Genomic Analysis, Progress and Future Perspectives in Dairy Cattle Selection: A Review

Inheritance of bovine lymphocyte intestinal retention defect disorder affects Holstein production performance and longevity

Improved methods previously developed for tracking new mutations within existing haplotypes for cholesterol deficiency (HCD) and muscle weakness (HMW) now also were applied to track the bovine lymphocyte intestinal retention defect (BLIRD) discovered in France. Gene tests were available in US data for HCD and HMW, but not yet for BLIRD. Haplotype statuses for 3 million genotyped animals that also had US phenotypes were used to compare recessive effects of BLIRD homozygotes with French estimates. Heifer livability was 97.6% for normal calves with no copies of the haplotype (code 0) but averaged 88.8% for 178 homozygotes (code 2) and 94.1% for 2,029 uncertain homozygotes (code 4), with corresponding estimates of -8.6% and -3.3% from an animal model. Haplotype carriers verified by pedigree (code 1) or uncertain carriers (code 3) were not affected. Yield trait effects for 412 code 2 homozygotes were -1,799 kg of milk, -63 kg of fat, and -55 kg of protein with a cost of -$1,206 using lifetime net merit values; other traits not yet studied may increase that cost. Mating a BLIRD carrier randomly to a population with 8.9% allele frequency would cause an economic loss of $1,653 × 0.089/2 = $74 because half of the progeny would inherit the carrier's normal allele. Those losses should already be reflected in evaluations that average the merit across normal, carrier, and homozygous daughters. Genomic predictions do not fully track those losses because new mutations are poorly correlated with nearby markers. However, US adjustments for future inbreeding automatically reduce evaluations of popular ancestors by more than the cost of these individual defects. Gene tests are needed for new mutations within common haplotypes because tracking can be difficult even with accurate pedigrees.

Integrative genomic analysis reveals shared loci for reproduction and production traits in Yorkshire pigs

BACKGROUND

Improving reproductive performance in Yorkshire pigs, a key maternal line in three-way crossbreeding systems, remains challenging due to low heritability and historical selection pressures favoring production traits. Identifying pleiotropic genetic variants that influence both reproduction and production traits is crucial for understanding their genetic interplay and enhancing molecular breeding strategies.

RESULTS

Genome-wide association studies (GWAS) using 2,764 individuals identified 264,660 significant loci associated with reproduction traits and 12,460 loci for production traits, with 73 independent signals, including genes such as SCLT1 and CAPN9. A total of 465,047 independent loci were identified, resulting in a genome-wide significance threshold of 2.15 × 10 - 6 . Genetic correlations analysis between reproduction and production traits across parities revealed varying trends, including a strengthening negative correlation between mean litter weight (MLW) and backfat thickness (BFT) with increasing parity (P1: r g =-0.0376; P2: r g =-0.1371; P3: r g =-0.1475). Given 1062 shared significant loci between MLW and BFT, local genetic correlation was calculated within the corresponding genomic regions, resulting in a weak correlation of 0.014. Transcriptome-wide association studies (TWAS) leveraging data from the PigGTEx project, which includes 9,530 RNA-sequencing samples across 34 tissues, revealed 2,143 significant genes, with 31 linked to total number of piglets born (TNB) and 133 to number of piglets born alive (NBA). These results highlight the importance of these genes in reproductive performance, with SCLT1 being notably significant in reproductive tissues. For MLW, integrating results from multiple analyses revealed CENPE as a strong candidate gene, exhibiting significant association and colocalization. Validation in an independent population (n = 300) showed that incorporating the top 0.2% of significant single nucleotide polymorphisms (SNPs) in the GFBLUP model improved predictive accuracy, increasing from 0.0168 to 0.0242 for MLW.

CONCLUSION

This study provides new insights into the pleiotropic genetic architecture underlying reproduction and production traits in Yorkshire pigs. Genetic correlations, shared loci, and candidate genes inform breeding program design. The increased accuracy of genomic selection using these significant loci highlights their practical utility in improving breeding efficiency. These findings suggest opportunities for refining selection strategies, although further research is warranted to fully realize their potential for enhancing breeding programs.

Ecuadorian Holstein-Friesian cattle paternal lineages: Demographic structure, inbreeding evolution, and genetic diversity

Holstein-Friesian cattle are the most important dairy breed worldwide. The main objective was to carry out a detailed pedigree evaluation of the Ecuadorian Holstein-Friesian cattle to investigate the demographic structure, inbreeding evolution, and genetic diversity of the official paternal lineages to determine the potential GD loss after the inclusion of modern Assisted Reproductive Technologies (ARTs). Official pedigree information from 28,893 Holstein-Friesian sires born between 1950 and 2021 and enrolled with the Ecuadorian Holstein-Friesian Association (AHFE, Ecuador) were recorded and evaluated from USA and Canada genetic official databases. After multiple-trait across-country genetic analyses the total population was divided into four subpopulations; i) 1950-1969: natural mating (NM) period; ii) 1970-1989: NM +  artificial insemination (AI) period; iii) 1990-2009: AI +  embryo transfer (ET) period; and iv) 2010-2021: AI +  ET +  genomic selection (GS) period. Demographic parameters [number of males, pedigree integrity (PI), and generation interval (GI)] were analysed. PI was analysed using known ancestors up to 4 generations considering the number of complete (GCom), maximum (GMax) and equivalent (GEqu) generations. Moreover, Inbreeding parameters [inbreeding coefficient (F), average relatedness (AR), coancestry (C), effective size (Ne), genetic conservation index (GCI)] and parameters related to the gene origin probability (number of founders (f), effective number of founders (fe), genetic conservation index (GCI), among others] were also analysed, together with the fe/f ratio, fge/fe ratio, genetic contributions, and genetic diversity loss (GD-loss) derived parameters. The results indicated that nearly all imported sires used in Ecuador born in the beginning of 1990s could be traced to just three countries, who together account for > 90% of paternal lineages. This fact indicates that GD has undergone a dramatic decrease during the past 30 years. The PCI for the three last periods were > 55%, and the trend was enhanced in the fourth chronological period till > 92%. The estimated proportion of random genetic drift in GD loss increased over time as well as the Ne that decreased by the time. In conclusion, the occurrence of AI +  ET +  GS period led to the major GD loss. Therefore, due to the extremely limited number of paternal lineages the strategy for recovering the minimal GD on the current and future Ecuadorian Holstein-Friesian cattle should reduce the inbreeding values by increasing the Ne using alternately the foreign genetic material and the national breeding stock.

Impact of Implementing Female Genomic Selection and the Use of Sex-Selected Semen Technology on Genetic Gain in a Dairy Herd in New Zealand

Genomic selection (GS) has changed cattle breeding, but its use so far has been in selecting superior bulls for breeding. However, its farm-level impact, particularly on female selection, remains less explored. This study aimed to investigate the impact of implementing GS to identify superior cows and using artificial mating of those cows with sex-selected semen in a New Zealand Holstein-Friesian (HF) dairy herd (n = 1800 cows). Heifers (n = 2061) born over four consecutive years between 2021 and 2024 were genotyped and their genomic breeding values (GBVs) were estimated. These heifers were ranked based on the Balanced Performance Index (BPI; DataGene, Dairy Australia) Lower-performing cows producing less than 15 L/day (or 20 L/day for older cows) and those with severe mastitis were culled. Cows were mated with HF genetics based on production and udder breeding values, while lower-performing cows were mated to beef genetics. Milking adult cows were mated to bulls with similar BPI value. Annual genetic change was measured using Australian breeding values (ABVg) for milk fat production (FAT), protein production (PROT), fertility (FER), Mastitis Resistance (MAS), and BPI. The genetic merits of the heifers improved annually, with BPI increasing from 136 to 184 between 2021 and 2023, corresponding to a financial gain of NZD 17.53 per animal per year. The predicted BPI gain from 2023 to 2026 is expected to rise from 184 to 384, resulting in a financial gain of NZD 72.96 per animal per year. Using sex-selected semen on the top 50% of BPI-rated heifers in 2024 further accelerated genetic gain. Predicted BPI values for progeny born in 2025 and 2026 are 320 and 384, respectively. These findings revealed that the female GS, combined with sex-selected semen from genomically selected bulls, significantly accelerates genetic gain by improving the intensity and accuracy of selection. The approach achieves genetic progress equivalent to what traditionally would have required eight years of breeding without female GS, and has potential to improve dairy herd performance and profitability.

