Molecular markers and their applications in cattle genetic research: A review

Genetic Parameters and Genomic Prediction for Calving Ease in Primiparous Nellore Heifers

The calving ease (CE) trait has recently been introduced in animal breeding programs, and studies on its genetic variability have proven essential for the genetic advancement of animals. An increase in dystocia rates in primiparous heifers has been observed due to the birth of heavier calves. As this is a new trait, no established model exists for its analysis. Thus, this study developed different statistical models to evaluate CE, aiming to estimate genetic parameters and perform genomic predictions for this trait. A total of 39,664 records of CE from primiparous Nellore heifers born between 2010 and 2017 were collected, belonging to the animal breeding program of the Nellore breed in Brazil, managed by the National Association of Breeders and Researchers (ANCP, Ribeirão Preto, Brazil). The results showed that direct heritability estimates ranged from 0.11 to 0.24, while maternal heritability estimates ranged from 0.09 to 0.11. Despite these low to moderate heritability estimates, the trait has potential for direct selection. Models incorporating the heifer category (HC) (early or traditional) and birth weight (BW), as well as the dam age at calving (DAC) and BW, were more suitable for estimating variance components. On the other hand, the model that considered only the HC and the model that included the DAC excelled in predictive ability, making them more appropriate for genomic predictions.

Nucleotide sequence variants, gene expression and serum profile of immune and antioxidant markers associated with brucellosis resistance/susceptibility in Shami goat

Brucellosis is a highly contagious zoonotic bacterial disease. It has considerable negative consequences on the animal production industry worldwide. The objective of this study was to investigate the genetic and molecular variations in Shami goat susceptible to Brucella infection. Blood samples were collected from fifty mature Shami goats (30 Brucella-infected does and 20 non-infection). DNA was extracted and selected parts the immunity; solute carrier family 11 member 1 (SLC11A1), toll-like receptor 1 (TLR1), toll-like receptor 9 (TLR9), SP110 nuclear body protein (SP110), the adenosine A3 receptor (ADORA3), caspase activating recruitment domain 15 (CARD15) and interferon regulatory factor 3 (IRF3), antioxidant glutathione peroxidase 1 (GPX1), nitric oxide synthase (NOS), NAD(P)H dehydrogenase [quinone] 1 (NQO1) and transcription factor NF-E2-related factor 2 (Nrf2) and erythritol related transketolase (TKT), ribose 5-phosphate isomerase (RPIA) and Adenosine monophosphate deaminase (AMPD) genes were sequenced. Likewise, the levels of gene expressions were investigated. The results identified polymorphic variants between healthy and infected does. Levels of gene expression of SLC11A1, TLR1, TLR9, SP110, ADORA3, CARD15, IRF3, HMOX1, TKT, RPIA and AMPD were significantly (P < 0.05) up regulated in the infected compared to the non-infected ones. On the other hand, GPX1, NOS, NQO1 and Nrf2 genes were significantly (P < 0.05) downregulated in the infected compared to the non-infected does. The results of serum profile indicated that there is a significant (P < 0.05) increase in the activities of AST, ALT, GGT, LDH, ALP as well as serum level of globulin, triglycerides, cholesterol, MDA, NO, IL-1β, TNF-α, IgM, IgG, haptoglobin and amyloid A. On the other hand, there were significant reductions in the glucose, total protein albumin, urea, calcium, inorganic phosphorus, sodium, copper, zinc, iron, TAC, GSH, SOD, GPx, IL-10 and fibrinogen in the infected compared to the non-infected does. Our results provide valuable information about the serum profile variations and putative genetic markers for Brucella infection in goats. This could be utilized in controlling goat brucellosis through selective breeding of natural resistant animals.

Applications of Next-Generation Sequencing Technologies and Statistical Tools in Identifying Pathways and Biomarkers for Heat Tolerance in Livestock

The climate change-associated abnormal weather patterns negatively influences the productivity and performance of farm animals. Heat stress is the major detrimental factor hampering production, causing substantial economic loss to the livestock industry. Therefore, it is important to identify heat-tolerant breeds that can survive and produce optimally in any given environment. To achieve this goal, a clearer understanding of the genetic differences and the underlying molecular mechanisms associated with climate change impacts and heat tolerance are a prerequisite. Adopting next-generation biotechnological and statistical tools like whole transcriptome analysis, whole metagenome sequencing, bisulphite sequencing, genome-wide association studies (GWAS), and selection signatures provides an opportunity to achieve this goal. Through these techniques, it is possible to identify permanent genetic markers for heat tolerance, and by incorporating those markers in marker-assisted breeding selection, it is possible to achieve the target of breeding for heat tolerance in livestock. This review gives an overview of the recent advancements in assessing heat tolerance in livestock using such 'omics' approaches and statistical models. The salient findings from this research highlighted several candidate biomarkers that have the potential to be incorporated into future heat-tolerance studies. Such approaches could revolutionise livestock production in the changing climate scenario and support the food demands of the growing human population.

Tailoring Genomic Selection for Bos taurus indicus: A Comprehensive Review of SNP Arrays and Reference Genomes

BACKGROUND

Advances in SNP arrays and reference genome assemblies have significantly transformed cattle genomics, particularly for Bos taurus indicus (Zebu cattle). Many commercial SNP arrays were originally designed for Bos taurus taurus, leading to ascertainment bias and the exclusion of crucial SNPs specific to Zebu populations. This review assesses progress in SNP array and reference genome development, with a focus on efforts tailored to Zebu populations and their impact on genomic selection and breeding efficiency.

