Estimation of genetic parameters and single-step genome-wide association studies for milk urea nitrogen in Holstein cattle

The main objectives of this study were to estimate genetic parameters for milk urea nitrogen (MUN) in Holstein cattle and to conduct a single-step (ss)GWAS to identify candidate genes associated with MUN. Phenotypic measurements from 24,435 Holstein cows were collected from March 2013 to July 2019 in 9 dairy farms located in the Beijing area, China. A total of 2,029 cows were genotyped using the Illumina 150K Bovine Bead Chip, containing 121,188 SNP. A single-trait repeatability model was used to evaluate the genetic background of MUN. We found that MUN is a trait with low heritability (0.06 ± 0.004) and repeatability (0.12). Considering similar milk production levels, a lower MUN concentration indicates higher nitrogen digestibility. The genetic correlations between MUN and milk yield, net energy concentration, fat percentage, protein percentage, and lactose percentage were positive and ranged from 0.02 to 0.26. The genetic correlation between MUN and somatic cell score (SCS) was negative (?0.18), indicating that animals with higher MUN levels tend to have lower SCS. Both ssGWAS and pathway enrichment analyses were used to explore the genetic mechanisms underlying MUN. A total of 18 SNP (located on BTA11, BTA12, BTA14, BTA17, and BTA18) were found to be significantly associated with MUN. The genes CFAP77, CAMSAP1, CACNA1B, ADGRB1, FARP1, and INTU are considered to be candidate genes for MUN. These candidate genes are associated with important biological processes such as protein and lipid metabolism and binding to specific proteins. This set of candidate genes, metabolic pathways, and their functions provide a better understanding of the genomic architecture and physiological mechanisms underlying MUN in Holstein cattle.     

Genome-wide association study for milk production traits in a Brazilian Holstein population

Advances in the molecular area of selection have expanded knowledge of the genetic architecture of complex traits through genome-wide association studies (GWAS). Several GWAS have been performed so far, but confirming these results is not always possible due to several factors, including environmental conditions. Thus, our objective was to identify genomic regions associated with traditional milk production traits, including milk yield, somatic cell score, fat, protein and lactose percentages, and fatty acid composition in a Holstein cattle population producing under tropical conditions. For this, 75,228 phenotypic records from 5,981 cows and genotypic data of 56,256 SNP from 1,067 cows were used in a weighted single-step GWAS. A total of 46 windows of 10 SNP explaining more than 1% of the genetic variance across 10 Bos taurus autosomes (BTA) harbored well-known and novel genes. The MGST1 (BTA5), ABCG2 (BTA6), DGAT1 (BTA14), and PAEP (BTA11) genes were confirmed within some of the regions identified in our study. Potential novel genes involved in tissue damage and repair of the mammary gland (COL18A1), immune response (LTTC19), glucose homeostasis (SLC37A1), synthesis of unsaturated fatty acids (LTBP1), and sugar transport (SLC37A1 and MFSD4A) were found for milk yield, somatic cell score, fat percentage, and fatty acid composition. Our findings may assist genomic selection by using these regions to design a customized SNP array to improve milk production traits on farms with similar environmental conditions.     

Short communication: Replication of genome-wide association studies for milk production traits in Chinese Holstein by an efficient rotated linear mixed model

Milk is regarded as an important nutrient for humans, and Chinese Holstein cows provide high-quality milk for billions of Chinese people. Therefore, detecting quantitative trait nucleotides (QTN) or candidate genes for milk production traits in Chinese Holstein is important. In this study, we performed genome-wide association studies (GWAS) in a Chinese Holstein population of 6,675 cows and 71,633 SNP using deregressed proofs (DRP) as phenotypes to replicate our previous study in a population of 1,815 cows and 39,163 SNP using estimated breeding values (EBV) as phenotypes. The associations between 3 milk production traits—milk yield (MY), fat percentage (FP), and protein percentage (PP)—and the SNP were determined by using an efficient rotated linear mixed model, which benefits from linear transformations of genomic estimated values and Eigen decomposition of the genomic relationship matrix algorithm. In total, we detected 94 SNP that were significantly associated with one or more milk production traits, including 7 SNP for MY, 76 for FP, and 36 for PP; 87% of these SNP were distributed across Bos taurus autosomes 14 and 20. In total, 83 SNP were found to be located within the reported quantitative trait loci (QTL) regions, and one novel segment (between 1.41 and 1.49 Mb) on chromosome 14 was significantly associated with FP, which could be an important candidate QTL region. In addition, the detected intervals were narrowed down from the reported regions harboring causal variants. The top significant SNP for the 3 traits was ARS-BFGL-NGS-4939, which is located within the DGAT1 gene. Five detected genes (CYHR1, FOXH1, OPLAH, PLEC, VPS28) have effects on all 3 traits. Our study provides a suite of QTN, candidate genes, and a novel QTL associated with milk production traits, and thus forms a solid basis for genomic selection and molecular breeding for milk production traits in Chinese Holstein.     