Reproductive Performance, Inbreeding, and Genetic Diversity in Montbeliarde Dairy Cattle Obtained by Absorption Crossing

Montbeliarde dairy cattle were introduced in Ecuador with the aim of ameliorating the production performance of other cattle breeds. The aim was to analyze the reproductive performance, demographic structure, inbreeding, and genetic diversity of Montbeliarde cattle obtained by absorption crossing. Official pedigree records from the Ecuadorian Montbeliarde Association were used. The total population was divided into seven populations: (i) historical (all individuals), (ii) 1999-2003, (iii) 2004-2008, (iv) 2009-2013, (v) 2014-2018, (vi) 2019-2023 (current), and (vii) reference (individuals with known parents). Demographic structure variables analyzed: pedigree completeness index (PCI), number of equivalents (GEqu), complete (GCom) and maximum (GMax) generations, and generation interval (GI). Inbreeding-derived variables analyzed: inbreeding (F), inbreeding increment (ΔF), average relatedness (AR), co-ancestry (C), non-random mating (α), effective population size (Ne), and genetic conservation index (GCI). Gene origin probability/genetic diversity variables analyzed: number of founders (f), effective number of founders (fe) and ancestors (fa), number of equivalent genomes (fg), fe/fa and fg/fa ratio, and DG losses. The databases were analyzed by ENDOG, POPREP, and CPC software. PCI in the historical population compared to the current population decreased from 72.95 to 65.87% (sire/dam pathway), while the GI decreased from 7.17 to 3.08 years when the historical and current populations were compared. Dam reproductive efficiency increased over time. Moreover, F = ~1%, AR = 2.06%, ΔF = 0.22%, C = 1.03%, α = -0.0077, GCI = 3.12, and Ne = 58 values were obtained. Gene origin probability in the reference population was f = 439, fa = 37, fe = 71.64, fg = 23.43, and fg/fe = 0.33, showing a GD loss due to unequal contribution of founders (0.55%) and bottleneck and genetic drift (4.25%). In conclusion, the Ecuadorian Montbeliarde cattle population displayed a relatively low diversity and high genetic relationship. Inbreeding levels increased while Ne values decreased over time. The introduction of new purebred bloodlines could be important to minimize the inbreeding levels ensuring the long-term conservation of this breed and minimizing GD loss.

Unravelling the Signature Follicular Fluid Metabolites in Dairy Cattle Follicles Growing Under Negative Energy Balance: An In Vitro Approach

The astringent selection criteria for milk-oriented traits in dairy cattle have rendered these animals prone to various metabolic disorders. Postpartum lactational peak and reduced feed intake lead to negative energy balance in cattle. As a compensatory mechanism, cattle start mobilizing fat reserves to meet the energy demand for vital body functions. Consequently, diminished glucose concentrations and elevated ketone body levels lead to poor ovarian function. The impaired follicular development and subpar oocyte quality diminish the conception rates, which poses significant economic repercussions. Follicular fluid is integral to the processes of follicular growth and oocyte development. Hence, the present study was performed to identify potential alterations in metabolites in the follicular fluid under in vitro culture conditions mimicking negative energy balance. Our results revealed nine distinct metabolites exhibiting differential expression in follicular fluid under negative energy balance. The differentially expressed metabolites were predominantly associated with pathways related to amino acid metabolism, lipid metabolism, signal transduction mechanisms, and membrane transport, alongside other biological processes. The identified signature metabolites may be further validated to determine oocyte fitness subjected to in vitro fertilization or embryo production from slaughterhouse source ovaries.

Maternal Genetic Diversity Analysis of Guanling Cattle by Mitochondrial Genome Sequencing

Owing to the unique geography and the isolated environment, Guanling cattle, which is one of five local cattle breeds in Guizhou, China, has developed unique characteristics. The number of pure Guanling cattle decreased markedly because of the hybridization with foreign breeds. In the present study, the maternal genetic diversity of 58 Guanling bulls was assessed by whole mitochondrial genome sequencing. Genetic polymorphisms and phylogenetic analyses classified Guanling cattle into two main lineages, where 43.10% of Guanling cattle were closely related to the foreign breeds and 56.90% displayed distinct features in mitochondrial genomic diversity. PCA analysis further separated Guanling cattle into four populations, one of which was clustered with the foreign breeds. The result of the structure plot and genetic polymorphisms revealed high genetic diversity within two populations that have a long genetic distance from the foreign breeds. Overall, our findings suggest that the whole mitochondrial genome sequencing analysis is a useful and reliable tool to study maternal genetic diversity and to identify the pure population of Guanling cattle. The results will be beneficial to the breeding management of Guanling cattle.

Evolution of Population Structure, Reproductive Performance, Inbreeding, and Genetic Diversity in Ecuadorian Charolais Cattle

The objective was to evaluate the evolution of the population structure, reproductive performance, inbreeding, and genetic diversity in Charolais cattle. Official genealogical information from the Ecuadorian Charolais Association was divided into five populations: (a) historical (total), (b) 2008-2012 (natural mating period), (c) 2013-2017 (natural mating + artificial insemination period), (d) 2018-2022 (artificial insemination + embryo transfer period), and (e) the reference (known sires and dams) from which the population structure was evaluated using pedigree completeness and the generation interval (GI). Meanwhile, for genetic diversity (GD), inbreeding (F), average relatedness (AR), and the effective population size (Ne) were estimated. The gene origin probability (number of founders, effective number of founders/ancestors, and number of founder genomes) explaining genetic variability, reproductive efficiency, the number of offspring per sire and dam, and the average ages of parents at the birth of their offspring were determined. The database was analyzed using the ENDOG, POPREP, and CFC software programs. The results indicate that pedigree completeness and the GI decreased over time among populations, although the first generation showed higher values. The sire gametic pathway was greater in all populations. F increased over time, although not markedly. Although Ne variations were observed, the levels remained above the recommended limit value. The GD loss increased progressively over time although the most recent population was not significantly affected. Finally, the female reproductive efficiency increased over time as well. In conclusion, the Charolais cattle GI should be reduced. After 2012, the use of Assisted Reproductive Technologies and breeding schemes raised the GD loss. Finally, the F increased over time although it could be reduced using foreign genetic resources in the current Ecuadorian Charolais population.

Proteomic identification of potential biomarkers for heat tolerance in Caracu beef cattle using high and low thermotolerant groups

BACKGROUND

Heat stress has deleterious effects on physiological and performance traits in livestock. Within this context, using tropically adapted cattle breeds in pure herds or terminal crossbreeding schemes to explore heterosis is attractive for increasing animal production in warmer climate regions. This study aimed to identify biological processes, pathways, and potential biomarkers related to thermotolerance in Caracu, a tropically adapted beef cattle breed, by proteomic analysis of blood plasma. To achieve this goal, 61 bulls had their thermotolerance evaluated through a heat tolerance index. A subset of 14 extreme animals, including the seven most thermotolerant (HIGH group) and the seven least thermotolerant (LOW group), had their blood plasma samples used for proteomic analysis by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The differentially regulated proteins detected between HIGH and LOW groups were used to perform functional enrichment analysis and a protein-protein interaction network analysis.

