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Simple Summary: Reproduction in Holstein cows is a critical factor influencing herd profitability. Heat stress (HS) caused by extremely warm climatic conditions disrupts several physiological processes, lowering fertility. Under the prospect of global warming, the selection of heat-tolerant cows able to maintain adequate reproductive performance during summer is favorable. The measurement of serum Anti-Müllerian hormone (AMH) has been proposed as a biomarker for fertility in Holstein cows, as well as single nucleotide polymorphisms (SNPs) associated with AMH. However, the HS that occurs in the summer of semi-arid regions appears to affect the predictability of the AMH marker(s). It could be due to a reduced ability of the follicle to synthesize AMH under HS conditions. In the current study, serum AMH was proved as an endocrine marker for fertility in cows subjected to a reproductive management program during summer but only if the heat stress did not exceed a moderate threshold. Polymorphisms within the AMH gene were validated as genetic markers associated with reproductive performance in cows exposed to either moderate or severe HS. However, due to the limited amount of variation accounted by these tools, their utility may be in conjunction with a genomic breeding value approach to help improve fertility in Holstein cows exposed to HS. Anti-Müllerian hormone (AMH) is proposed as a biomarker for fertility in cattle, yet this associative relationship appears to be influenced by heat stress (HS). The objective was to test serum AMH and AMH-related single nucleotide polymorphisms (SNPs) as markers potentially predictive of reproductive traits in dairy cows experiencing HS. The study included 300 Holstein cows that were genotyped using BovineSNP50 (54,000 SNP). A genome-wide association study was then executed. Nine intragenic SNPs within the pathways that influence the AMH gene were found important with multiple comparisons adjustment tests (p < 1.09 × 10−6). A further validation study was performed in an independent Holstein cattle population, which was divided into moderate (MH; n = 152) and severe heat-stressed (SH; n = 128) groups and then subjected to a summer reproductive management program. Serum AMH was confirmed as a predictor of fertility measures (p < 0.05) in MH but not in the SH group. Cows were genotyped, which revealed four SNPs as predictive markers for serum AMH (p < 0.01), reproductive traits (p < 0.01), and additional physiological variables (p < 0.05). These SNPs were in the genes AMH, IGFBP1, LGR5, and TLR4. In conclusion, serum AMH concentrations and AMH polymorphisms are proposed as predictive markers that can be used in conjunction with genomic breeding value approaches to improve reproductive performance in Holstein cows exposed to summer HS conditions. [ABSTRACT FROM AUTHOR]

Simple Summary: Holstein is the most popular dairy cattle breed worldwide due to its milk yield. When these cows are exposed to heat stress, they reduce feed intake and milk production in order to minimize body heat production. The large variability associated with this response appears to be genetically regulated. Therefore, we combined genomic and marker-assisted technologies with the objective to validate genetic markers associated with milk production and thermotolerance. A genome-wide association study detected six candidate single nucleotide polymorphisms (SNPs) as predictors for milk production in heat-stressed Holstein cows. Only three of these SNPs were further validated as markers for milk production and thermotolerance traits (i.e., rectal temperature and respiratory rate) in two independent Holstein cow populations. Such markers belong to genes that regulate metabolic functions needed to accomplish energy demands and minimal heat production. The results of this study revealed that heat-stressed Holstein cows with favorable markers were able to reduce rectal temperature and respiratory rate, which allowed them to maintain adequate milk production levels. In conclusion, we validated three genetic markers in heat-stressed Holstein dairy cows, which are useful to be included in selection programs to improve milk yield and tolerance to heat stress. Dairy production in Holstein cows in a semiarid environment is challenging due to heat stress. Under such conditions, genetic selection for heat tolerance appears to be a useful strategy. The objective was to validate molecular markers associated with milk production and thermotolerance traits in Holstein cows managed in a hot and humid environment. Lactating cows (n = 300) exposed to a heat stress environment were genotyped using a medium-density array including 53,218 SNPs. A genome-wide association study (GWAS) detected six SNPs associated with total milk yield (MY305) that surpassed multiple testing (p < 1.14 × 10−6). These SNPs were further validated in 216 Holstein cows from two independent populations that were genotyped using the TaqMan bi-allelic discrimination method and qPCR. In these cows, only the SNPs rs8193046, rs43410971, and rs382039214, within the genes TLR4, GRM8, and SMAD3, respectively, were associated (p < 0.05) with MY305, rectal temperature (RT), and respiratory rate. Interestingly, these variables improved as the number of favorable genotypes of the SNPs increased from 0 to 3. In addition, a regression analysis detected RT as a significant predictor (R2 = 0.362) for MY305 in cows with >1 favorable genotype, suggesting this close relationship was influenced by genetic markers. In conclusion, SNPs in the genes TLR4, GRM8, and SMAD3 appear to be involved in the molecular mechanism that regulates milk production in cows under heat-stressed conditions. These SNPs are proposed as thermotolerance genetic markers for a selection program to improve the milk performance of lactating Holstein cows managed in a semiarid environment. [ABSTRACT FROM AUTHOR]