On the genomic regions associated with milk lactose in Fleckvieh cattle

Lactose is a sugar uniquely found in mammals' milk and it is the major milk solid in bovines. Lactose yield (LY, kg/d) is responsible for milk volume, whereas lactose percentage (LP) is thought to be more related to epithelial integrity and thus to udder health. There is a paucity of studies that have investigated lactose at the genomic level in dairy cows. This paper aimed to improve our knowledge on LP and LY, providing new insights into the significant genomic regions affecting these traits. A genome-wide association study for LP and LY was carried out in Fleckvieh cattle by using bulls' deregressed estimated breeding values of first lactation as pseudo-phenotypes. Heritabilities of first-lactation test-day LP and LY estimated using linear animal models were 0.38 and 0.25, respectively. A total of 2,854 bulls genotyped with a 54K SNP chip were available for the genome-wide association study; a linear mixed model approach was adopted for the analysis. The significant SNP of LP were scattered across the whole genome, with signals on chromosomes 1, 2, 3, 7, 12, 16, 18, 19, 20, 28, and 29; the top 4 significant SNP explained 4.90% of the LP genetic variance. The signals were mostly in regions or genes with involvement in molecular intra- or extracellular transport; for example, CDH5, RASGEF1C, ABCA6, and SLC35F3. A significant region within chromosome 20 was previously shown to affect mastitis or somatic cell score in cattle. As regards LY, the significant SNP were concentrated in fewer regions (chromosomes 6 and 14), related to mastitis/somatic cell score, immune response, and transport mechanisms. The 5 most significant SNP for LY explained 8.45% of genetic variance and more than one-quarter of this value has to be attributed to the variant within ADGRB1. Significant peaks in target regions remained even after adjustment for the 2 most significant variants previously detected on BTA6 and BTA14. The present study is a prelude for deeper investigations into the biological role of lactose for milk secretion and volume determination, stressing the connection with genes regulating intra- or extracellular trafficking and immune and inflammatory responses in dairy cows. Also, these results improve the knowledge on the relationship between lactose and udder health; they support the idea that LP and its derived traits are potential candidates as indicators of udder health in breeding programs aimed to enhance cows' resistance to mastitis.     

Genome-wide association studies to identify quantitative trait loci affecting milk production traits in water buffalo

Water buffalo is the second largest resource of milk supply around the world, and it is well known for its distinctive milk quality in terms of fat, protein, lactose, vitamin, and mineral contents. Understanding the genetic architecture of milk production traits is important for future improvement by the buffalo breeding industry. The advance of genome-wide association studies (GWAS) provides an opportunity to identify potential genetic variants affecting important economical traits. In the present study, GWAS was performed for 489 buffaloes with 1,424 lactation records using the 90K Affymetrix Buffalo SNP Array (Affymetrix/Thermo Fisher Scientific, Santa Clara, CA). Collectively, 4 candidate single nucleotide polymorphisms (SNP) in 2 genomic regions were found to associate with buffalo milk production traits. One region affecting milk fat and protein percentage was located on the equivalent of Bos taurus autosome (BTA)3, spanning 43.3 to 43.8 Mb, which harbored the most likely candidate genes MFSD14A, SLC35A3, and PALMD. The other region on the equivalent of BTA14 at 66.5 to 67.0 Mb contained candidate genes RGS22 and VPS13B and influenced buffalo total milk yield, fat yield, and protein yield. Interestingly, both of the regions were reported to have quantitative trait loci affecting milk performance in dairy cattle. Furthermore, we suggest that buffaloes with the C allele at AX-85148558 and AX-85073877 loci and the G allele at AX-85106096 locus can be selected to improve milk fat yield in this buffalo-breeding program. Meanwhile, the G allele at AX-85063131 locus can be used as the favorable allele for improving milk protein percentage. Genomic prediction showed that the reliability of genomic estimated breeding values (GEBV) of 6 milk production traits ranged from 0.06 to 0.22, and the correlation between estimated breeding values and GEBV ranged from 0.23 to 0.35. These findings provide useful information to understand the genetic basis of buffalo milk properties and may play a role in accelerating buffalo breeding programs using genomic approaches.     

