Phenomics in Livestock Research: Bottlenecks and Promises of Digital Phenotyping and Other Quantification Techniques on a Global Scale.

Bottlenecks in moving genomics to real-life applications also include phenomics. This is true not only for genomics medicine and public health genomics but also in ecology and livestock phenomics. This expert narrative review explores the intricate relationship between genetic makeup and observable phenotypic traits across various biological levels in the context of livestock research. We unpack and emphasize the significance of precise phenotypic data in selective breeding outcomes and examine the multifaceted applications of phenomics, ranging from improvement to assessing welfare, reproductive traits, and environmental adaptation in livestock. As phenotypic traits exhibit strong correlations, their measurement alongside specific biological outcomes provides insights into performance, overall health, and clinical endpoints like morbidity and disease. In addition, automated assessment of livestock holds potential for monitoring the dynamic phenotypic traits across various species, facilitating a deeper comprehension of how they adapt to their environment and attendant stressors. A key challenge in genetic improvement in livestock is predicting individuals with optimal fitness without direct measurement. Temporal predictions from unmanned aerial systems can surpass genomic predictions, offering in-depth data on livestock. In the near future, digital phenotyping and digital biomarkers may further unravel the genetic intricacies of stress tolerance, adaptation and welfare aspects of animals enabling the selection of climate-resilient and productive livestock. This expert review thus delves into challenges associated with phenotyping and discusses technological advancements shaping the future of biological research concerning livestock.

Carcass characteristics, meat quality, and nutritional profiles of Mithun (Bos frontalis) meat reared under a semi-intensive system.

The present study aimed to determine carcass characteristics, meat quality, nutrient profiles, and sensory characteristics of Mithun meat. Sixteen Mithun were selected and divided into four groups, MM-4 (male; n = 4; <4 years of age), MM-47 (male; n = 4; 4-7 years of age), MF-4 (female; n = 4; <4 years of age), MF-47 (female; n = 4; 4-7 years of age). Carcass characteristics showed that adult males (MM-47) have significantly higher (P < 0.05) live weight, carcass weight, and meat-to-bone ratio. Fat (%) was significantly higher (P < 0.05), and deboned meat (%) was lower in MF-4 and MF-47, while marginal differences were observed in bone (%), dressing percentage, and offal yield between groups. Visible marbling increased with age and varied from "slight" to "small" in all groups. Nutrient profiling revealed a significantly higher (P < 0.05) fat percentage and cholesterol in MF-4 and MF-47. Fatty acid profile, amino acid profile, water-soluble vitamins, and minerals content did not differ between groups. However, lysine and leucine (essential amino acids) and glutamic acid and aspartic acid (nonessential amino acids) were most abundant. Effect of age was significant (P < 0.05) on juiciness, tenderness, and connective tissue residue scores. In conclusion, results indicate mithun meat is nutrient-rich regardless of the animal's age or sex.

Optimized addition of nitric oxide compounds in semen extender improves post-thaw seminal attributes of Murrah buffaloes.

Semen dilution and cryopreservation alter the homogeneity of seminal plasma, resulting in a non-physiological redox milieu and consequently poor sperm functionality. Considering the concentration-specific bimodal action of nitric oxide (NO) in the regulation of sperm functions, cryopreservation media supplemented with optimized concentrations can improve the semen attributes. The present study aimed to evaluate the effect of adding an optimized concentration of sodium nitroprusside (SNP) and N-nitro-L-arginine methyl ester (L-NAME) in an extender on in vitro semen quality. An aliquot of semen samples (n = 32) from Murrah buffalo bulls (n = 8) was divided into control (C) and treatment (T-I: SNP in extender at 1 µmol/L; T-II: L-NAME in extender at 10 µmol/L). Fresh semen quality parameters showed no significant difference at 0 h except for the structural integrity in the T-II group. Post-thaw semen quality parameters and sperm kinematics using computer-aided sperm analysis (CASA) revealed significantly higher (p < 0.05) cryoresistance in the treatment groups. Viability, acrosome integrity, and membrane integrity were significantly higher (p < 0.05) in both treatment groups; however, the results were pervasive in T-II. Lower abnormal spermatozoa were observed in both T-I and T-II. SNP supplementation led to a significant rise (p < 0.05) in NO, whereas L-NAME reduced the NO concentration in post-thawed samples, which was directly correlated with different sperm functionality and associated biomarkers viz. total antioxidant capacity (TAC) and thiobarbituric acid reactive substance (TBARS). It was concluded that the cryopreservation media supplemented with SNP and L-NAME at 1 µmol/L and 10 µmol/L, respectively, lower the cryo-damage and improve post-thaw seminal attributes.

Ovarian follicular dynamics, hormonal profiles and ovulation time in Mithun cows (Bos frontalis).

