Phenotypic Characterization and Multivariate Analysis to Explain Body Conformation in Lesser Known Buffalo (Bubalus bubalis) from North India

Genomic patterns of selection in morphometric traits across diverse Indian cattle breeds

This study seeks a comprehensive exploration of genome-wide selective processes impacting morphometric traits across diverse cattle breeds, utilizing an array of statistical methods. Morphometric traits, encompassing both qualitative and quantitative variables, play a pivotal role in characterizing and selecting livestock breeds based on their external appearance, size, and physical attributes. While qualitative traits, such as color, horn structure, and coat type, contribute to adaptive features and breed identification, quantitative traits like body weight and conformation measurements bear a closer correlation with production characteristics. This study employs advanced genotyping technologies, including the Illumina BovineSNP50 Bead Chip and next-generation sequencing methods like Reduced Representation sequencing, to identify genomic signatures associated with these traits. We applied four intra-population methods to find evidence of selection, such as Tajima's D, CLR, iHS, and ROH. We found a total of 40 genes under the selection signature, that were associated with morphometric traits in five cattle breeds (Kankrej, Tharparkar, Nelore, Sahiwal, and Gir). Crucial genes such as ADIPDQ, DPP6, INSIG1, SLC35D2 in Kankrej, LPL, ATP6V1B2, CDC14B in Tharparkar, HPSE2, PLAG1 in Nelore, PCSK1, PRKD1 in Sahiwal, and GNAQ, HPCAL1 in Gir were identified in our study. This approach provides valuable insights into the genetic basis of variations in body weight and conformation traits, facilitating informed selection processes and offering a deeper understanding of the evolutionary and domestication processes in diverse cattle breeds.

Prediction of Body Weight by Using PCA-Supported Gradient Boosting and Random Forest Algorithms in Water Buffaloes (Bubalus bubalis) Reared in South-Eastern Mexico

This study aims to use advanced machine learning techniques supported by Principal Component Analysis (PCA) to estimate body weight (BW) in buffalos raised in southeastern Mexico and compare their performance. The first stage of the current study consists of body measurements and the process of determining the most informative variables using PCA, a dimension reduction method. This process reduces the data size by eliminating the complex structure of the model and provides a faster and more effective learning process. As a second stage, two separate prediction models were developed with Gradient Boosting and Random Forest algorithms, using the principal components obtained from the data set reduced by PCA. The performances of both models were compared using R2, RMSE and MAE metrics, and showed that the Gradient Boosting model achieved a better prediction performance with a higher R2 value and lower error rates than the Random Forest model. In conclusion, PCA-supported modeling applications can provide more reliable results, and the Gradient Boosting algorithm is superior to Random Forest in this context. The current study demonstrates the potential use of machine learning approaches in estimating body weight in water buffalos, and will support sustainable animal husbandry by contributing to decision making processes in the field of animal science.

Discriminant analysis reveals differences in breed structure in river buffaloes of Maharashtra (India)

Buffaloes are a major milch species of India, and owning a true-to-breed buffalo herd is a reverie for livestock keepers, as it substantiates their incomes. Multivariate discriminate analysis is an efficient methodology to classify different farm animal populations based on canonical discriminant function. The present study was conducted on 392 adult buffaloes using 18 body biometric traits. Except for body height and body length, all the body characters revealed significant differences amongst the four buffalo populations. Unlike cattle, distance between horns and rump width were more discriminating factors, compared to body height, leg length, chest girth, and body length. We report the most suitable discriminate function which can discriminate with maximum between-group variation in four studied populations. Mahalanobis distances were calculated between populations and they ranged from 0.786 to 1.227. Purnathadi has revealed a distinct phenotypic structure, and these buffaloes have a distinct native breeding region comprising Akola, Amravati, and Buldhana districts of Maharashtra state. On the other hand, Elachpuri animals failed to depict physical and biometric discriminations from Nagpuri, Marathwadi, and Purnathadi buffalo populations, and Elachpuri can be considered as a strain of Nagpuri buffalo.