Single-step genome-wide association for selected milk fatty acids in Dual-Purpose Belgian Blue cows

The aim of this study was to estimate genetic parameters and identify genomic regions associated with selected individual and groups of milk fatty acids (FA) predicted by milk mid-infrared spectrometry in Dual-Purpose Belgian Blue cows. The used data were 69,349 test-day records of milk yield, fat percentage, and protein percentage along with selected individual and groups FA of milk (g/dL milk) collected from 2007 to 2020 on 7,392 first-parity (40,903 test-day records), and 5,185 second-parity (28,446 test-day records) cows distributed in 104 herds in the Walloon Region of Belgium. Data of 28,466 SNPs, located on 29 Bos taurus autosomes (BTA), of 1,699 animals (639 males and 1,060 females) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic best linear unbiased prediction approach. The proportion of genetic variance explained by each 25-SNP sliding window (with an average size of ~2 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Average daily heritability estimated for the included milk FA traits ranged from 0.01 (C4:0) to 0.48 (C12:0) and 0.01 (C4:0) to 0.42 (C12:0) in the first and second parities, respectively. Genetic correlations found between milk yield and the studied individual milk FA, except for C18:0, C18:1 trans, C18:1 cis-9, were positive. The results showed that fat percentage and protein percentage were positively genetically correlated with all studied individual milk FA. Genome-wide association analyses identified 11 genomic regions distributed over 8 chromosomes [BTA1, BTA4, BTA10, BTA14 (4 regions), BTA19, BTA22, BTA24, and BTA26] associated with the studied FA traits, though those found on BTA14 partly overlapped. The genomic regions identified differed between parities and lactation stages. Although these differences in genomic regions detected may be due to the power of quantitative trait locus detection, it also suggests that candidate genes underlie the phenotypic expression of the studied traits may vary between parities and lactation stages. These findings increase our understanding about the genetic background of milk FA and can be used for the future implementation of genomic evaluation to improve milk FA profile in Dual-Purpose Belgian Blue cows.     

Longitudinal genome-wide association studies of milk production traits in Holstein cattle using whole-genome sequence data imputed from medium-density chip data

Longitudinal traits, such as milk production traits in dairy cattle, are featured by having phenotypic values at multiple time points, which change dynamically over time. In this study, we first imputed SNP chip (50–100K) data to whole-genome sequence (WGS) data in a Chinese Holstein population consisting of 6,470 cows. The imputation accuracies were 0.88 to 0.97 on average after quality control. We then performed longitudinal GWAS in this population based on a random regression test-day model using the imputed WGS data. The longitudinal GWAS revealed 16, 39, and 75 quantitative trait locus regions associated with milk yield, fat percentage, and protein percentage, respectively. We estimated the 95% confidence intervals (CI) for these quantitative trait locus regions using the logP drop method and identified 581 genes involved in these CI. Further, we focused on the CI that covered or overlapped with only 1 gene or the CI that contained an extremely significant top SNP. Twenty-eight candidate genes were identified in these CI. Most of them have been reported in the literature to be associated with milk production traits, such as DGAT1, HSF1, MGST1, GHR, ABCG2, ADCK5, and CSN1S1. Among the unreported novel genes, some also showed good potential as candidate genes, such as CCSER1, CUX2, SNTB1, RGS7, OSR2, and STK3, and are worth being further investigated. Our study provided not only new insights into the candidate genes for milk production traits, but also a general framework for longitudinal GWAS based on random regression test-day model using WGS data.     

Genome-wide association study for milk production and conformation traits in Canadian Alpine and Saanen dairy goats

