Statistics of phenotype and SNP data
In this study, we analyzed 10 traits, including concentration of IgG, IgG1, IgG2, IgA and IgM in colostrum and serum. Mean and the corresponding standard deviations for the original and corrected phenotypic values with or without square root or log transformation were shown in Table 1.
Genome-wide association study
For the genotype imputation with the software Beagle 3.0.4, SNPs with R2 > 0.3 were retained  and the average allelic R2 of imputed genotypes was 74.8% , which made sure the accuracy of imputation and full use of chip data. With GCTA 1.90.2, no population substructure was observed form QQ plots (Figures. 1). In addition, the inflation factor (λ) estimated was from 0.98-1.02 for all traits, which indicated that our results can be accepted for further analysis.
For the contents of immunoglobulins in colostrum, as shown in Figure. 2 and Table 2, at genome-wide significant level, 3 SNPs (P<3.16E-6) located on BTA-20 (1 SNP) and 21 (2 SNPs) were found for concentration of IgG2 in colostrum. At suggestive significant level, a total of 11, 7 and 17 suggestive significant SNPs (P<6.32E-5) were detected for concentration of IgG, IgG1 and IgG2 in colostrum. Of these, the majority of them were located on BTA-21 (15 SNPs) while a few SNPs were located on BTA-1 (3 SNPs), 23 (2 SNPs), 24(7 SNPs), 3 (2 SNPs), 5 (1 SNP), 6 (1 SNP), 20 (2 SNPs), and 27 (2 SNPs). In addition, a total of 3 and 6 suggestive significant SNPs (P<6.32E-5) were detected for the concentration of IgA and IgM in colostrum and distributed in chromosomes 1 (1 SNP), 4 (1 SNP), 5 (1 SNP), 8 (1 SNP), 10 (2 SNPs), 15 (1 SNP) and 17 (2 SNPs). Associations between 4 SNPs and concentration of IgM in colostrum reached genome-wide significant level in chromosome 10 (2 SNPs) and 17 (2 SNPs) (P<3.16E-6).
For the immunoglobulins contents in serum, genome-wide significant associations between 17 SNPs and concentration of IgG2 were found in BTA-21 (16 SNPs) and 20 (1 SNP) (P<3.16E-6). Additionally, 22 suggestive significant SNPs (P<6.32E-5) were detected for IgG1 and IgG2 in serum. Of these, 15 SNPs were located on BTA-21 and the rest of them were on 28 (1 SNP), 19 (1 SNP), 7 (1 SNP), 19 (1 SNP), 12 (2 SNPs), and 20 (1 SNP) (Figure. 2 and Table 3). At both level, concentration of IgG in serum did not show any significant associations. For IgA and IgM in serum, 8 and 4 suggestive significant SNPs (P<6.32E-5) were identified in chromosomes 2 (1 SNP), 15 (3 SNPs), 18 (1 SNP), 25 (2 SNP), 29 (1 SNP), 4 (1 SNP), 6 (1 SNP) and 7 (2 SNPs) (Figure. 2 and Table 3). And 1 SNP associate with IgA in BTA-17 achieved genome-wide significant level (P<3.16E-6). The Manhattan plots for concentrations of IgG, IgG1, IgG2 IgA and IgM in colostrum and serum were shown in Figures. 2.
Haplotype Block Analysis
As shown in Figure. 2, with regards to the concentration of IgG in colostrum, 7 significant SNPs on BAT 24 (45.89–46.24Mb) generated a haplotype block (Figure. 3A) and 22 genes were found within this region after gene searching. As for the concentration of IgG2 in colostrum, 18 significant SNPs were found located on BTA-21 (66.58–71.39Mb) that contained 168 genes. In this region, we detected 3 haplotype blocks: block 1(14kb, 2 SNPs), block 2 (17kb, 3 SNPs) and block 3 (14kb, 2 SNPs) (Figure. 3B). For the concentration of IgG2 in serum, we detected 32 significant SNPs on BAT 21 (64.93–72.48Mb) that accommodate 204 genes and totally formed 3 haplotype blocks, including block 1 (18kb, 2 SNPs), block 2 (62kb, 4 SNPs) and block 3 (14kb, 2 SNPs) (Figure. 3C). Additionally, the haplotype block of IgG2 concentration in colostrum was covered in the block of IgG2 concentration in serum. However, few significant SNPs were observed within haplotype blocks for the other traits.
Candidate Genes and Function Analysis
For IgG in serum and colostrum, a total of 707 functional genes that contained or were near (within 1Mb) the identified significant SNPs were obtained based on the bovine genome assembly UMD3.1. In addition, 252 and 408 functional genes were identified that contained or were near the identified significant SNPs for IgA and IgM traits with distance of less than 1 Mb, respectively. After removing the duplicates of results, a total of 1,083 candidate genes were obtained for contents of immunoglobulins traits, 706 protein-coding genes, 60 miRNA genes, 45 spliceosomal RNAs, 76 small nucleolar RNAs and 196 novel genes (Additional file 3: Table S1). Out of these, with GO and KEGG analysis, 151 genes were observed participated in immune related pathways such as immune response, Fc gamma R-mediated phagocytosis, negative regulation of immunoglobulin secretion, humoral immune response, Fc-epsilon receptor and NF-kappaB signaling pathways, etc (Additional file 4:Table S2).
Based on the Cattle QTL database that has released 232 loci for immune capacity until now (April 26, 2020, http://www.animalgenome.org/cgi-bin/QTLdb/), we compared the physical positions of the 151 candidate genes with the peak of the known QTLs for immune capacity in dairy cattle, including IgG level, FMDV peptide-induced cell proliferation and ConA-induced cell proliferation. Consequently, 21 genes were found located within the QTL regions with distance to the peak positions of less than 1.0 cM so that they were considered as promising candidates for immunoglobulins level in serum and colostrum (Table 4). They were BR activator of RhoGEF and GTPase (ABR), translocase of inner mitochondrial membrane 22 (TIMM22), CRK proto-oncogene, adaptor protein (CRK), myosin IC(MYO1C), Rab interacting lysosomal protein (RILP), serpin family F member 2 (SERPINF2), AKT serine/threonine kinase 1 (AKT1), BAF chromatin remodeling complex subunit BCL11B (BCL11B), HHIP like 1 (HHIPL1),dynein cytoplasmic 1 heavy chain 1(DYNC1H1), heat shock protein 90 alpha family class A member 1(HSP90AA1), TNF receptor associated factor 3(TRAF3), kinesin light chain 1(KLC1), interleukin 6 (IL6), PYD and CARD domain containing (PYCARD), integrin subunit alpha M (ITGAM), transforming growth factor beta 1 induced transcript 1 (TGFB1I1), glucuronidase beta (GUSB), CGRP receptor component (CRCP), RAB guanine nucleotide exchange factor 1 (RABGEF1) and SBDS ribosome maturation factor (SBDS).