Multivariate analysis of morphometric traits of Malaimadu cattle-autochthonous draft cattle of south India

Malaimadu cattle is a less explored indigenous cattle germplasm reared in the Western Ghats area of Tamil Nadu, south India. This study aimed to analyze the morphological structure of the Malaimadu cattle using a multivariate approach that explains and best represents body conformation. Sixteen body measurements were obtained from 156 adult female cattle from their native breeding tract. The Nearest Neighbor Method of Hierarchical Cluster analysis was used to group the morphometric traits into clusters. Pearson's coefficients of correlation (r) were estimated to determine the phenotypic correlations between different body measurements. Traits were analyzed using varimax rotated principal component analysis (PCA) with Kaiser normalization. Cluster analysis categorizes morphometric traits into two distinct clusters with the first cluster formed by traits related to horns and face, while the second cluster denotes general body conformation. Out of 120 phenotypic correlations, 55 were significant of which 51 were positive correlations. The estimated correlation coefficient ranges between - 0.50 (body length and face width) to 0.85 (chest girth and body weight). PCA extracted six components representing 70.19% of the total variance, while the first principal component comprises chest girth (CG), body weight (BW), height at wither (HW), and Paunch girth (PG) alone accounts for 23.70% thereby describing the general size and shape of the animal. The multivariate approach has proven to be effective in differentiating Malaimadu cattle from other indigenous breeds of south India with clear morphometric differences that help in identifying the pure phenotype for future propagation and also for devising breeding strategies.

Principal component analysis of body biometric traits in Marathwadi buffaloes

The identification of livestock breed is a necessity for its long-term maintenance and utilisation. Principal component analysis of morphometric traits has proved successful for reduction in the number of features needed for morphological evaluation in livestock species, which keeps costs down and saves time and efforts. Eighteen body biometric traits, viz. Height at withers, Leg length, Neck length, Neck circumference, Body length, Chest girth, Abdominal girth, Face length, Face width, Ear length, Horn length, Horn base circumference, Distance between horns, Hip-bone distance, Pin-bone distance, Distance between hip and Pubis bone, Rump length and Tail length of 103 Marathwadi buffaloes were analysed by using Promax rotated PCA with Kaiser Normalization to explain body conformation. Highest correlation was observed between HW × LEG (0.77), KMO Measure of Sampling Adequacy was 0.794 while Bartlett’s test of Sphericity was significant with chi-square value of 640.494. PCA revealed five components which explained about 61.91% of the total variation. First component explained 31.05% describing general body conformation with highest loadings for BH, CG, LEG and HB. The communality ranged from 0.43 (HC) to 0.78 (FW). Total variance explained by second, third, fourth and fifth component was 10.83%, 7.34%, 6.75% and 5.92% respectively. The rotated pattern matrix showed higher loadings of NC, PG, FL for Marathwadi buffaloes. Traits having high loadings in pattern matrix had high correlation with the components under structure matrix. Present study suggested that PCA can successfully reduce the dimensionality and first PC can be used in the evaluation and comparison of body conformation in Marathwadi buffaloes.

Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India

To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.

Principal component analysis of linear type traits to explain body conformation in Murrah buffaloes

Linear type traits are important in terms of reflecting breed standards and in giving information about the developmental ability of the animals. For data analysis, principal component analysis (PCA) is most important technique when variables are correlated. The aim of present study was to make linear type traits unrelated and reduce their number to the extent which could be used in explaining body conformation in Murrah buffaloes. Measurements were recorded on a total of 81 adult Murrah buffaloes maintained at Buffalo Farm, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar for 11 linear type traits (top wedge angle, rump slope, rump width, hip bone distance, navel flap length, brisket distance, height at wither, body length, skin thickness at neck region, skin thickness at ribs region and skin thickness at rump region). Phenotypic correlations were calculated for considered traits and significant positive correlations varied from 0.26 to 0.67 in the present study. All 11 linear type traits were subjected to varimax rotated PCA with Kaiser Normalization to explain body conformation of Murrah buffaloes. Principal component analysis resulted into four components which described 69.522% of total variation and out of this, first component explained 28.678% variation. The communality ranged from 0.882 (rump slope) to 0.390 (naval flap length) and unique factors ranged from 0.118 to 0.610 for 11 different linear type traits. It was concluded that PCA was effective to reduce the number of variables required to explain the body conformation in Murrah buffaloes.