METHODS

We reviewed the relevant literature on the development of SNP arrays, reference genome assemblies, and SNP genotyping techniques used for Zebu cattle. Emphasis was placed on SNP arrays specifically designed for Zebu breeds, evaluating their contributions to genomic evaluations and identifying limitations in prediction accuracy.

RESULTS

Recent advancements, such as GeneSeek's low- and high-density SNP panels, have aimed to reduce ascertainment bias and include key SNPs for Zebu populations by providing breed-specific panels. These panels have been instrumental in identifying genomic regions associated with economically important traits in Nellore cattle. Studies show that tailored SNP arrays and breed-specific reference genomes can enhance genetic diversity assessment and improve genomic predictions, supporting more effective breeding programs for Zebu cattle.

CONCLUSIONS

Improved SNP arrays and breed-specific reference genomes are crucial for accurate genomic selection in Zebu cattle. Future efforts should prioritize expanding de novo genome assemblies, reducing ascertainment bias, and developing cost-effective genotyping solutions tailored to Zebu populations. Targeted genomic tools will ultimately enable more efficient breeding practices and enhance genomic selection for economically important traits in B. t. indicus cattle.

Climate Resilience in Farm Animals: Transcriptomics-Based Alterations in Differentially Expressed Genes and Stress Pathways

The livestock sector, essential for maintaining food supply and security, encounters numerous obstacles as a result of climate change. Rising global populations exacerbate competition for natural resources, affecting feed quality and availability, heightening livestock disease risks, increasing heat stress, and contributing to biodiversity loss. Although various management and dietary interventions exist to alleviate these impacts, they often offer only short-lived solutions. We must take a more comprehensive approach to understanding how animals adapt to and endure their environments. One such approach is quantifying transcriptomes under different environments, which can uncover underlying pathways essential for livestock adaptation. This review explores the progress and techniques in studies that apply gene expression analysis to livestock production systems, focusing on their adaptation to climate change. We also attempt to identify various biomarkers and transcriptomic differences between species and pure/crossbred animals. Looking ahead, integrating emerging technologies such as spatialomics could further accelerate genetic improvements, enabling more thermoresilient and productive livestock in response to future climate fluctuations. Ultimately, insights from these studies will help optimize livestock production systems by identifying thermoresilient/desired animals for use in precise breeding programs to counter climate change.

Identification of candidate SNPs associated with embryo mortality and fertility traits in lactating Holstein cows

Introduction: Targeted single nucleotide polymorphisms (SNPs) have been used in genomic prediction methodologies to enhance the accuracy of associated genetic transmitting abilities in Holstein cows. The objective of this study was to identify and validate SNPs associated with fertility traits impacting early embryo mortality. Methods: The mRNA sequencing data from day 16 normal (n = 9) and embryo mortality (n = 6) conceptuses from lactating multiparous Holstein cows were used to detect SNPs. The selection of specific genes with SNPs as preliminary candidates was based on associations with reproductive and fertility traits. Validation of candidate SNPs and genotype-to-phenotype analyses were conducted in a separate cohort of lactating primiparous Holstein cows (n = 500). After genotyping, candidate SNPs were filtered using a quality control pipeline via PLINK software. Continuous numeric and binary models from reproductive traits were evaluated using the mixed procedure for a generalized linear model-one way ANOVA or logistic regression, respectively. Results: Sixty-nine candidate SNPs were initially identified, but only 23 passed quality control procedures. Ultimately, the study incorporated 466 observations for statistical analysis after excluding animals with missing genotypes or phenotypes. Significant (p <0.05) associations with fertility traits were identified in seven of the 23 SNPs: DSC2 (cows with the A allele were older at first calving); SREBF1 and UBD (cows with the T or G alleles took longer to conceive); DECR1 and FASN (cows with the C allele were less likely to become pregnant at first artificial insemination); SREBF1 and BOLA-DMB (cows with the T allele were less likely to be pregnant at 150 days in milk). It was also determined that two candidate SNPs within the DSC2 gene were tag SNPs. Only DSC2 SNPs had an important allele substitution effect in cows with the G allele, which had a decreased age at first calving by 10 days. Discussion: Candidate SNPs found in this study could be used to develop genetic selection tools to improve fertility traits in dairy production systems.

DNA Polymorphisms and mRNA Levels of Immune Biomarkers as Candidates for Inflammatory Postpartum Disorders Susceptibility in Italian Buffaloes

The immunological genes that may interact with inflammatory postpartum diseases in Italian buffaloes were examined in this study. A total number of 120 female Italian buffaloes (60 normal and 60 with inflammatory reproductive diseases) were employed. Each buffalo's jugular vein was pierced to get five milliliters of blood. To obtain whole blood and extract DNA and RNA, the blood was placed within tubes containing sodium fluoride or EDTA anticoagulants. The immunological (IKBKG, LGALS, IL1B, CCL2, RANTES, MASP2, HMGB1, and S-LZ) genes' nucleotide sequence differences between healthy buffaloes and buffaloes affected by inflammatory reproductive diseases were found by employing PCR-DNA sequencing. According to Fisher's exact test (p ˂ 0.01), there were noticeably different probabilities of all major nucleotide changes spreading among buffalo groups with and without reproductive problems. Buffaloes were significantly more likely to express the examined genes when they had inflammatory reproductive diseases. The outcomes might support the significance of these markers' nucleotide variations and gene expression patterns as indicators of the prevalence of inflammatory reproductive disorders and provide a workable buffalo management policy.

