D NLRP9) were significantly associated with DPR (Table 2). The physical locationD NLRP9) were significantly

D NLRP9) were significantly associated with DPR (Table 2). The physical location
D NLRP9) were significantly associated with DPR (Table 2). The physical location of each SNP associated with DPR in the current study was PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27488460 compared to markers from the BovineSNP50 chip previously associated with DPR [7]. Figure 2 shows the relative location of the SNPs and the SNP50 marker effects. The SNP effects from the current custom array have a much greater effect on DPR than those found on the BovineSNP50 chip. The largest genetic standard deviation on the BovineSNP50 chip for DPR was 0.07 genetic standard deviations [7]; however, in the current study, the marker effect ranged from 0.44 to 1.78 (Additional file 3: Table S7). A literature search was conducted to determine if any SNPs previously related to fertility were within 100,000 bases of any of the SNPs related to DPR in the current study. The literature provided evidence for 3 other SNPs located close to SNPs from the current study. A SNP VelpatasvirMedChemExpress Velpatasvir inDGAT1, which is about 65,000 bp from the SNP in CPSF1, was associated with 28 and 56 day nonreturn rate to first service, age at puberty, number of inseminations per conception, and conception rate [56-58]. A SNP in TNF, which is about 25,000 bp from the SNP in NFKBIL1, was associated with early first ovulation in postpartum cows [59]. Also, a SNP in HSD14B14, which is about 60,000 bp from the SNP in FUT1, was associated with DPR [7]. Since these SNPs are close in distance, there could be linkage disequilibrium between them. Therefore, it is possible that either gene in each of the previous locations could contain the causative SNP.Effect of tissue type used for SNP discovery on probability of identifying SNPs associated with DPRAn analysis was performed to determine whether the tissue type used to identify genes for SNP discovery affected the probability that a gene was related to DPR (Additional file 3: Table S8). Using chi-square analysis,Cochran et al. BMC Genetics 2013, 14:49 http://www.biomedcentral.com/1471-2156/14/Page 12 ofTable 8 SNPs associated with fat yieldaSNP rs41766835 rs110541595 rs43114141 rs133674837 rs137601357 rs109621328 rs41711496 rs134432442 rs133449166 rs110629231 rs133175991 FGF2ag rs109247499 rs43703916 rs111027720 rs136457441 rs43321188 rs110365063 rsaGene 0 APBB1 ARL6IP1 AVP BDH2 CAST CD14 CD40 CPSF1 CSNK1E DNAH11 DZIP3 FGF2 FST MRPL48 PARM1 RPL26 SERPINE2 SLC18A2 TXNLeast-squares means (SEM) 1 6.22 (3.16) 5.83 (2.53) 6.03 (2.82) 3.71 (2.57) 8.56 (2.48) -0.36 (4.49) 7.94 (2.48) 19.88 (2.79) 9.75 (2.57) 7.78 (2.61) 5.65 (3.21) 7.56 (2.58) 10.96 (2.50) 12.51 (2.48) 4.84 (2.48) 6.36 (2.43) 11.63 (2.75) 14.21 (2.75) 13.18 (2.38) 2 12.64 (2.20) 12.47 (2.80) 12.53 (2.97) 13.03 (2.74) 4.87 (2.89) 10.42 (1.94) 12.40 (3.17) -0.39 (2.19) 4.72 (2.85) 10.96 (2.55) 11.90 (2.36) 11.43 (2.61) 1.75 (3.25) 6.04 (3.33) 18.09 (2.97) 13.19 (3.35) 8.10 (2.27) 7.25 (2.27) 5.89 (2.90) Effect 6.39 4.88 4.76 4.18 -6.38 11.34 4.34 -19.67 -5.19 5.40 6.61 4.87 -4.94 2.59 7.01 -0.84 2.24 2.98 -0.21 -0.06 (7.57) 3.52 (4.03) 3.31 (3.56) 7.70 (4.15) 18.50 (3.70) -15.29 (14.91) 3.72 (3.20) 37.64 (6.52) 15.18 (3.92) -1.91 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28300835 (4.66) -2.51 (8.81) 1.05 (4.24) 11.59 (3.27) 0.50 (3.43) 5.09 (3.45) 15.50 (3.55) -5.08 (5.73) -4.30 (5.73) 3.94 (3.80)Linear P value 0.0259 0.0341 0.0291 0.643 0.0033 0.0055 0.0479 <0.0001 0.0216 0.0197 0.0290 0.0304 0.0265 0.2581 0.0014 0.7208 0.3735 0.3407 0.9263 Q value 0.1474 0.1516 0.1474 0.2443 0.0587 0.0733 0.1965 0.0048 0.1474 0.1474 0.1474 0.1474 0.1474 0.3471 0.0373 0.5003 0.3831 0.3634 0.Dominance P value 0.9883 0.