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Background: Quantitative trait loci (QTL) are genomic regions that influence essential traits in livestock. Understanding QTL distribution and density across species' genomes is crucial for animal genetics research. Objectives: This study explored the QTLome of cattle, pigs, sheep, and chickens by analyzing QTL distribution and evaluating the correlation between QTL, gene density, and chromosome size with the aim to identify QTL-enriched genomic regions. Methods: Data from 211,715 QTL (1994–2021) were retrieved from the AnimalQTLdb and analyzed using R software v4.2.1. Unique QTL annotations were identified, and redundant or inconsistent data were removed. Statistical analyses included Pearson correlations and binomial, hypergeometric, and bootstrap-based enrichment tests. Results: QTL densities per Mbp were 10 for bovine, 4 for pig, 1 for sheep, and 3 for chicken genomes. Analysis of QTL distribution across chromosomes revealed uneven patterns, with certain regions enriched for QTL. Correlation analysis revealed a strong positive relationship between QTL and gene density/chromosome size across all species (p < 0.05). Enrichment analysis identified pleiotropic regions, where QTL affect multiple traits, often aligning with known candidate and major genes. Significant QTL-enriched windows (p < 0.05) were detected, with 699 (187), 355 (68), 50 (15), and 38 (17) genomic windows for cattle, pigs, sheep, and chickens, respectively, associated with overall traits (and specific phenotypic categories). Conclusions: This study provides critical insights into QTL distribution and its correlation with gene density, offering valuable data for advancing genetic research in livestock species. The identification of QTL-enriched regions also highlights key areas for future exploration in trait improvement programs. [ABSTRACT FROM AUTHOR]

Understanding the relationship between Raramuri Criollo cattle (RC) and their microbial ruminal ecosystem will help identify advantageous characteristics of adapted cattle as alternatives to achieve sustainable beef production systems. Our objective was to characterize the rumen microbiome of RC in comparison to Angus and Hereford breeds (European, E) and the cross between them (E × RC). Ruminal fluid was collected from 63 cows in their second productive cycle after grazing in the same paddock for 45 d, in the dry (n = 28) and rain (n = 35) seasons. DNA from ruminal fluid was isolated for 16s rRNA gene next-generation sequencing. The data were analyzed with QIIME2 and compared against the SILVA 16s rRNA database. Beta diversity was different (p < 0.05) between RC and E in both seasons. A microbial core was represented by the most abundant phyla. Planctomycetes and Spirochaetes represented above 1% in the rain season and below 1% in the dry one, whereas Euryarchaeota was below 1% and around 3%, respectively. LEfSe analysis identified differentiated (p < 0.05) key microbial groups that explain the differences between lineages at different taxonomic levels, reflecting the ability of the rumen ecosystem of RC cattle to adapt to hostile environmental conditions by having microbial groups specialized in the degradation of highly fibrous content. [ABSTRACT FROM AUTHOR]

Raramuri Criollo cattle (RC), a local heritage breed in the Chihuahua state of Mexico, are highly rustic and well-adapted animals that can contribute to cow productivity in a low-input cow-calf production system. The aim was to evaluate traits related to productive performance of purebred RC, Angus x RC (AC) and Hereford x Angus (HA) cows. Each cow breed group was randomly assigned to one of three pastures within each of two mountains dominant exposures and evaluated during 2022 and 2023 at Rancho Teseachi (28◦48′ N, 107◦25′ W) belonging to Universidad Autonoma de Chihuahua. The six grazing pastures ranged from 263 to 400 ha, with similar slope, altitude and water sources characteristics. The stocking rate was moderate (forage utilization <50%). Forage biomass availability for the period of use was sampled in October, and stocking rate adjusted accordingly in March. RC cows were bred with RC bulls, and AC and HA with Angus bulls. The breeding season was from September to November, and pregnancy diagnosis at mid-January. Non-pregnant cows were replaced by pregnant cows from other pastures of the same farm. Feed supplementation was limited in 2022 and according to nutritional requirements in 2023. Evaluated variables included calf birth (BW) and weaning weight adjusted (WW) to the average age at weaning (190 d in 2022 and 165 d in 2023); body condition score (BCS 1 to 9), cow body weight (CBW) at the beginning of the breeding season, as well as body weight of calf weaned by unit of cow weight (WW/CBW), and pregnancy rate (PR). A general linear model with fixed effects of breed group, sex, dominant exposure of mountains, their interaction, cow age subclass (Young, 4 yr; Middle, 5 to 8 yr; Adult, > 9 yr) and Julian date at calving as a covariate was adjusted using PROC GLM of SAS for continuous, normally distributed variables, and PROC CATMOD for pregnancy rate, leaving out sex and interaction effects. Means of BW and WW on calves from AC and HA cows were greater (P < 0.5) than those from RC cows in both years (Table 1). In 2022, the mean CBW of HA was greater (P < 0.5) than for AC, and this greater (P < 0.5) than for RC cows; BCS was greater for AC than for HA and RC, and PR lower (P < 0.5) for HA than for AC and RC. In 2023, there was no difference in CBW between AC and HA; BCS was similar (P > 0.05) among the three groups; and PR was the lowest (P < 0.5) for HA. The AC cows had the greatest WW/CBW mean (P < 0.5) in both years. Overall, using AC cows resulted on a combination of traits that outperformed on general productivity in the evaluated production system. [ABSTRACT FROM AUTHOR]

