Breed and adaptive response modulate bovine peripheral blood cells' transcriptome

Genetic Diversity, Population Structure and Selection Signature in Begait Goats Revealed by Whole-Genome Sequencing

Goats belong to a group of animals called small ruminants and are critical sources of livelihood for rural people. Genomic sequencing can provide information ranging from basic knowledge about goat diversity and evolutionary processes that shape genomes to functional information about genes/genomic regions. In this study, we exploited a whole-genome sequencing data set to analyze the genetic diversity, population structure and selection signatures of 44 individuals belonging to 5 Ethiopian goat populations: 12 Aberegalle (AB), 5 Afar (AF), 11 Begait (BG), 12 Central highlands (CH) and 5 Meafure (MR) goats. Our results revealed the highest genetic diversity in the BG goat population compared to the other goat populations. The pairwise genetic differentiation (FST) among the populations varied and ranged from 0.011 to 0.182, with the closest pairwise value (0.003) observed between the AB and CH goats and a distant correlation (FST = 0.182) between the BG and AB goats, indicating low to moderate genetic differentiation. Phylogenetic tree, ADMIXTURE and principal component analyses revealed a classification of the five Ethiopian goat breeds in accordance with their geographic distribution. We also found three top genomic regions that were detected under selection on chromosomes 2, 5 and 13. Moreover, this study identified different candidate genes related to milk characteristics (GLYCAM1 and SRC), carcass (ZNF385B, BMP-7, PDE1B, PPP1R1A, FTO and MYOT) and adaptive and immune response genes (MAPK13, MAPK14, SCN7A, IL12A, EST1 DEFB116 and DEFB119). In conclusion, this information could be helpful for understanding the genetic diversity and population structure and selection scanning of these important indigenous goats for future genetic improvement and/or as an intervention mechanism.

Effect of Slow-Release Urea Partial Replacement of Soybean Meal on Lactation Performance, Heat Shock Signal Molecules, and Rumen Fermentation in Heat-Stressed Mid-Lactation Dairy Cows

This study aimed to assess the effects of partially substituting soybean meal in the diet with slow-release urea (SRU) on the lactation performance, heat shock signal molecules, and environmental sustainability of heat-stressed lactating cows in the middle stage of lactation. In this study, 30 healthy Holstein lactating dairy cattle with a similar milk yield of 22.8 ± 3.3 kg, days in milk of 191.14 ± 27.24 days, and 2.2 ± 1.5 parity were selected and randomly allocated into two groups. The constituents of the two treatments were (1) basic diet plus 500 g soybean meal (SM) for the SM group and (2) basic diet plus 100 g slow-release urea and 400 g corn silage for the SRU group. The average temperature humidity index (THI) during the experiment was 84.47, with an average THI of >78 from day 1 to day 28, indicating the cow experienced moderate heat stress conditions. Compared with the SM group, the SRU group showed decreasing body temperature and respiratory rate trends at 20:00 (p < 0.1). The substitution of SM with SRU resulted in an increasing trend in milk yield, with a significant increase of 7.36% compared to the SM group (p < 0.1). Compared to the SM group, AST, ALT, and γ-GT content levels were significantly increased (p < 0.05). Notably, the levels of HSP-70 and HSP-90α were significantly reduced (p < 0.05). The SRU group showed significantly increased acetate and isovalerate concentrations compared with the SM group (p < 0.05). The prediction results indicate that the SRU group exhibits a significant decrease in methane (CH4) emissions when producing 1 L of milk compared to the SM group (p < 0.05). In summary, dietary supplementation with SRU tended to increase the milk yield and rumen fermentation and reduce plasma heat shock molecules in mid-lactation, heat-stressed dairy cows. In the hot summer, using SRU instead of some soybean meal in the diet alleviates the heat stress of dairy cows and reduces the production of CH4.

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

BACKGROUND

Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits.

RESULTS

SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117).

CONCLUSIONS

Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.

Pegbovigrastim Treatment around Parturition Enhances Postpartum Immune Response Gene Network Expression of whole Blood Leukocytes in Holstein and Simmental Cows

Simple Summary

The innate and adaptive immune system of dairy cows is impaired during the transition period, leading to an increase in susceptibility to infectious disease. Pegbovigrastim is a recombinant form of a granulocyte colony-stimulating factor that stimulates differentiation of hemopoietic stem cells to granulocytes and shortens maturation time within the bone marrow and release in circulation. The objective of the present study was to explore the effect of pegbovigrastim on whole blood leukocytes by analyzing the expression of 34 genes involved in immune and inflammatory responses immediately after calving in Simmental, a dual-purpose cow breed selected for both meat and milk production, and Holstein, a cow breed highly specialized for milk production. This study provides insight into immune cell functions impacted by pegbovigrastim treatment. Treatment of cows with pegbovigrastim increased the mRNA abundance level of most genes investigated, suggesting a thorough activation of the immune machinery during the critical post-partum period.

