The missing link between nature and nurture i.e. epigenetics is the process of turning genes on and off or can be explained as a phenomenon that includes all the process that affects phenotypic expressions without causing any alteration in the genetic sequence. Epigenetic regulation can be done by post-translational modification of histones but is also linked to the regulation of gene expression by non-coding RNAs, genome instabilities or any other force that could modify a phenotype. Epigenomic patterns in various tissues reveal the regulatory functions of epigenetic mechanisms in livestock growth and health. DNA methylation modifications can explain poor offspring performance due to maternal stressors like metabolic disorder, heat stress and negative energy balance. It is an attractive field for livestock breeding, as it can help identify missing causality and heritability of traits and diseases. Certain methylation patterns are more likely to increase in specific environments, explaining phenotypic diversity between individuals. Accurate recording of the environment and epigenomes can provide more accurate and precise calculations of phenotypic variance. Methods to estimate the contribution of epigenetics to covariance between relatives have been developed which can be beneficial for obtaining favorable methylation patterns that impact disease resistance and economic traits.

Epigenetics: Unraveling Hidden Phenotypic Diversity in Livestock

Background: For this study, information was gathered on 6785 Chokla sheep at the Central Sheep and Wool Research Institute in Bikaner, Rajasthan, India and documented between 1974 and 2020.&nbsp; 
 
Methods: (Co)variance components and genetic parameters of weight at birth (BW), weaning (WW), 6, 9 and 12 months of age (6W,9W and YW, respectively) of Chokla sheep, were estimated by average algorithm restricted maximum likelihood (AIREML), fitting six different animal models with various combinations of direct and maternal effects. 
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Result: The direct heritability estimates increased from birth to twelve months of age and values for all the body weight traits except birth weight (0.170) were moderate (0.30-0.50). The maternal influence diminished as age increases and maternal genetic effect (m2) was found to be important and sizeable at weaning stage (0.181). Maternal permanent environmental variance was found to influence the early body weight traits. Negative and high estimate of covariance between direct and maternal effects, resulted in highly inflated values of additive heritability. In this condition, it is more useful to use the total heritability (h2t) for evaluation of the response for selection based on phenotypic values to prevent the use of biased estimates of additive heritability. Genetic and phenotypic correlations among body weights at different ages were positive and ranged from medium to high.

Estimates of Maternal Effect and (co)Variance Components for BodyWeight at Different Ages by Animal Model in Chokla Sheep

<div>Background: The present study is focused on documentation of the husbandry practices and phenotypic characterization of Bidri goats, which is essential in recognition and improvement of this breed. 
 
Methods: A total of 20 random flocks in 7 villages were investigated. Data was collected as per the standard format suggested by ICAR-NBAGR (2012) and was statistically analyzed using analysis of variance in R software environment. 
 
Result: The average flock size of these goats was 33.43&plusmn;4.73. The smaller flocks were generally housed in the part of residence, whereas, larger flocks (30-40 goats) were housed separately. Random mating was observed as males and females were grazed and housed together. These goats were predominantly black (73%), but black with white patches on ears, forehead, neck and knees (18%) and black with brown coat color (9%) were also found. The eyelids, muzzle and hooves were generally black in color and few exceptions were also seen. The forehead was straight in most of the goats but it was convex and concave shaped in very few. In these goats, 78 per cent were horned and were generally upwards, backwards, outward and curved, 13 per cent had downwards, backwards, outward and curved horns. Majority of these goats have pendulous ears and very few had horizontal ears. The average age at first estrus, first kidding, weaning age and kidding interval observed were 10.33&plusmn;0.24, 17.57&plusmn;0.40, 4-6 and 8.48&plusmn;0.38 months, respectively. Usually the first kidding was single; twinning and triplet was 40 and 5 per cent of the breedable does, respectively. The mean body weight was 32.88&plusmn;1.04 kg in bucks and 30.08&plusmn;0.59 kg in does. Bidri goats are distinct and selective breeding would improvise the economic traits in these goats.</div>

​Husbandry Practices and Phenotypic Characterization of Bidri Goats in Karnataka

<div>Background:&nbsp;In Pakistan, the naked neck chickens are characterized on the base of plumage colors such as black, white black, light brown and dark brown. There is scanty of information on hatching traits in different phenotypes of naked neck chicken. The current study aimed to investigate and compare the hatching traits in four phenotypes of naked neck chicken (black, white black, light brown and dark brown). 
 
Methods:&nbsp;In total, 300 females (20 weeks old) comprising four plumage colors (black, white black, light brown and dark brown), 75 from each, were randomly assigned to 20 replicates (15/replicate) under a completely randomized design (CRD). Number of settable eggs, fertility, hatch of fertile, hatchability, embryonic mortality and chick quality parameters were evaluated. 
 