RESULTS

A total of 217 proteins were detected only in the HIGH thermotolerant group and 51 only in the LOW thermotolerant group. In addition, 81 and 87 proteins had significantly higher and lower abundancies in the HIGH group, respectively. Regarding proteins with the highest absolute log-fold change values, we highlighted those encoded by DUSP5, IGFALS, ROCK2, RTN4, IRAG1, and NNT genes based on their functions. The functional enrichment analysis detected several biological processes, molecular functions, and pathways related to cellular responses to stress, immune system, complement system, and hemostasis in both HIGH and LOW groups, in addition to terms and pathways related to lipids and calcium only in the HIGH group. Protein-protein interaction (PPI) network revealed as important nodes many proteins with roles in response to stress, hemostasis, immune system, inflammation, and homeostasis. Additionally, proteins with high absolute log-fold change values and proteins detected as essential nodes by PPI analysis highlighted herein are potential biomarkers for thermotolerance, such as ADRA1A, APOA1, APOB, APOC3, C4BPA, CAT, CFB, CFH, CLU, CXADR, DNAJB1, DNAJC13, DUSP5, FGA, FGB, FGG, HBA, HBB, HP, HSPD1, IGFALS, IRAG1, KNG1, NNT, OSGIN1, PROC, PROS1, ROCK2, RTN4, RYR1, TGFB2, VLDLR, VTN, and VWF.

CONCLUSIONS

Identifying potential biomarkers, molecular mechanisms and pathways that act in response to heat stress in tropically adapted beef cattle contributes to developing strategies to improve performance and welfare traits in livestock under tropical climates.

Effect of Age at First Calving on the Reproduction Parameters, Metabolic Profile, and Fatty Acid Composition of Polish Holstein Friesian (PHF) and Crossbreds PHF × Swedish Red (SRB) Cattle

BACKGROUND

The high dairy production of Polish Holstein Friesian (PHF) cows determines high energy requirements in the early stages of lactation. Unfortunately, it is very often difficult to meet this demand through feedstuffs; therefore, homeostasis may be disturbed and metabolic diseases may occur, causing a majority of cows' health problems. Breeders are, therefore, looking for alternatives to the PHF breed using crossbreeding.

METHODS

This experiment involved 30 PHF cows and 30 PHF × Swedish Red (SRB) crossbred hybrid cows, divided into two age groups, <2 years and >2 years, at first calving. Milk and blood samples were collected at 35 ± 5 days postpartum for analysis. Data on reproductive performance were also analyzed.

RESULTS

This study revealed lower milk production for the crossbreds hybrid (27.44 kg compared to 32.08 kg), with a higher basic composition content than PHF cows (fat: 3.97% compared to 3.83%, protein: 3.53% compared to 3.27%). The heifers of the crossbreds hybrid reached sexual maturity earlier but did not affect the lower age at first calving. Dividing the cows into age categories provided a more detailed perspective of the impact of genotypic differences on reproductive and metabolic profiles in PHF and PHF × SRB cattle. The findings highlight the importance of considering age-specific effects when assessing the performance and health of dairy cattle with diverse genotypes.

CONCLUSIONS

The choice between PHF and PHF × SRB should depend on the specific goals and priorities of the cattle farming operation. Factors such as overall milk yield requirements, market demands, reproductive management strategies, and health considerations should be carefully evaluated to determine the most suitable breed for a given farming context.

Impact of Heat Stress on Milk Yield, Milk Fat-to-Protein Ratio, and Conception Rate in Thai-Holstein Dairy Cattle: A Phenotypic and Genetic Perspective

Heat stress severely affects dairy cattle production and reproduction performances in tropical regions. Genetic selection to maintain adequate yield and reproductive performance while enhancing their ability to withstand heat is essential for improving the genetics of dairy cows. Therefore, in this study, we aimed to estimate genetic parameters affecting production and reproduction performances under heat stress conditions in dairy cattle and to investigate the threshold point of heat stress for milk yield (MY), milk fat-to-protein ratio (FPR), and conception rate (CR) in Thai-Holstein dairy cattle. The data included 168,124 records related to MY and milk FPR and 21,278 records of CR in Thai-Holstein dairy cattle, covering the period from 1990 to 2007. A multiple-trait threshold-linear random regression model based on a Bayesian approach via Gibbs sampling was used to estimate variance components, genetic parameters (heritability values, and genetic correlations), and decline rates for each studied trait. The threshold point of heat stress was identified as a temperature and humidity index (THI) of 76. At THI76, a decline was observed in the MY, milk FPR, and CR of Thai dairy cattle. The heritability estimates for MY, milk FPR and CR were 0.347 ± 0.032, 0.293 ± 0.021, and 0.032 ± 0.001, respectively. The genetic correlation between MY and milk FPR and MY and CR were -0.24 and -0.53, respectively, whereas those between milk FPR and heat tolerance as well as between CR and heat tolerance were -0.48 and -0.49, respectively. In addition, the decline rates in MY, milk FPR, and CR were found to be associated with a high percentage of Holstein genetics. In conclusion, the results obtained in this study reveal that the simultaneous consideration of the MY, milk FPR, CR, and heat tolerance traits of Thai-Holstein dairy cattle is possible. In addition, developing a genetic model that incorporates THI is essential for sustainably addressing heat stress problems.

Validating genomic predictions for economic traits in purebred U.S. dairy heifers

Most genotypes in the National Cooperator Database now originate from cows, but most previous studies validating genomic predictions have primarily focused on bulls. This study paired official within-breed genomic predicted transmitting ability (GPTA) and parent average (PA) for genotyped heifer calves born between 2019 and 2021 using the August 2021 database with their corresponding performance deviations (PDEV) for 17 different traits. The PDEV data became available when the heifers completed their first lactation and were extracted from the August 2023 database in which at least one PDEV value for those 17 traits existed for each genotyped heifer record. The separate breed analyses included records for 219 Ayrshires (AY), 2,715 Brown Swiss (BS), 1,055 Guernseys (GU), 949,904 Holsteins (HO), and 125,275 Jerseys (JE). These validation cows were heifer calves born between 2019 and 2021. However, due to timing or recording patterns, each trait had missing or incomplete PDEV data, leading to unbalanced distributions of records across traits. The squared accuracy of genomic prediction, or genomic reliability (r2), was divided by the corresponding heritability for each trait, as only the heritable portion of cow records could be predicted, and this reliability varied across different traits and breeds. For HO and JE, the predictive ability of GPTA outperformed PA in predicting cow PDEV for yield, productive life, somatic cell score, fertility, and health traits. The improvement ranged from 33% to 142% compared with the predictive ability of the PA. However, the results for AY, BS, and GU breeds were less consistent due to the smaller number of genotyped heifers. The r2 gains in those breeds were smaller and aligned with the published reliabilities of GPTA. Weighted and unweighted regressions of PDEV on GPTA and PA traits mostly exceeded the expected value of 2.00 when predicting the future trait PDEV using GPTA or PA. The larger number of observations and lower standard error of the weighted regression coefficient prediction in HO and JE breeds contributed to more stable and consistent regression coefficients for all traits except milk fever and heifer livability. Our study suggests that herd owners may experience greater benefits from genomics than originally forecast.