Haplotype-based association study of production and reproduction traits in multigenerational Vrindavani population

Haplotype-based association analysis promises to reveal important information regarding the effect of genetic variants on economic traits of interest. The present study aimed to evaluate the haplotype structure of Vrindavani cattle and explore the association of haplotypes with (re)production traits of economic interest. Genotyping array data of medium density (Bovine50KSNP BeadChip) on 96 randomly selected Vrindavani cows was used in the present study. Genotypes were called in GenomeStudio program while quality control was undertaken in PLINK using standard thresholds. The phenotypic traits used in the present study included age at first calving, dry days, lactation length, peak yield, total lactation milk yield, inter-calving period and service period. The haplotype structure of Vrindavani population was assessed, using a sliding window of 20 SNP with a shift of 5 SNPs at a time, in terms of the size of haplotype blocks regarding their length (in Kb) and frequency in chromosome-wise fashion. Haplotype blocks were assessed for possible association with important production and reproduction traits across three lactation cycles in Vrindavani cattle population. The first ten principal components were included in the model for haplotype-based association analysis to correct for stratification effects of assessed individuals. Multiple haplotypes were found to be associated with age at first calving, total lactation milk yield, peak yield, dry days, inter-calving period and service period. Various candidate genes were found to overlap haplotypes that were significantly associated with age at first calving (CDH18, MARCHF11, MYO10, FBXL7), total lactation milk yield (TGF, PDE1A, and COL8A1), peak yield (PPARGC1A, RCAN1, KCNE1, SMIM34 and MRPS6), dry days (CPNE4, ACAD11 and MRAS), inter-calving period (ABCG5, ABCG8 and COX7A2L) and service period (FOXL2 and PIK3CB). The putative candidate genes overlapping the significantly associated haplotypes revealed important pathways affecting the production and reproduction performance of animals. The identified genes and pathways may serve as good candidate markers to select animals for improved production and reproduction performance in future generations.

Genetic diversity and within-breed variation in three indigenous Ethiopian sheep based on whole-genome analysis

The objective of this work was to study genetic diversity by comparing whole genome sequence data of Rutana, Gumuz and Washera sheep found in Amhara and Benishanguel gumuz regional states of Ethiopia. We employed variant calling format tools version 0.1.15 to calculate some genetic diversity indices such as observed heterozygosity, expected heterozygosity, inbreeding coefficient, and nucleotide diversity. The results revealed that, observed heterozygosity ranged from 0.33 in Gumuz to 0.34 in Rutana and Washera sheep. Expected heterozygosity ranged from 0.37 in Rutana to 0.38 in Gumuz and Washera sheep. Expected heterozygosity was found to be higher than observed heterozygosity. Higher inbreeding coefficient (0.12) was recorded for Gumuz sheep compared to 0.09 of Rutana and Washera sheep. Mean nucleotide diversity values were 0.0029, 0.0030 and 0.0028 for Gumuz, Rutana and Washera sheep, respectively. Higher values of nucleotide diversity were recorded. Population structure analysis using principal component analysis revealed no clear separation between Gumuz, Rutana and Washera sheep populations with possibility of gene flow attributed to geographical location proximity. The smaller population size, closed breeding system, genetic drift and uncontrolled (non-random) mating might lead to higher rate of inbreeding in Gumuz, Rutana and Washera sheep, requiring timely intervention. This intervention helps to prevent inbreeding depression and extinction of these valuable breeds of sheep, which helps in sustaining the livelihood of sheep keepers in lowlands and highlands. Nevertheless, the whole-genome analysis revealed high within-breed variation. Uncovered areas of studies like mapping quantitative trait loci, identifying genes underpinning productivity traits such as carcass quantity and meat quality could be carried out on diversified sheep resources identified by the current study. Identifying the genomic regions and biological pathways that contribute to explaining variability in these traits is of great importance for selection purposes. Designing conservation-based within-breed sheep selective breeding programs are recommended considering economically important traits into account.

Management of Genetic Variation in the Gamete Bank of the Endangered Lake Minnow Eupallasella percnurus, Using Genassemblage 2.2 Software

The management of genetic resources deposited in gene banks requires knowledge of the genetic profiles of the gamete donors and bioinformatics tools to process this information. In this work, we show how to use Genassemblage 2.2 software in managing the genetic variation deposited in a bank of cryopreserved semen. Our demonstration was based on the leuciscid fish species, lake minnow Eupallasella percnurus, which is designated as endangered in Poland. The semen samples (n = 192) were taken from four Polish lake minnow populations and frozen in the gene bank. Fin clips were taken and DNA extracted. Across 13 investigated microsatellite loci, 21-53 alleles were identified in each population and 66 in the entire group of samples. The module "Management of genetic variation in gamete bank" of Genassemblage 2.2 software was used to find the set of samples that will preserve 100% of the detected allelic diversity in the next generation. Our results showed that a small group of 4-19 semen samples was enough to transfer all alleles detected across this set of samples. We, therefore, recommend Genassemblage 2.2 as a convenient tool for the detection of genetic differences between donors, the construction of optimal sets of samples for conservation of genetic variation, and for managing genetic variation deposited in gamete banks. Consequently, it can be used in breeding human-dependent populations and to optimize the use of genetic diversity in samples in the gamete banks. It can be especially useful for conserving populations of species characterized by low genetic variation, such as the lake minnow.