Several polymorphisms in the coding region of the myostatin (MSTN) gene have been associated with the double-muscled (DM) phenotype in different species. An experimental herd of purebred Raramuri criollo cattle in Chihuahua, Mexico, has been selectively managed for beef production during the last 15 yr. Recently, two calves where visually identified as DM animals. The aim of this study was to identify changes in the MSTN gene sequence, associated with the two DM individuals and to screen for carriers of the potential polymorphisms within this herd. The DM paternity of the calves was verified by the SeekSire bovine parentage testing of NEOGEN (Lincoln, NE). A 6.6 Kb fragment of the MSTN gene were amplified by PCR and sequenced using Illumina DNA prep kit in a MiniSeq platform. The resulting reads were analyzed using different bioinformatic programs. SNPs were generated in VCF files and filtered by the following criteria: variant confidence normalized by depth of variant samples (QD) < 2.0, mapping quality (MQ) < 40.0, strand bias(FS) > 60.0. The deduced myostatin protein and the three-dimensional model were obtained with bioinformatic tools. Once a novel variant was identified, a real-time PCR protocol was developed to genotype 100 and 97 herdmates, the allelic and genotypic frequencies were estimated. A 9-bp deletion was identified at the same position as the 11-bp deletion (g.821to 831del11) of the Belgian Blue MSTN allele (Figure 1). Although the latter allele has been found in three Spanish cattle breeds ancestrally related to Raramuri criollo, this is the first report of the 9-bp deletion in the MSTN gene. Such deletion results in the loss of three highly conserved amino acids residues (274, 275 and 276) in MSTN, but does not lead to a premature stop codon as in the case of the 11-bp deletion characteristic to DM Belgian Blue. The in silico three-dimensional MSTN conformation obtained for this allele has some structural differences compared with the protein reference model. The allelic frequencies were 0.85 and 0.15 for the MSTN+ and MSTNdel alleles, respectively, whereas the genotypic frequencies were 0.71, 0.01 and 0.28 for MSTN+/MSTN+, MSTNdel/MSTNdel MSTN+/MSTNdel genotypes, respectively. Controlled mattings to generate different genotypes in the research herd would allow to continue studying the effects of this MSTN gene variant on productive performance, forage behavior, husbandry and carcass and meat quality traits known to be affected by the DM phenotype in beef cattle. [ABSTRACT FROM AUTHOR]

The insulin-like growth factor-1 (IGF-1), a key hormone in muscle development was investigated for single-nucleotide polymorphisms (SNPs) upstream of the IGF-1 gene and their effects upon its cognate mRNA and hormone levels in sheep. A 70 d feeding trial was conducted with 22 F1 (Dorper × Pelibuey) lambs, individually allocated and fed a diet with a forage-to-concentrate ratio of 36:64 and 17% crude protein. Sequence analyses of 265 bp upstream the IGF-1 gene revealed the variant NC_040254.1:g.[184028491G > C;184028493G > A]. These SNPs generate alleles A and B, with frequencies of 0.66 and 0.34 in F1 lambs and of 0.73 and 0.27 in 81 pure Dorper lambs, respectively. Females were grouped by genotype AA, AB and BB (n = 3). IGF-1 hormone concentrations at 14, 42 and 70 d were higher (p < 0.05) in AA lambs compared to AB + BB lambs. The IGF-1 mRNA level was 2.6-fold higher in AA animals (n = 5, p < 0.05) than in AB + BB lambs (n = 7). A DNA binding site for the Inhibitor of Growth family member 4 (ING4) was found in allele B but not in allele A, which could explain the lower mRNA and hormone expression levels for AB + BB animals. The variant reported here appears to function as an eQTL with a negative effect on the level of IGF-1. [ABSTRACT FROM AUTHOR]