An overview of recent technological developments in bovine genomics

Cattle are regarded as highly valuable animals because of their milk, beef, dung, fur, and ability to draft. The scientific community has tried a number of strategies to improve the genetic makeup of bovine germplasm. To ensure higher returns for the dairy and beef industries, researchers face their greatest challenge in improving commercially important traits. One of the biggest developments in the last few decades in the creation of instruments for cattle genetic improvement is the discovery of the genome. Breeding livestock is being revolutionized by genomic selection made possible by the availability of medium- and high-density single nucleotide polymorphism (SNP) arrays coupled with sophisticated statistical techniques. It is becoming easier to access high-dimensional genomic data in cattle. Continuously declining genotyping costs and an increase in services that use genomic data to increase return on investment have both made a significant contribution to this. The field of genomics has come a long way thanks to groundbreaking discoveries such as radiation-hybrid mapping, in situ hybridization, synteny analysis, somatic cell genetics, cytogenetic maps, molecular markers, association studies for quantitative trait loci, high-throughput SNP genotyping, whole-genome shotgun sequencing to whole-genome mapping, and genome editing. These advancements have had a significant positive impact on the field of cattle genomics. This manuscript aimed to review recent advances in genomic technologies for cattle breeding and future prospects in this field.

Genomic selection for crop improvement in fruits and vegetables: a systematic scoping review

To ensure the nutritional needs of an expanding global population, it is crucial to optimize the growing capabilities and breeding values of fruit and vegetable crops. While genomic selection, initially implemented in animal breeding, holds tremendous potential, its utilization in fruit and vegetable crops remains underexplored. In this systematic review, we reviewed 63 articles covering genomic selection and its applications across 25 different types of fruit and vegetable crops over the last decade. The traits examined were directly related to the edible parts of the crops and carried significant economic importance. Comparative analysis with WHO/FAO data identified potential economic drivers underlying the study focus of some crops and highlighted crops with potential for further genomic selection research and application. Factors affecting genomic selection accuracy in fruit and vegetable studies are discussed and suggestions made to assist in their implementation into plant breeding schemes. Genetic gain in fruits and vegetables can be improved by utilizing genomic selection to improve selection intensity, accuracy, and integration of genetic variation. However, the reduction of breeding cycle times may not be beneficial in crops with shorter life cycles such as leafy greens as compared to fruit trees. There is an urgent need to integrate genomic selection methods into ongoing breeding programs and assess the actual genomic estimated breeding values of progeny resulting from these breeding programs against the prediction models.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01497-2.

Correlation of sperm motility, acrosome integrity, protamine deficiency, and DNA fragmentation in proven and unproven Friesian Holstein bulls

Objective

The evaluation of frozen semen quality is an essential aspect in determining male fertility for artificial insemination programs. This study aims to evaluate the characteristics of Friesian Holstein (FH) bull-frozen semen in different classes (proven and unproven) based on protein profiling and molecular evaluation.

Materials and Methods

This study used frozen semen straws from FH bulls selected according to criteria for proven (6 individuals) and unproven (6 individuals) bulls produced by the Singosari AI Center (AIC). Sperm motility parameters were assessed using Computer Assisted Semen Analysis (CASA Supervision®, Germany), while sperm viability and abnormality were evaluated through eosin-nigrosin staining under a microscope at 400´ magnifications. The integrity of the sperm plasma membrane was determined using the hypoosmotic swelling test, and acrosome integrity was analyzed using the fluorescein isothiocyanate PNA-propidium iodide staining method. Protamine deficiency was quantified using Chromomycin A3 fluorescence staining, while DNA fragmentation was assessed using the acridine orange technique.

Results

The findings demonstrated that there were no statistically significant differences (p > 0.05) in the assessed parameters of frozen semen quality between FH-proven and unproven bulls. Furthermore, in FH-proven bulls, a negative correlation was observed between protamine deficiency and acrosome integrity (r = -0.528) and between protamine deficiency and sperm DNA fragmentation (r = -0.467). The parameters of protamine deficiency in unproven bulls exhibited a positive correlation with sperm progressive motility.

Conclusion

The frozen semen quality of FH bulls in different classes (proven and unproven) was found to be equally good. Molecular-based analysis allows for a more accurate determination of semen quality. These findings are significant for bull breeding stations when comprehensively evaluating semen quality.

Mammary fat globules as a source of mRNA to model alterations in the expression of some milk component genes during lactation in bovines

BACKGROUND

The milk's nutritional value is determined by its constituents, including fat, protein, carbohydrates, and minerals. The mammary gland's ability to produce milk is controlled by a complex network of genes. Thereby, the fat, protein, and lactose synthesis must be boost in milk to increase milk production efficiency. This can be accomplished by fusing genetic advancements with proper management practices. Therefore, this study aimed to investigate the association between the Lipoprotein lipase (LPL), kappa casein CSN3, and Glucose transporter 1 (GLUT1) genes expression levels and such milk components as fat, protein, and lactose in different dairy breeds during different stages of lactation.

METHODS

To achieve such a purpose, 94 milk samples were collected (72 samples from 36 multiparous black-white and red-white Holstein-Friesian (HF) cows and 22 milk samples from 11 Egyptian buffaloes) during the early and peak lactation stages. The milk samples were utilized for milk analysis and genes expressions analyses using non- invasive approach in obtaining milk fat globules (MFGs) as a source of Ribonucleic acid (RNA).

RESULTS

LPL and CSN3 genes expressions levels were found to be significantly higher in Egyptian buffalo than Holstein-Friesian (HF) cows as well as fat and protein percentages. On the other hand, GLUT1 gene expression level was shown to be significantly higher during peak lactation than early lactation. Moreover, lactose % showed a significant difference in peak lactation phase compared to early lactation phase. Also, fat and protein percentages were significantly higher in early lactation period than peak lactation period but lactose% showed the opposite pattern of Egyptian buffalo.

CONCLUSION

Total RNA can be successfully obtained from MFGs. The results suggest that these genes play a role in glucose absorption and lactose synthesis in bovine mammary epithelial cells during lactation. Also, these results provide light on the differential expression of these genes among distinct Holstein-Friesian cow breeds and Egyptian buffalo subspecies throughout various lactation phases.

New mutation within a common haplotype is associated with calf muscle weakness in Holsteins

A recessive haplotype resulting in elevated calf mortality but with apparent incomplete penetrance was previously linked to the end of chromosome 16 (78.7-80.7 Mbp). Genotype analysis of 5.6 million Holsteins indicated that the haplotype was common and traced back to 1952, with a key ancestor born in 1984 (HOUSA1964484, Southwind) identified from chip genotypes as homozygous for the suspect haplotype. Sequence data from Southwind (an affected calf) and the sire of the affected calf were scanned for candidate mutations. A missense mutation with a deleterious projected impact at 79,613,592 bp was homozygous in the affected calf and heterozygous in the calf's sire and Southwind. Sequence data available from the Cooperative Dairy DNA Repository for 299 other Holsteins indicated a 97% concordance with the haplotype and an 89% call rate. The exon amino acid sequence appears to be broadly conserved in the CACNA1S gene, and mutations in humans and mice can cause phenotypes of temporary or permanent paralysis analogous to those in calves with the haplotype causing muscle weakness (HMW). Improved methods for using pedigree to track new mutations within existing haplotypes were developed and applied to the haplotypes for both muscle weakness and Holstein cholesterol deficiency (HCD). For HCD, concordance of the gene test with its haplotype status was greatly improved. For both defects, haplotype status was matched to heifer livability records for 558,000 calves. For HMW, only 46 heifers with livability records were homozygous and traced only to Southwind on both sides. Of those, 52% died before 18 mo at an average age of 1.7 ± 1.6 mo, but that death rate may be underestimated if only healthier calves were genotyped. The death rate was 2.4% for noncarriers. Different reporting methods or dominance effects may be needed to include HMW and other partially lethal effects in selection and mating. Direct tests are needed for new mutations within existing common haplotypes because tracking can be difficult even with accurate pedigrees when the original haplotype has a high frequency.