Abstract

Pegbovigrastim is a commercial long-acting analog of bovine granulocyte colony-stimulating factor (rbG-CSF) that promotes the increased count and functionality of polymorphonuclear cells in dairy cows around the time of parturition. We hypothesized that pegbovigrastim administered to periparturient cows at approximately seven days before parturition and within 24 hours after calving could affect the profiles of gene networks involved in leukocyte function. Blood was collected on Day 3 after calving from treated groups (pegbovigrastim (PEG); 13 Simmental (seven multiparous and six primiparous) and 13 Holstein (seven multiparous and six primiparous) cows) that received pegbovigrastim (Imrestor; Elanco Animal Health) and controls (CTR; 13 Simmental (seven multiparous and six primiparous) and 13 Holstein (six multiparous and seven primiparous) cows) that received saline solution. Blood from all cows was sampled from the jugular vein in a PAXgene Blood RNA System tube (Preanalytix, Hombrechtikon, Switzerland) for RNA extraction. The RT-qPCR analysis was performed to investigate a panel of 34 genes of interest, representing recognition, immune mediation, migration, cell adhesion, antimicrobial strategies, inflammatory cascade, oxidative pattern, and leukotrienes in whole blood leukocytes. Normalized data were subjected to the MIXED model of SAS (ver. 9.4) with treatment, breed, parity, and their interaction as fixed effects. Compared with CTR, whole blood leukocytes of PEG cows had higher expression of genes involved in recognition and immune modulation (CD14, CD16, MYD88, TLR2, and TLR4), cell adhesion (ITGB2, ITGAL, TLN1, SELL, SELPLG, and CD44), antimicrobial activity (MMP9, LTF, and LCN2), and inflammatory cascade (CASP1, TNFRSF1A, IL1B, IL1R, IL18, IRAK1, NLRP3, and S100A8). This suggested an improvement of migration, adhesion, and antimicrobial ability and an enhanced inflammatory response, which in turn could trigger immune cell activation and enhance function. Expression of SOD2 and ALOX5 was also greater in the PEG group. In contrast, compared with CTR cows, PEG led to lower expression of RPL13A, ALOX15, IL8, and TNF. Overall, leukocytes from Simmental compared with Holstein cows had greater expression of IDO1, RPL13A, ALOX5, CD44, CX3CR1, ITGB2, and TNFA, whereas expression of CD16 and TLR2 was lower. Overall, compared with multiparous cows, primiparous cows had higher expression of IL1B, IL18, MYD88, SELL, and TLR2 and lower expression of MMP9. Simmental cows seemed more sensitive to induction of the immune system after calving, as revealed by the greater abundance of genes involved in immune system adaptation, regardless of pegbovigrastim treatment. Primiparous cows undergoing a new stress condition with respect to older cows were characterized by leukocytes with a higher inflammatory response. In conclusion, pegbovigrastim led to higher expression levels of most genes involved in the processes investigated, suggesting a thorough activation of the immune machinery during the critical post-partum period.

Short communication: Inflammation, migration, and cell-cell interaction-related gene network expression in leukocytes is enhanced in Simmental compared with Holstein dairy cows after calving

The aim of this study was to investigate changes in the abundance of genes involved in leukocyte function between cows highly specialized for milk production (Holstein, n = 12) and cows selected for meat and milk (Simmental, n = 13). Blood was collected on d 3 after calving in PAXgene tubes (Preanalytix, Hombrechtikon, Switzerland) to measure mRNA abundance of 33 genes. Normalized gene abundance data were subjected to MIXED model ANOVA using SAS (SAS Institute Inc. Cary, NC). Simmental cows had greater transcript abundance of proinflammatory cytokines and receptor genes (IL1B, TNF, IL1R, TNFRSF1A), cell migration- and adhesion-related genes (CX3CR1, ITGB2, CD44, LGALS8), and the antimicrobial IDO1 gene. In contrast, compared with Holstein cows, Simmental cows had lower abundance of the toll-like receptor (TLR) recognition-related gene TLR2, the antimicrobial-related gene LTF, and S100A8, which is involved in cell maturation, regulation of inflammatory processes, and immune response. These results revealed that breed plays an important role in the modulation of genes involved in immune adaptation and inflammatory response, and the immune system of Simmental cows could potentially have a more acute response in early lactation. In turn, this might be beneficial for mounting a more efficient response after calving and allow for a smoother homeorhetic adaptation to lactation.