Immune mechanisms, resistance genes, and their roles in the prevention of mastitis in dairy cows

Mastitis is one of the most important diseases of the mammary gland. The increased incidence of this disease in cows is due to the breeding of dairy cattle for higher yields, which is accompanied by an increased susceptibility to mastitis. Therefore, the difficulty involved with preventing this disease has increased. An integral part of current research is the elimination of mastitis in order to reduce the consumption of antibiotic drugs, thereby reducing the resistance of microorganisms and decreasing companies' economic losses due to mastitis (i.e. decreased milk yield, increased drug costs, and reduced milk supply). Susceptibility to mastitis is based on dairy cows' immunity, health, nutrition, and welfare. Thus, it is important to understand the immune processes in the body in order to increase the resistance of animals. Recently, various studies have focused on the selection of mastitis resistance genes. An important point is also the prevention of mastitis. This publication aims to describe the physiology of the mammary gland along with its immune mechanisms and to approximate their connection with potential mastitis resistance genes. This work describes various options for mastitis elimination and focuses on genetic selection and a closer specification of resistance genes to mastitis. Among the most promising resistance genes for mastitis, we consider CD14, CXCR1, lactoferrin, and lactoglobulin.

Breeding of African sheep reared under low-input/output smallholder production systems for trypanotolerance

Trypanosomiasis is a disease caused by unicellular protozoan parasites. Small ruminants succumb to trypanosomiasis in areas of high tsetse fly challenge, resulting in serious economic loss often to farmers in low-input smallholder systems. At present, trypanosomiasis is treated with trypanocidal drugs, but access to these can be limited, and increasing parasite resistance raises questions about their efficacy. The development of trypanotolerance in small ruminant flocks through targeted breeding strategies is considered a sustainable and economical option for controlling African trypanosomiasis. Recently, quantitative trait loci (QTLs) associated with trypanotolerance traits in sheep have been reported. The results of these studies form the basis for more studies to identify QTLs associated with trypanosomiasis resistance, particularly in African livestock species. For example, signatures of positive selection for trypanotolerance have been identified using genome-wide single-nucleotide polymorphism data. However, there are several challenges in performing genetic analyses using data from low-input smallholder systems, including a lack of recorded pedigree and production records and the need for large sample sizes when flock sizes are often fewer than 50 animals. Breeding strategies to improve trypanotolerance should also preserve existing genetic diversity as well as minimize excessive genetic introgression by trypanosusceptible breeds. This review discusses the possibilities of breeding for trypanosome tolerance/resistance in low-input/low-output small ruminant production systems. Potential challenges are outlined, and potential available genetic resources are described as a foundation for future work.

Association of single nucleotide polymorphisms in the CAPN, CAST, LEP, GH, and IGF-1 genes with growth parameters and ultrasound characteristics of the Longissimus dorsi muscle in Colombian hair sheep

Recognition of the genes that influence livestock production characteristics has allowed researchers to identify single nucleotide polymorphisms (SNPs) associated with phenotypic traits that contribute to higher productivity. The objective of this research was to associate SNPs in the genes calpain (CAPN), calpastatin (CAST), leptin (LEP), growth hormone (GH), and insulin-like growth factor 1 (IGF-1) with the growth characteristics birth weight (BW), weaning weight adjusted at 120 days (WW), daily pre-weaning gain (PRADG), adjusted weight at 210 days (AW210), and daily post-weaning gain (POADG), and the measures of the Longissimus dorsi muscle based on ultrasound, namely loin eye area (LEA), loin depth (LD), and back fat thickness (BFT), in Colombian hair sheep (OPC). The association between phenotypic and genotypic characteristics was made using the PLINK v.1.9 program using linear regression analysis. There was a statistically significant association (p < 0.05) between the CAST polymorphism (M/N) and BW, a tendency (p = 0.07) for an association between the T → C SNP of the CAPN gene and AW210, and a trend (p = 0.07) for an association between the A → G SNP of the IGF-1 locus and POADG. The LEA and BFT characteristics were not associated with a SNP, while PL was significantly affected by SNPs in the GH and IGF-1 genes. In conclusion, all the genes evaluated were polymorphic, the CAST gene significantly influenced BW, and the GH and IGF-1 genes were associated with LD characteristics. These results could be used to identify individuals with favorable genotypes to implement a marker-assisted selection method.

Single nucleotide polymorphisms and metabolic biochemical profile of productive markers characterize three European breeds of dairy cattle

The objective of this study was to investigate polymorphisms of DGAT1, FABP, OLR1 and ATP1A1 genes using PCR-DNA sequencing, and to associate these genetic structures to changes in metabolic biochemical markers and milk composition indicators in a total of 90 dairy cows of the Holstein, Simmental, and Brown Swiss breeds (30 cows each). PCR was carried out for amplification of 411-bp of DGAT1, 525-bp of FABP, 582-bp of OLR1, and 300-bp of ATP1A1 genes. Three breeds’ nucleotide sequence variations in the form of single nucleotide polymorphisms (SNPs) were detailed by DNA sequencing analysis. Chisquare analysis showed that the distribution of all discovered SNPs varied significantly (P < 0.001). Biochemical indices in cow’s serum revealed no significant difference in serum total protein, albumin, and total cholesterol among the three breeds. However, triglyceride showed a significant increase in Simmental compared to either Holsteins or Brown Swiss, while the highest mean value of triiodothyronine (T3) and tetraiodothyronine (T4) was detected in Holstein dairy cows The milk composition indicators analysis revealed that milk protein, sugar, and density were significantly higher in Holsteins than both Simmental and Brown Swiss. Meanwhile, milk fat and total solids revealed a significantly higher increase in Simmental than both brown Swiss and Holstein. As a result, the metabolic biochemical markers profile along with the identified SNPs could be used as a candidate and a reference guide for effective characterization of the Holstein, Simmental, and Brown Swiss breeds, leading to the creation of a marker-assisted selection system for production traits in dairy cattle breeds.