Machine Learning to Predict Pregnancy in Dairy Cows: An Approach Integrating Automated Activity Monitoring and On-Farm Data

Automated activity monitoring (AAM) systems are critical in the dairy industry for detecting estrus and optimizing the timing of artificial insemination (AI), thus enhancing pregnancy success rates in cows. This study developed a predictive model to improve pregnancy success by integrating AAM data with cow-specific and environmental factors. Utilizing data from 1,054 cows, this study compared the pregnancy outcomes between two AI timings-8 or 10 h post-AAM alarm. Variables such as age, parity, body condition, locomotion, and vaginal discharge scores, peripartum diseases, the breeding program, the bull used for AI, milk production at the time of AI, and environmental conditions (season, relative humidity, and temperature-humidity index) were considered alongside the AAM data on rumination, activity, and estrus intensity. Six predictive models were assessed to determine their efficacy in predicting pregnancy success: logistic regression, Bagged AdaBoost algorithm, linear discriminant, random forest, support vector machine, and Bagged Classification Tree. Integrating the on-farm data with AAM significantly enhanced the pregnancy prediction accuracy at AI compared to using AAM data alone. The random forest models showed a superior performance, with the highest Kappa statistic and lowest false positive rates. The linear discriminant and logistic regression models demonstrated the best accuracy, minimal false negatives, and the highest area under the curve. These findings suggest that combining on-farm and AAM data can significantly improve reproductive management in the dairy industry.

Chromosome Transplantation: Opportunities and Limitations

There are thousands of rare genetic diseases that could be treated with classical gene therapy strategies such as the addition of the defective gene via viral or non-viral delivery or by direct gene editing. However, several genetic defects are too complex for these approaches. These "genomic mutations" include aneuploidies, intra and inter chromosomal rearrangements, large deletions, or inversion and copy number variations. Chromosome transplantation (CT) refers to the precise substitution of an endogenous chromosome with an exogenous one. By the addition of an exogenous chromosome and the concomitant elimination of the endogenous one, every genetic defect, irrespective of its nature, could be resolved. In the current review, we analyze the state of the art of this technique and discuss its possible application to human pathology. CT might not be limited to the treatment of human diseases. By working on sex chromosomes, we showed that female cells can be obtained from male cells, since chromosome-transplanted cells can lose either sex chromosome, giving rise to 46,XY or 46,XX diploid cells, a modification that could be exploited to obtain female gametes from male cells. Moreover, CT could be used in veterinary biology, since entire chromosomes containing an advantageous locus could be transferred to animals of zootechnical interest without altering their specific genetic background and the need for long and complex interbreeding. CT could also be useful to rescue extinct species if only male cells were available. Finally, the generation of "synthetic" cells could be achieved by repeated CT into a recipient cell. CT is an additional tool for genetic modification of mammalian cells.

Multi-omics integration identifies regulatory factors underlying bovine subclinical mastitis

BACKGROUND

Mastitis caused by multiple factors remains one of the most common and costly disease of the dairy industry. Multi-omics approaches enable the comprehensive investigation of the complex interactions between multiple layers of information to provide a more holistic view of disease pathogenesis. Therefore, this study investigated the genomic and epigenomic signatures and the possible regulatory mechanisms underlying subclinical mastitis by integrating RNA sequencing data (mRNA and lncRNA), small RNA sequencing data (miRNA) and DNA methylation sequencing data of milk somatic cells from 10 healthy cows and 20 cows with naturally occurring subclinical mastitis caused by Staphylococcus aureus or Staphylococcus chromogenes.

RESULTS

Functional investigation of the data sets through gene set analysis uncovered 3458 biological process GO terms and 170 KEGG pathways with altered activities during subclinical mastitis, provided further insights into subclinical mastitis and revealed the involvement of multi-omics signatures in the altered immune responses and impaired mammary gland productivity during subclinical mastitis. The abundant genomic and epigenomic signatures with significant alterations related to subclinical mastitis were observed, including 30,846, 2552, 1276 and 57 differential methylation haplotype blocks (dMHBs), differentially expressed genes (DEGs), lncRNAs (DELs) and miRNAs (DEMs), respectively. Next, 5 factors presenting the principal variation of differential multi-omics signatures were identified. The important roles of Factor 1 (DEG, DEM and DEL) and Factor 2 (dMHB and DEM), in the regulation of immune defense and impaired mammary gland functions during subclinical mastitis were revealed. Each of the omics within Factors 1 and 2 explained about 20% of the source of variation in subclinical mastitis. Also, networks of important functional gene sets with the involvement of multi-omics signatures were demonstrated, which contributed to a comprehensive view of the possible regulatory mechanisms underlying subclinical mastitis. Furthermore, multi-omics integration enabled the association of the epigenomic regulatory factors (dMHBs, DELs and DEMs) of altered genes in important pathways, such as 'Staphylococcus aureus infection pathway' and 'natural killer cell mediated cytotoxicity pathway', etc., which provides further insights into mastitis regulatory mechanisms. Moreover, few multi-omics signatures (14 dMHBs, 25 DEGs, 18 DELs and 5 DEMs) were identified as candidate discriminant signatures with capacity of distinguishing subclinical mastitis cows from healthy cows.

CONCLUSION

The integration of genomic and epigenomic data by multi-omics approaches in this study provided a better understanding of the molecular mechanisms underlying subclinical mastitis and identified multi-omics candidate discriminant signatures for subclinical mastitis, which may ultimately lead to the development of more effective mastitis control and management strategies.

Association of three single nucleotide polymorphisms in the LPIN1 gene with milk production traits in cows of the Yaroslavl breed

Lipin-1 is a member of the evolutionarily conserved family of proteins and is expressed predominantly in adipose tissue and skeletal muscle. On the one hand, lipin-1 is an enzyme that catalyzes the dephosphorylation of phosphatidic acid to diacylglycerol (DAG) and thus participates in the metabolic pathways of biosynthesis of storage lipids in the cell, membrane phospholipids, and intracellular signaling molecules. On the other hand, lipin-1 is able to be transported from the cytoplasm to the nucleus and is a coactivator of lipid metabolism gene transcription. It was shown, using the analysis of single nucleotide polymorphism (SNP) associations, that the lipin-1 coding gene (LPIN1) is a promising candidate gene for milk production traits in Holstein and Brown Swiss cows. However, it is unclear how much of its effect depends on the breed. The Yaroslavl dairy cattle breed was created in the 18-19 centuries in Russia by breeding northern Great Russian cattle, which were short and poor productive, but well adapted to local climatic conditions and bad food base. It was shown by whole genome genotyping and sequencing that the Yaroslavl breed has unique genetics compared to Russian and other cattle breeds. The aim of the study was to assess the frequency of alleles and genotypes of three SNPs in the LPIN1 gene and to study the association of these SNPs with milk production traits in Yaroslavl cows. Blood samples from 142 cows of the Yaroslavl breed were obtained from two farms in the Yaroslavl region. Genotyping of SNPs was carried out by polymerase chain reaction-restriction fragment length polymorphism method. Associations of SNPs with 305-day milk yield, fat yield, fat percentages, protein yield, and protein percentages were studied from the first to the fourth lactation. Statistical tests were carried out using a mixed linear model, taking into account the relationship between individuals. We identified three SNPs - rs110871255, rs207681322 and rs109039955 with a frequency of a rare allele of 0.042-0.261 in Yaroslavl cows. SNP rs110871255 was associated with fat yield during the third and fourth lactations. SNP rs207681322 was associated with milk yield for the second, third and fourth lactations, as well as protein yield for the third lactation. Thus, we identified significant associations of SNPs rs207681322 and rs110871255 in the LPIN1 gene with a number of milk production traits during several lactations in Yaroslavl cows.

