Introduction
In India, total milk production was 187.75 million tonnes in 2018–2019 with an increase of 6.5% over the previous year. As per BAHS (2019), buffaloes (49%) contribute the most to the total milk production in the country followed by cattle (48%) and goats (3%). Out of the total milk production, ∼48.82 million tonnes (26%) is contributed by crossbred cattle, indicating the importance of crossbred cattle in India. There is a marked increase in demand of milk and milk products with the rise in the human population numbers. Milk production potential of indigenous cattle can be improved through selective and crossbreeding. Selection of dairy animals is usually done based on the production performance of animals. Any selection or breeding programme in dairy animals requires an understanding of the genetic parameters of performance traits. The importance of estimating genetic and phenotypic parameters in the populations of interest has been depicted by some researchers (Ebangi et al., Reference Ebangi, Erasmus, Neser and Tawah2000; Plasse et al., Reference Plasse, Verde, Fossi, Romero, Hoogesteijn, Bastidas and Bastardo2002). Therefore, there is a need to understand the genetic and phenotypic relationships between various lactation traits, as well as the extent of genetic variation in these traits. Genetic progress in any trait achieved through selection is also determined by the heritability of the trait. Several factors influence the precision of genetic parameters, including the data and information provided, statistical model used, and the method used to estimate covariance.
Previously, researchers (Saha et al., Reference Saha, Joshi and Singh2010; Taggar et al., Reference Taggar, Das, Kumar and Mahajan2014; Ratwan et al., Reference Ratwan, Mandal, Kumar, Kumar and Chakravarty2016, Reference Ratwan, Mandal, Kumar and Chakravarty2017) have estimated the genetic parameters of production and reproduction traits in crossbred cattle using maximum likelihood methods. According to Pollak et al. (Reference Pollak, Werf and Quaas1983), using a multitrait model allows all information available from an animal to be incorporated, increasing the accuracy of genetic parameter estimates. Published literature (Aspilcueta-Borquis et al., Reference Aspilcueta-Borquis, Bignardi, Seno, Camargo, Munoz-Berrocal, Albuquerque, Di Palo and Tonhati2010; Kumar et al., Reference Kumar, Vohra, Ratwan, Valsalan, Patil and Chakravarty2016; Ratwan et al., Reference Ratwan, Kumar, Kumar, Chakravarty and Mandal2018, Reference Ratwan, Kumar, Chakravarty and Mandal2019; Worku et al., Reference Worku, Gowane, Kumar, Joshi, Gupta and Verma2021) has documented the use of restricted maximum likelihood (REML) and Bayesian approaches for the estimation of covariance components and genetic parameters of performance traits in various species. The Bayes approach unravels the problem of limited sample size by providing an accurate a posteriori distribution for any large or small data from which interpretations can be inferred. Likelihood function tends to conquer a priori information, while establishing a posteriori distribution, therefore the parameters estimated coincide with the findings obtained through frequentist methods based on likelihood functions. However, when the sample size is large enough, the maximum likelihood technique gives well defined features, which may not be true for a small sample size (Gianola and Fernando, Reference Gianola and Fernando1986). To the best of our knowledge, there have been no studies in India to estimate the genetic parameters of production and reproduction traits in Jersey crossbred cattle using a Bayesian approach. Therefore, the present study aimed to estimate the genetic parameters of production and reproduction traits in Jersey crossbred cattle using a Bayesian approach.
Materials and methods
Location of farm
The study was conducted on Jersey crossbred cattle kept at the Eastern Regional Station, National Dairy Research Institute, Kalyani, West Bengal, India. On 22.59°N latitude and 88.29°E longitude, the farm is situated at an average altitude of 9.75 m above mean sea level. Hot and humid weather prevails in the area. Average highest and lowest annual temperatures are 41°C and 10°C, respectively. The highest humidity is 91%, and the minimum humidity is 58%, with average annual rainfall of ∼1250 mm. Between July and October, there is the most precipitation (83%). Therefore, it is evident that Jersey crossbred animals maintained at the farm are exposed to a wide range of environmental conditions.