Increasing the productivity of Canadian dairy goats is critical to the competitiveness of the sector; however, little is known about the underlying genetic architecture of economically important traits in these populations. Consequently, the objectives of this study were as follows: (1) to perform a single-step GWAS for milk production traits (milk, protein, and fat yields, and protein and fat percentages in first and later lactations) and conformation traits (body capacity, dairy character, feet and legs, fore udder, general appearance, rear udder, suspensory ligament, and teats) in the Canadian Alpine and Saanen breeds; and (2) to identify positional and functional candidate genes related to these traits. The data available for analysis included 305-d milk production records for 6,409 Alpine and 3,434 Saanen does in first lactation and 5,827 Alpine and 2,632 Saanen does in later lactations; as well as linear type conformation records for 5,158 Alpine and 2,342 Saanen does. Genotypes were available for 833 Alpine and 874 Saanen animals. Both single-breed and multiple-breed GWAS were performed using single-trait animal models. Positional and functional candidate genes were then identified in downstream analyses. The GWAS identified 189 unique SNP that were significant at the chromosomal level, corresponding to 271 unique positional candidate genes within 50 kb up- and downstream, across breeds and traits. This study provides evidence for the economic importance of several candidate genes (e.g., CSN1S1, CSN2, CSN1S2, CSN3, DGAT1, and ZNF16) in the Canadian Alpine and Saanen populations that have been previously reported in other dairy goat populations. Moreover, several novel positional and functional candidate genes (e.g., RPL8, DCK, and MOB1B) were also identified. Overall, the results of this study have provided greater insight into the genetic architecture of milk production and conformation traits in the Canadian Alpine and Saanen populations. Greater understanding of these traits will help to improve dairy goat breeding programs.     

Fine-mapping of BTA17 using imputed sequences for associations with de novo synthesized fatty acids in bovine milk

The aim of this study was to fine-map a genomic region associated with milk fatty acids (FA) on Bos taurus autosome (BTA) 17. This genomic region has been discovered with 50,000 (50k) single nucleotide polymorphisms (SNP) imputed to 777,000 (777k) SNP. In this study, high-density genotypes were imputed to whole-genome sequences level to identify candidate gene(s) associated with milk FA composition on BTA17. Phenotypes and genotypes were available for 1,640 cows sampled in winter, and for 1,581 cows sampled in summer. Phenotypes consisted of gas chromatography measurements in winter and in summer milk samples of 6 individual FA and the indicator of de novo synthesis, C6:0–C14:0. Genotypes consisted of imputed 777k SNP, and 89 sequenced ancestors of the population of genotyped cows. In addition, 450 whole-genome sequences from the 1,000 Bull Genome Consortium were available. Using 495 Holstein-Friesian sequences as a reference population, the 777k SNP genotypes of the cows were imputed to sequence level. We then applied single-variant analyses with an animal model, and identified thousands of significant associations with C6:0, C8:0, C10:0, C12:0, C14:0, and C6:0–C14:0. For C8:0 in summer milk samples, the genomic region located between 29 and 34 Mbp on BTA17 revealed a total of 646 significant associations. The most significant associations [–log₁₀(P-value) = 7.82] were 8 SNP in perfect linkage disequilibrium. After fitting one of these 8 SNP as a fixed effect in the model, and re-running the single-variant analyses, no further significant associations were found for any of the 6 FA or C6:0–C14:0. These findings suggest that one polymorphism underlying this QTL on BTA17 influences multiple de novo synthesized milk FA. Thirteen genes in the QTL region were identified and analyzed carefully. Six out of the 8 SNP that showed the strongest associations were located in the La ribonucleoprotein domain family, member 1B (LARP1B) gene, and we suggest LARP1B as a primary candidate gene. Another gene of interest for this QTL region might be PKL4. None of these suggested candidate genes have previously been associated with milk fat synthesis or milk FA composition.     

Genome-wide association study of normal and atypical progesterone profiles in Holstein-Friesian dairy cows

Female fertility has a major role in dairy production and affects the profitability of dairy cattle. The genetic progress obtained by traditional selection can be slow because of the low heritability of classical fertility traits. Endocrine fertility traits based on progesterone concentration in milk have higher heritability and more directly reflect the cow's own reproductive physiology. The aim of our study was to identify genomic regions for 7 endocrine fertility traits in dairy cows by performing a genome-wide association study with 54,000 SNP. The next step was to fine-map targeted genomic regions with significant SNP using imputed sequences to identify potential candidate genes associated with the normal and atypical progesterone profiles. The association between a SNP and a phenotype was assessed by a single SNP analysis, using a linear mixed model that included a random polygenic effect. Phenotypes and genotypes were available for 1,126 primiparous and multiparous Holstein-Friesian cows from research herds in Ireland, the Netherlands, Sweden, and the United Kingdom. In total, 44 significant SNP associated with 7 endocrine fertility traits were identified on Bos taurus autosome (BTA) 1–4, 6, 8–9, 11–12, 14–17, 19, 21–24, and 29. Three chromosomes, BTA8, BTA17, and BTA23, were imputed from 54,000 SNP genotypes to the whole-genome sequence level with Beagle version 4.1. The fine-mapping identified several significant associations with delayed cyclicity, cessation of cyclicity, commencement of luteal activity, and inter-ovulatory interval. These associations may contribute to an index of markers for genetic improvement of fertility. Several potential candidate genes reported to affect reproduction were also identified in the targeted genomic regions. However, due to high linkage disequilibrium, it was not possible to identify putative causal genes or polymorphisms for any of the regions.     

