Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution.
We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats.
Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.

High resilience against diseases, changing environmental conditions, and other stress factors and the ability to efficiently recover to normal status, is becoming increasingly important in pig production. Finding new phenotypes that relate to resilience is a crucial step for improving the resilience of pigs through selection. The objective of this study was to extract resilience-related phenotypes based on fluctuations in daily feed intake (DFI, g) and time spent in feeding per day (TPD, min) and to estimate the heritability of these traits and genetic correlations with production traits (PT). Resilience-related traits with high enough heritability and with either favorable or neutral genetic correlation with PT could be used in the selection program to improve the productivity and welfare of pigs. In this study, we used data from 7,347 Finnish Yorkshire, Landrace, and crossbred pigs raised at the test station. Six pig-specific resilience-related phenotypes were extracted from the individual DFI and TPD: root mean square error (RMSE), quantile regression (QR), and coefficient of variation (CV). RMSE was calculated from the differences between the actual DFI (or TPD) and the pig-specific predicted values. QR was based on the number of days that a pig belonged to the group with the lowest 5% of pigs based on DFI (or TPD), and CV was calculated over the daily observations of DFI (or TPD). PT included average daily gain (ADG, g), backfat thickness (BF, mm), and feed conversion rate (FCR, g/g). The heritability estimates for resilience-related traits varied between 0.07 ± 0.02 (QRDFI) and 0.20 ± 0.03 (RMSETPD). The genetic correlations between resilience-related traits and PT were mostly neutral, but for example, RMSEDFI had a favorable genetic correlation with FCR and BF but an unfavorable correlation with ADG. Lastly, we observed that pigs belonging to the lowest 10% group based on their breeding value (BV) for QRTPD had a lower proportion (10% incidence) of sick days compared to the highest 10% BV group (30% incidence). Therefore, pigs exhibiting small TPD variation (related to high resilience) tend to be less susceptible to sickness than pigs with large TPD variation (related to low resilience). Given its moderate heritability, neutral genetic correlation with PT, and positive effect on health, QRTPD can be considered the most promising resilience-related trait in the Finnish production system.
Improving resilience, i.e., the capacity to respond to the impacts of stressors and to effectively recover to normal status, is a promising approach to enhancing the well-being of pigs and the productivity of the pig industry. Animals with high resilience can maintain their performance under challenging conditions. However, obtaining heritable measurements and indicators of resilience is challenging. One indicator of resilience is fluctuation in daily feed intake (DFI) and time spent in feeding per day (TPD). In our study, the proportion of days during which a particular pig belongs to the lowest 5% of pigs based on TPD (QRTPD) turned out to be the most promising resilience-related trait. This trait is moderately inheritable and has only a weak genetic correlation with production traits (PTs). Pigs with the most favorable breeding values (BVs) for QRTPD had four times fewer sick days than pigs with less favorable BVs for QRTPD. Overall, selecting QRTPD would improve pig resilience and health without negative effects on PTs.

Genomic structural variants (SVs) constitute a significant proportion of genetic variation in the genome. The rapid development of long-reads sequencing has facilitated the detection of long-fragment SVs. There is no published study to detect SVs using long-read data from sheep. We applied a long-read mapping approach to detect SVs and characterized a total of 30,771 insertions, deletions, inversions and translocations. We identified 716, 916, 842 and 303 specific SVs in Southdown sheep, Alpine merino sheep, Qilian White Tibetan sheep and Oula sheep, respectively. We annotated these SVs and found that these SV-related genes were primarily enriched in the well-established pathways involved in the regulation of the immune system, growth and development and environmental adaptability. We detected and annotated SVs based on NGS resequencing data to validate the accuracy based on third-generation detection. Moreover, five candidate SVs were verified using the PCR method in 50 sheep. Our study is the first to use a long-reads sequencing approach to construct a novel structural variation map in sheep. We have completed a preliminary exploration of the potential effects of SVs on sheep.

Duroc pigs are popular crossbred terminal sires, and accurate assessment of genetic parameters in the population can help to rationalize breeding programmes. The principle aim of this study were to evaluate the genetic parameters of production (birth weight, BW; age at 115 kg, AGE; feed conversion ratio, FCR) and body size (body length, BL; body height, BH; front cannon circumference, FCC) traits of Duroc pigs. The second objective was to analyze the fit of different genetic assessment models. The variance components and correlations of BW (28,348 records), AGE (28,335 records), FCR (11,135 records), BL (31,544 records), BH (21,862 records), and FCC (14,684 records) traits were calculated by using DMU and AIREMLF90 from BLUPF90 package. In the common environment model, the heritability of BW, AGE, FCR, BL, BH, and FCC traits were 0.17 ± 0.014, 0.30 ± 0.019, 0.28 ± 0.024, 0.16 ± 0.013, 0.14 ± 0.017, and 0.081 ± 0.016, with common litter effect values of 0.25, 0.20, 0.18, 0.23, 0.19, and 0.16, respectively. According to the results of the Akaike information criterion (AIC) calculations, models with smaller AIC values have a better fit. We found that the common environment model with litter effects as random effects for estimating genetic parameters had a better fit. In this Model, the estimated genetic correlations between AGE with BW, FCR, BL, BH, and FCC traits were -0.28 (0.040), 0.76 (0.038), -0.71 (0.036), -0.44 (0.060), and -0.60 (0.073), respectively, with phenotypic correlations of -0.17, 0.52, -0.22, -0.13 and -0.24, respectively. In our analysis of genetic trends for six traits in the Duroc population from 2012 to 2021, we observed significant genetic trends for AGE, BL, and BH. Particularly noteworthy is the rapid decline in the genetic trend for AGE, indicating an enhancement in the pig\'s growth rate through selective breeding. Therefore, we believe that some challenging-to-select traits can benefit from the genetic correlations between traits. By selecting easily measurable traits, they can gain from synergistic selection effects, leading to genetic progress. Conducting population genetic parameter analysis can assist us in devising breeding strategies.