Porcine Reproductive and Respiratory Syndrome (PRRS) is a viral disease that seriously affects the swine industry. The main method of control is vaccination, which has shown variable effectiveness partly attributed to genetic variability in sows. The objective was to validate single-nucleotide polymorphisms (SNPs) associated with performance traits following PRRS vaccination in replacement sows. A population of 100 Landrace(¾) / Yorkshire(¼) commercial line sows of 6 months of age, an average weight of 108 kg, and negative for PRRS virus were used. After an acclimatization stage, sows were vaccinated against PRRS (day 0). Daily weight gain (DWG) and rectal temperature (RT) were recorded on days 0, 7, 14, 21, and 28. A blood sample was individually collected on day 40 and used for DNA extraction and genotyping of 59 SNPs. These SNPs were previously identified through genomic analysis as associated with a vaccination response indicator. The 59 SNPs were validated in this study using a statistical mixed-effects model that included DWG or RT as response variables. From 59 SNPs, 5 of them were associated with DWG (P < 0.05), and 3 with RT (P < 0.05). Interestingly, the SNPs in the genes DENND5A (rs81409931 and rs81216494) and COL22A1 (rs329119519 and rs81381462) were associated with both DWG and RT, and they showed a higher allele contribution effect on phenotypes. These 2 genes appeared to be functionally related to DWG; therefore, their corresponding 4 SNPs are proposed as genetic markers associated with the response to PRRS vaccination in replacement sows from southern Sonora. [ABSTRACT FROM AUTHOR]

Cattle living in the Rocky Mountains (elevations of >1,500 m) are often at risk of contracting high altitude disease. Low atmospheric pressure at high altitudes causes pulmonary hypertension and potentially right heart failure. Pulmonary arterial pressure (PAP) is an indicator for pulmonary hypertension. PAP measurements of <41 mmHg are categorized as low risk for the development of pulmonary hypertension at high altitudes. Genetic resilience to the disease is possible and can be achieved through breed or within breed selection. Here, we explored differences between Angus raised at 2,150 m divided into low (<41 mmHg; n = 24) and high PAP (>41 mmHg; n = 41) groups and Salers (n = 24) at loci associated with PAP. The Salers sampled, a French mountainous breed (<4,800 m elevation), were all full blood. The mean Angus PAP score was 49 ± 2.1 mmHg (range 35 to 115). To determine the population structure between the two breeds, 121,756 SNP pruned from the 777,972 SNP on BovineHD BeadChip were evaluated using Admixture to infer ancestral populations. Previously identified SNP (n = 40) associated with PAP in Angus cattle through genome-wide association studies were used to assess the genetic diversity of both breeds. Chi-square tests were performed to identify statistical differences among the allele frequencies and breed groups. We used TreeSelect to identify allele frequency divergence from a central node due to selection. Admixture revealed by the lowest cross validation error that two distinct populations existed. Chi-square tests of SNP genotypic frequencies among the groups revealed that 23 of the 40 SNP differed (P < 0.025). Sixteen SNP differed between both low and high PAP Angus groups versus Salers. Also these results show the high PAP Angus genotypic frequencies differentiated themselves from the low PAP Angus genotypic frequencies. However, both high and low PAP Angus group allele frequencies showed evidence of approaching the frequencies observed in Salers. TreeSelect identified four SNP under selection. Of those SNP, three allele frequencies were similar between low PAP Angus and Salers, suggesting natural or artificial selection for both populations. These results indicate that genetic diversity exists between Angus and Salers cattle, which can be used to increase resilience to high altitude disease. Therefore, cattle breeders may choose to address such a problem through breed choice, selection within a breed, or both. [ABSTRACT FROM AUTHOR]