Multivariate analysis of body morphometric traits in conjunction with performance of reproduction and milk traits in crossbred progeny of Murrah × Jafarabadi buffalo (Bubalus bubalis) in North-Eastern Brazil

We studied the relationship between body morphometric traits, and their underlying association with milk production (MP), lactation length (LL), first calving interval (FCI) and subsequent calving interval (CI) of crossbred progeny of Murrah × Jafarabadi buffalo aiming to assist in selection programs. We carried out principal component analysis (PCA) of the body morphometric traits, which include breast width (BW), thigh width (THW), hip width (HW), rump width (RW), rump length (RL), body depth (BD), body length (BL), height withers (HEW), rear height (RH), shoulder width (SW), thorax width (TW), loin width (LW), distance from the head to ischium (DHI), and thoracic perimeter (TP). We determined the association of morphometric traits with milk/reproduction traits using canonical correlation analysis (CCA). The analysis revealed that the first six PCA accounted for 82.14% of the total observed variation, and the traits THW, HW, TW, LW, RW, HEW, TP, RH, and BW, accounted for almost half (48.00%) of the total variance indicating a higher contribution in body structural conformation. The first canonical function was significant (p<0.05), accounted for 72.46% of the total variance, and the canonical correlation was 0.56, indicating the dependence between both groups of traits. Higher canonical loadings were obtained for LL (0.49), FCI (0.46), BW (-0.71), BL (-0.56), DHI (-0.34), HEW, (-0.38) and TP (-0.50). These traits were most important for the derivation of canonical statistical variables, and presented a higher canonical correlations (r) between the dependent (LL/FCI) and independent (BW, BL, DHI, HEW and TP) groups. The results could suggest that the body morphometric traits THW, HW, TW, LW, RW, HEW, BD, TP, RH, and BW could play important role in body structural composition, indicating a suitable functional type, and aid designing of selection programs for buffalo breeding.

Phenotypic characterization, management and socio-economic impact of Purnathadi buffaloes

A survey was conducted in breeding tract of Purnathadi buffalo with the aim to record its physical, phenotypic and performance traits as well as management practices and the socio economic status were assessed. Purnathadi is a medium sized buffalo, docile in nature with a typical whitish to brown coat colour. Physical and morphometric traits are not only important to identify the group of animals but because of their relationship with performance traits. The studied population of Purnathadi buffalo breed was homogeneous and possessed distinct physical characters those could form the base for identification. Purnathadi buffaloes were preferred by the small and marginal farmers due to low animal cost, high fat% in milk, good reproductive performance and low maintenance cost on feeding and management, however, non-availability of frozen semen and low preference towards maintenance of breeding bull is a major limitation for genetic improvement and conservation of Purnathadi buffaloes. Further, detailed studies for its complete characterization and genetic comparison with other breeds of the region are necessary to register and recognize Purnathadi as separate breed of buffalo, so that breeding plan for conservation and genetic improvement could be designed. This shall increase the interest and confidence of its keepers towards their own germplasm, the Purnathadi buffalo.

Multivariate analysis of biometric traits and their shared variance in Chhattisgarhi buffalo

Principal component analysis (PCA) with a varimax rotation was applied to 18 highly inter-correlated body biometric traits in 157 adult female water buffalo from Chhattisgarh state of India to deduce the components that control body conformation, suitable for use in buffalo breeding, and to reveal the main sources of their shared variability. First principal component explained 34.47% of total variance in body biometric traits and can be used in the evaluation and comparison of body morphology in female water buffaloes using body height, neck circumference, rump width, leg length, paunch girth, chest girth and tail length. The shared variability due to common variance ranged from 92% (horn length) to 51% (rump length) whereas 8 to 49% of their variation was contributed by unique variance specific for each trait in Chhattisgarhi buffaloes.

Identification and characterization of Chhattisgarhi buffalo population in India

Chhattisgarhi buffalo are raised in North and Central parts of Chhattisgarh. They are medium sized buffaloes having triple purpose utility viz. milk, drought and manure, which makes them economical to their keepers. Average milk production in buffaloes was around 4 kg/day with a peak milk yield of 6 kg and buffalo bullocks were preferred over cattle bullocks for cultivating rice fields. Physical and phenotypic characterization of Chhattisgarhi buffalo reveals that the population does not resemble other extant breeds of the region and has a unique management system, therefore, we may conclude that Chhattisgarhi buffalo is unique and distinct population. We recommend that Chhattisgarhi buffalo should be registered and recognized as separate breed of buffalo in India.