Data
Analysis was carried out on the data of Jersey crossbred cattle spread over a span of 41 years (1974–2014). Incomplete records because of illness or abortion were not considered in the study. Animals having a 305-day milk yield less than 500 kg and a lactation length (LL) less than 100 days were also not considered in the present study. Pedigree viewer software (Kinghorn and Kinghorn, Reference Kinghorn and Kinghorn2015) was used to test the duplicity and bisexuality in pedigree records. Data were divided into seven periods (<1985, 1986–1990, 1991–1995, 1996–2000, 2001–2005, 2006–2010 and 2011–2014) and three seasons, which were winter (November–February), summer (March–June) and rainy (July–October). The parity of animals was classified into seven groups, i.e. 1–6 and 7 for all the animals having a parity >6. Based on the level of inheritance, Jersey crossbred animals were classified into nine genetic groups, i.e. 50% J × 50% RS, 50% J × 50% T, 50% J × 25% (HF/BS) × 25% (Sahiwal/RS), 50% J × 25% T × 25% (RS/Desi), 50% J × 50% (any two other breeds), 50% J miscellaneous group, < 50% J, >50% to 62.5% J and >62.5% J; in which J: Jersey; RS: Red Sindhi; T: Tharparkar; HF: Holstein-Friesian; and BS: Brown-Swiss.
Traits
Traits considered for this study were 305-day milk yield (305MY), total milk yield (TMY), peak yield (PY), lactation length (LL), calving interval (CI) and two production efficiency traits, which were total milk yield per day of lactation length (TMY/LL) and total milk yield per day of calving interval (TMY/CI) in Jersey crossbred cattle. Data structure summary and descriptive statistics for the considered traits are presented in Table 1.
Statistical analyses
Least squares analysis (Harvey, Reference Harvey1990) was done to assess the effect of non-genetic factors viz., period of calving, season of calving, parity and genetic group of animals on the considered traits and significant factors were finally included in the model as fixed effects. The GIBBS3F90 (BLUPF90 family) programme was used to estimate the variance and (co)variance components of investigated traits using a Bayesian approach in multitrait analysis (Misztal et al., Reference Misztal, Tsuruta, Lourenco, Aguilar, Legarra and Vitezica2015). The model of analysis included fixed effects of period of calving, season of calving, parity and genetic group of animals and random effects were additive genetic, permanent environmental and residual effects. The following model was applied:
where y is a vector of observed traits (305MY, TMY, PY, LL, CI, TMY/LL and TMY/CI); X: incidence matrix of fixed effects (period of calving, season of calving, parity and genetic group of animals); β: vector of fixed effects; Z: incidence matrix of additive genetic random effects; a: vector of additive genetic random effects; W: incidence matrix of permanent environmental random effect; p: vector of permanent environmental random effects; and e: vector of random error effects. Inverted Wishart distribution (Sorensen and Gianola, Reference Sorensen and Gianola2007) was supposed for the fully conditional posterior distributions of random effect matrices.
The posterior densities of (co)variance components were calculated using the Gibbs sampler. With a burn-in period of 1 lakh cycle, and a sampling interval of 100 cycles, a chain length of 10 lakhs cycles was established, resulting in 9000 samples for further analysis. Graphical inspection (traceplots and histogram) using gnuplot was used to confirm convergence. Effective samples (9000) in the analysis were used to derive descriptive statistics of posterior distribution for each trait. The reliability was measured using the highest posterior density (HPD) area, which provided a range that contained 95% of the samples.