Milk recording data indicates the importance of fertility, including age at first calving, on the progression of first lactation cows to second lactation

Dairy farmers do not recoup the rearing costs incurred from birth to first calving until second lactation but varying proportions of first lactation cows are removed from the herd before second calving. Herein, we used milk recording data to examine the outcomes and performance of first lactation cows to gain insight into farmer decisions to keep or remove them from the herd. An InterHerd+ dataset derived from 500 milk recording dairy herds in UK was used to examine first lactation cows which calved in 2020. Of 29,128 first lactation cows that calved in 2020, 82.6% remained within the herd and re-calved, 4.9% conceived but exited the herd before re-calving, 6.0% were served but exited the herd after failing to conceive and 6.6% exited the herd without being served. The fertility data on these cows support the logical conclusion that farmers retain cows that are served and conceive sooner, possibly in order to keep within a broadly seasonal calving pattern. Cows which were served but not conceived had a median AFC 16-20 days greater than the median AFC for those that conceived. Farmers may also be retaining cows with relatively high milk yields and lower somatic cell counts, or these parameters may be an indicator of a range of attributes affecting the farmer's decision. The data also suggest that farmers are rearing more replacements than required, because over one third of the cows removed in first lactation are never served, and 70% of these are sold within 120 days post-partum. These cows had a significantly older median age at first calving of 818 days, but their early removal without serving suggests there is an oversupply of replacements forcing farmers to dispose of these cows early in lactation. In order to develop a deeper understanding of herd turnover and replacement, future work could examine cow removals in lactation 2 onwards.

Farmers' preferences for breeding goal traits and selection indexes for Slovenian dairy cattle

The aim of the study was to determine the role played by farmers' sociodemographic factors in the characteristics of dairy farmers' breeding goals and how they are clustered in Slovenia. Understanding how farmers formulate their breeding objectives is crucial because their perspectives may diverge from those of the stakeholders engaged in selection and breeding. Involving farmers in the process of setting breeding goals can improve the use of selection tools and confidence in the selection process. For a more complete picture of how farmers view breeding work, their expectations, and the changes they would prefer to see in the future in terms of new traits and a total merit index, a mixed methods approach was used. Initially, 3 focus groups with 30 participants were conducted on the following main topics: farmers' needs and attitudes regarding genomic selection, the main barriers and advantages to adopting genomic selection, the design of a total merit index, and preferences for breeding goals. To generalize the results to the whole population, an additional online questionnaire was sent to dairy farmers affiliated with Slovenian breeding associations, with 212 farmers responding. Based on how the farmers distributed weights across the trait categories in the total merit index, a cluster analysis identifies 3 distinct groups of farmers. Milk production proved to be an important common factor for all farmers, especially production-focused ones. Functionality-focused farmers expressed the strongest preference for fertility (22%), longevity (18%), and animal health (18%), whereas resilience-focused farmers concentrated on fertility (13%), health (13%), longevity (11%), and workability (11%). Yet, the results also showed that dairy farmers hold quite similar preferences for breeding goal traits, with animal health and welfare, reproductive traits, dominating across the sample and environmental and meat traits being the least important. The quantitative analysis of the preference for new environmental traits showed that farmers express less importance to them due to pressure and negative public opinion about the environmental impact of dairy farming. The focus group participants, although acknowledging that adaptation to climate change and heat stress will be essential, were even more negative about traits related to greenhouse gas emissions, which can be attributed to negative public opinion and constraints on agricultural activity.

A simulation study comparing advanced marker-assisted selection with genomic selection in tree breeding programs

Advances in DNA sequencing technologies allow the sequencing of whole genomes of thousands of individuals and provide several million single nucleotide polymorphisms (SNPs) per individual. These data combined with precise and high-throughput phenotyping enable genome-wide association studies (GWAS) and the identification of SNPs underlying traits with complex genetic architectures. The identified causal SNPs and estimated allelic effects could then be used for advanced marker-assisted selection (MAS) in breeding programs. But could such MAS compete with the broadly used genomic selection (GS)? This question is of particular interest for the lengthy tree breeding strategies. Here, with our new software "SNPscan breeder," we simulated a simple tree breeding program and compared the impact of different selection criteria on genetic gain and inbreeding. Further, we assessed different genetic architectures and different levels of kinship among individuals of the breeding population. Interestingly, apart from progeny testing, GS using gBLUP performed best under almost all simulated scenarios. MAS based on GWAS results outperformed GS only if the allelic effects were estimated in large populations (ca. 10,000 individuals) of unrelated individuals. Notably, GWAS using 3,000 extreme phenotypes performed as good as the use of 10,000 phenotypes. GS increased inbreeding and thus reduced genetic diversity more strongly compared to progeny testing and GWAS-based selection. We discuss the practical implications for tree breeding programs. In conclusion, our analyses further support the potential of GS for forest tree breeding and improvement, although MAS may gain relevance with decreasing sequencing costs in the future.

Factors Influencing the Maturation and Developmental Competence of Yak (Bos grunniens) Oocytes In Vitro

The yak (Bos grunniens) is a unique breed living on the Qinghai-Tibet Plateau and its surrounding areas, providing locals with a variety of vital means of living and production. However, the yak has poor sexual maturity and low fertility. High-quality mature oocytes are the basis of animal breeding technology. Recently, in vitro culturing of oocytes and embryo engineering technology have been applied to yak breeding. However, compared to those observed in vivo, the maturation rate and developmental capacity of in vitro oocytes are still low, which severely limits the application of in vitro fertilization and embryo production in yaks. This review summarizes the endogenous and exogenous factors affecting the in vitro maturation (IVM) and developmental ability of yak oocytes reported in recent years and provides a theoretical basis for obtaining high-quality oocytes for in vitro fertilization and embryo production in yaks.

Genome-Wide Association Studies for Body Conformation Traits in Korean Holstein Population

The objective of this study was to identify quantitative trait loci (QTL) and nearby candidate genes that influence body conformation traits. Phenotypic data for 24 body conformation traits were collected from a population of 2329 Korean Holstein cattle, and all animals were genotyped using the 50 K Illumina bovine SNP chip. A total of 24 genome-wide significant SNPs associated with 24 body conformation traits were identified by genome-wide association analysis. The selection of the most promising candidate genes was based on gene ontology (GO) terms and the previously identified functions that influence various body conformation traits as determined in our study. These genes include KCNA1, RYBP, PTH1R, TMIE, and GNAI3 for body traits; ANGPT1 for rump traits; MALRD1, INHBA, and HOXA13 for feet and leg traits; and CDK1, RHOBTB1, and SLC17A1 for udder traits, respectively. These findings contribute to our understanding of the genetic basis of body conformation traits in this population and pave the way for future breeding strategies aimed at enhancing desirable traits in dairy cattle.

Association of Phenotypic Markers of Heat Tolerance with Australian Genomic Estimated Breeding Values and Dairy Cattle Selection Indices

Dairy cattle predicted by genomic breeding values to be heat tolerant are known to have less milk production decline and lower core body temperature increases in response to elevated temperatures. In a study conducted at the University of Melbourne's Dookie Robotic Dairy Farm during summer, we identified the 20 most heat-susceptible and heat-tolerant cows in a herd of 150 Holstein Friesian lactating cows based on their phenotypic responses (changes in respiration rate, surface body temperature, panting score, and milk production). Hair samples were collected from the tip of the cows' tails following standard genotyping protocols. The results indicated variation in feed saved and HT genomic estimated breeding values (GEBVs) (p ≤ 0.05) across age, indicating a potential for their selection. As expected, the thermotolerant group had higher GEBVs for HT and feed saved but lower values for milk production. In general, younger cows had superior GEBVs for the Balanced Performance Index (BPI) and Australian Selection Index (ASI), whilst older cows were superior in fertility, feed saved (FS), and HT. This study demonstrated highly significant (p ≤ 0.001) negative correlations (-0.28 to -0.74) between HT and GEBVs for current Australian dairy cattle selection indices (BPI, ASI, HWI) and significant (p ≤ 0.05) positive correlations between HT and GEBVs for traits like FS (0.45) and fertility (0.25). Genomic selection for HT will help improve cow efficiency and sustainability of dairy production under hot summer conditions. However, a more extensive study involving more lactating cows across multiple farms is recommended to confirm the associations between the phenotypic predictors of HT and GEBVs.