Whole-Genome comparative analysis reveals genetic mechanisms of disease resistance and heat tolerance of tropical Bos indicus cattle breeds

The Bos indicus cattle breeds have been naturally selected over thousands of years for disease resistance and thermo-tolerance. However, a genetic mechanism of these specific inherited characteristics needs to be discovered. Hence, in this study, the whole-genome comparative analysis of Bos indicus cattle breeds of Kangayam, Tharparkar, Sahiwal, Red Sindhi, and Hariana of the Indian subcontinent was conducted. The genetic variants identification analysis revealed a total of 15,58,51,012 SNPs and 1,00,62,805 InDels in the mapped reads across all Bos indicus cattle breeds. The functional annotation of 17,252 genes that comprised both, SNPs and InDels, of high functional impact on proteins, has been carried out. The functional annotation results revealed the pathways that were involved in the innate immune response including toll-like receptors, a retinoic acid-inducible gene I like receptors, NOD-like receptors, Jak-STAT signaling pathways, and the non-synonymous variants in the candidate immune genes. Further, we also identified several pathways involved in heat shock response, hair and skin properties, oxidative stress response, osmotic stress response, thermal sweating, feed intake, metabolism, and the non-synonymous variants in the candidate thermo-tolerant genes. These pathways and genes were directly or indirectly contributing to the disease resistance and thermo-tolerance adaptations of Bos indicus cattle breeds.

Exploring the relationship between polymorphisms of leptin and IGF-1 genes with milk yield in indicine and taurine crossbred cows

Leptin an adipokine plays a significant role in several physiological processes and has been indicated as a candidate gene for marker-assisted selection for high-yielding cows. Insulin-like growth factor-1 (IGF-1) hormone plays an important physiological role in growth, development, metabolism, and lactation in bovines. It is believed to be one of the main mediators of energy balance effects on the reproductive performance of dairy cows after calving. The present investigation was carried out to identify the novel polymorphisms in exon 3 region of leptin and exon 3 partial intron 3 of IGF-1 genes and their association with the milk production performance in indicine and taurine crossbred (Karan Fries) cows. Blood samples were collected from 160 apparently healthy Karan Fries (KF) cows. Four SNPs (single-nucleotide polymorphisms) at positions rs29004508 (C > T), rs29004509 (C > T), rs29004510 (T > C), and rs29004511 (T > C) in leptin gene and two SNPs at positions rs133251968 (C > A) and rs137289661 (C > T) in IGF-1 gene were found in KF cows; however, rs29004509 (C > T) had a positive correlation (r = 0.376; P < 0.05) with milk yield. The genetic variants observed in exon 3 region of leptin gene and their association with milk yield traits revealed the importance of CT genotype, which had been useful for genetic improvement of KF cow for milk production traits and can also be utilized as a potential genetic marker to select appropriate animals.

Is neutral genetic diversity related to quantitative variation in semen traits in bulls?

Conservation decisions based on neutral genetic diversity have been observed to promote retention of useful quantitative variation in biological populations. An experiment was undertaken to determine the association between microsatellite marker polymorphisms and phenotypic variation in semen production and cryosurvival traits in bulls. Thirty-five ejaculates were collected from ten bulls of two breeds and evaluated before and after cryopreservation for several semen traits. The bulls were also genotyped using a set of sixteen bovine-specific microsatellite marker loci. Fixation indices (F_ST ), heterozygosity and Nei's genetic distance measures were computed from allele frequency data for each of the bulls. Molecular and phenotypic data were used to compute tri-distance matrices for the ten bulls and correlated using Mantel's test in GenAIEx 6.5. The study revealed extensive heterogeneity in semen traits, heterozygosity and F_ST values among the bulls. Large pairwise phenotypic and genetic distances were also observed. Correlation between pairwise genetic distances and phenotypic distances was significant and highly positive for sperm viability (r = .61, p < .001) and moderately positive for sperm motility (r = .40-42, p < .05) variables. For sperm morphology, ejaculate volume and sperm concentration, correlation with genetic distances was positive, low and not significantly different from zero (p > .05). A tendency for a triangular-shaped relationship between genetic and phenotypic distances for post-thaw motility and viability traits was also observed. Accordingly, association with neutral genetic diversity was absent for semen production traits and moderate to highly positive for sperm cryosurvival traits. Given these findings, conservation decisions based on neutral genetic diversity may capture variation in some adaptive traits, but not others.

Discovery of SNPs and indel 11-bp of the myostatin gene and its association with the double-muscled phenotype in Belgian blue crossbred cattle

Determining double muscle based on the myostatin (MSTN) gene in Belgian blue (BB), Peranakan Ongole (PO) and BB × PO crossbred cattle is very important for crossbreeding programs. This study aimed to investigate single-nucleotide polymorphisms (SNPs) and 11-bp deletions in the coding region of the MSTN gene and their relationship with the double-muscled phenotype in BB × PO crossbred cattle. A total of 86 blood samples were collected from 28 individual BB, 43 individual PO, and 15 individual BB × PO crossbred cattle. SNPs and indel 11-bp variation in the coding region of the MSTN gene were found using the sequencing method, followed by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. The MSTN gene in the coding region was detected in four SNPs found in PO cattle and its crossbreed. However, the four SNPs could not differentiate normal and double-muscled phenotypes although they are polymorphic. Moreover, in this study, an 11-bp deletion in exon 3 of the MSTN gene in BB cattle was found. In this case, by applying the PCR-RFLP technique using the restriction enzyme NmuCI (Tsp45I) in indel 11-bp, the genotypes that were successfully observed were +/+, +/del.11, and del.11/del.11.