Genome-wide association study for selected cheese-making properties in Dual-Purpose Belgian Blue cows

This study aimed to estimate genetic parameters and identify genomic region(s) associated with selected cheese-making properties (CMP) in Dual-Purpose Belgian Blue (DPBB) cows. Edited data were 46,301 test-day records of milk yield, fat percentage, protein percentage, casein percentage, milk calcium content (CC), coagulation time (CT), curd firmness after 30 min from rennet addition (a30), and milk titratable acidity (MTA) collected from 2014 to 2020 on 4,077 first-parity (26,027 test-day records), and 3,258 second-parity DPBB cows (20,274 test-day records) distributed in 124 herds in the Walloon Region of Belgium. Data of 28,266 SNP, located on 29 Bos taurus autosomes (BTA) of 1,699 animals were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 25 consecutive SNPs (with an average size of ～2 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Heritability estimates for the included CMP ranged from 0.19 (CC) to 0.50 (MTA), and 0.24 (CC) to 0.41 (MTA) in the first and second parity, respectively. The genetic correlation estimated between CT and a30 varied from ?0.61 to ?0.41 and from ?0.55 to ?0.38 in the first and second lactations, respectively. Negative genetic correlations were found between CT and milk yield and composition, while those estimated between curd firmness and milk composition were positive. Genome-wide association analyses results identified 4 genomic regions (BTA1, BTA3, BTA7, and BTA11) associated with the considered CMP. The identified genomic regions showed contrasting results between parities and among the different stages of each parity. It suggests that different sets of candidate genes underlie the phenotypic expression of the considered CMP between parities and lactation stages of each parity. The findings of this study can be used for future implementation and use of genomic evaluation to improve the cheese-making traits in DPBB cows.     

Genome-wide association study identifies loci influencing natural antibody titers in milk of Dutch Holstein-Friesian cattle

Natural antibodies (NAb) are produced without any antigenic stimulation as a part of the innate immune system and provide a first line of defense against pathogens. Hence, they may be a useful trait when estimating an animal's potential immune competence and in selection for disease resistance. The aim of this study was to identify genomic regions associated with different NAb traits in milk and potentially describe candidate genes. Milk samples from 1,695 first-lactation Holstein Friesian cows with titer measurements for keyhole limpet hemocyanin, lipopolysaccharide, lipoteichoic acid, and peptidoglycan-binding total NAb and isotypes IgG₁, IgM, and IgA were used. Genome-wide association study analyses were performed using imputed 777K SNP genotypes, accounting for relationships using pedigree information. Functional enrichment analysis was performed on the significantly associated genomic regions to look for candidate genes. For IgM NAb, significant associations (false discovery rate <0.05) were found on Bos taurus autosome (BTA) 17, 18, and 21 with candidate genes related to immunoglobulin structure and early B cell development. For IgG₁, associations were found on BTA3, and we confirmed a quantitative trait loci on BTA21 previously reported for IgG NAb in serum. Our results provide new insights into the regulation of milk NAb that will help unravel the complex relationship between milk immunoglobulins and disease resistance in dairy cattle.     

Genome-wide association study and in silico functional analysis of the number of embryos produced by Holstein donors

Superovulation or ovum pick-up and in vitro fertilization are technologies used to produce an increased number of embryos from elite females. Embryo production traits have been shown to be heritable, but the genes that cause this variability have not yet been assessed. The main objectives of this study were to perform a genome-wide association study (GWAS) to find single nucleotide polymorphisms (SNP) associated with embryo production traits and to identify candidate genes affecting the number of embryos produced by Holstein donors in Canada that may provide insight into the regulation of embryo production. Breeding values were estimated and de-regressed for all donors and sires using a data set of 150,971 records of superovulation or ovum pick-up and in vitro fertilization. A total of 11,607 animals were genotyped, but of that number only 5,118 were genotyped with at least a 50K SNP panel and had a de-regressed estimated breeding value reliability of at least 10%. For the GWAS, 606,406 imputed SNP on 29 autosomal chromosomes were considered after applying quality control measures. A single-SNP univariate mixed linear animal model was used to perform the GWAS, and a 5% false discovery rate was applied to adjust for multiple testing. We found 36 and 14 significant SNP associated with the total number of embryos and the number of viable embryos, respectively, with most of them located on chromosome 11. Using these significant SNP, positional genes located within 10,000 bp upstream and downstream of the SNP were retrieved. Thirteen genes were harboring or near the significant SNP for the total number of embryos, 4 of them also being near the significant SNP for viable embryos. Some of these genes (CRB2, DENND1A, MAD1L1, NDUFA8, PTGS1) could be considered as potential positional candidate genes related to the number of embryos produced by a donor. This list will need to be validated in an independent population to confirm the role of the genes for embryo production.     