Influence of dairy farmers' knowledge on their attitudes towards breeding tools and genomic selection

Understanding farmers' attitudes towards traits is critical for developing appropriate breeding goals for dairy production. In response to a research gap in regards to the influence of farmers' knowledge of breeding tools, this study aimed to determine the effect of farmers' knowledge on their attitudes towards the use of breeding tools and traits in typical family-owned farms in Slovenia. An online questionnaire was sent to dairy farmers affiliated with Slovenian breeding associations, and 256 dairy farmers responded. The analysis was conducted in three steps. First, the basic response patterns according to the farmers' knowledge level were determined using latent class analysis. Second, farmers' attitudes towards breeding tools were assessed by 15 statements using principal component analysis. Finally, we were interested in the relationship between farmers' attitudes and knowledge about selection. The results showed that farmers had more knowledge about the benefits of genomic selection, followed by general knowledge about breeding values and the definition of genomic selection, and they had the least knowledge about the reference population. Farmers with more knowledge were statistically significantly more likely than farmers with less knowledge to have higher education, be younger, have a larger herd size, have higher milk production per cow, have the intent to increase herd size and milk quantity, and use genomically tested bulls. No significant relationship was found between belonging to a specific knowledge class and the main breed in the herd, the farmer's gender, production system, or farming in less-favoured areas. The results also show that farmers basically agree that they need written recorded performance data about a bull/cow to know exactly how good the animal is, that the genetic merit (breeding value) of bulls/cows adds to the performance of their progeny, that it is very important to maintain the breed characteristics of bulls/cows, that cooperation in being able to compare animals with other farmers is essential for improving herd performance, and that the possibilities of selecting dairy cows with genomic selection and monogenetic traits must be fully exploited, indicating a positive attitude towards genomic selection. The level of knowledge was shown to influence attitudes towards various aspects of breeding. It was found that the higher the level of knowledge, the more positive the attitude towards genetic and genomic selection, and the more negative the attitude towards traditional selection.

Genomic and Phenotypic Udder Evaluation for Dairy Cattle Selection: A Review

The traditional point of view regarding dairy cattle selection has been challenged by recent genomic studies indicating that livestock productivity prediction can be redefined based on the evaluation of genomic and phenotypic data. Several studies that included different genomic-derived traits only indicated that interactions among them or even with conventional phenotypic evaluation criteria require further elucidation. Unfortunately, certain genomic and phenotypic-derived traits have been shown to be secondary factors influencing dairy production. Thus, these factors, as well as evaluation criteria, need to be defined. Owing to the variety of genomic and phenotypic udder-derived traits which may affect the modern dairy cow functionality and conformation, a definition of currently important traits in the broad sense is indicated. This is essential for cattle productivity and dairy sustainability. The main objective of the present review is to elucidate the possible relationships among genomic and phenotypic udder evaluation characteristics to define the most relevant traits related to selection for function and conformation in dairy cattle. This review aims to examine the potential impact of various udder-related evaluation criteria on dairy cattle productivity and explore how to mitigate the adverse effects of compromised udder conformation and functionality. Specifically, we will consider the implications for udder health, welfare, longevity, and production-derived traits. Subsequently, we will address several concerns covering the application of genomic and phenotypic evaluation criteria with emphasis on udder-related traits in dairy cattle selection as well as its evolution from origins to the present and future prospects.

Effects of recombinant FSH (bscrFSH) and pituitary FSH (FSH-p) on embryo production in superovulated dairy heifers inseminated with unsorted and sex-sorted semen

Superovulation is a drug-based method used in cattle to stimulate the ovarian folliculogenesis and the number of oocytes and transferable embryos. The present study aimed to test the effects of recombinant FSH (bscrFSH) and pituitary FSH (FSH-p) on ovarian response and in vivo embryo production in superovulated dairy heifers inseminated with unsorted and sex-sorted semen. Forty healthy Holstein heifers subjected to a superovulation (SOV) protocol by using FSH-p or bscrFSH were divided randomly into four groups: a) FSH-p inseminated with unsorted semen (USP; n = 10), b) FSH-p inseminated with sex-sorted semen (SSP; n = 10), c) bscrFSH inseminated with unsorted semen (USR; n = 10), and d) bscrFSH inseminated with sex-sorted semen (SSR; n = 10). Ultrasonography was carried out on Day 8 (estrus) and Day 15 (embryo collection) to evaluate the ovarian structures [follicles (FL), corpora lutea (CL), and non-ovulated follicles (NOFL)]. Embryonic-derived parameters were scored on Day 15 [total structures collected (TS), unfertilised oocytes (UFOs), total embryos (TEs), transferable embryos (TFEs), freezable embryos (FEs), and degenerated embryos (DEs)]. No differences were observed regarding ovarian structures (FL and NOFL) irrespective of SOV protocol or group assessed (P > 0.05). CL increased in bscrFSH-derived SOV protocol (P < 0.05). On Day 15, the embryonic-derived parameters TEs, TFEs, and FEs decreased in SSP/SSR compared to USP/USR (P < 0.05). Differences were observed regarding UFOs, with a greater number in SSP and SSR (P = 0.01). In conclusion, the bscrFSH-derived SOV protocol showed improved results compared to FSH-p-derived SOV protocol regarding ovarian (CL) and embryo-derived (TFE) parameters irrespective of the type of semen used.

Genome-Wide Association Study for Body Conformation Traits and Fitness in Czech Holsteins

The aim of this study was a genome-wide association study (GWAS) on conformation traits using 25,486 genotyped Czech Holsteins, with 35,227 common SNPs for each genotype. Linear trait records were collected between 1995 and 2020. The Interbull information from Multiple Across Country Evaluation (MACE) was included for bulls that mostly had daughter records in a foreign country. When using the Bonferroni correction, the number of SNPs that were either significant or approached the significance threshold was low-dairy capacity composite on BTA4, feet and legs composite BTA21, total score BTA10, stature BTA24, body depth BTA6, angularity BTA20, fore udder attachment BTA10. Without the Bonferroni correction, the total number of significant or near of significance SNPs was 32. The SNPs were localized on BTA1,2,4,5,6,7,8,18,22,25,26,28 for dairy capacity composite, BTA15,21 for feet and legs composite, BTA10 for total score, BTA24 stature, BTA6,23 body depth, BTA20 angularity, BTA2 rump angle, BTA9,10 rear legs rear view, BTA2,19 rear legs side view, BTA10 fore udder attachment, BTA2 udder depth, BTA10 rear udder height, BTA12 central alignment, BTA24 rear teat placement, BTA8,29 rear udder width. The results provide biological information for the improvement of body conformation and fitness in the Holstein population.