Result:&nbsp;The results showed higher settable eggs, fertility and hatchability in black, dark brown and light brown phenotypes than that of the white black whereas better hatch of fertile and reduced embryonic mortality were recorded in black and dark brown phenotypes as compared to white black. Better chick quality was observed in dark brown phenotype followed by light brown, black and then white black. Phenotypes other than white black had better hatching performance, hence could be used to revive backyard poultry farming.</div>

​​Comparative Evaluation of Hatching Traits in Four Phenotypes of Naked Neck Chicken

<div>Background: Kachchhi-Sindhi horses are famous for their &lsquo;Rewal chal&rsquo; (a unique style of running). These horses dominantly exist in the western-northern border of India adjoining Pakistan. The breeding tract of these horses is Surat, Navsari, Kachchh district of Gujarat and Jaisalmer-Barmer districts of Rajasthan in India. Most familiar colors in the Kachchhi-Sindhi horses are bay and chestnut. Roman nose, ears curved at tips but not touching each other, short back, short pastern length, broader hoof for better grip and docile temperament are major characteristics of these horses. 
 
Methods: The present study is an effort to phenotypically characterize Kachchhi-Sindhi horse breed based on their different biometric indices for selection and conservation of stallions and mares for breeding purposes by private breeders. Fourteen biometric indices were recorded for phenotypic characterization of each breed viz., height at wither (HW), body length (BL), heart girth (HG), neck length (NL), face length (FL), face width (FW), pole, ear length (EL), ear width (EW), foreleg length (FLL), canon, pastern, hoof length (HoL) and hoof width (HoW). On average, these horses stand 148 cm height, have a body length of ~140 cm, a heart girth of ~165 cm, an ear length of ~15 cm and a face length of ~61 cm. 
 
Result: Horse keepers sustain horses in intensive as well as an extensive system of rearing. It has also been ascertained from various sources that horse number is declining rapidly, however, breed population statistics are not available. There is, therefore, an urgent need to conserve this breed. Proper managemental practices and conservation efforts will pave the way for the multiplication of this valuable equine genetic resource of India.</div>

<div>Phenotypic Characterization of Kachchhi-Sindhi Horses of India</div>

<div>Background: Notable advancements in the selection indices have led to the development of exceptional breeding strategies, which have eventually led to the selection of elite dairy animals. The comparison of trends is facilitated by their estimation which permit the assessment of progress in a particular trait. The purpose of this study was to investigate genetic trends in economic traits of Murrah buffaloes, which is predominantly present as a high milk producer using the regression method. The study was designed to estimate the phenotypic, genetic and environmental trends, which represent the changes accrued over time and hence, determines the efficiency of breeding programme. 
 
Methods: The present study was conducted on 659 Murrah buffaloes, sired by 188 bulls, over a period of 27 years (1991-2017). The economic traits studied were first lactation milk yield (FLMY), first lactation length (FLL), age at first calving (AFC), first calving interval (FCI), first service period (FSP) and first dry period (FDP). The phenotypic trends were obtained as regression of population performance on year and the genetic trends were obtained by Smith method I and II. 
 
Result: The results revealed that the phenotypic trends obtained were significant and desirable for all the traits except for first lactation length, which was non-significant. The standard errors obtained by Smith method-I were higher than those obtained from method-II. As the Smith method-II avoids year to year fluctuations in the environment and those of contemporaries, it gives more realistic estimate as compared to the first method with lower standard error.</div>

<div>Estimation of Phenotypic and Genetic Trends in Economic Traits of Murrah Buffaloes</div>

Background: The advancements achieved in artificial intelligence (AI) technology in recent decades have not yet been equaled by agricultural phenotyping approaches that are both rapid and precise. Efficient crop phenotyping technologies are necessary to enhance crop improvement endeavors in order to fulfill the projected demand for food in future.&nbsp; 
 
Methods: This work demonstrates a method for non-destructive physiological state phenotyping of plants using cutting-edge image processing methods in conjunction with chlorophyll fluorescence imaging. Key fluorescence metrics, such as fv/fm and NPQ, were extracted from images taken at different phases of development via processing. In addition, this research explores the transformative role of automated image analysis in high-throughput phenotyping of legume traits. A comprehensive examination of recent studies reveals the diverse applications of machine learning and deep learning algorithms in capturing morphological traits, assessing physiological parameters, detecting stress and diseases in various legume species. The comparative analysis underscores the superiority of automated systems over traditional methods, emphasizing scalability and efficiency. Challenges, including algorithm sensitivity and environmental variability, are identified, urging further refinement. Recommendations advocate for standardized metrics, interdisciplinary collaborations and user-friendly platforms to enhance accessibility. As the field evolves, the integration of automated image analysis holds promise for revolutionizing legume phenotyping, accelerating crop improvement and contributing to global food security in sustainable agriculture. 
 
Result: The findings demonstrate that the proposed method is effective in illuminating how plants respond to their environment, hence promoting advancements in plant phenotyping and agricultural research.

