Inputs for optimizing selection platform for milk production traits of dairy Sahiwal cattle.

The premises for the potential success of molecular breeding is the ability to identify major genes associated with important dairy related traits. The present study was taken up with the objectives to identify single nucleotide polymorphism (SNP) of bovine MASP2 and SIRT1 genes and its effect on estimated breeding values (EBVs) and to estimate genetic parameters for lactation milk yield (LMY), 305-day milk yield (305dMY), 305-day fat yield (305dFY), 305-day solid not fat yield (305dSNFY) and lactation length (LL) in Sahiwal dairy cattle to devise a promising improvement strategy. Genetic parameters and breeding values of milk production traits were estimated from 935 Sahiwal cattle population (1979-2019) reared at National Dairy Research Institute at Karnal, India. A total of 7 SNPs, where one SNP (g.499C>T) in exon 2 and four SNPs (g.576G>A, g.609T>C, g.684G>T and g.845A>G) in exon 3 region of MASP2 gene and 2 SNPs (g.-306T>C and g.-274G>C) in the promoter region of SIRT1 gene were identified in Sahiwal cattle population. Five of these identified SNPs were chosen for further genotyping by PCR-RFLP and association analysis. Association analysis was performed using estimated breeding values (n = 150) to test the effect of SNPs on LMY, 305dMY, 305dFY, 305dSNFY and LL. Association analysis revealed that, three SNP markers (g.499C>T, g.609T>C and g.-306T>C) were significantly associated with all milk yield traits. The estimates for heritability using repeatability model for LMY, 305dMY, 305dFY, 305dSNFY and LL were low, however the corresponding estimates from first parity were 0.20±0.08, 0.17±0.08, 0.13±0.09, 0.13±0.09 and 0.24, respectively. The repeatability estimates were moderate to high indicating consistency of performance over the parities and hence reliability of first lactation traits. Genetic correlations among the traits of first parity were high (0.55 to 0.99). From the results we could conclude that optimum strategy to improve the Sahiwal cattle further would be selecting the animals based on their first lactation 305dMY. Option top include the significant SNP in selection criteria can be explored. Taken together, a 2-stage selection approach, select Sahiwal animals early for the SNP and then on the basis of first lactation 305dMY will help to save resources.

Worku D ，Gowane G ，Alex R ，Joshi P ，Verma A ... -  《PLoS One》

Associations between polymorphisms of LAP3 and SIRT1 genes with clinical mastitis and milk production traits in Sahiwal and Karan Fries dairy cattle.

Bovine mastitis continues to remain as the most challenging disease in dairy cattle, as a result improvement of selection methods has great economic relevance while a deeper understanding of the genetic mechanisms regulating milk production traits and mastitis is of general scientific interest. This study aimed to evaluate the association of SNPs of the LAP3 and SIRT1 genes with estimated breeding values (EBVs) of milk production traits and clinical mastitis in dairy cattle of Indian origin. DNA samples from 263 animals (Sahiwal and Karan Fries cattle) were genotyped by PCR-RFLP to assess their pattern of genetic variation. EBVs of milk production traits and phenotypic records of incidences of clinical mastitis were used for association analysis. A total of 9 SNPs were identified, including three (rs110932626: A>G, rs716493845: C>T and rs43702363: C>T) in intron 12, four (g.24904G>C, rs110839532: G>T, rs43702361: T>C and rs41255599: C>T) in exon 13 and within 3'UTR of LAP3 gene and two (rs110250233: G>A and rs42140046: C>G) in the promoter region of SIRT1 gene. Eight of these identified SNPs were chosen for subsequent genotyping and association analyses. Association analysis revealed that SNP rs41255599: C>T was significantly associated with lactation milk yield, 305-day milk yield, 305-day fat yield, 305-day solid not fat yield, lactation length and incidence of clinical mastitis (p < 0.05) in Sahiwal cattle. For Karan Fries cattle, two SNPs including rs110932626: A>G and rs43702363: C>T showed significant association with 305-day milk yield. Overall, these findings provide evidence for association of the LAP3 gene with milk production traits and clinical mastitis in dairy cattle, indicating the potential role of LAP3 variants in these traits.

Worku D ，Gowane GR ，Mukherjee A ，Alex R ，Joshi P ，Verma A ... -  《Veterinary Medicine and Science》

Estimation of genetic parameters for production and reproductive traits in Indian Karan-Fries cattle using multi-trait Bayesian approach.