Short communication: Validation of somatic cell score–associated loci identified in a genome-wide association study in German Holstein cattle

Recently, we identified 6 genomic loci affecting daughter yield deviations (DYD) for somatic cell score (SCS) in a genome-wide association study (GWAS) performed with German Holstein bulls. In the current study, we tested if these loci were associated with SCS in cows using their own performance data. The study was performed with 1,412 German Holstein cows, of which 483 were daughters of 71 bulls that had been used in the GWAS. We tested 10 single nucleotide polymorphisms (SNP) representing 6 genomic regions that were associated with DYD for SCS in bulls. All tested SNP were significant in cows. Seven of them, located on Bos taurus autosomes (BTA) 6, 13, and 19, had the same direction of effect as those previously reported in the bull population. The most significant associations were detected on BTA6 and BTA19, accounting for 1.8% of the total genetic variance. The major allele of the 2 SNP on BTA6 and the minor allele of the 2 SNP on BTA19 were favorable for lower SCS. The differences between the homozygous genotype classes were up to 15,000 cells/mL. The verification of SNP associated with SCS in this study provides further evidence for the functional role of the linked genomic regions for immune response and contributes to identification of causative mutations. In particular, SNP with minor frequency of the favorable allele possess high potential to reduce SCS in German Holstein cattle by selection.     

Genome-wide association studies (GWAS) and post-GWAS analyses for technological traits in Assaf and Churra dairy breeds

This study aimed to perform a GWAS to identify genomic regions associated with milk and cheese-making traits in Assaf and Churra dairy sheep breeds; second, it aimed to identify possible positional and functional candidate genes and their interactions through post-GWAS studies. For 2,020 dairy ewes from 2 breeds (1,039 Spanish Assaf and 981 Churra), milk samples were collected and analyzed to determine 6 milk production and composition traits and 6 traits related to milk coagulation properties and cheese yield. The genetic profiles of the ewes were obtained using a genotyping chip array that included 50,934 SNP markers. For both milk and cheese-making traits, separate single-breed GWAS were performed using GCTA software. The set of positional candidate genes identified via GWAS was subjected to guilt-by-association-based prioritization analysis with ToppGene software. Totals of 84 and 139 chromosome-wise significant associations for the 6 milk traits and the 6 cheese-making traits were identified in this study. No significant SNPs were found in common between the 2 studied breeds, possibly due to their genetic heterogeneity of the phenotypes under study. Additionally, 63 and 176 positional candidate genes were located in the genomic intervals defined as confidence regions in relation to the significant SNPs identified for the analyzed traits for Assaf and Churra breeds. After the functional prioritization analysis, 71 genes were identified as promising positional and functional candidate genes and proposed as targets of future research to identify putative causative variants in relation to the traits under examination. In addition, this multitrait study allowed us to identify variants that have a pleiotropic effect on both milk production and cheese-related traits. The incorporation of variants among the proposed functional and positional candidate genes into genomic selection strategies represent an interesting approach for achieving rapid genetic gains, specifically for those traits difficult to measure, such as cheese-making traits.     