High altitude disease (HAD) is of low incidence but occurs in cattle at altitudes of >1,500 m. Histopathologically, this condition is characterized by pulmonary arterial vasoconstriction resulting in reduced diameter of arterioles, subsequently causing pulmonary hypertension and right heart failure. Mean pulmonary arterial pressure (mPAP) is commonly used as an indicator trait of pulmonary hypertension leading to HAD. Animals with mPAP measurements of <41 mmHg are considered to be of low risk for the development of HAD. Because mPAP is a trait difficult to measure, studies have identified SNP that may be of interest in selecting cattle more tolerant of higher altitudes. These SNP, if evaluated in polygenic models, could elucidate ways to implement genomic selection by establishing genetic pathways that will identify cattle better suited for high altitudes. In previous genome-wide association studies (GWAS), SNP were associated with mPAP as well as traits of birth weight, milking ability, weaning weight, post-weaning gain, and yearling weight. The objective of this study was to identify relationships among previously identified SNP by means of an association weight matrix (AWM) with mPAP as the primary trait of interest. Significant SNP from six GWAS were included in the AWM if they accounted for >0.001% of the genetic variance for mPAP. Based on that criterion, 954 SNP were identified for the AWM. Those SNP specifically associated with mPAP were then utilized to calculate the average number of phenotypes (Ap) a SNP should be associated in order to be included in the AWM. By averaging the number of additional phenotypes that SNP related to mPAP were associated with, an Ap of 0.266 was obtained, which was then rounded to one. All SNP that were significant at a genetic variance of >0.001% and associated with at least one phenotype were included in the AWM. Results indicated that significant SNP for the AWM spanned all 29 autosomal chromosomes as well as the X chromosome. Of the 262 SNP associated with mPAP, 17, 19, and 11 were associated with birth, weaning, and yearling weights, respectively. This supports previous studies indicating that the genetic correlations between mPAP and performance traits were weak to moderate rg < 0.27. Results from this study can be utilized to construct gene networks of SNP that are associated with mPAP as an effort to develop multi-trait genomic selection tools for high altitude beef production systems. [ABSTRACT FROM AUTHOR]

Grazing distribution is important for pasture management in beef cattle production systems. In mountainous terrain, abiotic factors such as steep slope and high elevation often yield concentrated grazing near riparian areas and limited livestock use in uplands. While management practices (fencing, water development, and herding) are effective in improving grazing distribution, these practices are costly and labor intensive. Previous research suggests that the traits used in indices to quantify grazing distribution are moderately heritable; therefore, genomic selection could be used to improve grazing distribution. Five QTL and underlying candidate genes (ACN9, FAM48A, GRM5, MAML3, and RUSC2) have been determined to be associated with grazing distribution traits in cattle. The objective of this study was to further examine these candidate genes and identify SNP that may then be incorporated into a previously developed 50-SNP panel used for genotype associations with grazing distribution phenotypes. Sequencing of RNA (RNA-Seq) yielded 30 million reads (single-read) per sample from 6 tissues (aorta, LM muscle, lung, pulmonary artery, and right and left ventricle) collected as part of an altitude tolerance study of Angus cattle. These tissues were from 10 steers with outlying pulmonary arterial pressure observations and unique sires. Sequences were assembled to the annotated bovine reference genome (UMD3.1; release annotation 87) and analyzed using CLC Genomics Workbench (version 8.0). Variant detection was performed using two methods: (1) individual samples and (2) a pool of all samples. No variants were detected in GRM5, MAML3, and RUSC2; however, individual sample analysis identified 30 SNP within ACN9 and FAM48A, and pooled sample analysis identified 184 SNP within ACN9 and FAM48A. Twenty-one SNP were identified in both approaches. The Ensemble Variant Effect Predictor was used to determine the functional consequence of each SNP. Of the 21 SNP, 16 were intronic, four were exonic, and one was reported to be a downstream variant and a splice acceptor variant. The SNP discovered using RNASeq technology were compared to the exonic SNP in dbSNP within the 5 candidate genes. There were 1,663 exonic SNP in dbSNP in these genes. One synonymous SNP, located within ACN9 (rs382949979), was observed in both data from RNASeq and dbSNP. In summary, 21 SNP were discovered in two of the five candidate genes underlying QTL associated with grazing distribution. These SNP will be incorporated in a new genotyping panel to examine associations with the grazing distribution phenotypes. [ABSTRACT FROM AUTHOR]