Estimates of variance components are needed for implementing genetic selection. This study was conducted to genetic parameters for production and reproductive traits on Indian Karan-Fries cattle using multi-trait repeatability animal model. Data collected from ICAR-National Dairy Research Institute, Karnal, India (from 1988 to 2019) were used. Single-trait and multi-trait repeatability animal models were used for parameter estimation. The posterior mean of Heritability estimates for 305-day milk yield (305-DMY), lactation milk yield (LMY), lactation length (LL) were 0.20 ± 0.03, 0.19 ± 0.03 and 0.06 ± 0.02, respectively. For age at first calving (AFC), calving interval (CI), and days open (DO), the posterior mean of heritability estimates were 0.24 ± 0.08, 0.06 ± 0.01, and 0.07 ± 0.02, respectively. The repeatability estimates for 305-DMY, LMY, LL, CI, and DO were 0.37 ± 0.02, 0.34 ± 0.02, 0.15 ± 0.02, 0.09 ± 0.02, and 0.12 ± 0.02, respectively. Genetic correlation between milk production traits (305-DMY, LMY, and LL) was positive and strong (> 0.80). However, the genetic correlation between milk production trait and AFC ranges from - 0.31 to 0.12. Unfavorable strong genetic correlations were observed between production and reproductive traits (CI and DO) with values ranged from 0.5 to 0.7. Phenotypic correlations among 305-DMY, LMY, and LL were generally positive and high. The moderate heritability estimates and potential genetic variation for 305-DMY, TMY, and AFC suggested that genetic gain can be obtained for these traits through genetic selection. Low heritability estimates found for LL, CI and DO, indicating that the possibility of changing these traits through genetic selection is small. High genetic correlation observed between productive and fertility traits were unfavorable. The existed strong genetic and phenotypic correlation estimates between CI and DO indicates that recording only one of them would be sufficient in the herd. As the multi-trait model showed slight improvements in the h as well as r estimates for both productive and reproductive traits over univariate analysis, future selection with a multi-trait animal model applying Bayesian approach would be recommended.

Worku D ，Gowane GR ，Kumar R ，Joshi P ，Gupta ID ，Verma A ... -  《-》

Single Nucleotide Polymorphisms of NUCB2 and their Genetic Associations with Milk Production Traits in Dairy Cows.

We previously used the RNA sequencing technique to detect the hepatic transcriptome of Chinese Holstein cows among the dry period, early lactation, and peak of lactation, and implied that the nucleobindin 2 () gene might be associated with milk production traits due to its expression being significantly increased in early lactation or peak of lactation as compared to dry period ( value < 0.05). Hence, in this study, we detected the single nucleotide polymorphisms (SNPs) of and analyzed their genetic associations with milk yield, fat yield, fat percentage, protein yield, and protein percentage. We re-sequenced the entire coding and 2000 bp of 5' and 3' flanking regions of by pooled sequencing, and identified ten SNPs, including one in 5' flanking region, two in 3' untranslated region (UTR), and seven in 3' flanking region. The single-SNP association analysis results showed that the ten SNPs were significantly associated with milk yield, fat yield, fat percentage, protein yield, or protein percentage in the first or second lactation ( values <= 1 × 10 and 0.05). In addition, we estimated the linkage disequilibrium (LD) of the ten SNPs by Haploview 4.2, and found that the SNPs were highly linked in one haplotype block (D' = 0.98-1.00), and the block was also significantly associated with at least one milk traits in the two lactations ( values: 0.0002-0.047). Further, we predicted the changes of transcription factor binding sites (TFBSs) that are caused by the SNPs in the 5' flanking region of , and considered that g.35735477C>T might affect the expression of by changing the TFBSs for ETS transcription factor 3 (ELF3), caudal type homeobox 2 (CDX2), mammalian C-type LTR TATA box (VTATA), nuclear factor of activated T-cells (NFAT), and v-ets erythroblastosis virus E26 oncogene homolog (ERG) (matrix similarity threshold, MST > 0.85). However, the further study should be performed to verify the regulatory mechanisms of and its polymorphisms on milk traits. Our findings first revealed the genetic effects of on the milk traits in dairy cows, and suggested that the significant SNPs could be used in genomic selection to improve the accuracy of selection for dairy cattle breeding.

Han B ，Yuan Y ，Li Y ，Liu L ，Sun D ... -  《Genes》

Genome-wide association for milk production traits and somatic cell score in different lactation stages of Ayrshire, Holstein, and Jersey dairy cattle.

We performed genome-wide association analyses for milk, fat, and protein yields and somatic cell score based on lactation stages in the first 3 parities of Canadian Ayrshire, Holstein, and Jersey cattle. The genome-wide association analyses were performed considering 3 different lactation stages for each trait and parity: from 5 to 95, from 96 to 215, and from 216 to 305 d in milk. Effects of single nucleotide polymorphisms (SNP) for each lactation stage, trait, parity, and breed were estimated by back-solving the direct breeding values estimated using the genomic best linear unbiased predictor and single-trait random regression test-day models containing only the fixed population average curve and the random genomic curves. To identify important genomic regions related to the analyzed lactation stages, traits, parities and breeds, moving windows (SNP-by-SNP) of 20 adjacent SNP explaining more than 0.30% of total genetic variance were selected for further analyses of candidate genes. A lower number of genomic windows with a relatively higher proportion of the explained genetic variance was found in the Holstein breed compared with the Ayrshire and Jersey breeds. Genomic regions associated with the analyzed traits were located on 12, 8, and 15 chromosomes for the Ayrshire, Holstein, and Jersey breeds, respectively. Especially for the Holstein breed, many of the identified candidate genes supported previous reports in the literature. However, well-known genes with major effects on milk production traits (e.g., diacylglycerol O-acyltransferase 1) showed contrasting results among lactation stages, traits, and parities of different breeds. Therefore, our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the analyzed traits across breeds, parities, and lactation stages. Further functional studies are needed to validate our findings in independent populations.

Oliveira HR ，Cant JP ，Brito LF ，Feitosa FLB ，Chud TCS ，Fonseca PAS ，Jamrozik J ，Silva FF ，Lourenco DAL ，Schenkel FS ... -  《-》