Genome wide mining of SNPs and INDELs through ddRAD sequencing in Sahiwal cattle.

The study was conducted in Sahiwal cattle for genome wide identification and annotation of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) in Sahiwal cattle. The double digest restriction-site associated DNA (ddRAD) sequencing, a reduced representation method was used for the identification of variants at nucleotide level. A total of 1,615,211 variants were identified at RD10 and Q30 consisting of 1,480,930 SNPs and 134,281 INDELs with respect to the Bos taurus reference genome. The SNPs were annotated for their location, impact and functional class. The SNPs identified in Sahiwal cattle were found to be associated with a total of 26,229 genes. A total of 1819 SNPs were annotated for 209 candidate genes associated with different production and reproduction traits. The variants identified in the present study may be useful to strengthen the existing bovine SNP chips for reducing the biasness over the taurine cattle breeds. The diversity analysis provides the insight of the genetic architecture of the Sahiwal population Studied. The large genetic variations identified at the nucleotide level provide ample scope for implementing an effective and efficient breed improvement programme for increasing the productivity of Sahiwal cattle.

Genetic aspects of Wood's lactation curve parameters in Jersey crossbred cattle using Bayesian approach.

The study was undertaken to estimate the genetic parameters of lactation curve parameters of Wood's function in Jersey crossbred cattle using the Bayesian approach. Data on 33,906 fortnightly test day milk yields of 1,718 lactation records of Jersey crossbred cows, maintained at the ICAR-National Dairy Research Institute in West Bengal, were collected over a period of 40 years. The lactation curve parameters including 'a' (initial milk yield after calving), 'b' (ascending slope up to peak yield) and 'c' (descending slope after peak yield) and lactation curve traits, peak yield (ymax), time of peak yield (tmax) and persistency of milk yield (P) of individual cow for each lactation were estimated using the incomplete gamma function (Wood's model) by fitting the Gauss-Newton algorithm as an iteration method using PROC NLIN procedure of SAS 9.3. Variance components and genetic parameters of lactation curve parameters/traits were estimated by a repeatability animal model using the Bayesian approach. Estimates of heritabilities were found to be 0.18 ± 0.05, 0.09 ± 0.03 and 0.11 ± 0.04 for parameters 'a', 'b' and 'c', respectively and 0.24 ± 0.05, 0.12 ± 0.04, and 0.15 ± 0.05 for ymax, tmax and P, respectively. Repeatability estimates were 0.31 ± 0.03, 0.21 ± 0.04 and 0.30 ± 0.04 for parameters 'a', 'b' and 'c' respectively and 0.39 ± 0.03, 0.24 ± 0.03 and 0.37 ± 0.03 for ymax, tmax and p, respectively. Genetic correlations among lactation curve parameters/traits ranged from -0.75 to 0.95. Existence of genetic correlations among lactation curve parameters/traits indicated substantial genetic and physiological relationships among lactation curve parameters/traits of Jersey crossbred cattle.

Genome-wide identification and annotation of SNPs for economically important traits in Frieswal™, newly evolved crossbred cattle of India.

The Frieswal™ is a crossbred cattle evolved by ICAR-Central Institute for Research on Cattle utilizing more than 15,000 cattle maintained at more than 37 military farms spread all over the agro-climatic regions of the country. The ddRAD sequencing method was used to identify and annotate the SNPs and INDELs. The results of variant calling revealed 1,487,851 SNPs and 128,175 INDELs at a read depth of 10. A total of 3,775,079 effects were identified, and majority (66.41%) of the effects were in the intron region of the genome followed by intergenic (21.87%). Majority (99.18%) of the variants had the modifier effect. The results revealed a higher magnitude of transitions as compared to the transversion. The classification of SNPs by functional class revealed a majority of missense (43%) and silent (56%) effects. Out of 26,278 genes identified, 1841 SNPs were annotated in 207 candidate genes responsible for various milk production and reproduction traits. The observed heterozygosity was 0.2804 against the expected heterozygosity value of 0.2978. The overall average inbreeding coefficient (FIS) was 0.0604. The pathway analysis revealed that the prolactin signaling pathway (GO:0038161) was significant biological process complete for both milk production and reproduction traits. The SNP variations can be effectively used as markers for early and accurate identification of the QTLs and for formulating an efficient and effective breed improvement program in Frieswal™ cattle. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03701-0.

Effect of lameness (hoof disorders) on productivity of Karan Fries crossbred cows.

In present study production performance of 96 lame cows was compared with 67 healthy cows. No significant effect of parity and year of calving on milk yield were observed but the effect of season of calving was significant (P < 0.01). Effect of lameness on milk yield at the second, third and fourth months and 305 days was highly significant (P < 0.01), and was also significant (P < 0.05) on lactation yield of the fifth and tenth months. The effect of lameness on monthly and 305-day milk yield was significant (P < 0.01) only for those cows diagnosed lame before calving and during the first month of lactation. The differences in mean monthly yield were highly significant (P < 0.01) at the second, third and fourth months; and significant (P < 0.05) in the first and fifth months. The loss in the first lactation month of cows which were diagnosed as lame in the second month, was found to be significant (P < 0.05). Thus the yield of the month previous to the diagnosis (sub-clinical stage) was also affected. A significant (P < 0.01) total loss of 498.95 kg of milk yield was observed during a period of 305 days.