The number of lambs per birth expressed as prolificacy is a key trait that determines productive efficiency in sheep. However, the optimal litter size depends on the production system, since the milk production of the ewe impacts the postnatal development of lambs. Milk yield, in turn, is related to the expression of the SLC2A1 gene in mammary epithelial cells. This gene encodes the solute carrier/glucose transporter 1 and is upregulated in peak/mid lactation. To assess the productive efficiency of twinning ewes in regard to SLC2A1 expression, the objective of this study was to measure the mRNA levels of SLC2A1 in milk somatic cells (MSC) of Pelibuey ewes lambing twins. Healthy ewes (n = 8), three primiparous and five multiparous, were selected to quantify and compare abundance of SLC2A1 mRNA. Management was under feedlot conditions, and the milk samples were taken between 16 and 20 d post-lambing. Total RNA was purified from MSC and SLC2A1 mRNA abundance were measured by RT-qPCR, relative to β-actin as reference gene. The total birth weight (TBW) and weaning weight of their lambs were recorded, calculating the total weight of lamb weaned (TWLW). TBW, TWLW and relative expression of SLC2A1 were analyzed with PROC GLM of SAS, whereas the Pearson correlation coefficient between TWLW and relative expression of SLC2A1 was calculated using PROC CORR of SAS. Although there was no statistical difference in TBW (P = 0.13) and TWLW (P = 0.38) between lambing groups, a numerical difference was observed both in TBW (5.7 ± 0.54 and 6.9 ± 0.42) and in TWLW (21.5 ± 3.94 and 26.2 ± 3.05) for primiparous and multiparous, respectively. The abundance of SLC2A1 mRNA were 3.1-fold change (P = 0.0005) greater in MSC of primiparous ewes than in the multiparous ones (Figure 1). In multiparous ewes a positive correlation, r = 0.96 (P = 0.01) was found between TWLW and relative expression of SLC2A1. It is concluded that greater relative expression of SLC2A1 in young prolific ewes could be a compensatory mechanism to produce more milk to feed their lambs, even with a smaller udder volume. Such findings give way for further research on the subject. [ABSTRACT FROM AUTHOR]

The Chihuahuan Criollo cattle is a genetic resource with special adaptive characteristics to rough, arid and semi-arid ecosystems. There is a great interest in incorporating such adaptations into beef production systems as one of the strategies for sustainable production to face the climate change challenge. Reproductive success is determinant to achieve sustainability in animal production systems. Most research efforts to improve reproductive efficiency have focused on the study of females. However, it has been shown that much of the economic losses caused by embryonic deaths are due to the bull. The aim of this study was to evaluate the quality of thawed semen from Angus and Criollo bulls kept in a low-input system. Thirteen healthy bulls (n = 7 Angus and 6 = Chihuahuan Criollo), with an average age of 4.3 ± 0.48 yr, grazing in the same rangeland and subjected to natural pasture conditions, were studied. Semen obtained by electroejaculation, were frozen and subsequently thawed for analyses. Characteristics of motility, vitality (V), morphology (M) and plasma membrane integrity (PMI) were evaluated in fresh and thawed semen, whereas movement kinetics (MK) and acrosome reaction (AR) were evaluated in thawed semen. Statistical analysis was performed using the PROC GLM of SAS Studio 2022 including the fixed effects of breed, semen condition and their interaction for variables of progressive motility (PM), V, M, PMI and the effect of breed for variables of MK and AR. As expected, PM and V were less (P < 0.05) in thawed (57.93 ± 4.1 and 53.69 ± 2.7) compared with fresh (72.64 ± 3.9 and 74.98 ± 2.6) semen, whereas no differences (P > 0.05) were found in M. However, the interaction between semen condition and breed for PMI tended to the significance (P = 0.08) with a PMI of 68.95 ± 4.6 and 58.98 ± 4.3 for Criollo and Angus, respectively, in fresh semen, whereas in thawed semen this difference was inverted (52.08 ± 4.6 and 58.40 ± 4.6). It is important to note that the semen retained quality traits with values above the minimum accepted for use in artificial insemination, despite the scarcity of resources of the system in which the animals were kept. There were no differences by breed in the main MK variables; however, AR reported as live unreacted sperm was less (P < 0.05) in Criollo (40.49 ± 4.49) compared with Angus bulls (58.48 ± 4.49). In conclusion, it is important to incorporate the assessment of membrane integrity and acrosome reaction in thawed semen evaluation to obtain a more accurate prediction of the potential fertility of samples, even if motility parameters appear to be optimal. [ABSTRACT FROM AUTHOR]

