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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]

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 FecGE allele of the ovine GDF9 gene has been reported segregating in the Pelibuey hair type breed in México. Homozygous E/E ewes reproduce normally, in contrast to the sterility of homozygous ewes reported for other GDF9 variants. Thus, potential exists to cross homozygous and carrier Pelibuey ewes with meat type rams of low-prolificacy but welladapted breeds to obtain F1 commercial flock ewes. The aim was to evaluate ewe productivity, as total lamb weight weaned (TWW), of FecGE carrier vs non-carrier F1 Dorper x Pelibuey ewes. Sixty one first lambing ewes (34 carrier and 27 non-carrier) equally served with two Texel rams were used. Management was under feedlot conditions. Genotyping was done by real time PCR (StepOnePlus) using the FAMACTTCAAACAGTTTCTTTTTMGBNFQ and VICTCAAACAGTGTCTTTTTMGBNFQ probes (Applied Biosystems). Type of birth (TB; twins vs single) and weaning (TW) were analyzed with PROC CATMOD of SAS. Fixed effects of ewe genotype (carrier vs non-carrier), contemporary group and ram of service were included in a logistic generalized linear model. Lamb weaning weights were adjusted to a common age of 75 d and by sex. Equivalent to male average birth lamb weight (ABW), average weaning lamb weight (AWW) and TWW per ewe were analyzed with PROC GLM of SAS. Carrier ewes had more twins (P < 0.01) for TB (75 vs 19.4 %) and TW (58.8 vs 21.7 %) than non-carrier ewes. Equivalent to male ABW on carrier ewes was less (P < 0.05; 3.17 ± 0.21 vs 3.97 ± 0.20 kg) than for non-carrier ewes but not difference (P > 0.05) was observed for AWW (21.96 ± 0.85 vs 22.93 ± 0.90 kg). Ewe productivity, as indicated by TWW, was greater (P < 0.05; 33.16 ± 1.78 vs 27.23 ± 1.88 kg) for FecGE carrier ewes than for the non-carrier ones. More research on this topic deserves further attention, especially under range conditions, with multiple parity ewes, different years and reproductive activity seasons, using a larger simple. [ABSTRACT FROM AUTHOR]

Reports in the literature suggest that a transient surge of ghrelin secretion (TSGS) just before a scheduled meal may be triggered by an appetite mechanism. Also, it is known that circulating ghrelin concentrations fluctuate relative to nutritional status and influence feeding behavior. The aim of the present study was to search for genetic variants in five selected genes (GHRL, GHSR1a, MBOAT4, NPY and AgRP) within the ghrelin gene (GHRL) interaction network. gDNA was extracted from the six highest- and six lowest-RFI Hampshire non-castrated male lambs, out of a total of 25 lambs in a 56-d GrowSafe SystemsÒ feeding trial and the complete genes were amplified by PCR. Libraries were prepared and sequenced in the ILLUMINA platform MiniSeq Sequencing System. Variations were identified using the genomic variant call format (GVCF) workflow with HaplotypeCaller using the reference genome oviAri 4 - Oar_v4 (GCA_000298732.2). One hundred and ninety-two SNPs were found in the five analyzed genes. Most of them had been reported in the SNPs data base. Linear models including each SNP genotype at a time as fixed effects, in addition to ADG and mid test metabolic body weight as covariates for some variables, were adjusted. Forty-three of these SNPs had different genotype frequencies in the two RFI groups, and appear to be associated (p < 0.05) with traits such as RFI, feed intake (FI), feed conversion (FC) and ghrelin hormone concentration in plasma (GHRL) at the TSGS; especially SNPs rs399405301, rs421869734, rs604106535, rs417836509, rs600356564, rs590893697 at the MBOAT4 gene which resulted highly significant (p < 0.01) for RFI and GHRL. The SNP rs423156356 at the GHSR1a gene was highly significant (p < 0.01) for FI and FC. These SNPs (Table 1) have the potential to be used as genetic markers for improvement of feed efficiency in Hampshire sheep, but validation on a larger sample deserves further research efforts. [ABSTRACT FROM AUTHOR]

The aim was to explore potential differences on ghrelin plasm concentrations between efficient and inefficient lambs within a transient surge of ghrelin secretion just before a scheduled meal feeding. Six high- (256±19 g) and six low-RFI (-242±19 g) Hampshire entire male lambs (Age=168±2 d and BW=63±5 kg) were taken out of 25 individuals in a 56-d GrowSafe SystemsÒ feeding trial. After a 10-d adaptation to a once-daily ad-libitum feed offering (0900 h), at d11 three lambs from each RFI group continued the oncedaily feeding schedule (FED), whereas feed was withheld from the other three lambs (FAST) from each RFI group for 24-h (d11 to d12). Blood samples were collected via indwelling jugular catheter. In d11, ghrelin plasm concentrations were determined by ELISA in all animals at 0800, 0840, 0900, 1000 and 1100, and d12 at 0900, 1000 and 1100 in the FAST group. A linear model for repeated measures was adjusted with PROC MIXED of SAS. Plasm ghrelin levels began to increase at 0800, and RFI groups reached significant difference (P < 0.05) within both FED and FAST groups at 0840, with the greatest difference at peak concentrations at 0900 h (3.9±0.2 vs 2.4±0.2 and 3.9±0.2 vs 3.0±0.2 ng/ml for high vs low RFI, respectively). In the descendent phase of the curve for the FED group, one hour after feeding, ghrelin plasm concentration levels continued to be greater (P < 0.05) for high RFI vs low RFI animals and reached basal levels by 1100 h. For the FAST group, ghrelin concentrations continued to increase averaging maximum concentrations at the end of feed restriction, 0900 h of d12, being 4.9±0.2 ng/mL for the high RFI animals and 3.5±0.2 ng/mL for the low RFI ones. In conclusion, high RFI lambs show more pronounced transient surge of ghrelin secretion just before a scheduled meal feeding than low RFI lambs. [ABSTRACT FROM AUTHOR]

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