Results and Discussion
In the present study, averages for 305MY, TMY, PY, LL, CI, TMY/LL and TMY/CI were 2355.16 kg, 2614.61 kg, 12.59 kg, 357.33 days, 441.05 days, 7.48 kg/day and 6.29 kg/day, respectively, in Jersey crossbred cattle. Vijayakumar et al. (Reference Vijayakumar, Singaravadivelan, Silambarasan, Ramachandran and Churchil2019) reported the average value for 305-day milk yield as 2459.27 ± 68.98 kg in Jersey crossbred cattle that was comparatively higher compared with our findings. Taggar et al. (Reference Taggar, Das, Kumar and Mahajan2014) and Ratwan et al. (Reference Ratwan, Mandal, Kumar, Kumar and Chakravarty2016) observed lower (2104.14 ± 38.79 and 2141.26 ± 79.32, respectively) 305MY in Jersey crossbred cattle. Total milk yield as reported by Mandal et al. (Reference Mandal, Roy, Ghosh, Chatterjee and Das2013) was comparatively higher (2881.35 kg) compared with the present study, while Varaprasad et al. (Reference Varaprasad, Raghunandan, Kumar and Prakash2013) and Ratwan et al. (Reference Ratwan, Mandal, Kumar, Kumar and Chakravarty2016) observed lower TMY in Jersey crossbred cattle. Peak yield (11.89 kg) as observed by Ratwan et al. (Reference Ratwan, Mandal, Kumar, Kumar and Chakravarty2016) in Jersey crossbred cattle was in line with the present study. Taggar et al. (Reference Taggar, Das, Kumar and Mahajan2014) reported comparatively lower (340.99 ± 5.91 days) LL in Jersey crossbred cattle maintained in a sub-temperate region. Vijayakumar et al. (Reference Vijayakumar, Singaravadivelan, Silambarasan, Ramachandran and Churchil2019) reported almost similar LL (364.21 ± 9.52 days) and average daily milk yield (8.06 ± 0.23 kg/day), however, the CI (460.56 ± 11.08 days) observed by them was higher compared with the present study. Calving interval observed by Vinothraj et al. (Reference Vinothraj, Subramaniyan, Venkataramanan, Joseph and Sivaselvam2016) was higher (489.12 ± 6.45 days) compared with the present study. Average PY and daily milk yield obtained in the present study corroborated the findings of Taggar et al. (Reference Taggar, Das, Kumar and Mahajan2014) in Jersey crossbred cattle, however they found a comparatively lesser (5.65 ± 0.09) mean value for TMY/CI. Ratwan et al. (Reference Ratwan, Mandal, Kumar, Kumar and Chakravarty2016) also reported similar PY in Jersey crossbred cattle. Ratwan et al. (Reference Ratwan, Mandal, Kumar and Chakravarty2017) observed TMY per day of CI as 5.91 ± 0.23 kg/day that was in agreement with the present results.
It was observed from the graphics of heritability estimates (Fig. 1) that the burn-in duration chosen was sufficient to reach convergence in all the considered traits. According to Resende et al. (Reference Resende, Duda, Guimaraes and Fernandes2001), in Bayesian analysis, the number of samples discarded during the burn-in period and the serial correlation established between samples in the Markov chain are important considerations.
Estimates of heritability (h2) and permanent environment effect (c2)
Variance components as estimated for 305MY, TMY, PY, LL, CI, TMY/LL and TMY/CI in Jersey crossbred cattle are presented in Table 2. Residual variance component estimates were found to be high compared with additive genetic variance for all the considered traits in the present study. Worku et al. (Reference Worku, Gowane, Kumar, Joshi, Gupta and Verma2021) reported similar findings for 305-day milk yield, however Singh et al. (Reference Singh, Singh, Singh, Prakash, Ambhore, Sahoo and Dash2016) observed higher additive genetic and permanent environment variances compared with residual variance for test-day milk yield in Holstein crossbred cattle.
σa 2, additive genetic variance estimates; σc 2, permanent environmental variance estimates; σr 2, residual variance estimates; σp 2, phenotypic variance estimates; h2, heritability estimates; c2, permanent environmental variance estimates as proportions of phenotypic variance estimates; r, repeatability; PSD, posterior standard deviation; HPD, highest posterior density.