The QTLome represents the collection of QTLs (quantitative trait loci) documented for each trait within a specific species, detailing the position, effect, and mode of inheritance of each locus. Despite the abundance of known QTLs for productive traits in cattle, only a few genes have been identified as selection markers. This study aimed to prioritize genes within validated QTLs associated with crucial traits in cattle by integrating this information with RNAseq data. Initially, bovine QTLs (n = 161,730) were sourced from the AnimalQTLdb database (version 44), and both graphical and quantitative analyses were conducted using R software. Only annotations within the UMD 3.1 genome were considered, with overlapping QTLs from the same scientific report grouped together. Following quality control measures, the number of QTLs was reduced to 37,146. Validated QTLs were determined by identifying overlapping annotations from various studies or those within a distance of < 1 Mb for the same phenotypic trait, resulting in a total of 3,856 validated QTLs. For gene prioritization, validated QTLs were selected based on semen traits and residual feed intake (RFI). Transcriptomes corresponding to these traits were sourced from NCBI (PRJNA516089 and PRJEB7696). Sequence filtering was performed using the fastp program, and transcript counts were obtained with SALMON software. Sequences were aligned to the Ensembl UMD 3.1 reference genome (version 94), and differential expression analysis was conducted using the R package DESeq2, considering only the group factor (high/low) for each trait (fertility/ RFI). Integration of QTLs and transcriptomes utilized the methodology of the cageminer R package, which prioritizes candidate genes within validated QTLs, identifies those grouped in co-expression modules enriched by reference genes, and correlates with the study phenotype (biserial r > 0.2). Reference genes were obtained from Ignatieva et al. (2021 PMID 34290736) and Chen et al. (2021; PMID 33664767). Among the 18 validated QTLs for semen traits, four candidate genes (TSPAN6, QSER1, ADRB2, AKAP4) were identified. Except for ADRB2, these genes exhibited significant differential expression (P < 0.05) in contrasting groups of Holstein cattle. They are associated with semen traits and perform functions such as regulation of spermatogenesis, development, activation, and cell growth. Regarding RFI, 127 validated QTLs yielded 205 prioritized genes, of which 123 showed significant differential expression (P < 0.05) in divergent groups of the Nelore breed. These genes are involved in the immune response and the polymerization and organization of actin filaments, processes that have been reported as biologically relevant to RFI. The implemented strategy was efficient for gene prioritization through the integration of QTLs and RNAseq. [ABSTRACT FROM AUTHOR]

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The prototype of Pura Raza Española horse depends on the equestrian disciplines and establishes the breeding selection objectives; the selection criteria are developed from zoometric measures (ZM), which are subject to multiple direct and maternal genetic effects. The objective of this study was to evaluate the magnitude of the maternal genetic effects, based on the (co)variances, if they are equal to or different from zero. Our database included information of 1806 equines born from 2004 to 2013, with data of eight ZM (mean in cm ± SD): thoracic perimeter (TP; 189.3±8.9), knee perimeter (KP; 32.3±1.8), cannon perimeter (CP; 20.4±1.3), scapular-ischial length (SIL; 160.7±5.9), chest width (CW; 43.1±3.0), height of the substernal space (HSS; 83.1±5.1), chest height (CH; 73.2±4.3), and withers height (WH; 157.8±4.3). We conducted the analysis with a mixed model that included the fixed effects of contemporary groups (ranch, year, time, and sex) and the age covariable of the individual; as random, the direct (D) and maternal (M) genetic effects, plus the covariance between them, (C). By alternating maternal genetic effects, we compared the models: D, DM, and DMC. We selected the models using the likelihood-ratio test. The pedigree was made up of 7498 animals. We estimated the direct (h²) and maternal (m²) heritabilities, as well as the genetic correlations (rg). For the analysis, we used the software MTDFREML. The maternal genetic effects in CH and CP were statistically not different from zero (p±0.05); in the other ZM, the DMC model was the most fit. The h² oscillated between 0.09 (CH) and 0.65 (WH), with an average of 0.40. The m² fluctuated between 0.17 (HSS) and 0.23 (WH), with an average of 0.19. All the rg were negative, between ±0.37 (WH) and ±0.99 (HSS), which must be considered in the genetic improvement of the ZM. [ABSTRACT FROM AUTHOR]