Genetic parameters and weighted single-step genome-wide association study for supernumerary teats in Holstein cattle

Supernumerary teats (SNT) are a common epidermal abnormality of udders in mammals. The SNT negatively affect machine milking ability, udder health, and animal welfare and sometimes act as reservoirs for undesirable bacteria, resulting in economic losses on calves and lactating cows due to the cost of SNT removal surgery, early culling, and low milk yield. This study aimed to analyze the incidence and genetic parameter of SNT and detect SNT-related genes in Chinese Holstein cattle. In this study, the incidence of SNT was recorded in 4,670 Chinese Holstein cattle (born between 2008 and 2017) from 2 farms, including 734 genotyped cows with 114,485 SNPs. The SNT had a total frequency of 9.8% and estimated heritability of 0.22 (SE = 0.07), which were obtained using a threshold model in the studied Chinese Holstein population. Furthermore, we calculated approximate genetic correlations between SNT and the following indicator traits: 12 milk production, 28 body conformation, 5 fertility and reproduction, 5 health, and 9 longevity. Generally, the estimated correlations, such as 305-d milk yield for third parity (−0.55; SE = 0.02) and age at first calving in heifer (0.19; SE = 0.03), were low to moderate. A single-step GWAS was implemented, and 10 genes associated with SNT located in BTA4 were identified. The region (112.70–112.90 Mb) on BTA4 showed the highest genetic variance for SNT. The quantitative trait loci on BTA4 was mapped into the RARRES2 gene, which was previously shown to affect adipogenesis and hormone secretion. The WIF1 gene, which was located in BTA5, was also considered as a candidate gene for SNT. Overall, these findings provide useful information for breeders who are interested in reducing SNT.     

Genome-wide association study of milk fatty acid composition in Italian Simmental and Italian Holstein cows using single nucleotide polymorphism arrays

Bovine milk is important for human nutrition, but its fat content is often criticized as a risk factor in cardiovascular disease. Selective breeding programs could be used to alter the fatty acid (FA) composition of bovine milk to improve the healthiness of dairy products for human consumption. Here, we performed a genome-wide association study (GWAS) on bovine milk to identify genomic regions or specific genes associated with FA profile and to investigate genetic differences between the Italian Simmental (IS) and Italian Holstein (IH) breeds. To achieve this, we first characterized milk samples from 416 IS cows and 436 IH cows for their fat profile by gas chromatography. Subjects were genotyped with single nucleotide polymorphism array and a single-marker regression model for GWAS was performed. Our findings confirm previously reported quantitative trait loci strongly associated with bovine milk fat composition. More specifically, our GWAS results revealed significant signals on chromosomes Bos taurus autosome 19 and 26 for milk FA. Further analysis using a gene-centric approach and pathway meta-analysis identified not only some well-known genes underlying quantitative trait loci for milk FA components, such as FASN, SCD, and DGAT1, but also other significant candidate genes, including some with functional roles in pathways related to “Lipid metabolism.” Highlighted genes related to FA profile include ECI2, PCYT2, DCXR, G6PC3, PYCR1, and ALG12 in IS, and CYP17A1, ACO2, PI4K2A, GOT1, GPT, NT5C2, PDE6G, POLR3H, and COX15 in IH. Overall, the breed-specific association outcomes reflect differences in the genetic backgrounds of the IS and IH breeds and their selective breeding histories.     

A genome-wide association study for left-sided displacement of the abomasum using a high-density single nucleotide polymorphism array

Left-sided displacement of the abomasum (LDA) is a frequent disease in dairy cattle causing significant financial losses for dairy farmers. Heritability (h²) of this complex disease was estimated at up to 0.5 in German Holstein (GH) cattle. Using the Bovine High Density BeadChip (Illumina Inc., San Diego, CA) comprising 588,753 single nucleotide polymorphisms (SNP) after quality control for 126 LDA cases and 280 population-based controls, we used a mixed linear model analysis in a genome-wide association study (GWAS). We identified 6 genomic regions for LDA on bovine chromosomes 2, 8, 13, 20, 24, and X that were significantly associated with LDA. Each of these regions was covered by 4 to 12 LDA-associated SNP. Single SNP within these regions explained up to 7.3% of the phenotypic variance. An independent sample of 1,554 GH cows, including 539 controls and 1,015 cases, were genotyped for 8 SNP highly associated with LDA on Bos taurus autosomes (BTA) 2, 8, 13, and 24, as well as 6 SNP located in previously identified LDA regions on BTA1, 5, 11, and 27 using competitive allele-specific PCR genotyping technology (KASP). The analysis using the KASP genotypes confirmed LDA-associated loci on BTA2, 8, 13, and 27. These genomic regions may contribute to the susceptibility to LDA in Holstein cows and may harbor functional variants for LDA.     