In the present study, marginal posterior means (HPD of 95%) of heritability for 305MY, TMY, PY, LL, CI, TMY/LL and TMY/CI were 0.31 (0.180–0.431), 0.29 (0.148–0.408), 0.27 (0.147–0.383), 0.16 (0.069–0.254), 0.15 (0.062–0.236), 0.29 (0.172–0.417), and 0.27 (0.149–0.375), respectively. Heritability estimate for 305MY, as reported by Missanjo et al. (Reference Missanjo, Imbayarwo-Chikosi and Halimani2013), was in agreement with the present findings, although Ratwan et al. (Reference Ratwan, Kumar, Chakravarty and Mandal2019) reported higher (0.55) heritability estimates for 305MY in dairy cattle using REML. Worku et al. (Reference Worku, Gowane, Kumar, Joshi, Gupta and Verma2021) observed lower (0.20 ± 0.03) heritability estimates for 305-day milk yield in Karan-Fries (Holstein cross) cattle using a Bayesian approach. Ratwan et al. (Reference Ratwan, Kumar, Chakravarty and Mandal2019) reported higher (0.50) heritability estimates for TMY in Jersey crossbred cattle using REML, however Worku et al. (Reference Worku, Gowane, Kumar, Joshi, Gupta and Verma2021) observed lower (0.18 ± 0.03) heritability for the same trait in Holstein crossbred cattle using a Bayesian approach. Heritability estimate for PY, as obtained in the present study, was in line with the results of Rekaya et al. (Reference Rekaya, Carabaño and Toro2000). In contrast, Lakshmi et al. (Reference Lakshmi, Gupta, Prakash, Sudhakar and Sharma2010) reported lower (0.16) heritability of PY in Holstein cattle. Ratwan et al. (Reference Ratwan, Kumar, Chakravarty and Mandal2019) reported comparatively higher heritability estimates for PY (0.41) in Jersey crossbred cattle using a REML animal model. Moderate heritability values for 305MY, TMY and PY indicated the existence of adequate additive genetic diversity in these traits to respond to selection combined with better herd management.
For LL, Ratwan et al. (Reference Ratwan, Kumar, Chakravarty and Mandal2019) reported higher (0.25) heritability estimates in Jersey crossbred cattle, although several workers (Dash et al., Reference Dash, Gupta, Avtar, Chakravarty, Mohanty, Panmei and Pushp2016; Ayalew et al., Reference Ayalew, Aliy and Negussie2017; Getahun et al., Reference Getahun, Beneberu and Lemma2020; Worku et al., Reference Worku, Gowane, Kumar, Joshi, Gupta and Verma2021) reported comparatively lower heritability of LL in different cattle breeds. Heritability estimates (0.18), as reported by Usman et al. (Reference Usman, Guo, Suhail, Ahmed, Qiaoxiang, Qureshi and Wang2012) for LL in Holstein cattle, corroborated the present findings. Ali et al. (Reference Ali, Muhammad Suhail and Shafiq2019) observed a similar (0.14 ± 0.21) heritability estimate for CI in different cattle breeds reared under subtropical conditions. In Jersey crossbred cattle, Kumar and Mandal (Reference Kumar and Mandal2021) reported comparatively higher (0.20) heritability of CI using REML. Heritability for CI, as reported by Worku et al. (Reference Worku, Gowane, Kumar, Joshi, Gupta and Verma2021) in Holstein crossbred cattle, was lower compared with the present study. The reason for the differences in heritability estimates by different methods may be attributed to the method of estimation and, additionally, heritability can alter over time due to changes in genetic values and environmental factors.
