0.35 for UFA to 0.86 for SFA when modeling with the G matrix. In the first lactation stage, larger additive genetic variances under HSC compared with TNC indicate climate sensitivity for C18:0, PUFA, and UFA. Climate sensitivity was also reflected by pronounced chromosome-wide genetic variances for HSR of PUFA and UFA in the first stage of lactation. For all FA under TNC, HSC, and HSR, quite large genetic variance proportions were explained by BTA14. In GWAS, 30 SNP (within or close to 38 potential candidate genes) overlapped for HSR of the different FA. One unique potential candidate gene (AMFR) was detected for HSR of PUFA, 15 for HSR of SFA (ADGRB1, DENND3, DUSP16, EFR3A, EMP1, ENSBTAG00000003838, EPS8, MGP, PIK3C2G, STYK1, TMEM71, GSG1, SMARCE1, CCDC57, and FASN) and 3 for HSR of UFA (ENSBTAG00000048091, PAEP, and EPPK1). The identified unique genes play key roles in milk FA synthesis and are associated with disease resistance in dairy cattle. The results suggest consideration of FA in combination with climatic responses when inferring genetic mechanisms of heat stress in dairy cows.

A comprehensive study was conducted to assess the effects of seasonal transition and temperature humidity index (THI) on the adaptive responses in crossbred dairy cows reared in a tropical savanna region. A total of 40 lactating dairy cattle reared by small-scale dairy farmers in Bengaluru, India, were selected for this study. The research period comprised the transitioning season of summer to monsoon, wherein all traits were recorded at two points, one representing late summer (June) and the other early monsoon (July). A set of extensive variables representing physiological responses (pulse rate, respiration rate, rectal temperature, skin surface temperature), hematological responses (hematological profile), production (test day milk yield, milk composition) and molecular patterns (PBMC mRNA relative expression of selective stress response genes) were assessed. A significant effect of seasonal transition was identified on respiration rate (RR), skin surface temperature, mean platelet volume (MPV), platelet distribution width (PDWc), test day milk yield and on milk composition variables (milk density, lactose, solids-not-fat (SNF) and salts). The THI had a significant effect on RR, skin surface temperature, platelet count (PLT), plateletcrit (PCT) and PDWc. Lastly, THI and/or seasonal transition significantly affected the relative PBMC mRNA expression of heat shock protein 70 (HSP70), interferon beta (IFNβ), IFNγ, tumor necrosis factor alpha (TNFα), growth hormone (GH) and insulin-like growth factor-1 (IGF-1) genes. The results from this study reveal environmental sensitivity of novel physiological traits and gene expressions to climatic stressors, highlighting their potential as THI-independent heat stress biomarkers.

This genome-wide association study (GWAS) aimed to identify sequence variants (SVs) and candidate genes associated with fertility and health in endangered German Black Pied cattle (DSN) based on whole-genome sequence (WGS) data. We used 304 sequenced DSN cattle for the imputation of 1797 genotyped DSN to WGS. The final dataset included 11,413,456 SVs of 1886 cows. Cow traits were calving-to-first service interval (CTFS), non-return after 56 days (NR56), somatic cell score (SCS), fat-to-protein ratio (FPR), and three pre-corrected endoparasite infection traits. We identified 40 SVs above the genome-wide significance and suggestive threshold associated with CTFS and NR56, and three important potential candidate genes (ARHGAP21, MARCH11, and ZNF462). For SCS, most associations were observed on BTA 25. The GWAS revealed 61 SVs, a cluster of 10 candidate genes on BTA 13, and 7 pathways for FPR, including key mediators involved in milk fat synthesis. The strongest associations for gastrointestinal nematode and Dictyocaulus viviparus infections were detected on BTA 8 and 24, respectively. For Fasciola hepatica infections, the strongest associated SVs were located on BTA 4 and 7. We detected 200 genes for endoparasite infection traits, related to 16 pathways involved in host immune response during infection.

Greenhouse gas emissions from livestock farming and in particular enteric methane (CH₄) from ruminants are criticized for being one of the main contributors to climate change. Different breeding, feeding and management strategies are tested to decrease these emissions, but a status quo analysis is also relevant to implement such measures. The present study aimed to analyze the concentration of CH₄ in air exhaled by dairy cows along a rural-urban gradient of Bangalore, India. Urban, mixed and rural areas were defined based on a survey stratification index (SSI) comprising build-up density and distance to the city center. Using a laser methane detector (LMD), CH₄ concentration was determined in 2-min spot measurements of exhaled air of 448 cows at three equally spaced visits between June 2017 and April 2018. Mean, maximum and CH₄ concentration per duration of the overall measurement, eructation and respiration bouts were calculated. For the overall mean and respiration bouts, CH₄ concentration was higher in cows from urban areas, which had also higher milk yield than cows from mixed and rural areas. Although no differences were found in terms of the intake level of fibrous diet components, the type of measurement location (indoor, half-outdoor or outdoor) and pasture access had an impact on CH₄ concentration. To our knowledge, this is the first study using the LMD on-farm and in an urbanizing environment. The LMD measurements show variations in enteric CH₄ emissions along the rural-urban gradient of Bangalore that reflect differences in dairy husbandry systems governed by the social-ecological context.

Gastrointestinal nematodes (GIN), liver flukes (Fasciola hepatica) and bovine lungworms (Dictyocaulus viviparus) are the most important parasitic agents in pastured dairy cattle. Endoparasite infections are associated with reduced milk production and detrimental impacts on female fertility, contributing to economic losses in affected farms. In quantitative-genetic studies, the heritabilities for GIN and F. hepatica were moderate, encouraging studies on genomic scales. Genome-wide association studies (GWAS) based on dense single nucleotide polymorphism (SNP) marker panels allow exploration of the underlying genomic architecture of complex disease traits. The current GWAS combined the identification of potential candidate genes with pathway analyses to obtain deeper insights into bovine immune response and the mechanisms of resistance against endoparasite infections. A 2-step approach was applied to infer genome-wide associations in an endangered dual-purpose cattle subpopulation [Deutsches Schwarzbuntes Niederungsrind (DSN)] with a limited number of phenotypic records. First, endoparasite traits from a population of 1166 Black and White dairy cows [including Holstein Friesian (HF) and DSN] naturally infected with GIN, F. hepatica and D. viviparus were precorrected for fixed effects using linear mixed models. Afterwards, the precorrected phenotypes were the dependent traits (rFEC-GIN, rFEC-FH, and rFLC-DV) in GWAS based on 423,654 SNPs from 148 DSN cows. We identified 44 SNPs above the genome-wide significance threshold (pBonf = 4.47 × 10− 7), and 145 associations surpassed the chromosome-wide significance threshold (range: 7.47 × 10− 6 on BTA 1 to 2.18 × 10− 5 on BTA 28). The associated SNPs identified were annotated to 23 candidate genes. The DAVID analysis inferred four pathways as being related to immune response mechanisms or involved in host-parasite interactions. SNP effect correlations considering specific chromosome segments indicate that breeding for resistance to GIN or F. hepatica as measured by fecal egg counts is genetically associated with a higher risk for udder infections. We detected a large number of loci with small to moderate effects for endoparasite resistance. The potential candidate genes regulating resistance identified were pathogen-specific. Genetic antagonistic associations between disease resistance and productivity were specific for specific chromosome segments. The 2-step approach was a valid methodological approach to infer genetic mechanisms in an endangered breed with a limited number of phenotypic records.