Genetic variability and biodiversity of Ukrainian Gray cattle by the BoLA-DRB3 gene

At the current stage of genetic studies of cattle, more and more attention is being drawn to autochthonous breeds. Native cattle have a number of prominent phenotypic traits and have preserved unique genes and their combinations lost by modern commercial breeds, which would be valuable to use in selective programs. We surveyed polymorphism of the Ukrainian autochthonous Gray breed according to alleles of exon 2 of the BoLA-DRB3 gene. The uniqueness of the gene lies in the broad variability of its allele variants. Significant informativeness at DNA level is quite important for genetic studies. We surveyed allele polymorphism using the PCR-RLFP method on DNA isolated from 88 samples of blood of cows and 5 samples of sperm. We identified 28 alleles, of which 23 variants were nomenclature ones and 5 (jba, *jab, *jbb, *nad and *nda) were “without established nomenclature”, their share accounting for 8.9%. Four alleles *06, *12, *16 and *jba had a frequency above 5% and occupied 69.9% of the breed’s allele fund overall. The commonest allele was BoLA-DRB3.2*16 (44.1%). In total, we found 40 genotypes. Considering the significant dominance of variant *16, as expected, 5 genotypes with its inclusion occurred: *16/*16, *12/*16, *06/*16, *16/*24 and *jba/*16. It was present in the genotype of two out three studied animals. Parameters of heterozygosity, effective number of alleles, Shannon and Pielou indices indicate that Ukrainian Gray cattle are characterized by lowest level of genetic variability and biodiversity according to the BoLA-DRB3 gene compared with other breeds. Due to significant dominance of allele *16, the breed has no inbred motifs. We noted deviation toward increase in homozygosity without deviations from the norm of the distribution according to Hardy-Weinberg equilibrium. The obtained results will be used for genetic-populational programs with the purpose of improving the genetic potential of cattle breeds in terms of economically beneficial traits and diseases of cattle.

Effect of GH p.L127V Polymorphism and Feeding Systems on Milk Production Traits and Fatty Acid Composition in Modicana Cows

Growth hormone participates in the regulation of lactation and lipid metabolism. A trial study was conducted to evaluate the effects of genetic polymorphism at GH p.L127V and its interaction with feeding system (extensive, EX; semi-intensive, SI) on milk traits and fatty acids composition in Modicana cows. In the semi-intensive farm (SI) diet consisted of hay, concentrate and 2 h of grazing. In the extensive farm (EX) feeding consisted in 8 h of grazing and hay. The frequencies of LL, LV and VV genotypes were, respectively: 0.64, 0.34, 0.02. GH polymorphism and its interaction with feeding system did not influence milk yield and composition. Cows carrying LL genotype produced milk with lower 6:0 and 8:0 and higher 16:1 c9 and 18:1 c9, total UFA and total MUFA. Feeding significantly affected fatty acids: in EX cows lower SFA and higher PUFA and UFA were found, compared to SI cows. The lower, more favorable atherogenic index of milk from EX system was coherent with the improved healthy characteristics of milk from animals fed almost exclusively on pasture. A significant interaction genotype x feeding system was evident for 18:1, higher in the LL cows only in the EX system, but not in the SI system.

Associations of CAST, CAPN1 and MSTN Genes Polymorphism with Slaughter Value and Beef Quality – A Review

The slaughter value of cattle and beef quality are influenced by many factors, which can generally be divided into antemortem (breed, sex, age, housing system, diet, pre-slaughter handling) and postmortem (post-slaughter processing, chilling temperature, packaging). Studies of many authors have shown that meat quality traits can be also influenced by the individual genetic background of an animal. Numerous studies have been conducted worldwide to determine the functions of various genes as well as polymorphisms with potential effects on fattening and slaughter value of cattle and on beef quality. This study reviews the most important research done on the associations of polymorphisms in the calpain, calpastatin and myostatin genes with carcass traits and beef quality. Knowledge about the genes and chromosome regions associated with desired meat quality characteristics may prove very helpful when selecting pairs for mating and estimating the breeding value of offspring, mainly because it is difficult to improve meat quality traits based on conventional selection methods due to their low heritability and polygenic regulation. Furthermore, meat quality evaluation is expensive and can only be carried out after slaughter.

Effects of polymorphism of myostatin and fatty acid-binding protein 4 genes on the chemical composition of meat in cull female Aceh cattle

Aim:

This study aimed to investigate the association of single nucleotide polymorphism of the myostatin (MSTN) and fatty acid-binding protein 4 (FABP4) genes on the total water, ash, fat, protein, and cholesterol contents of sirloin (gluteus medius muscle) and silverside (biceps femoris muscle) meats of cull female Aceh cattle.