A Practical Application of Genomic Predictions for Mastitis Resistance in Italian Holstein Heifers

Heifers are a fundamental resource on farms, and their importance is reflected in both farm management and economy. Therefore, the selection of heifers to be reared on a farm should be carefully performed to select only the best animals. Genomic selection is available nowadays to evaluate animals in a fast and economic way. However, it is mainly used on the sire line and on performance traits. Ten farms were selected based on their 5-year records of average somatic cell count and evenly classified into high (>300,000 cells/mL) and low somatic cell count (<150,000 cells/mL). Genomic indexes (regarding both wellness and productive traits) were evaluated in 157 Italian Holstein heifers reared in the selected ten farms (90 from high-cells farms and 67 from low-cells ones). Linear mixed models were fitted to analyze the effects of the abovementioned genomic indexes on related phenotypes. Results have shown that farms classified into low somatic cell count had an overall better animal genomic pool compared to high somatic cell count ones. Additionally, the results shown in this study highlighted a difference in wellness genomic indexes in animals from farms with either a high or a low average somatic cell count. Applying genomic tools directly to heifer selection could improve economic aspects related to herd turnover.

An Appropriate Genetic Approach for Improving Reproductive Traits in Crossbred Thai-Holstein Cattle under Heat Stress Conditions

Thailand is a tropical country affected by global climate change and has high temperatures and humidity that cause heat stress in livestock. A temperature−humidity index (THI) is required to assess and evaluate heat stress levels in livestock. One of the livestock types in Thailand experiencing heat stress due to extreme climate change is crossbred dairy cattle. Genetic evaluations of heat tolerance in dairy cattle have been carried out for reproductive traits. Heritability values for reproductive traits are generally low (<0.10) because environmental factors heavily influence them. Consequently, genetic improvement for these traits would be slow compared to production traits. Positive and negative genetic correlations were found between reproductive traits and reproductive traits and yield traits. Several selection methods for reproductive traits have been introduced, i.e., the traditional method, marker-assisted selection (MAS), and genomic selection (GS). GS is the most promising technique and provides accurate results with a high genetic gain. Single-step genomic BLUP (ssGBLUP) has higher accuracy than the multi-step equivalent for fertility traits or low-heritability traits.

Historical Evolution of Cattle Management and Herd Health of Dairy Farms in OECD Countries

This work aimed to review the important aspects of the dairy industry evolution at herd level, interrelating production with health management systems. Since the beginning of the industrialization of the dairy cattle sector (1950s), driven by the need to feed the rapidly growing urban areas, this industry has experienced several improvements, evolving in management and technology. These changes have been felt above all in the terms of milking, rearing, nutrition, reproductive management, and design of facilities. Shortage of labor, emphasis on increasing farm efficiency, and quality of life of the farmers were the driving factors for these changes. To achieve it, in many areas of the world, pasture production has been abandoned, moving to indoor production, which allows for greater nutritional and reproductive control of the animals. To keep pace with this paradigm in milk production, animal health management has also been improved. Prevention and biosecurity have become essential to control and prevent pathologies that cause great economic losses. As such, veterinary herd health management programs were created, allowing the management of health of the herd as a whole, through the common work of veterinarians and farmers. These programs address the farms holistically, from breeding to nutrition, from prevention to consultancy. In addition, farmers are now faced with a consumer more concerned on animal production, valuing certified products that respect animal health and welfare, as well as environmental sustainability.

A review of inbreeding depression in dairy cattle: current status, emerging control strategies, and future prospects

Dairy cattle breeding has historically focused on relatively small numbers of elite bulls as sires of sons. In recent years, even if generation intervals were reduced and more diverse sires of sons could have been selected, genomic selection has not fundamentally changed the fact that a large number of individuals are being analyzed. However, a relatively small number of elite bulls are still siring those animals. Therefore inbreeding-derived negative consequences in the gene pool have brought concern. The detrimental effects of non-additive genetic changes such as inbreeding depression and dominance have been widely disseminated while seriously affecting bioeconomically important parameters because of an antagonistic relationship between dairy production and reproductive traits. Therefore, the estimation of benefits and limitations of inbreeding and variance of the selection response deserves to be evaluated and discussed to preserve genetic variability, a significant concern in the selection of individuals for reproduction and production. Short-term strategies for genetic merit improvement through modern breeding programs have severely lowered high-producing dairy cattle fertility potential. Since the current selection programs potentially increase long-term costs, genetic diversity has decreased globally as a consequence. Therefore, a greater understanding of the potential that selection programs have for supporting long-term genetic sustainability and genetic diversity among dairy cattle populations should be prioritized in managing farm profitability. The present review provides a broad approach to current inbreeding-derived problems, identifying critical points to be solved and possible alternative strategies to control selection against homozygous haplotypes while maintaining sustained selection pressure. Moreover, this manuscript explores future perspectives, emphasizing theoretical applications and critical points, and strategies to avoid the adverse effects of inbreeding in dairy cattle. Finally, this review provides an overview of challenges that will soon require multidisciplinary approaches to managing dairy cattle populations, intending to combine increases in productive trait phenotypes with improvements in reproductive, health, welfare, linear conformation, and adaptability traits into the foreseeable future.

The Contribution of Copy Number Variants and Single Nucleotide Polymorphisms to the Additive Genetic Variance of Carcass Traits in Cattle

The relative contributions of both copy number variants (CNVs) and single nucleotide polymorphisms (SNPs) to the additive genetic variance of carcass traits in cattle is not well understood. A detailed understanding of the relative importance of CNVs in cattle may have implications for study design of both genomic predictions and genome-wide association studies. The first objective of the present study was to quantify the relative contributions of CNV data and SNP genotype data to the additive genetic variance of carcass weight, fat, and conformation for 945 Charolais, 923 Holstein-Friesian, and 974 Limousin sires. The second objective was to jointly consider SNP and CNV data in a least absolute selection and shrinkage operator (LASSO) regression model to identify genomic regions associated with carcass weight, fat, and conformation within each of the three breeds separately. A genomic relationship matrix (GRM) based on just CNV data did not capture any variance in the three carcass traits when jointly evaluated with a SNP-derived GRM. In the LASSO regression analysis, a total of 987 SNPs and 18 CNVs were associated with at least one of the three carcass traits in at least one of the three breeds. The quantitative trait loci (QTLs) corresponding to the associated SNPs and CNVs overlapped with several candidate genes including previously reported candidate genes such as MSTN and RSAD2, and several potential novel candidate genes such as ACTN2 and THOC1. The results of the LASSO regression analysis demonstrated that CNVs can be used to detect associations with carcass traits which were not detected using the set of SNPs available in the present study. Therefore, the CNVs and SNPs available in the present study were not redundant forms of genomic data.

Identification and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr

Whole genome sequencing of bovine breeds has allowed identification of genetic variants in milk protein genes. However, functional repercussion of such variants at a molecular level has seldom been investigated. Here, the results of a multistep Bioinformatic analysis for functional characterization of recently identified genetic variants in Brazilian Gyr and Guzerat breeds is described, including predicted effects on the following: (i) evolutionary conserved nucleotide positions/regions; (ii) protein function, stability, and interactions; (iii) splicing, branching, and miRNA binding sites; (iv) promoters and transcription factor binding sites; and (v) collocation with QTL. Seventy-one genetic variants were identified in the caseins (CSN1S1, CSN2, CSN1S2, and CSN3), LALBA, LGB, and LTF genes. Eleven potentially regulatory variants and two missense mutations were identified. LALBA Ile60Val was predicted to affect protein stability and flexibility, by reducing the number the disulfide bonds established. LTF Thr546Asn is predicted to generate steric clashes, which could mildly affect iron coordination. In addition, LALBA Ile60Val and LTF Thr546Asn affect exonic splicing enhancers and silencers. Consequently, both mutations have the potential of affecting immune response at individual level, not only in the mammary gland. Although laborious, this multistep procedure for classifying variants allowed the identification of potentially functional variants for milk protein genes.