Reproductive performance in Holstein dairy cattle managed during summer in southern Sonora is a challenge because of high ambient temperature and relative humidity. Both of these factors contribute to heat stress, which influences cow behavior. The physiological response of cows to heat stress is one component of a system-wide gene network. Within this environment, a superior cow's ability to get pregnant early during postpartum is favorable as to reduce the trait days open and to increase productive life. Recently, many reproductive specialists have recommended using pregnancy rate as a measure of reproductive success, after converting this trait into a quantitative value using a linear formula. In comparison to the traditional measure of days open, pregnancy rate calculation includes more easily cows that do not become pregnant; furthermore, the output variable indicates that larger values are more desirable, and therefore, more understandable by dairy producers. The objective herein was to predict pregnancy rate in lactating Holstein cows using molecular markers associated with fertility in Holstein cows under a heat-stressed environment. This study included 500 cows from three dairy herds located in the Yaqui Valley of Sonora. A blood sample was collected from every cow and spotted onto FTA cards. The DNA was extracted from each card and used to genotype 179 tag SNP within 43 genes in the prolactin and GH-IGF1 pathways. Five SNP within the genes IGFBP7, IGFBP2, PAPPA1, SSTR2, and STAT6 were associated with pregnancy rate using a mixed effects model. The genotype term was later included in this model to calculate allele substitution effects. Molecular breeding values of the individual cows were calculated by summing the additive genotype effect for each SNP that showed a significant independent association with pregnancy rate, and the average MBV was 0.46 ± 0.01%. Two statistical regression models were used to predict the variable pregnancy rate: a full model that included effects of days and number of lactations, contemporary group (e.g., farm management group), health status, and MBV and a reduced model that only included MBV. Coefficients of determination were 37.61% and 3.07% for full and reduced models, respectively (P < 0.01). These results indicate that five SNP explained only a small proportion of the additive genetic variance for pregnancy rate. Additional research is needed to understand if these results are due to low heritability/repeatability of a fertility and (or) if these results are also influenced by heat stress. [ABSTRACT FROM AUTHOR]

At altitudes of >1,800 m, measurements of mean pulmonary arterial pressures (mPAP) have been used as an indicator trait of pulmonary hypertension and risk of right-sided heart failure in cattle. Genotypes from a G/A SNP (rs208684340) in the oxygen-dependent domain of the endothelial PAS domain protein 1 (EPAS1) gene were determined for yearling Angus cattle classified into mPAP risk categories (low, moderate, high) of heart failure. The A allele of this SNP was hypothesized to be associated with high altitude-induced hypoxemia. The initial objective of this study was to survey genotypic frequencies in Angus cattle at high altitude ranches in the Rocky Mountain west (elevation 1,850 to 2,800 m) and at low altitude ranches (elevation 91 to 1,192 m) in several states. For the latter, a random sampling (n = 118) of 1,275 Angus cattle from low altitude beef production systems in California, Missouri, Iowa, Texas, and New Mexico were genotyped. The mPAP phenotype was not collected for cattle residing at these altitudes. The percentages of cattle with genotypes G/G, G/A, and A/A were 64.4, 33.9, and 1.7%, respectively, with a MAF of 18.6%. Also, bulls, steers, and heifers (n = 690 progeny of 99 sires) from 4 Angus seedstock herds managed at high elevation were genotyped. The percentages of these cattle with genotypes G/G, G/A, and A/A were 48.7, 34.3, and 17.0%, respectively. The overall minor allele frequency (MAF; A allele) was 34.1% and mPAP averaged 40.6 ± 8.8 mmHg with a range of 28 to 126 mmHg. The MAF for the low, moderate, and high-risk categories were 35.4, 31.0, and 36.3%, respectively. No differences were observed for MAF between mPAP risk categories (P > 0.05). A second objective of this research was to evaluate the genotype to phenotype association of this SNP with mPAP phenotypes in the Colorado State University Beef Improvement Center (CSU-BIC; elevation 2,150 m) Angus herd. Genotypes from 496 Angus cattle were utilized in the association between this SNP and mPAP. Hardy-Weinberg equilibrium (P = 0.07) was not violated. A linear mixed model analysis with fixed effects of genotype, mPAP date, age, and a random effect of sire suggested genotype was not a predictor (P = 0.5) of mPAP and explained only 0.02% of the variation in mPAP. These results do not support the hypothesis that the A allele of this SNP (rs208684340) in the EPAS1 gene was associated with altitude-induced hypoxemia in cattle. [ABSTRACT FROM AUTHOR]