This study provides estimates on genetic parameters, inbreeding depression and purging for meat performance measures from 25 German sheep breeds. All German meat, merino sheep breeds and breeds of other breeding directions with a sufficient number of pedigree and performance data were included in this study. Phenotypic traits retrieved from the national database OviCap were evaluated: daily weight gain, meatiness score and ultrasound measurements for muscle and fat thickness. We employed animal models to estimate heritability, variance and covariance components for these meat performance traits as well as inbreeding depression and purging. The heritabilities, on average, reached estimates of 0.55, 0.34, 0.53 and 0.61 for daily weight gain, meatiness score and ultrasound measurements for muscle and fat thickness, respectively. We estimated the linear regression slopes for the individual rate of inbreeding, new and ancestral inbreeding, as well as the inbreeding coefficient and its interaction with the inbreeding coefficient of Ballou, employing animal models with non-genetic effects and the additive genetic effect of the animal. Across all breeds, inbreeding was only significant for daily weight gain, whereas for all other traits, estimates were not significant. Within sheep breeds, we found significant inbreeding depression for daily weight gain in German Mutton Merino and German Blackheaded Mutton as well as for the meatiness score in German Whiteheaded Mutton. Significant effects for purging, based on ancestral inbreeding and the interaction effect of the classical inbreeding coefficient with the inbreeding coefficient of Ballou, were not obvious either across or within any sheep breed. A 1% increase in inbreeding significantly decreased the phenotypic trait median of daily weight gain across all sheep breeds by 0.50% and 0.70% of phenotypic and genetic standard deviation, respectively. Purging effects due to ancestral inbreeding were not significant in any breed or across breeds. The results of this study may indicate that inbreeding depression may be more harmful in traits under stronger selection than in traits that exert low selection pressure. The results of this study demonstrate the different effects that result in meat performance traits due to inbreeding. With increasing rates of inbreeding and critical effective population sizes, selection intensity for breeding objectives has to be critically reviewed for each sheep breed. Inbreeding depression and purging should be evaluated in order to prevent a decrease in trait means due to inbreeding and to determine whether detrimental alleles are eliminated.

This trial was carried out to find out the effects of the parent flock and hatching time of broiler chickens on the production traits and bacteriota development of animals. Two sets of 730 hatching eggs were collected from two different parent flocks with ages of 25 and 50 weeks. In the hatchery, both groups were divided into two subgroups: those hatched during the first 10 and the subsequent 10 h of the hatching window. A feeding trial was carried out afterwards, using the four treatments in six replicate floor pens and feeding commercial starter, grower, and finisher diets that contained all the nutrients according to the breeder\'s recommendations. The day-old chickens of the older parent flock and those hatched later were heavier, and this advantage remained until the end of the production period. The different ages and origins of the parent flocks failed to modify the microbiological parameters of the chicken\'s ceca; however, the hatching time significantly influenced the different bacteriota diversity indices: the late-hatched chickens showed higher Bacteroidetes and lower Firmicutes and Actinobacteria abundances at day 11. These treatments resulted in differences in the main families, Ruminococcaceae, Lactobacillaceae, and Bacteroidaceae. These differences could not be found at day 39.

OBJECTIVE: This study aims to investigate the genetic structure and characteristics of the Angus cattle population in Hungary. The survey was performed with the assistance of the Hungarian Hereford, Angus, Galloway Association (HHAGA).
METHODS: Genetic parameters of 1,369 animals from 16 Angus herds were analyzed using the genotyping results of 12 microsatellite markers with the aid of PowerMarker, Genalex, GDA-NT2021, and STRUCTURE software. Genotyping of DNA was performed using an automated genetic analyzer. Based on pairwise identity by state values of animals, the Python networkx 2.3 library was used for network analysis of the breed and to identify the central animals.
RESULTS: The observed numbers of alleles on the 12 loci under investigation ranged from 11 to 18. The average effective number of alleles was 3.201. The overall expected heterozygosity was 0.659 and the observed heterozygosity was 0.710. Four groups were detected among the 16 Angus herds. The breeders\' information validated the grouping results and facilitated the comparison of birth weight, age at first calving, number of calves born and productive lifespan data between the four groups, revealing significant differences. We identified the central animals/herd of the Angus population in Hungary. The match of our group descriptions with the phenotypic data provided by the breeders further underscores the value of cooperation between breeders and researchers.
CONCLUSIONS: The observation that significant differences in the measured traits occurred among the identified groups paves the way to further enhancement of breeding efficiency. Our findings have the potential to aid the development of new breeding strategies and help breeders keep the Angus populations in Hungary under genetic supervision. Based on our results the efficient use of an upcoming genomic selection can, in some cases, significantly improve birth weight, age at first calving, number of calves born and the productive lifespan of animals.