Single-step genomic best linear unbiased predictor genetic parameter estimations and genome-wide associations for milk fatty acid profiles,interval from calving to first insemination,and ketosis in Holstein cattle

Milk fatty acids (FA) have been suggested as biomarkers for early-lactation metabolic diseases and for female fertility status. The aim of the present study was to infer associations between FA, the metabolic disorder ketosis (KET), and the interval from calving to first insemination (ICF) genetically and genomically. In this regard, we focused on a single-step genomic BLUP approach, allowing consideration of genotyped and ungenotyped cows simultaneously. The phenotypic data set considered 38,375 first-lactation Holstein cows, kept in 45 large-scale co-operator herds from 2 federal states in Germany. The calving years for these cows were from 2014 to 2017. Concentrations in milk from the first official milk recording test-day for saturated, unsaturated (UFA), monounsaturated (MUFA), polyunsaturated, palmitic, and stearic (C18:0) FA were determined via Fourier-transform infrared spectroscopy. Ketosis was defined as a binary trait according to a veterinarian diagnosis key, considering diagnoses within a 6-wk interval after calving. A subset of 9,786 cows was genotyped for 40,989 SNP markers. Variance components and heritabilities for all Gaussian distributed FA and for ICF, and for binary KET were estimated by applying single-step genomic BLUP single-trait linear and threshold models, respectively. Genetic correlations were estimated in series of bivariate runs. Genomic breeding values for the single-step genomic BLUP estimations were dependent traits in single-step GWAS. Heritabilities for FA were moderate in the range from 0.09 to 0.20 (standard error = 0.02–0.03), but quite small for ICF (0.08, standard error = 0.01) and for KET (0.05 on the underlying liability scale, posterior standard deviation = 0.02). Genetic correlations between KET and UFA, MUFA, and C18:0 were large (0.74 to 0.85, posterior standard deviation = 0.14–0.19), and low positive between KET and ICF (0.17, posterior standard deviation = 0.22). Genetic correlations between UFA, MUFA, and C18:0 with ICF ranged from 0.34 to 0.46 (standard error = 0.12). In single-step GWAS, we identified a large proportion of overlapping genomic regions for the different FA, especially for UFA and MUFA, and for saturated and palmitic FA. One identical significantly associated SNP was identified for C18:0 and KET on BTA 15. However, there was no genomic segment simultaneously significantly affecting all trait categories ICF, FA, and KET. Nevertheless, some of the annotated potential candidate genes DGKA, IGFBP4, and CXCL8 play a role in lipid metabolism and fertility mechanisms, and influence production diseases in early lactation. Genetic and genomic associations indicate that Fourier-transform infrared spectroscopy FA concentrations in milk from the first official test-day are valuable predictors for KET and for ICF.     

The genetic architecture of milk ELISA scores as an indicator of Johne's disease (paratuberculosis) in dairy cattle

Johne's disease (or paratuberculosis), caused by Mycobacterium avium ssp. paratuberculosis (MAP) infection, is a globally prevalent disease with severe economic and welfare implications. With no effective treatment available, understanding the role of genetics influencing host infection status is essential to develop selection strategies to breed for increased resistance to MAP infection. The main objectives of this study were to estimate genetic parameters for the MAP-specific antibody response using milk ELISA scores in Canadian Holstein cattle as an indicator of resistance to Johne's disease, and to unravel genomic regions and candidate genes significantly associated with MAP infection. After data editing, 168,987 milk ELISA records from 2,306 herds, obtained from CanWest Dairy Herd Improvement, were used for further analyses. Variance and heritability estimates for MAP infection status were determined using univariate linear animal models under 3 scenarios: (a) SCEN1: the complete data set (all herds); (b) SCEN2: herds with at least one suspect or test-positive animal (ELISA optical density ≥0.07); and (c) SCEN3: herds with at least one test-positive animal (ELISA optical density ≥0.11). Heritability estimates were calculated as 0.066, 0.064, and 0.063 for SCEN1, SCEN2, and SCEN3, respectively. The correlations between estimated breeding values for resistance to MAP infection and other economically important traits, when significant, were favorable and of low magnitude. Genome-wide association analyses identified important genomic regions on Bos taurus autosome (BTA)1, BTA7, BTA9, BTA14, BTA15, BTA17, BTA19, and BTA25 showing significant association with MAP infection status. These regions included 2 single nucleotide polymorphisms located 2 kb upstream of positional candidate genes CD86 and WNT9B, which play key roles in host immune response and tissue homeostasis. This study revealed the genetic architecture of MAP infection in Canadian Holstein cattle as measured by milk ELISA scores by estimating genetic parameters along with the identification of genomic regions potentially influencing MAP infection status. These findings will be of significant value toward implementing genetic and genomic evaluations for resistance to MAP infection in Holstein cattle.