Materials and Methods:

This analysis covered a total of 27 cull female Aceh cattle slaughtered at the Animal Slaughterhouse of Banda Aceh that was purposively selected based on hair color referred to the criteria described in the Decree of Ministry of Agriculture of the Republic of Indonesia. Genomic DNA was extracted from 25 mg of fresh meat using the spin column method before subjected to a polymerase chain reaction amplification using primer sets specific for 1346-bp and 275-bp fragments of MSTN and FABP4, respectively. A 4-h digestion reaction was done separately for the MSTN/HaeIII and FABP4/NlaIII loci genotyping. The total protein, ash, and fat of the meat were measured using the Indonesian National Standard (SNI) methods whereas its cholesterol content was determined using the AOAC method. The association between each polymorphism and the variation in meat chemical parameters was analyzed using the Pearson correlation test.

Results:

The results showed that the MSTN/HaeIII locus was polymorphic in Aceh cattle, but the FABP4/NlaIII locus was monomorphic. Meat chemical parameters were not influenced by different commercial cuts and MSTNgenotypes, showing that there was no association between different commercial cuts, cattle hair colors, and MSTN/HaeIII and FABP4/NlaIII markers with the meat chemical parameters in Aceh cattle.

Conclusion:

These results suggest that focusing on the novel effects of MSTN and FABP4 gene polymorphisms on meat production traits might not be useful for marker-assisted selection in Aceh cattle.

DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria

Within Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.

Association of BoLA-DRB3.2 alleles with fusobacteriosis in cows

The Major Histocompatability Complex (MHC) determines the immune response to pathogens, and its genes are promising candidates for the search of associations with diseases. A special role is played by BoLA-DRB3 gene, the product of which directly participates in the binding of alien antigens and conditions the specificity of the immune response. The second exon of this gene codes β1-domain of class II antigens, which is necessary for binding a broad spectrum of alien antigens. Exon 2 of BoLA-DRB3 gene is extremely polymorphic, giving the possibility to search the associations of its alleles with various diseases. The article provides the results of the study on polymorphism of alleles of BoLA-DRB3.2 gene for detection of its associations with sensitivity to fusobacteriosis (necrobacteriosis) of cows. The survey was performed using PCR-RFLP method with DNA of blood from 176 cows of two herds of Ukrainian black-and-white dairy breed. As a result of the studies, in the first herd, 25 BoLA-DRB3.2 alleles were found. In the selections of nectobacteriosis susceptible and resistant cows, we found 22 and 21 variants respectively. In the second herd, in the general selection and group of healthy animals, 27 alleles were typed, and 22 in the group of susceptible cows. BoLA-DRB3.2*22 allele was the commonest in both herds in both general selections and groups of nectobacteriosis-resistant cows. In the selection of susceptible animals, the commonest was the variant BoLA-DRB3.2*16. We determined statistically significant associations of BoLA-DRB3.2 alleles with sensitivity to nectobacteriosis of cattle. BoLA-DRB3.2*03 and *22 alleles associate with nectobacteriosis-resistant, while *16 and *23 – with nectobacteriosis-susceptible cows of the both studied groups. Also, in the first herd, another allele was found – *24, indicating close relationship with the disease. The studies of polymorphism of BoLA-DRB3 gene expand the knowledge about genetic peculiarities of the Ukrainian black-and-white dairy breed. The identified molecular-genetic markers could be useful for breeders whose work is oriented towards the formation of herds which are resistant to diseases of the limbs in cattle.

MALDI-TOF-MS-based high throughput genotyping of mutations associated with body measurement traits in cattle

Exploration of genes in relation to body measurement traits through large-scaled mutation identification is highly conductive for the genomics-assisted breeding of superior productivity cattle. In this investigation, 31 objective mutations were genotyped synchronously in 384 yellow cattle of 8 breeds through the application of optimized MALDI-TOF-MS and multiplex PCR techniques. High genotyping rate was obtained as well as greatly decreased cost which was below one thirtieth of the routine analysis. Results from genotyping revealed 23 mutations as valid mutations in the studied cattle population with gene heterozygosity and effective allele number varying from 0.0052 to 0.4998 and 1.0052 to 1.9991, respectively. Among the 23 effective mutations, 12 was classified as moderate polymorphism (0.25 < PIC < 0.5) while the other 11 belonged to low polymorphism (PIC < 0.25), 7 mutations did not obey the HW equilibrium (p < 0.05) and linkage mainly appeared between mutations of UCP2 and PTHR1 genes. Furthermore, 8 body measurement traits in the 384 cattle were recorded to validate their association with tag mutations, and significant correlations were found in 12 mutations of 9 genes including PTHR1, CDK6, IHH, HHIP, GHRL, COL1A1, INS, GDF5 and UCP2, of which, PTHR1 was proved to be the most potential contributor to bone modeling in cattle. Results highlight the potential application value of 12 novel mutations in enhancing cattle production traits as well as the high genotyping rate achieved by MALDI-TOF-MS coupled with multiplex PCR technique.