The composition and abundance of microorganisms in the gastrointestinal tract of cows are complex and extensive, and they play a crucial role in regulating nutrient digestion, absorption, maintaining digestive tract stability, and promoting the production and health of the host. The fermentation carried out by these microorganisms in the gastrointestinal tract is fundamental to the health and productivity of cows. Rumen microorganisms produce the majority of enzymes required to break down feed substrates, such as cellulose, protein, lipids, and other plant materials, through fermentation. This process provides energy metabolism substrates that satisfy approximately 70% of the host\'s energy requirements for physiological activities. Gut microorganisms primarily decompose cellulose that is difficult to digest in the rumen, thereby providing heat and energy to the hosts. Additionally, they have an impact on host health and productivity through their role in immune function. Understanding the composition and function of the cow gut microbiota can help regulate dairy cattle breeding traits and improve their health status. As a result, it has become a popular research topic in dairy cattle breeding. This article provides a review of the composition, structure, physiological characteristics, and physiological effects of the cow gut microbiota, serving as a theoretical foundation for future studies that aim to utilize the gut microbiota for dairy cattle breeding or improving production traits. It may also serve as a reference for research on gut microbiota of other ruminants.

This study aimed to identify the optimum level of supplementary feeds on the carcass traits and meat quality of Jamuna basin lambs. Forty selected lambs were divided into four treatments such as T0 (no concentrate supplementation), T1 (1% concentrate feed), T2 (1.5% concentrate feed) and T3 (2% concentrate feed) having ten lambs per treatment. The data were analyzed through Completely Randomized Design (CRD) with SAS software. Hot carcass, dressing percentage, head, leg, neck, loin, heart, and spleen weight were showed significantly (p < 0.05) higher values with increasing concentrate feed. The crude protein (CP), ether extract (EE) and ash values were significantly increased (p < 0.001) except T2 treatment. The ultimate pH was significantly increased except T2 and cooked pH was significantly decreased (p < 0.001) except T3 treatment. Drip loss and cooking loss (CL) % had significantly reduced (p < 0.001) except T3 treatment. The water holding capacity (WHC) % was significantly increased (p < 0.001) except T3 treatment. The score of color, juiciness and tenderness were significantly different (p < 0.001). Flavor and overall acceptability score were significantly increased (p < 0.05) in different treatments. The color values L* and b* had significantly changed (p < 0.001) and a* value was found significantly higher (p < 0.05) in all treatments. Hence, 12 months of aged lambs with 1.5% concentrate feed showed better performances on carcass, nutritional, physicochemical, sensory and instrumental color values to increase the carcass and the meat quality of lambs.

This research investigated the growth and other production traits of four distinct lines (L1, L2, L3, and L4) of Japanese quail (Cortunix japanoica) kept in the tropical climate of Tamil Nadu, India. The traits related to body weight at different weeks and weight gain were measured in 180 birds (90 males and 90 females) per line up to the fifth week of age, and then 90 birds (females only) from the sixth to the 16th week of age, with egg production and feed efficiency parameters measured in 10 observations per line. The traits were analysed using the General Linear Model procedure, and Tukey\'s HSD was used to test for statistical differences (p < 0.05) between the means for subclasses under a specific effect. The results revealed a highly significant difference (p < 0.01) in body weight from hatch to fifth week of age. At 5th week of age, the L3 and L2 did not differ (p > 0.05) based on Tukey test; therefore, both presented the highest values and were statistically significant (p < 0.01) with L4 with a lowest value of 203.62 g. The cumulative fifth week feed conversion ratio showed non-significant difference (p > 0.05) at first and second week, and highly significant difference (p < 0.01) from third to fifth week of age. The age at 50 per cent egg production was 60.2 (L4), 61.4 (L2), 65.1 (L3) and 66.0 (L1) days and the L1 egg production differed significantly (p < 0.01) from L4 line. The highest bodyweight (g) during the laying period (at 15 weeks of age) was observed in L2 (327.08) and L3 (326.54) and differed significantly (p < 0.01) from L1 (309.24) as well as L4 (288.69) lines. The mean egg weight (g) of different lines showed non-significant difference (p > 0.05) at all weeks, except at 11th week of age (p < 0.01). The mean feed consumption (g)/bird/day differed significantly (p < 0.01) from 6th to 16th week of age, except at sixth and eighth week of age, where it was non-significant (p > 0.05). The overall feed efficiency/dozen of eggs (from 6th to 16th weeks) ranged from 1.33 (L1) to 1.98 (L3). The livability from 6 to 16 weeks of age was 100 per cent in all the lines. In order to boost Japanese quail production in the tropics, L3 and L4 may be selected for body weight and egg production, respectively.