Genomic evaluation of milk yield in a smallholder crossbred dairy production system in India.

BACKGROUND: India is the largest milk producer globally, with the largest proportion of cattle milk production coming from smallholder farms with an average herd size of less than two milking cows. These cows are mainly undefined multi-generation crosses between exotic dairy breeds and indigenous Indian cattle, with no performance or pedigree recording. Therefore, implementing genetic improvement based on genetic evaluation has not yet been possible. We present the first results from a large smallholder performance recording program in India, using single nucleotide polymorphism (SNP) genotypes to estimate genetic parameters for monthly test-day (TD) milk records and to obtain and validate genomic estimated breeding values (GEBV). RESULTS: The average TD milk yield under the high, medium, and low production environments were 9.64, 6.88, and 4.61 kg, respectively. In the high production environment, the usual profile of a lactation curve was evident, whereas it was less evident in low and medium production environments. There was a clear trend of an increasing milk yield with an increasing Holstein Friesian (HF) proportion in the high production environment, but no increase above intermediate grades in the medium and low production environments. Trends for Jersey were small but yield estimates had a higher standard error than HF. Heritability estimates for TD yield across the lactation ranged from 0.193 to 0.250, with an average of 0.230. The additive genetic correlations between TD yield at different times in lactation were high, ranging from 0.846 to 0.998. The accuracy of phenotypic validation of GEBV from the method that is believed to be the least biased was 0.420, which was very similar to the accuracy obtained from the average prediction error variance of the GEBV. CONCLUSIONS: The results indicate strong potential for genomic selection to improve milk production of smallholder crossbred cows in India. The performance of cows with different breed compositions can be determined in different Indian environments, which makes it possible to provide better advice to smallholder farmers on optimum breed composition for their environment.

Genetic and non-genetic factors affecting conception rate of frozen semen in small holder dairy farmer system of rural India.

Fertility traits are as important as production traits in crossbred bovine population. Assessment of the fertility of bull in any frozen semen production program and evaluation of the conception rate under actual field conditions provide valuable information. The objective of this retrospective study was to estimate the effect of genetic and non-genetic influence on conception rate of frozen semen bulls maintained at Bharatiya Agro-Industries Foundation (BAIF) Pune based on the conception rate in cattle population of small holder dairy farmer system. The data comprising of 1,08,238 insemination records pertaining to 83 Holstein Friesian pure and crossbred bulls available at BAIF Pune were used to analyze conception rate. The fixed effect solutions and covariance components were estimated by linear mixed model using the restricted maximum likelihood method in WOMBAT software. The genetic correlations were estimated using bivariate analysis between post thaw motility and conception rate. The study was based on fertility related information from cows maintained in different villages of India and thus reflects the actual fertility of frozen semen used. The study was suggestive of influence of very small fraction of genetic effect and higher impact of management effect on conception rate. Fertility-related information available from this study is an invaluable asset in decision making process of breeding policies.