Principal component analysis of biometric traits to explain body conformation in Kajali sheep of Punjab, India

Different body biometric traits were analysed in Kajali ewes (395) of Punjab (India) using varimax rotated principal components (PCA) with Kaiser Normalization to explain their body conformation and were subsequently used to predict adult body weight. These traits revealed that Kajali sheep were large in size and suitable for mutton production. The positive and highly significant phenotypic correlations among most of the traits indicates high predictability among these traits. PCA extracted major three components which explained 68.66% of total variation of body biometry. First component described the body size and explained about 36% of total variation. It was represented by high component loadings for chest girth, paunch girth and body weight. The second component described the tail length, height and ear length and explained about 21% variation. The communalities ranges between 0.33 (face length) to 0.87 (chest girth). The lower communality of face length and ear length indicates that these traits are less effective to explain the body conformation. The study suggested that PCA could be used in breeding programme for phenotypic selection of Kajali ewes and PCA is more appropriate compared to multiple regression analysis in predicting adult body weight. In predicting body weight using multiple regression analysis, chest girth alone accounted for 55% of total variation in body weight whereas, use of first principal component as a single predictor explained 79% of total variance and the best prediction equation (R2 = 0.83) was obtained after inclusion of second and third component in the model.

Study of the dairy characters of lactating Murrah buffaloes on the basis of body parts measurements

AIM

The aim of the study was to correlate the milk yield of Murrah buffaloes with certain body parts measurements.

MATERIALS AND METHODS

A total of 70 lactating Murrah buffaloes were selected from Buffalo Farm, Lala Lajpat Rai University of Veterinary and Animal Science, Hisar and were randomly selected in a range from first to fifth parity. Traits studied were 305 days milk yield (MY), body weight (BW), body length (BL), muzzle width (MW), height at wither (HW), abdominal girth (AG), chest girth (CG), body depth fore, body depth rear, hip bone distance (HBD), pin bone distance (PBD), skin thickness (STK), and tail length (TL). Data were collected and statically analyzed by Pearson's correlation method.

RESULT

The result of this study showed that Murrah buffaloes had the average 2604.8±39.5 kg for MY, 556.1±4.9 kg for BW, and 152.2±0.8 cm for BL. This study showed that buffaloes had positive significant (p<0.05) correlation between MY and BW (0.26). Highly significant (p<0.01) correlation was observed between MY and AG (0.64), MW (0.42). Significant (p<0.01) negative correlation was observed between MY and STK (-0.79). Different body part measurements (BW, BL, HW, AG, CG, MW, TL, BD, PBD, HBD, STK) were significantly correlated with each other.

CONCLUSION

This study can be helpful as a selection tool to enhance and evaluate the production potential by setting standards of Murrah buffalo breed. BW, abdominal growth, muzzle thickness, and STK were found key factors while selecting a dairy Murrah buffalo.

Principal component analysis of biometric traits to reveal body confirmation in local hill cattle of Himalayan state of Himachal Pradesh, India

AIM

In the present study, biometric traits (body length [BL], heart girth [HG], paunch girth (PG), forelimb length (FLL), hind limb length (HLL), face length, forehead width, forehead length, height at hump, hump length (HL), hook to hook distance, pin to pin distance, tail length (TL), TL up to switch, horn length, horn circumference, and ear length were studied in 218 adult hill cattle of Himachal Pradesh for phenotypic characterization.

MATERIALS AND METHODS

Morphological and biometrical observations were recorded on 218 hill cattle randomly selected from different districts within the breeding tract. Multivariate statistics and principal component analysis are used to account for the maximum portion of variation present in the original set of variables with a minimum number of composite variables through Statistical software, SAS 9.2.

RESULT

Five components were extracted which accounted for 65.9% of variance. The first component explained general body confirmation and explained 34.7% variation. It was represented by significant loading for BL, HG, PG, FLL, and HLL. Communality estimate ranged from 0.41 (HL) to 0.88 (TL). Second, third, fourth, and fifth component had a high loading for tail characteristics, horn characteristics, facial biometrics, and rear body, respectively.

CONCLUSION

The result of component analysis of biometric traits suggested that indigenous hill cattle of Himachal Pradesh are small and compact size cattle with a medium hump, horizontally placed short ears, and a long tail. The study also revealed that factors extracted from the present investigation could be used in breeding programs with sufficient reduction in the number of biometric traits to be recorded to explain the body confirmation.