The study aimed to evaluate follicular dynamics and concentrations of estradiol-17ß (E2), progesterone (P4), follicle stimulating hormone (FSH) and luteinizing hormone (LH) during the oestrous cycle and to determine ovulation time in Mithun cows. Ovaries of experimental cows (n = 7) were examined daily by transrectal-ultrasonography for three consecutive oestrous cycles (n = 21). The characteristics of follicular waves, dominant follicle, largest subordinate follicle and corpus luteum and ovulation time were evaluated. The plasma samples were analysed throughout the interovulatory interval to determine the differences in the hormonal profiles (E2, P4, FSH and LH) between different follicular wave cycles. Out of eighteen oestrous cycles analysed, three-wave follicular cycles were maximum (n = 12: 66.66%) followed by two (n = 4: 22.22%) and four waves (n = 2: 11.11%). The two and three waves were statistically compared, and no significant (p > .05) differences were observed in day of wave emergence, number of follicles (≥3 mm) recruited, maximum diameter of the ovulatory dominant follicle, growth rates of ovulatory and anovulatory dominant follicles and maximum diameter of corpus luteum. The diameter of dominant follicles was significantly (p < .05) greater than subordinate follicles in both ovulatory and anovulatory waves. No significant differences were observed in peak concentrations of estradiol-17ß and follicle stimulating hormone between ovulatory and anovulatory waves in all wave cycles. A preovulatory luteinizing hormone surge was observed a day before ovulation in all wave cycles. Progesterone concentrations were lower than 0.5 ng/ml during oestrus and increased sharply to the maximum levels of ≥3.8 ng/ml in all wave cycles. Ovulation time (mean ± SEM), irrespective of follicular waves was 10.5 ± 0.64 h after the end of oestrus. It was concluded that Mithun cows have a preponderance of three follicular waves with little difference between the two- and three-follicular waves and ovulation occurred 10.5 h after the end of oestrus.

Bimodal interplay of reactive oxygen and nitrogen species in physiology and pathophysiology of bovine sperm function.

Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are the mediators of redox activity and are known to perform concentration-specific bimodal roles. At lower concentrations, serves as a molecular messenger and signaling molecule while at higher concentrations induces stress which in turn alters the sperm's functional characteristics. Production of ROS and RNS cannot be prevented entirely and should not be followed as a pragmatic approach as they are involved in numerous sperm physiological functions. When the antioxidants defense armory is meager, excess generation of these species cross the physiological limits and inactivates essential metabolic enzymes and disrupts signal transduction altering normal sperm functions. As per the available literature, oxidants mostly arise as a result of pathological conditions or cryopreservation-induced injury. Dead and debilitated or abnormal spermatozoa and associated leukocytes release free radicals in an excess amount which elicits oxidative and nitrosative stressors that are potentially toxic to cryosurviving sperm. ROS plays a double edge sword effect on sperm function, as regulators of physiological mechanisms at low levels and as toxicants when produced at high concentrations. Recently nitric oxide (NO.) has emerged as a potential regulator of sperm physiology, in addition, found to mediate homeostasis of the seminal plasma microenvironment when semen samples are incubated with optimal concentrations of NO. compounds. The NO. compounds can provide some resistance to future stresses which are not usually harnessed by using the defensive strategy of supplementing antioxidants. Therefore, through the optimized addition of NO. donor and inhibitor in extender, the free radical-induced damage can be avoided without inhibiting their essential physiological effects on fertilization and subsequent embryo development. This article is intended to describe the role of reactive oxidants in the physiology and pathophysiology of spermatozoa and their relationship with various seminal attributes.

Comparative ejaculatory response, fresh and frozen semen quality and fertility to artificial vagina vs electroejaculation method of semen collection in mithun (Bos frontalis) bulls.

The study aimed to describe a comparative ejaculatory response, fresh and frozen-thawed semen quality and fertility of semen collected by artificial vagina and electroejaculation in mithun. Experimental bulls were divided into two groups, G-I: young bulls (n = 4; 4-5 years of age) and G-II: older bulls (n = 4; 8-10 years of age). Sixteen ejaculates were collected from each group G-I (AV1 ) and G-II (AV2 ) by artificial vagina method (control). Thirty-six ejaculates were collected from the same bulls from each group G-I (EE1 ) and G-II (EE2 ) by electroejaculation method (treatment). The study did not reveal any significant (p > 0.05) difference in the ejaculatory responses between EE1 and EE2 . Mann-Whitney U test indicated that salivation discomfort sign score was significantly (p < 0.05) higher in EE1 . Fresh and frozen-thawed semen quality parameters, and motility and velocity profiles recorded by computer-assisted sperm analyser were significantly (p < 0.05) lower in electroejaculation than the artificial vagina. The conception rates (AV1 vs EE1 & AV2 vs EE2 ) at day 35-45 post insemination were nonsignificantly higher (p > 0.05) in the artificial vagina group. It concluded that, although artificial vagina method has better semen quality, nevertheless, electroejaculation has the potential for semen collection from free-range mithun bulls to incorporate in assisted reproductive technology procedures.

Implications of cryopreservation on structural and functional attributes of bovine spermatozoa: An overview.

Sperm cryopreservation is an important adjunct to assisted reproduction techniques (ART) for improving the reproductive efficiency of dairy cattle and buffaloes. Improved understanding of mechanisms and challenges of bovine semen cryopreservation is vital for artificial insemination on a commercial basis. Although cryopreservation of bovine spermatozoa is widely practiced and advanced beyond that of other species, there are still major gaps in the knowledge and technology. Upon cryopreservation, disruption of spermatozoal plasma membrane configuration due to alterations in metabolic pathways, enzymes and antioxidants activity add to lower efficiency with loss of sperm longevity and fertilising ability. Therefore, the effective amalgamation of cryo-variables like ambient temperature, cooling and thawing rates, nucleation temperature, type and concentration of the cryoprotectant, seminal plasma composition, free radicals and antioxidant status are required to optimise cryopreservation. Novel strategies like supplementation of cholesterol-loaded cyclodextrins (CLC), nanovesicles, osteopontin, antioxidants, etc., in an extender and recent techniques like nano-purification and modified packaging have to be optimised to ameliorate the cryodamage. This article is intended to describe the basic facts about the sperm cryopreservation process in bovine and the associated biochemical, biophysical, ultra-structural, molecular and functional alterations.