Leveraging Image Analysis for High-throughput Phenotyping of Legume Plants

Vachellia karroo is an important pasture legume which fixes nitrogen through its symbiotic relationship with rhizobia. Thirty two indigenous rhizobia were isolated from four different morphotypes of V. karroo obtained from four agro-ecologically diverse areas of South Africa. Phenotypic characterization of isolates revealed that they have the same colony morphology. Numeric analysis of the isolates&rsquo; phenotypic characteristics produced six clusters at 83% level of relative similarity. High variation of the isolates growth in different temperatures, salt concentration, pH, antibiotic resistance and heavy metal resistance was also noted. Carbon source utilization was generally the same for all isolates. Isolates that tolerated a wide range of test conditions are recommended as potentially highly competitive V. karroo inoculants for use in various climatic and soil conditions.

Phenotypic characterisation of rhizobia nodulating different&nbsp;morphotypes of Vachellia karroo

<div>Background: Pedigree method of breeding in predominantly self-pollinated crop like dolichos bean enable exploiting only fixable genetic effects as a result of rapid increase in homozygosis. One or a few cycles of inter-mating in F2 generation help create populations with high frequency of desired recombinants which otherwise cannot be realized in later generations. The objective of the present investigation was to assess the impact of inter se mating in F2 population on nine quantitative traits&rsquo; (QTs) mean and variability parameters. 
 
Methods: Randomly selected 20 pairs of a single cross-derived F2 plants with flowering synchrony were inter se mated. Progenies derived from 20 paired crosses (designated as BIP F3 progenies) and those (F3) derived from their 40 F2 parents were evaluated for 9 QTs. Statistics such as mean, absolute range (AR) and standardized range (SR), variance (&sigma;2), additive genetic variance (&sigma;2A) and narrow-sense heritability (NS-h2) were estimated. BIP F3 progenies were compared with those of F3 progenies for QTs mean, AR/SR, &sigma;2, &sigma;2A and NS-h2. Significance of differences between BIP F3 progenies and F3 progenies for mean and &sigma;2 were examined using two-sample t test and Levene&rsquo;s tests, respectively.&nbsp; 
 
Result: The random mating in F2 population was effective in increasing the means, variances, &sigma;2A and NS-h2 of racemes plant-1, fresh pods node-1, fresh pods plant-1 and fresh pod yield plant-1 in dolichos bean. Considering that random mating followed by selfing is a method of genetic improvement for future breeding rather than for immediate use, our results suggest long-term genetic gain and better prospects of deriving superior pure-lines with desired traits/combination of traits from inter-mated population in dolichos bean.</div>

<div>Effect of F2 Inter se Mating on Quantitative Traits Mean, Range, Variance and Heritability in Dolichos Bean (Lablab purpureus L. Sweet var. Lignosus)</div>

<div style="text-align: justify;">Animal coloration is a powerful model for studying the genetic mechanisms that determine animal phenotypes. But, there has not been comprehensive characterization of the molecular basis of the complex patterns of coat color phenotype variation in wild boars. This study results indicated that the wild-type allele E+ of the MC1R gene was a dominant allele in wild boars and was not responsible for black, brown or other coat color phenotypes. A novel mutation c.695 T &gt; C was identified in the 3&cent;-UTR of the ASIP gene. The association analysis showed that the C mutation allele was highly significantly associated with wild-type coat colors between wild boars and Western pig breeds (P=1.35E-33). A non-synonymous g.2254 G &gt; A substitution was found in exon 2 of the TYRP1 gene (p.143His&gt;Arg). The association analysis demonstrated that the G mutation allele was also significantly associated with wild-type coat colors between wild boars and Western pig breeds (P = 5.09E-10). In short, a few mutation sites in MC1R, ASIP, and TYRP1 genes were identified and surveyed several polymorphisms molecular variations in Chinese wild boars. In our identified mutations have caused the morphological diversity in wild boars, but did not influence coat color phenotype variation in some domesticated pig breeds. The conclusion was obtained that some mutations in color-associated genes were associated with wild-type coat colors in wild boar population, and that similar coat colorations observed in domesticated pig and wild boars can be the product of underlying differences in the genetic basis of color variants.&nbsp;</div>

The mutations within MC1R, TYRP1, ASIP genes and their effects on phenotypes of coat color in wild pigs (Sus scrofa ussuricus )

Epigenetics: Unraveling Hidden Phenotypic Diversity in Livestock

Estimates of Maternal Effect and (co)Variance Components for BodyWeight at Different Ages by Animal Model in Chokla Sheep

Husbandry Practices and Phenotypic Characterization of Bidri Goats in Karnataka

Comparative Evaluation of Hatching Traits in Four Phenotypes of Naked Neck Chicken

Phenotypic Characterization of Kachchhi-Sindhi Horses of India

Estimation of Phenotypic and Genetic Trends in Economic Traits of Murrah Buffaloes

Leveraging Image Analysis for High-throughput Phenotyping of Legume Plants

Phenotypic characterisation of rhizobia nodulating different morphotypes of Vachellia karroo

Effect of F₂ Inter se Mating on Quantitative Traits Mean, Range, Variance and Heritability in Dolichos Bean (Lablab purpureus L. Sweet var. Lignosus)

The mutations within MC1R, TYRP1, ASIP genes and their effects on phenotypes of coat color in wild pigs (Sus scrofa ussuricus )