In the present study, heritability of daily milk yield, i.e. TMY/LL, was observed as 0.28 and this was similar to the results of Getahun et al. (Reference Getahun, Tadesse, Hunde and Lemma2021) in crossbred cows in Ethiopia. Heritability for daily milk yield as observed by Getahun et al. (Reference Getahun, Beneberu and Lemma2020) in Jersey cattle maintained in Ethiopian highland environment was comparatively lower (0.11) compared with the present study. Penasa et al. (Reference Penasa, Cecchinato, Battagin, De Marchi, Pretto and Cassandro2010) also reported lower (0.18) heritability estimates for daily milk yield in Burlina cattle using a Bayesian approach. Ratwan et al. (Reference Ratwan, Kumar, Kumar, Chakravarty and Mandal2018) reported the high heritability (0.47) for TMY per day of LL, although for milk yield per day of CI they observed similar (0.25) heritability estimates. Heritability estimates for TMY/LL and TMY/CI, as observed by Saha et al. (Reference Saha, Joshi and Singh2010) in Holstein crossbred cattle, were higher (0.39) compared with our study.
The present study also revealed that permanent environmental variance estimates as proportions of phenotypic variance estimates (c2) varied from 0.16 to 0.28 for the all considered traits (Table 2). Aspilcueta-Borquis et al. (Reference Aspilcueta-Borquis, Bignardi, Seno, Camargo, Munoz-Berrocal, Albuquerque, Di Palo and Tonhati2010) reported similar (0.23) c2 estimates for milk yield in buffaloes using the same methodology, however Ojango and Pollot (Reference Ojango and Pollott2001) reported c2 as 0.05 and 0.03 for 305MY and LL in Holstein cattle. Edriss et al. (Reference Edriss, Nilforooshan and Sadeghi2006) reported lower estimates of c2 for milk yield in Iranian Holstein cattle. Ratwan et al. (Reference Ratwan, Kumar, Kumar, Chakravarty and Mandal2018) also observed comparatively lower (0.12) permanent environment effects for the trait TMY/CI using derivative-free REML in Jersey crossbred cattle.
Repeatability estimates
Repeatability estimates for 305MY, TMY, PY, LL, CI, TMY/LL and TMY/CI as obtained in Jersey crossbred cattle were 0.57, 0.58, 0.51, 0.34, 0.31, 0.54 and 0.49, respectively. High repeatability estimates for 305MY, TMY and PY in the current study suggested the use of first lactation records for early evaluation of Jersey crossbred cattle for future selection. Pereira et al. (Reference Pereira, Suzuki, Hagiya, Yoshizawa, Tsuruta and Misztal2001) reported the repeatability estimates of milk yield as 0.53 in Japanese Holstein cattle, which was in line with the present study. Similar estimates of repeatability of milk yield were obtained by Visscher and Thompson (Reference Visscher and Thompson1992) using a repeatability animal model. Worku et al. (Reference Worku, Gowane, Kumar, Joshi, Gupta and Verma2021) reported repeatability estimates for 305MY and TMY as 0.37 and 0.34 that were relatively lower compared with the present study. Ilahi et al. (Reference Ilahi, Hammouda and Othmane2012) also reported relatively lower (0.38) repeatability of 305MY in Tunisian Holstein cattle, although Hermiz and Hadad (Reference Hermiz and Hadad2020) reported comparatively higher (0.67) repeatability of TMY in different cattle breeds. Ghafoor et al. (Reference Ghafoor, Khan and Khan1992) reported repeatability of PY as 0.33 in Tharparkar cows that was lower compared with present study. For LL, different workers (Ojango and Pollot, Reference Ojango and Pollott2001; Ayalew et al., Reference Ayalew, Aliy and Negussie2017; Worku et al., Reference Worku, Gowane, Kumar, Joshi, Gupta and Verma2021) reported lower repeatability estimates varying from 0.11 to 0.15 in different breeds of cattle. Islam et al. (Reference Islam, Akhtar, Hossain, Rahman and Hossain2017) observed repeatability estimates as 0.30 for CI in Holstein cattle that were in concordance with present study, however in Jersey crossbred cattle they reported comparatively lower repeatability (0.13) for the same trait.
