Association of lameness and mastitis with return-to-service oestrus detection in the dairy cow

Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology

BACKGROUND

The accurate identification of the functional elements in the bovine genome is a fundamental requirement for high-quality analysis of data informing both genome biology and genomic selection. Functional annotation of the bovine genome was performed to identify a more complete catalog of transcript isoforms across bovine tissues.

RESULTS

A total of 160,820 unique transcripts (50% protein coding) representing 34,882 unique genes (60% protein coding) were identified across tissues. Among them, 118,563 transcripts (73% of the total) were structurally validated by independent datasets (PacBio isoform sequencing data, Oxford Nanopore Technologies sequencing data, de novo assembled transcripts from RNA sequencing data) and comparison with Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive data from different technologies such as whole transcriptome termini site sequencing, RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression, chromatin immunoprecipitation sequencing, and assay for transposase-accessible chromatin using sequencing. A large proportion of identified transcripts (69%) were unannotated, of which 86% were produced by annotated genes and 14% by unannotated genes. A median of two 5' untranslated regions were expressed per gene. Around 50% of protein-coding genes in each tissue were bifunctional and transcribed both coding and noncoding isoforms. Furthermore, we identified 3,744 genes that functioned as noncoding genes in fetal tissues but as protein-coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 annotated gene borders compared to Ensembl or NCBI annotations. The resulting bovine transcriptome was integrated with publicly available quantitative trait loci data to study tissue-tissue interconnection involved in different traits and construct the first bovine trait similarity network.

CONCLUSIONS

These validated results show significant improvement over current bovine genome annotations.

Effect of retained placenta and clinical mastitis on reproduction parameters, immune response, and steroidogenic receptors gene expression in postpartum crossbred dairy cows

The purpose of this study was to evaluate the effect of retained placenta (RP) and clinical mastitis (CM) on the reproductive efficiency of crossbred dairy cows during the postpartum period and the effect in some innate immune system indicators. For this, two experiments were carried out. In the first, a total of 232 cows were evaluated and divided as: healthy control (n = 184), RP (n = 22), and CM (n = 26) groups. The RP and CM was evaluated until 30 days postpartum (DPP) and reproductive rates were measured. In experiment 2, cows were divided in control (n = 10), RP (n = 10), and CM (n = 30) groups. Between 40 and 50 DPP, clinical, gynecological examination and endometrial cytobrush were performed to evaluate subclinical endometritis (SE) and gene expression of interleukins 1β (IL-1β) and 6 (IL-6), chemokine ligand 5 (CCL5), estrogen α (ESR1), and progesterone (PGR) receptors by qRT-PCR analysis. In experiment 1, the conception rate at 1st artificial insemination (AI) was lower in RP and CM groups and pregnancy rate at 150 days decreased in CM group. Calving-to-1st AI interval and days open were shorter in healthy cows. In experiment 2, the occurrence of SE was 26.7% and higher in RP and CM groups. The expression of IL-1β increased in RP and CM groups, while IL-6 was less expressed in RP group. The CCL5, ESR1, and PGR were similar between groups. In conclusion, cows with RP and CM had their reproductive efficiency negatively affected and had they initial pro-inflammatory response improved by the increase of IL-β.

Resynchronizing the first eligible estrus in dairy cattle after a prior insemination and fertility of the prior insemination after gonadotropin-releasing hormone and progesterone treatments

The hypothesis of this study tested whether application of designed treatments to synchronize estrus in nonpregnant previously inseminated lactating dairy cows increased the proportion of nonpregnant cows in estrus before early pregnancy diagnosis on Day 32 after the previous insemination (Day 0) and increase fertility of the pretreatment insemination. A progesterone insert (CIDR) and GnRH were applied to cows after insemination to resynchronize the returning estrus of cows that failed to conceive on Day 0. The combination of GnRH (Day 14) and a CIDR insert (d 17 through 24) in experiment 1 (n = 347 cows) did not increase (P = 0.13) the proportion of nonpregnant cows returning to estrus before pregnancy diagnosis, but increased (P < 0.01) the synchrony of their return by 24.4% points, and delayed (P < 0.01) that return by 2.3 ± 0.3 d compared with controls. Ovulation risk after GnRH treatment on Day 14 was only 10%. For cows that failed to return to estrus before Day 32, progesterone concentration on Days 14 and 17 were less than that in cows that returned to estrus by Day 32 and in pregnant cows. Cows that returned to estrus had larger follicles and fewer numbers of CL on Day 21 than pregnant cows and cows that failed to return to estrus, but concentrations of pregnancy-associated glycoproteins on Day 28 indicated that cows failing to return to estrus were likely pregnant but suffered embryo death. In experiment 2 (n = 881), use of GnRH alone (Day 7), a CIDR insert alone (Days 14 through 21), or in combination, failed to increase the proportion of nonpregnant cows in estrus before pregnancy diagnosis on Day 32 compared with controls. Cows receiving the CIDR insert had increased (P < 0.01) synchrony of estrus by 24-34% points compared with cows that did not receive a CIDR insert. More cows receiving GnRH had 2 or more CL on Days 14 and 21 compared with controls. Ovulation risk after GnRH on Day 7 was greater than 66%. In both experiments combined, treatments with GnRH or GnRH + CIDR insert increased (P = 0.015) pretreatment pregnancy per AI by 7.1% points, but did not affect pregnancy loss. Although administering GnRH with or without a CIDR insert synchronized returns to estrus, treatments failed to increase the proportion of nonpregnant cows reinseminated before pregnancy diagnosis, but increased pretreatment pregnancy risk.