The porcine reproductive and respiratory syndrome (PRRS) is a viral disease that decreases the reproductive performance in breeding sows and leads to economic losses to the swine industry. The objective of the present study was to identify single nucleotide polymorphisms (SNP) associated to the number of live-born piglets in the first (LBP1) and second birth (LBP2) in breeding sows exposed to PRRS virus. The study included 100 pregnant females of the Landrace(?)/ Yorkshire(?) line, 75 of which were infected with the PRRS virus and 25 were free of PRRS. Individual blood samples (6-8 drops) were obtained and spotted onto FTA cards and subsequently processed for DNA extraction, which was genotyped using a 10,000 SNP chip for genomic profile. Resulting genotypes were analyzed using a multi-locus mixed model that detected three SNP associated to LBP1 and five SNP associated to LBP2 (P<0.001). These eight SNP were validated using an associative mixed effects model which included the terms genotype and age of dam as fixed effects, and sire as random effect. Allele substitution effects were estimated using the same model including the term genotype as covariate. The SNP rs81276080, rs81334603 and rs80947173 were associated to LBP1 (P<0.001), whereas the SNP rs81364943, rs80859829, rs80895640, rs80893794 and rs81245908 were associated to LBP2 (P<0.001). Only two SNP were in functional chromosomal regions and the remainder SNP were within an intergenic position. In conclusion, these results suggest the existence of gene variants associated with the reproductive performance of sows infected with the PRRS virus. [ABSTRACT FROM AUTHOR]

• SNPs in heat-stress related genes were associated with fertility traits in Holstein cows. • Gene markers allowed to construct an MBV capable to predict pregnancy rate in cows. • Heritability estimates were 0.06 for days open (DO) and 0.04 for pregnancy rate (PR) • The additive genetic variance explained by the MBVs was 2.5% for DO and 9.6% for PR. • Significant correlations among molecular and quantitative predictors were detected. Reproductive management in lactating Holstein cattle is a challenge for dairy producers in Northwestern Mexico where a semi-desert, yet humid, environment is predominant. Under such conditions, a superior cow's ability to get pregnant early during postpartum is desirable to reduce the number of days open and improve fertility parameters. The objective of this study was to predict days open (DO) and pregnancy rate (PR) using molecular markers associated with fertility in lactating Holstein cows managed in a warm climate. This study included 510 cows from three dairy herds located in the Yaqui Valley of Sonora. A blood sample was collected from every cow and spotted onto FTA cards. Each cow was genotyped for 179 tag single nucleotide polymorphisms (SNPs) within 43 genes in the prolactin and GH-IGF1 pathways. An association mixed-effects model identified three SNPs within the genes AVPR1A, PRLR and SSTR2 associated with DO (P < 0.05), and five SNPs within the genes IGFBP2, IGFBP5, PRLR, PIAS1 and SSTR2 associated with PR (P < 0.05). The SNP effects were estimated and used to calculate the individual molecular breeding values (MBV) for DO and PR. Average MBV were 20.91 ± 0.21 d and 0.29 ± 0.003% for DO and PR, respectively. The correlation between the MBV and DO was 0.0008 (P = 0.968), whereas correlation between MBV and the estimated breeding value (EBV) for DO was −0.16 (P < 0.001) with an adjusted coefficient of determination (R 2) of 2.5%. For PR, its correlation with the MBV was 0.15 (P < 0.001) with a R 2 of 2.2%, whereas the correlation between MBV and the EBV for PR was 0.31 (P < 0.001) with a R 2 of 9.6%. Heritability estimates were 0.06 ± 0.11 and 0.04 ± 0.06 for DO and PR, respectively. In conclusion, candidate gene SNPs from the prolactin and GH-IGF1 pathways were effectively used to construct an MBV for fertility traits in heat-stressed Holstein cattle. These SNPs explained only a small amount of variation for PR, but not for DO; therefore, additional research using denser SNP panels and a larger population is suggested to improve the power of the MBV as genetic predictor for fertility traits in lactating dairy cows managed under warm environmental conditions. [ABSTRACT FROM AUTHOR]