Correlation estimates
Estimates of correlations between traits can be obtained using multiple-trait analysis, which cannot be done using single-trait analyses. The oscillations in the samples obtained for the genetic correlations did not show extensive dispersion, indicating that the burn-in period utilized in the analysis was acceptable and permitted chain convergence (Gelfand and Smith, Reference Gelfand and Smith1990). In the current study, maximum (0.97) genetic correlation was observed between 305MY and TMY, indicating that consideration of 305MY instead of TMY in breeding programmes would suffice. Strong positive genetic correlation between 305MY and TMY as obtained in current study was in agreement with the findings of several workers (Ayalew et al., Reference Ayalew, Aliy and Negussie2017; Worku et al., Reference Worku, Gowane, Kumar, Joshi, Gupta and Verma2021). Genetic correlations between production traits (305MY, TMY, PY) were observed as strongly positive, varying from 0.85–0.97 (Table 3) and these corresponded with the results of Worku et al. (Reference Worku, Gowane, Kumar, Joshi, Gupta and Verma2021) in Holstein crossbred cattle. In the present study, genetic correlation between 305MY and PY was observed as 0.90, which agreed with the results of Ratwan et al. (Reference Ratwan, Mandal, Kumar, Kumar and Chakravarty2016) in Jersey crossbred cattle. Ratwan et al. (Reference Ratwan, Mandal, Kumar, Kumar and Chakravarty2016) reported comparatively higher (0.62) genetic correlation between LL and PY in Jersey crossbred cattle. Genetic correlations between milk yield and CI were also found to be positive in this study. Makgahlela et al. (Reference Makgahlela, Banga, Norris, Dzama and Ng’ambi2007) reported a high positive genetic correlation between CI and yield traits in South African Holstein cattle. Positive genetic correlations of CI with 305-day milk yield and TMY suggested that animals having more milk yield tended to have longer CI, pointing towards the unfavourable relationship between production and reproduction traits. Several studies (Berry et al., Reference Berry, Buckley, Dillon, Evans, Rath and Veerkamp2003; Wall et al., Reference Wall, Brotherstone, Woolliams, Banos and Coffey2003; Ratwan et al., Reference Ratwan, Chakravarty and Kumar2022) have revealed the antagonistic relationships between production and reproduction traits in cattle.
PSD, posterior standard deviation; HPD, highest posterior density.
Permanent environment correlation estimates between different considered traits varied from low to high, as presented in Table 4. Permanent environment correlations between production (305MY, TMY and PY) and production efficiency traits (TMY/LL and TMY/CI) were high. The present study revealed the permanent environment correlations between LL and CI as 0.86, however Worku et al. (Reference Worku, Gowane, Kumar, Joshi, Gupta and Verma2021) reported slightly higher (0.92) estimates among the same traits. From Table 5, it is obvious that the estimates of residual correlations among the considered traits varied from −0.28 (CI and TMY/CI) to 0.86 (305MY and TMY). Except for a few traits, residual correlations were positive and high, suggesting that the traits are dependent on environment. Therefore, by altering the environmental factors, influencing one trait, it is feasible to alter the other trait in a parallel direction.
PSD, posterior standard deviation; HPD, highest posterior density.
PSD, posterior standard deviation; HPD, highest posterior density.
In conclusion, the present study was conducted to estimate the genetic parameters of performance traits in Jersey crossbred cattle using a Bayesian method. Moderate heritability values for 305MY, TMY, PY and production efficiency traits indicated the presence of sufficient additive genetic variability in these traits and rapid genetic improvement is feasible through a selection process. Heritability estimates for LL and CI were low suggesting a lesser chance of improvement in these traits through selection. Repeatability of 305MY, TMY and PY was found be high in our study suggesting the use of first lactation records for early evaluation of Jersey crossbred cattle for future selection. The high genetic correlation between 305MY and PY suggested the probable use of peak yield for early selection of superior animals.
Acknowledgements
The authors appreciate the facilities provided by the Director cum Vice Chancellor ICAR-NDRI, Karnal and Head ERS, ICAR-NDRI Kalyani, as well as the financial support provided by ICAR. We would like to thank the staff of the cattle farm for their hard work and dedication towards maintaining the animals and records of the farm.
Declaration of competing interest
Authors declare that they have no conflict of interest.
Funding statement
There is no funding to report for the present work.