Insight in Leptin Gene Polymorphism and Impact on Milk Traits in Autochtonous Busha Cattle

Leptin, a biomolecule secreted by adipose tissue, enchances productivity in cattle, especially affecting milk traits. The aim of this study was to detect leptin gene polymorphism on exon 3 (A59V locus) and intron 2 (SAU3AI locus) in the endangered population of autochtonous Busha cattle and associations with milk traits. The study included 46 cows: 36 Busha and 10 half-bred. Milk analyses comprised determination of somatic cell counts, fat, protein, lactose, total solids and solids-not-fat (SNF) concentrations and freezing point depression (FPD). Polymorphisms were determined by PCR-RFLP technique. A single A59V genotype (CC) was affirmed, and two SAU3AI genotypes, AA and AB, with frequencies of 78.26% and 21.74%, respectively. Comparing the obtained results for chemical characteristics of milk between cows with AA and AB, no significant differences were found, except for SNF content and FPD values. Cows with AA genotype had significantly lower (p=0.021) average SNF content (8.74%) in milk compared to the average SNF content (9.28%) in those with genotype AB, while cows with genotype AA (−0.54°C) had significantly higher (p=0.004) average FPD values than those with AB genotype (−0.58°C). The absence of BB genotype and significant differences in the investigated functional traits between two SAU3AI genotypes and the absence of A59V polymorphism (presence of only CC genotype) show that the Busha cattle breed, although being an autochtonous low-producing native breed used for meat and milk production, harbours polymorphism on gentic markers characteristic of high production dairy cows.

Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan

The primary goal of cattle genomics is the identification of genome-wide polymorphism associated with economically important traits. The bovine genome sequencing project was completed in 2009. Since then, using massively parallel sequencing technologies, a large number of Bos taurus cattle breeds have been resequenced and scanned for genome-wide polymorphisms. As a result, a substantial number of single nucleotide polymorphisms (SNPs) have been discovered across European Bos taurus genomes, whereas extremely less number of SNPs are cataloged for Bos indicus breeds. In this study, we performed whole-genome resequencing, reference-based mapping, functional annotation and gene enrichment analysis of 20 sires representing eleven important Bos indicus (indicine) breeds of Pakistan. The breeds sequenced here include: Sahiwal, Red Sindhi, Tharparkar and Cholistani (tropically adapted dairy and dual purpose breeds), Achai, Bhagnari, Dajal and Lohani (high altitude adapted dual and drought purpose breeds); Dhanni, Hisar Haryana and Gabrali (dairy and light drought purpose breeds). A total of 17.4 billion QC passed reads were produced using BGISEQ-500 next generation sequencing platform to generate 9 to 27-fold genome coverage (average ~16×) for each of the 20 sequenced sires. A total of 67,303,469 SNPs were identified, of which 3,850,365 were found novel and 1,083,842 insertions-deletions (InDels) were detected across the whole sequenced genomes (491,247 novel). Comparative analysis using coding region SNPs revealed a close relationship between the best milking indicine breeds; Red Sindhi and Sahiwal. On the other hand, Bhagnari and Tharparkar being popular for their adaptation to dry and extremely hot climates were found to share the highest number of SNPs. Functional annotation identified a total of 3,194 high-impact (disruptive) SNPs and 745 disruptive InDels (in 275 genes) that may possibly affect economically important dairy and beef traits. Functional enrichment analysis was performed and revealed that high or moderate impact variants in wingless-related integration site (Wnt) and vascular smooth muscle contraction (VSMC) signaling pathways were significantly over-represented in tropically adapted heat tolerant Pakistani-indicine breeds. On the other hand, vascular endothelial growth factor (VEGF) and hypoxia-inducible factor 1 (HIF-1) signaling pathways were found over-represented in highland adapted Pakistani-indicine breeds. Similarly, the ECM-receptor interaction and Jak-STAT signaling pathway were significantly enriched in dairy and beef purpose Pakistani-indicine cattle breeds. The Toll-like receptor signaling pathway was significantly enriched in most of the Pakistani-indicine cattle. Therefore, this study provides baseline data for further research to investigate the molecular mechanisms of major traits and to develop potential genomic markers associated with economically important breeding traits, particularly in indicine cattle.

The application of gene marker-assisted selection and proteomics for the best meat quality criteria and body measurements in Qinchuan cattle breed

In the past few decades, enhancement of animal productivity has been gaining increasing attention among decisions-makers, politicians, mangers, and breeders, because of the increasing of world population and shortage of natural resources. The selection of high productivity animals is the main goal, through the application of genetic improvement programs. The use of molecular genetics has conferred significant breeding advantages over conventional breeding techniques. In this regard, many economic characteristics are controlled by a small number of multiple gene loci, each of which is responsible for trait diversity and hence they are referred to as quantitative trait loci (QTL). Single-nucleotide polymorphisms (SNPs), which have recently been discovered through DNA sequencing, are considered one of the most useful types of genetic marker. SNPs are found where different nucleotides occur at the same position in the DNA sequence. They are found in both coding and noncoding regions of the genome and are present at one SNP in every 1000 b. Strategies for the identification and application of markers are based on reference to examples of loci that can control various traits. Furthermore, markers for growth, body measurements, and meat quality traits are preferred, because they can be used to predict the performance of animals, via blood samples, in the first few days of animal life. Marker-assisted selection using SNPs, such asSIRT1, SIRT2, LPL, CRTC2, SIX4, UCPs, and ZBTB38as selection criteria of body measurements and meat traits in beef cattle, will be beneficial in selection and breeding programs. The proteomic is a novel marker and a new approache of biotechnology which increases the understanding of the biological processes, besides being a remarkable biomarker that interrelated to growth and meat quality traits. Proteomics is a vigorous tool as usage for deduces molecular processes between quality traits and muscle proteins, which are helpful in analyzing the mechanisms of biochemistry that influence quality. So they could be potential biomarker for some meat quality traits. Among them, Actin, Myosin, Heat shock proteins are used a novel approaches in the field of biotechnology to understand the proteomics changes. This review article highlights the novel findings on the potential use of MAS and proteomics as biomarker for the selection for meat quality and carcass traits in Qinchuan cattle breed.